Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

Michael Feig^*^†^‡

, Isseki Yu^§^∥, Po-hung Wang^§, Grzegorz Nawrocki^†, and Yuji Sugita^‡^§^∥^⊥

^† Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States

^‡ Quantitative Biology Center, RIKEN, Kobe, Japan

^§ Theoretical Molecular Science Laboratory, RIKEN, Wako, Japan

^∥ iTHES Research Group, RIKEN, Wako, Japan

^⊥ Advanced Institute for Computational Science, RIKEN, Kobe, Japan

J. Phys. Chem. B, 2017, 121 (34), pp 8009–8025

DOI: 10.1021/acs.jpcb.7b03570

Publication Date (Web): June 30, 2017

*Address: 603 Wilson Road, Room BCH 218, East Lansing, MI, 48824. E-mail: feig@msu.edu. Phone: +1 (517) 432-7439. Fax: +1 (517) 353-9334.

ACS Editors' Choice - This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.

Cite this:J. Phys. Chem. B 121, 34, 8009-8025

Biography

Michael Feig is a Professor of Biochemistry & Molecular Biology at Michigan State University, USA. He obtained a Diplom degree in Physics from the Technical University of Berlin, Germany, continued the study of Computational Chemistry resulting in a Ph.D. degree at the University of Houston, Texas, USA, and completed postdoctoral training at The Scripps Research Institute in La Jolla, California, USA, before becoming faculty at MSU in 2003. His primary interests are in the development and application of molecular modeling and molecular dynamics techniques to biological questions, especially to connect biomolecular structure and dynamics of single molecules to biological function at the cellular level.

Biography

Isseki Yu is a Research Scientist at Interdisciplinary Theoretical Science Research Group (iTHES), RIKEN, in Japan. He also works as a member of Theoretical Molecular Science Laboratory, RIKEN. He obtained his Ph.D. in engineering at Yokohama National University in 2003. He was a postdoctoral fellow in Nagoya University (2003–2008) and an assistant professor in Aoyama Gakuin University (2008–2013). In 2013, he joined the Theoretical Molecular Science Laboratory, RIKEN, and started to investigate the cellular environment with large-scale molecular dynamics simulations.

Biography

Po-hung Wang is a Postdoctoral Researcher at the Theoretical Molecular Science Laboratory, RIKEN, Japan. In 2013, he obtained his Ph.D. in Physics in the University College London, UK. During his Ph.D. study, his primary interest was small molecule transport in proteins. After joining RIKEN, he shifted his focus to the study of various interactions between macromolecules in crowded environments using molecular simulations.

Biography

Grzegorz Nawrocki completed his M.S. degree in Biophysics at Jagiellonian University, Poland. He earned his Ph.D. in Biophysics at Polish Academy of Sciences, Poland, where he worked with Professor Marek Cieplak on characterizing interactions of biomolecules with the surfaces of solid bodies. Currently, he is a Postdoctoral Research Associate at Michigan State University working on developing force fields and analysis methods for molecular dynamics simulations. He studies diffusion, stability, and interactions of proteins and lipid bilayers in the crowded cellular environment.

Biography

Yuji Sugita is a Chief Scientist at Theoretical Molecular Science Laboratory, RIKEN, in Japan. He also works as a team leader at Laboratory of Molecular Function Simulation, RIKEN, and at Computational Biophysics Research Team, RIKEN. He obtained his Ph.D. in chemistry at Kyoto University in 1998, working with Nobuhiro Go. He was a postdoctoral fellow in RIKEN (1998), a research associate in IMS (1998–2002), and a lecturer in the University of Tokyo (2002–2007). In 2007, he joined RIKEN as a PI (Associate Chief Scientist) and was promoted to Chief Scientist in 2012. His group is primarily working on the development of a high-performance molecular dynamics program for investigating the structure–dynamics–function relationship of biomolecules in cellular environments.

Abstract

The effects of crowding in biological environments on biomolecular structure, dynamics, and function remain not well understood. Computer simulations of atomistic models of concentrated peptide and protein systems at different levels of complexity are beginning to provide new insights. Crowding, weak interactions with other macromolecules and metabolites, and altered solvent properties within cellular environments appear to remodel the energy landscape of peptides and proteins in significant ways including the possibility of native state destabilization. Crowding is also seen to affect dynamic properties, both conformational dynamics and diffusional properties of macromolecules. Recent simulations that address these questions are reviewed here and discussed in the context of relevant experiments.

Introduction

Realistic biological environments involve a high degree of complexity and crowding at the molecular level that is still only at the beginning of being fully understood.(1-5) Increasing evidence suggests that crowding can markedly affect biomolecular structure, dynamics, and thus possibly their function.(6) The most obvious aspect of cellular crowding, a greatly diminished free volume with mostly entropic consequences, has long been studied in various ways using experiments, theory, and simulation.(7-12) However, the degree to which artificial crowders approximate real cellular environments or even reproduce just excluded-volume effects without any other artifacts is unclear.(6, 13-15) At the same time, increasing attention is now focused on the effects of interactions between the cellular components(16-24) and altered solvent properties,(25-30) often contributing enthalpically,(15, 31, 32) as well as the consequences of a substantial compositional heterogeneity present in biological cells.(33, 34)

The concentration of biological macromolecules in cells is between 100 and 450 g/L, occupying 5–40% of the cytoplasmic volume.(35) In addition, structural elements such as the cytoskeleton, compartments, and membrane surfaces are present, whereas genomic DNA fills out eukaryotic nuclei and a good fraction of prokaryotic cells. A variety of metabolites, small molecules that are intermediates of metabolic reactions such as phosphates, carbohydrates, amino acids, alcohols, vitamins, and other cofactors, as well as ions at significant concentrations further contribute to the rich physicochemical environment inside living cells. Experiments that are carried out under in vivo conditions or in the presence of cell extracts face substantial technical challenges.(1, 2, 25, 36) Often, it is difficult to achieve sufficient resolution to provide detailed insights, although recent progress especially with in-cell nuclear magnetic resonance (NMR)(24, 37-55) and in-cell fluorescence spectroscopy(56-58) techniques is encouraging. An alternative is computational modeling, which can describe the structure and dynamics of biomolecules with high resolution in both space and time within model and resource limitations.(59) In particular, molecular dynamics (MD) simulations using atomistic force fields are a popular avenue for studying biological systems. However, MD studies have so far largely focused on single molecules or complexes without considering crowded environments, even as multimillion atom systems are now becoming feasible,(60-62) whereas questions in regard to crowding have been addressed mostly with simplified models.(10) This may reflect in part the computational costs involved with fully atomistic detailed models of crowded environments, but the more important constraint is that sufficient experimental data for building high-resolution models of biological environments has not been readily available. There has also been a lack of suitable experimental data that predictions from simulating such models could be compared to. However, there is a recent influx of data from high-throughput experiments that probe the composition of a cell,(63-65) and new experiments can directly probe macromolecule structure and dynamics in cellular environments.(16-22, 25, 32, 37, 40, 41, 44-46, 49, 54, 56, 66-85) This now enables and, we would argue, requires detailed computational studies of realistic models of crowded biological environments to connect with the newly emerging experimental data and generate new hypotheses.(86)

Key Questions

The questions to be addressed here revolve around the structure, interactions, and dynamics of biomolecules, proteins, nucleic acids, and metabolites in cellular environments. Essentially, the key point is to determine to what extent the vast amount of knowledge about the biomolecular structure–dynamics–function paradigm generated during decades of structural biology and mechanistic analyses of biological function under in vitro conditions translates to real biological environments and ultimately what makes up life.(87) The end point is a fully integrated view of biology that scales from single molecules to whole-cell models(88, 89) to explain life based on physical and chemical principles.(90)

Structure and Stability

Most of the knowledge about protein structure has been derived from crystallography where the environment, although relatively dense in terms of packing, lacks the heterogeneity of biological environments and where packing contacts are more likely related to artifacts than being representative of what would be seen in crowded biological environments. Structures based on nuclear magnetic resonance (NMR), on the other hand, are traditionally obtained under dilute conditions that are far from crowded cellular environments. Thus, it remains largely unclear whether and how the structure and stability of proteins, and more broadly the conformational energy landscape, is affected by crowding in the cell.(91) Simple arguments based on a volume exclusion effect due to crowding focus on a shift in populations toward compact states on an otherwise largely unchanged landscape,(11) but this view conflicts with recent experiments.(17, 22, 23, 73, 92, 93) Largely unaltered conformations in vivo vs in vitro are seen with in-cell solution NMR(40, 44) and solid-state (SS) NMR,(54) but other evidence from experiments and simulations indicates that cellular environments may remodel the folded or unfolded ensemble or both(16, 17, 49, 71, 94-100) with potentially varying effects in different cellular compartments.(82) This suggests a more complicated picture where it is unclear whether remodeling of the ensemble is again driven mostly by entropic volume exclusion effects or by more enthalpic effects due to interactions with protein crowders and other components of the biological environment.(16, 17) Significant crowding effects are also expected for intrinsically disordered peptides (IDPs) where extended and dynamic ensembles have to be accommodated under crowded environments.(37, 69, 75, 76, 83, 100, 101)

Although proteins have received most of the attention, similar, less well-explored questions have been raised about how nucleic acid structures may act as crowders(43) or be affected by crowded cellular environments compared to what we know about DNA and RNA from crystallography and solution NMR studies.(102-109)

Dynamics

Biomolecular dynamics links structure with function, and it is equally unclear how it may be affected in the context of cellular environments. Conformational dynamics is a key mechanistic factor in most biological macromolecules, and any effect of cellular crowding on such dynamics would directly impact biological function. There is some insight into altered folding kinetics under crowded conditions,(48, 56, 80, 82) and a few studies suggest that the internal backbone and side chain dynamics on sub-microsecond time scales remain largely unaltered.(78, 110-112) On the other hand, only a few studies have examined how functionally relevant motions in the native state, e.g., dynamics related to allosteric mechanisms, ligand binding, or catalysis, and dynamics of intrinsically disordered peptides may change upon crowding.(113-115) This leaves many open questions yet to be addressed.

Diffusional motions of biomolecules in cellular environments, on the other hand, are somewhat better understood. Diffusion rates are a key determinant for the kinetics of many biological processes. Ligand diffusion is rate-limiting in many enzyme reactions, and protein diffusion is an important factor in most protein–protein and protein–nucleic acid interactions.(116-120) There is a general understanding that diffusion of proteins is slowed down by about 1 order of magnitude under crowded conditions due to increased viscosity and interactions with crowder molecules,(77, 121-124) although this may not be generally true for natively disordered proteins.(122) Anomalous diffusion results in diffusion rates varying on different time scales due to confinement within cellular compartments and caging effects due to temporary encapsulation by larger crowders.(34, 123, 125-128) However, details of how diffusion is modulated by different cellular microenvironments and by the presence of DNA or membrane surfaces have remained unclear.(77) There is also an incomplete understanding of how smaller molecules, metabolites and other ligands navigate the dense cellular environments where available space is not just limited and solvent viscosity may be altered but where the various macromolecular surfaces also provide ample opportunities for distractions that could, for example, slow down diffusion toward an enzyme active site.(129)

Interactions

Cellular crowding undoubtedly increases the opportunities for frequent encounters of biomolecules due to weak interactions.(79, 130, 131) It is not clear, however, whether such soft interactions simply hinder diffusion and alter the conformational energy landscape as discussed above or whether interactions between biomolecules are altered with possible functional implications.(16, 66, 70, 74, 84, 132) Crowding has been found to affect native complex formation(31, 68, 133-135) and aggregation,(136-138) while other evidence indicates enhanced formation of nonspecific complexes between proteins in the cellular milieu.(14) Weak interactions under highly crowded conditions may further lead to protein-enriched regions, forming distinct phases within the cell such as droplets with gel-like characteristics.(139, 140)

Metabolite–protein interactions are also subject to crowding effects. Studies of substrate binding and product release during enzyme reactions under crowded conditions have suggested crowding effects.(129) Moreover, effective metabolite concentrations in vivo may be reduced as a result of metabolites being sequestered from bulk solvent by nonspecific binding to biomolecular surfaces,(141) whereas competition by promiscuous interactions with the environment, on the other hand, may modulate specific binding of ligands to target binding sites.(132, 142)

Solvent and Membrane Environments

Finally, a fundamental question is how the solvent environment is altered in the presence of biomolecules at very high concentrations. Simple geometric considerations suggest that, although water still makes up about 70% of the cytoplasm, only a relatively small fraction is actually bulk-like, as defined by water molecules being several layers away from the closest macromolecule. This has been shown to impact water dynamics,(29, 143) viscosity,(66, 144, 145) and dielectric properties,(26, 146) which then in turn may further exacerbate crowding effects on the macromolecules compared to dilute environments.(29) While experiments have provided varying insights,(28, 147) a more detailed analysis of the properties of aqueous solvent inside biological cells is desirable. There are also many unanswered questions about how membrane bilayers respond to crowding,(148) both inside the membrane by membrane proteins and outside by a crowded cytoplasm and how membrane surfaces modulate crowding effects in the cytoplasms.

A full review of all experiments, simulations, and theoretical studies that have looked at these questions is not possible here. Instead, the specific focus of this article is to highlight recent advances based on computer simulations of dense macromolecular systems in atomistic detail, and relate those findings to experimental studies, both past and future.

Cellular Environments in Computer Simulations

Computer simulations have examined biological systems at a wide range of scales from full atomistic detail to very coarse representations. Most simulations of crowded cellular environments have involved simplified models where macromolecules, crowder molecules, and the solvent environment are represented with different degrees of coarse-graining.(95-98, 127, 149-152) For example, coarse-grained models of proteins in the presence of spherical crowders without any explicit representation of solvent are one avenue for studying the effect of crowding on protein folding or association equilibria,(30, 153) whereas Brownian, Stokesian, or other stochastic dynamics simulations of rigid protein models at different levels of detail have offered insights into how crowding modulates diffusive properties.(127, 151, 154-158) Another possibility is postprocessing of trajectories using particle-insertion methods.(159) All of these approaches involve simplifications that are attractive for saving computational costs and have allowed the exploration of relatively long time scales, in the range of micro- to milliseconds. However, there are significant trade-offs as intermolecular interactions and solvent effects often do not fully reflect cellular environments and intramolecular dynamics may be neglected or not fully accounted for.

As with any modeling, the degree of detail should match the questions that are being asked and an in silico model of a complete cell does not necessarily have to include every atom that is present. However, we argue that the central questions that are being asked here, conformational sampling, stability, and dynamics of biomolecules in the cellular environment, require, at the minimum, a model with the following features: (1) Proteins, nucleic acids, and metabolites should be fully flexible with an interaction potential that is able to maintain native states under dilute conditions but that can also sample non-native states in response to interactions with cellular components. (2) Weak interactions between the cellular components are physically accurate and predictive without requiring previous knowledge about specific complexes, since nonspecific interactions dominate in cellular environments. (3) The essential characteristics of the solvent environment are captured including an ability to reflect altered solvent behavior under crowded conditions such as reduced solvent dynamics and hydrodynamics interactions.

These requirements are a tall order for most coarse-grained approaches that typically focus only on certain aspects while failing to capture other features. For example, Go models can describe the thermodynamics of protein folding and complex association assuming that the structures of the end states are known and may offer some insight into how crowding shifts populations between known states.(160-162) However, perturbations of the energy landscape toward unknown conformational states that may be induced as a result of crowding are difficult to capture with structure-based models. On the other hand, simulations of rigid or spherical biomolecules via Brownian and Stokesian dynamics schemes can describe diffusive properties well,(155, 157, 163, 164) but these approaches neglect intramolecular dynamics and conformational sampling. More sophisticated physics-based coarse-grained models(165) such as PRIMO,(166) OPEP,(150) or COFFDROP(167) that are combined with implicit solvent and/or models for hydrodynamic interactions(156) are in a better position to satisfy these criteria, as the increased level of model detail requires fewer constraints and provides more transferability and ability to capture the various features outlined above. Such models can at least at a general qualitative level capture the main features of biomolecular structure and dynamics cellular environments.(149, 168, 169) Atomistic simulations, with explicit(26, 143, 170-176) or implicit solvent,(27, 97, 98) or multiscale models, where atomistic and coarse-grained resolutions are mixed,(169) provide even greater levels of detail and can, at least in principle, satisfy all of the requirements for modeling crowded cellular environments outlined above. However, because the balance between molecular stability, weak interactions, and solvent interactions in crowded environments depends on subtle shifts between enthalpic and entropic energy terms, the major challenge is an accurate interaction potential, both at the coarse-grained and atomistic level that can accurately reproduce both intra- and intermolecular interactions.(177-179) For example, just a slight unbalance between protein–protein and protein–water interactions is enough to lead to aggregation(177) and overcompaction artifacts(180, 181) with significantly mispredicted diffusive properties being one consequence. The choice of the water model is also a concern, since the most widely used models (SPC/E(182) and TIP3P(183)) significantly mispredict viscosity and dielectric properties(26, 184, 185) which in turn impacts macromolecular properties.(185) Therefore, future efforts should continue the improvement of force fields(186-192) to better balance the interactions between the various cellular components.

Another issue is the high computational cost of the most detailed models that limits the time scales that can be accessed. Current computer hardware, especially GPUs and other many-core coprocessors such as Intel Xeon Phi and high-performance simulation software,(193-198) are now allowing for atomistic simulations of biomolecules in crowded cellular environments on time scales well into the microsecond regime with millisecond dynamics being within reach now(199) and probably becoming routine within a decade. While such time scales are short compared to most functional dynamics of biological processes, they cover the majority of diffusive processes within the cell for all but the very largest particles such as ribosomes based on the extrapolation of sub-microsecond diffusion rates in crowded environments estimated from simulation.(173) Therefore, the development of more accurate coarse-grained models that can describe biomolecular dynamics on millisecond to second time scales remains an attractive goal in the foreseeable future. The length of the simulations also determines the degree of sampling and the statistical significance of properties determined via averaging. However, this is a minor issue, since parallel computing architectures facilitate replicate simulations and crowded systems with multiple copies of a given system of interest allow ensemble averaging in addition to time averaging.

One strategy for overcoming limitations in simulation times is the use of enhanced sampling techniques(200) such as umbrella sampling,(201) generalized-ensemble methods,(202, 203) metadynamics,(204) λ-dynamics,(205) or accelerated MD,(206) just to name a few. These methods generally focus on specific processes where significant kinetic barriers hinder sampling, and they are usually used to extract thermodynamic quantities such as ligand binding affinities. So far, enhanced sampling methods have not seen extensive use, in part because there is still very limited knowledge about what states may exist under crowded conditions and enhanced sampling methods are less advantageous for exploratory simulations where little is known about a system’s behavior. However, as more information is becoming available, the energetics of protein–protein or protein–ligand interactions or conformational dynamics between different states seen under crowded conditions are good problems for using enhanced sampling. Enhanced sampling methods are also less effective for accelerating processes that are limited by slow diffusion, a major factor in crowded cellular environments. Diffusion-limited processes can be accelerated, however, by using mean-field models of cellular environments,(27, 103, 152) although the implicit models have other drawbacks, as they may oversimplify cellular environments(169) and the extraction of kinetic properties is hindered. Developing enhanced sampling methods that target the sampling of diffusion-limited processes while fully capturing all components of cellular environments and allowing the extraction of thermodynamic and kinetic properties remains a significant challenge that we hope can be addressed in the future with new methods.

While it is clear that the simulation of crowded cellular environments is still in its infancy, the aim of this Feature Article is to review what has been reported so far from molecular simulations of proteins in dense cosolvents,(97, 98, 112, 143, 207, 208) of dense peptide and protein solutions,(26, 29, 143, 159, 170-172, 174, 175, 209-213) and of more complex models of cellular environments.(112, 163, 168, 214)

Atomistic Simulations of Cellular Crowding

Table 1 gives an overview of crowding simulations studied via atomistic models in recent years. We selected studies of peptides and proteins where at least the solute for which crowding effects are studied is represented in atomistic detail but allowed for crowders and/or solvent environments to be modeled in a coarse-grained or implicit fashion. We included simulations of dense amino acid and peptide systems, as they offer insight into protein amino acid interactions under crowded conditions. Despite some overlap, we did not consider simulations involving amyloidogenic peptides.(216) The concentrations of solutes in those studies are generally low compared to crowded environments, whereas their analysis primarily focuses on their aggregation propensities offering less insights into cellular crowding. In addition to studies of peptides and proteins, there are also a few studies involving nucleotides and nucleic acids under crowded and concentrated conditions,(103, 217-219) but since general insights have remained limited, these studies will also not be discussed here.

Table 1. Simulations of Crowded Peptide and Protein Systems with Atomistic Detail

solutes^a	solvent	sampling	year	group^ref
Gly/Val/Phe/Asn (50–300 g/L)	expl. water	1 μs MD	2013	Elcock(178)
Gly/Ala/Val/Phe (50–300 g/L)	expl. water	10 ns MD	2015	Price(175)
(GlySer)₂ (9–560 g/L)	TIP3P water	8 μs MD	2014	Rao(29)
27 × (Xxx^l)₄ (40 mM; 10–30 g/L)	expl. water	100 ns MD	2016	Taiji(213)
Gly₅ (0.03/0.3 M; 10/100 g/L)	TIP3P water	100 ns MD	2014	Pettitt(176)
1 × Ala/Ala₁₅/melittin	GB^k (ε = 2–80)	44–83 ns ReX^e-MD	2008	Feig(27)
1 × Trp-cage/melittin + 8 × protein G (CG) (40% vol; 540 g/L)	GB^k (ε = 80)	20 ns ReX^e-MD	2012	Feig(169)
1 × chignolin, 0–8 × HS^c (0–40% vol)	TIP4P water	1 μs MD	2012	Rajagopalan(215)
1 × Trp-cage + 8 × BPTI (7% vol; 95 g/L), 8 × HS^c (7%/20% vol)	implicit	10⁷ ReX^e-MC moves	2015	Irbäck(98)
1 × Trp-cage/GB1m3 + 8 × BPTI (7% vol; 95 g/L), 8 × GB1^d (7% vol; 95 g/L), 8 × HS^c (20% vol)	implicit	10⁷ ReX^e-MC moves	2016	Irbäck(97)
4/8 × villin^b (6/9.2 mM; 25/40 g/L)	SPC wat./NaCl	50–200 ns MD	2014	Zagrovic(177)
8 × GB1^d (10–30% vol; 135–405 g/L), 4 × GB1^d/8 × villin^b (10–43% vol; 135–580 g/L)	TIP3P water	300 ns MD	2012; 2013	Sugita/Feig(26, 171)
1 × CI2,^f 8 × lysozyme (100 g/L), 8 × BSA^g (100 g/L)	TIP3P water	100–250 ns MD	2012	Sugita/Feig(170)
1/4 × ubiquitin (16% vol; 216 g/L), 19/157 metabolites	TIP3P water, KCl, MgCl₂	200 ns MD	2011	Guallar(207)
1 × ubiquitin, glucose (325 g/L)	TIP3P water	500 ns MD	2013	Dal Peraro(112)
1–3 × ubiquitin, glucose (108/325 g/L)	TIP3P water	600 ns MD, 30–70 ns ReX^e-MD	2014	Dal Peraro(208)
3 × ubiquitin, Glu/Arg/glucose (300 g/L)	TIP3P water	600–800 ns MD	2016	Dal Peraro(143)
1 × ACTR^h/6 × NCBDⁱ/1 × IRF-3^j (175–296 g/L), 4 × ACTR^h/24 × NCBDⁱ/4 × IRF-3^j (183 g/L)	TIP3P water	100 ns–3 μs MD	2016	Orozco(174)
8 × BSA^g (400 g/L), 88 × GB1^d (400 g/L), 132 × villin^b (400 g/L)	TIP3P water	100 ns MD	2017	Sugita/Feig(172)
100s–1000s of proteins/RNA (300 g/L), 5000–40,000s of metabolites	TIP3P water	20–140 ns MD	2016	Sugita/Feig(173)

Reported concentrations are underlined.

Villin headpiece.

Hard sphere.

B1 subunit of protein G.

Replica exchange sampling; given times are per replica.

Chymotrypsin inhibitor 2.

Bovine serum albumin.

Activator for thyroid hormone and retinoid receptor.

Nuclear coactivator-binding domain of CREB.

Interferon regulatory transcription factor.

Generalized Born implicit solvent.

Any amino acid.

As a representative overview of the kind of systems that are now being studied in atomistic detail via computer simulations, Figure 1 shows models that have been studied recently in our group. The systems range from mixtures of a few proteins at different concentrations to models of cytoplasmic environments with thousands of macromolecules. The number of atoms in these systems ranges from 50K to 100M atoms, and the time scales that were reached varied between tens of nanoseconds and microseconds. In all of these cases, all-atom force fields were used to describe the solutes, aqueous solvent, and any other molecules such as metabolites that were present, allowing for unrestrained dynamics of all components. On the basis of simulations of such systems, exciting new ideas have been found for how the stability and dynamics of proteins may be modulated by interactions with other molecules in the cell.

Figure 1. Crowded and cellular systems studied via molecular dynamics simulations: Concentrated solution of villin in explicit water and ions (top left); chymotrypsin inhibitor 2 (CI2; blue) in the presence of bovine serum albumin (BSA) crowders with explicit water (top right); model of a bacterial cytoplasm consisting of proteins, RNA, metabolites, ions, and water shown only for part of the system in cyan (bottom).

Solute Interactions

A key feature of crowded environments is the opportunity for frequent encounters between biomolecules. The well-understood volume-exclusion effect of crowding typically assumes crowder molecules that are repulsive or at least not attractive so that such interactions would be minimized to just unavoidable random collisions. However, atomistic simulations of crowded environments have shown many examples of attractive interactions between proteins(97, 98, 170, 171, 173, 174, 177) and between proteins and other molecules such as metabolites.(143, 173, 207) Such interactions are generally nonspecific; i.e., the formed complexes cover a broad range of arrangements and do not correspond to specific functional complexes, but they have the potential to significantly perturb protein structure and dynamics over solutes in dilute environments that are free from such contacts. Weak transient interactions, commonly termed quinary interactions,(2) nevertheless, do have the potential to be functionally relevant, for example, to bring enzymes involved in a common metabolic pathway into proximity to facilitate substrate channeling.(173) Whether such close interactions are formed depends greatly on the involved partners. For example, chymotrypsin inhibitor 2 (CI2) interacts extensively with lysozyme but hardly at all with bovine serum albumin (BSA), whereas BSA prefers to interact with other BSA molecules.(170) A similar finding was reported for Trp-cage in the presence of protein G vs bovine pancreatic trypsin inhibitor (BPTI) crowders, with BPTI more strongly self-interacting with other BPTI molecules.(97) Differential protein interaction propensities can be traced to the nature of the amino acids decorating the surface of different proteins that lead to charge differences(98) and hydrophobic patches(97, 171) along with sufficiently good shape complementarity to allow close interactions. Simulations of dense solutions of amino acids and small peptides(29, 143, 175, 176, 178, 213) have offered additional insights into which amino acids are more favorable to interact(178) and how such interactions are formed via hydrogen bonding,(176, 213) aromatic ring interactions,(213) dipole–dipole interactions,(176) or mediation via water molecules.(29) Generally, the degree to which amino acid interactions were found to be favorable reflects established hydrophobicity profiles;(213) e.g., isoleucine, leucine, and valine readily interact due to their hydrophobicity, whereas basic and acidic residues strongly prefer to remain solvated.(143, 213) There are differences that can be at least in part be explained by strong intermolecular self-interactions, e.g., between asparagine and glutamine side chains,(213) but variations were also seen as a function of the force field that was used.(178, 213)

A concern that has been raised is whether the overall strength of peptide–peptide and protein–protein interactions in dense solutions is correctly calibrated in the current generation of force fields. On the basis of simulations of villin, it has been suggested that protein–protein interactions may be overall too strong relative to protein–water interactions.(177) This would also be generally consistent with the observation that intrinsically disordered peptides are too compact with most force fields(220-222) unless amino acid–water interactions are enhanced.(180, 191) However, simulations of concentrated amino acids and peptides seem to come to the opposite conclusion that solubilities are significantly overestimated compared to experimental values.(176, 178) This is clearly an area that will require further attention, but significant challenges exist in how to effectively compare with experimental measurements. For example, the extraction of solubilities that are comparable with macroscopic measurements, while possible in principle,(176) requires a system with a large number of solutes that are simulated over long enough times to overcome kinetic bottlenecks of aggregate formation. Another possibility is to match rotational and/or translational diffusion rates for concentrated solutions as the slow-down in diffusion upon crowding is expected to depend upon the extent of protein interactions(170) while deviations from nonideal behavior vary with the crowder type.(123) A meaningful comparison between experiments and simulations also requires long simulations as well as reliable force field parameters for solutes and solvent and faces potential experimental difficulties in analyzing highly retarded and likely complex dynamics in concentrated solutions, e.g., via nuclear magnetic resonance (NMR) spectroscopy.(81, 175)

Apart from interactions between peptides and proteins, some studies have examined interactions with high concentrations of smaller cosolvents such as metabolites(173, 207) or glucose(112, 143, 208) or osmolytes such as trimethylamine N-oxide (TMAO).(223) The general finding is that such molecules may interact extensively with protein solutes(172, 207) or among themselves,(207) displace water molecules,(143) and further affect the structure and/or dynamics of proteins as a consequence of such interactions.(173) The simulations can be compared with experiments(224-227) by quantifying preferential solvation via the integration of MD-derived density fluctuation of water and cosolvents to obtain Kirkwood–Buff integrals.(228-232) While this approach can be readily applied for proteins in two-component, or at the most, three-component solvents with small cosolvent molecules, the extension to cellular environments where a large number of components are present and density distributions of larger molecules such as proteins do not converge well is not as straightforward.

Protein Structure Stability

A central question is whether crowded cellular environments affect the stability of protein native states and, more broadly, whether the conformational landscape is modulated over dilute conditions. As mentioned already above, one aspect of crowding, the reduction of accessible volume, is well understood and generally believed to stabilize the native state as the most compact state a given protein will assume.(233) Unfortunately, such a simple view is not borne out in the atomistic simulations of peptides and proteins under crowded conditions. Instead, the simulations suggest that crowded cellular environments may perturb the native state, either directly due to interactions with other solutes(170, 173) or indirectly due to altered solvent properties (see example in Figure 2).(26, 27, 29, 172) There is also evidence from simulation that crowding may not just affect the native state but also folding intermediates(215) or the unfolded ensemble based on the analysis of an intrinsically disordered peptide.(174)

Figure 2. Villin native state destabilization under crowded conditions.

One theme for such native state perturbations is the competition between inter- and intramolecular interactions that can lead to a shift toward more extended states. Examples range from concentrated (GlySer)₂ solutions,(29) Trp-cage in the presence of protein G(169) or BPTI,(97, 98) villin in villin/protein G mixtures,(171) pyruvate dehydrogenase α subunit in a cytoplasmic environment,(173) and ordered and natively disordered proteins in a heterogeneous environment.(174) The presumed general mechanism in all of these cases is that favorable intermolecular interactions with peptide or protein crowders combined with an overall reduction of solvent exposure due to complex formation can drive partial unfolding. However, specific interactions with crowders such as edge-to-edge β-sheet interactions may also have the opposite effect of stabilizing the native state, as demonstrated for the GB1m3 hairpin.(97)

A second theme is the modulation of secondary structure propensities as a result of crowder interactions. While this has been systematically analyzed using coarse-grained models,(95, 96) atomistic simulations have provided evidence for an apparent stabilization of secondary structure elements, especially helices, as a result of crowding.(27, 97, 98, 174) One way to understand that is via crowder amino acid side chain interactions that stabilize helices(95) or β-hairpin turns.(97, 98) Another interpretation is based on a reduced dielectric response of solvent in crowded environments(26, 27) where intramolecular hydrogen bonding would be strengthened as a result of reduced electrostatic screening.(27)

A third theme is a disruption of the hydrophobic core that would lead to a general destabilization of natively folded peptides.(27, 29, 169, 174) This could simply be a corollary of a shift toward extended states driven by protein–protein interactions, but it may also be understood in the context of a reduced dielectric response of the solvent that would imply a weakened hydrophobic effect.(27)

Finally, a newly emerging theme is the role of metabolites in modulating protein structure. Functionally relevant ligand-induced conformational changes are well documented,(234) and it is easy to imagine that nonspecific metabolite interactions could have similar effects. Indeed, in a recent study of a model for a bacterial cytoplasm, nonspecific binding of negatively charged metabolites was found to modulate the structure of phosphoglucokinase and induce structural compaction via electrostatic screening.(173)

Experimental validation of the specific effects seen in the different simulations is largely missing so far and is therefore difficult to tell how real the specific effects seen in the simulations are. We imagine that it would be relatively straightforward to test the predicted effects of metabolites on protein structures, whereas in-cell NMR(24, 38, 41, 42, 44-46, 115) and fluorescence techniques(56, 58, 235) should be able to test how real the crowding-induced perturbations of the conformational ensembles are. Specifically, the hope would be that the experiments could identify the presence of the predicted non-native subpopulations in the presence of certain protein crowders, but it may be challenging to discern minor populations of heterogeneous non-native conformations induced by crowding in vivo.(38) Other avenues for comparing the simulations with experiments would be to identify key residues based on the simulations that appear to play a role in facilitating crowding-induced structural changes and propose experimentally testable mutations that should be resistant to crowding effects on structural stability.

While the results from specific simulations are questionable without experimental validation, the overall picture from the simulations taken together is that the conformational landscape of proteins may become perturbed as a result of nonspecific weak interactions in cellular environments and a resulting competition between intra- and intermolecular interactions that can stabilize non-native states. The possibility of native-state destabilization in vivo is generally consistent with experiments,(22, 23) but the simulations, furthermore, suggest specific mechanisms by which the energy landscape may be altered such as direct contacts with nearby crowder protein surfaces that shift the balance toward unfolded states and a role of altered solvent properties and metabolites. Nevertheless, much remains to be learned about more general principles that would, for example, allow predictions of how the structure and stability of a specific protein may be affected by cellular environments. Such insight is desirable to advance the fundamental understanding of biology, but it is also practically relevant in the context of protein design and therapeutic developments involving protein targets.

Protein Dynamics

Dynamics is what connects structure to function for all but a few proteins. The dynamics of proteins spans a wide range of time scales and covers internal, conformational rearrangements as well as diffusive motions. Internal dynamics may be further distinguished into fluctuations around the native state and conformational transitions between different states including the folding–unfolding transition. The available simulations suggest that fluctuations around the native state, as measured by S² order parameters or Debye–Waller B-factors, are only moderately affected by crowding.(97, 98, 143, 174, 208) Other results point at increased fluctuations as a result of protein–protein contacts in CI2 when interacting with lysozyme,(170) whereas somewhat reduced backbone dynamics were observed in other studies as a result of crowding.(112, 174) Experiments also indicate moderate effects of crowding on fast internal motions but a stronger influence on slower conformational dynamics.(41, 110, 236) A more detailed understanding of how crowding may affect internal dynamics beyond these general observations can be gained from direct comparisons between MD and NMR,(143) but further studies are needed to address this question. A somewhat clearer picture exists for the kinetics of conformational transitions between different states. Crowding with either proteins(174) or glucose(143, 208) led to a significant slowdown in conformational sampling. A similar conclusion was also reached for (GlySer)₂.(29) The slowdown in conformational transitions has been correlated with crowders, such as glucose, or water molecules becoming trapped between solutes and exhibiting slow diffusion and long residence times.(29, 208) It remains difficult, however, to clearly separate cause and effect with respect to retarded solvation causing slow conformational dynamics or vice versa. In any case, as conformational transitions are essential in many biological mechanisms, understanding how much such kinetic processes are slowed down in cellular environments is critical for fully understanding biological processes.

Translational and rotational diffusion is well-known to be significantly slower under crowded conditions (by about a factor of 10).(237-240) Furthermore, experiments show varying degrees of deviations from nonideality with respect to how the observed diffusion slows down with increased viscosity as a function of crowder type (proteins vs nonproteins and also between different proteins) that are taken to indicate different degrees of protein–crowder interactions.(121-123) Diffusion rates from atomistic simulations under crowded conditions are generally consistent with these observations,(170, 173, 175, 208) and simulations clearly show a slowdown in diffusion that strongly depends on protein–protein interactions.(170, 173) This means in the context of a diverse cytoplasmic environment that different copies of the same protein may experience very different diffusion rates depending on the local environment. Or for a given molecule, diffusion may vary significantly on μs–ms time scales as different local environments are sampled as the molecule diffuses across a cell.(173) In addition, there is evidence for anomalous diffusion as a result of caging by crowders, especially when interactions with those crowders are weak.(170) One may take that argument a step further to postulate that a diffusing protein molecule in a heterogeneous cellular environment should experience a spectrum of diffusion time scales as crowders of different sizes and with different levels of attraction are encountered. This analysis informs dynamic models of processes at cellular levels that require diffusion rates as input.(241)

Taken together, new insight into the dynamics of biomolecules under crowded conditions from the simulations is a significant degree of heterogeneity in the diffusion on microsecond time scales, while other findings so far are largely confirming more general observations that are known already from experiments. We believe that simulations are especially valuable for describing how dynamics varies over different time scales in the presence of crowding. This will require that more efforts are made to extend future simulations of crowded systems well into the tens of microseconds regime which is technically becoming possible with specialized hardware such as the Anton 2 supercomputer.(242)

Solvent Properties

Most of the simulations discussed here involve explicit solvent. Therefore, the analysis of how crowding and cellular environments affects solvent properties is straightforward. The first realization from such analysis is that bulk-like water, defined here as water molecules beyond the second solvation layer from the closest macromolecular solute, only represents a small fraction under cellular conditions with macromolecular concentrations of 30–40% vol.(26) For concentrations beyond 40% vol, even water molecules in the second solvation layer become rare. This means that under crowded conditions most of the water is either in the first solvation shell in direct contact with a macromolecular solute or sufficiently close to still experience the electric field of a solute (see Figure 3). While this has only a minor impact on water structure, analyzed in terms of pairwise radial distribution and hydrogen bonding,(26, 29) water dynamics has been found to be more strongly altered. According to the simulations, self-diffusion of water is reduced and residence times are increased significantly upon crowding.(26, 29) Further analysis suggest that the crowding effects vary with the size of the protein crowders.(172) Smaller proteins led to a more pronounced slowdown in dynamics than large proteins at the same volume fraction, essentially as a result of larger protein surface areas for the smaller crowders.

Figure 3. Interfacial water under crowded conditions with one (1) or two (2) layers of water between noninteracting proteins.

As a further indication of reduced dynamics, the dielectric response of water is also lowered to values between 20 and 60,(26) in agreement with experimental measurements.(146) The dielectric response of the entire cellular environment is more difficult to assess. Polar and charged metabolites and ions may increase the polarizability,(207) while proteins with interior dielectric constants lower than pure water(243, 244) would be expected to reduce the overall dielectric response. A net decrease in the dielectric response in cellular environment would also be consistent with a tendency toward native-state destabilization with a partial loss of the hydrophobic core and an increase in secondary structure formation as discussed above.

Taken together, the simulations suggest that solvent exhibits significantly altered properties in crowded environments which in turn is expected to affect biomolecular structure, dynamics, and function. The general idea is that crowding reduces water dynamics and lowers the dielectric response which in turn suggests a reduced hydrophobic effect in crowded cellular environments. There is limited experimental data consistent with this picture,(146) but further experimental probes that quantify solvent dynamics and describe electrostatic properties under crowded conditions are needed to validate the theoretical predictions.(32)

Limitations and Failures with Current Simulations

Since most simulations on crowded cellular systems lack direct experimental validation so far, it is difficult to assess how realistic the predictions made by the simulations really are. We expect that the overall picture of altered conformational landscapes and reduced diffusional dynamics as a result of intermolecular interactions with crowders is largely correct but there are indications that protein–protein interactions could be too strong(177) and that there is a bias toward the sampling of compact states vs more disordered states due to force field artifacts(180, 191, 220-222) limiting the ability to accurately describe conformational ensembles of peptides and proteins under crowded conditions. Ongoing force field improvements are aimed at addressing such problems.(186) The other major issue are the relatively short time scales in the atomistic simulations published to date that have largely limited the study of dynamics to sub-microsecond time scales. Although longer time scales can be reached with coarse-grained models,(154, 155) such models do not provide as much detailed insight and a major challenge going forward is how to extend atomistic simulations of crowded systems further into the μs–ms regime. Quantitative studies of dynamics are also affected by the venerable three-site TIP3P and SPC/E water models in common use today that do not describe viscosity and dielectric properties of water as well as newer, more expensive four- and five-site models.(245, 246) The use of the newer water models may appear straightforward, but the main challenge is that the current force fields will need to be reparametrized to be compatible with these water models while the higher computational costs due to the additional sites further limit the time scales that can be reached in simulations.

Connections with Experiment

The recent detailed atomistic simulations of crowded cellular environments have been motivated and enabled by experiments in the growing field of cellular structural biology.(24, 38, 39, 41, 42, 44-46, 54, 56, 85, 247) There are increasing opportunities now to advance the field by complementing the experiments with simulations,(143, 170, 171) where the role of simulations is ideally to provide more detailed insights and make predictions that can then be validated via additional experiments. Especially new NMR and fluorescence experiments(5, 6, 15, 17, 19, 20, 22, 44, 48-50, 52, 54, 56, 71, 73, 75, 82, 84, 92, 105, 108, 132, 248) are well suited to connect simulations with experiments as the experimental observables can be extracted easily from simulations and the high resolution in both spatial and temporal scales, especially with NMR, matches the level of detail in MD results well. As the experiments offer insights into biomolecular structures under concentrated conditions in vitro and in vivo, simulations can provide additional details about the exact mechanisms by which the structure and dynamics of a given system may be altered as a result of quinary interactions with cellular environments. Simulations are in principle able to combine dynamic and structural analyses for a given protein in the presence of crowders and make a direct connection with how crowding interactions lead to a modified structural ensemble. One advantage of simulations is that even minor populations can be observed that could be more difficult to detect experimentally and simulations can, at least in principle, pinpoint and quantify which interactions with other molecules in a more complex cell-like environment are most relevant for explaining crowding effects observed, for example, via in-cell NMR experiments. It is also possible to consider a variety of mutants for both the protein that is studied and the crowder proteins to obtain a more detailed view of how individual residues contribute to crowding effects. The results of such simulations would then lead directly back to experimentally testable hypotheses with respect to mutant proteins predicted to exhibit altered susceptibility to crowding effects.

As new simulations and experiments of cell-like environments have just recently begun to emerge in parallel, there are not many examples of direct comparisons yet as different systems have been studied via experiment and simulation. Focusing both sides, experiments and simulations, on the same systems in the same environments will be necessary to lead to more productive and meaningful interactions. However, coordinating experiments and simulations is not without challenges. Experimental systems may involve large crowders such as bovine serum albumin (BSA) that are computationally costly to study via simulation or involve complex in vivo environments that are basically impossible to reproduce exactly in silico. On the other hand, some computational studies involve systems that are difficult to prepare or analyze experimentally such as highly concentrated protein solutions(171) or involve probe molecules at low concentrations in highly complex environments.(173) Nevertheless, there are questions raised by recent simulations that could be tested experimentally, such as, for example, the idea that the two domains of phosphoglucokinase are closer in cellular environments because of electrostatic effects,(173) and variations in secondary structure propensities as a function of crowder interactions.(95, 96) On the other hand, recent experiments of altered protein stabilities of small proteins like CI2,(22) protein L,(73) protein G,(71) and SH3(48) in the presence of protein crowders as well as cosolute and crowding effects on the binding energetics of a dimer-forming protein G variant,(68) just to give some examples, are a strong motivation for simulations to determine the exact mechanisms by which destabilization occurs.

Finally, direct imaging methods are rapidly advancing in recent years and super-resolution microscopy(249) and high-resolution cryo-electron microscopy(250) are primed to study the structure and dynamics of cellular environments, especially if the resolution both in space and time can be further increased.

Next Steps

Detailed simulations of crowded cellular environments have so far largely focused on proteins and protein crowders. There is also some insight into the role of metabolites as cosolvents under crowded conditions, but there is clearly room for additional studies to explore how metabolites may modulate biomolecular structure and dynamics in crowded environments. A related and possibly more important question is how metabolites behave in the presence of high concentrations of biomolecules where there are ample opportunities for nonspecific interactions that could reduce effective concentrations and distract from finding enzyme active sites. Insight into such questions would be especially relevant for understanding the dynamics of drug molecules where the kinetics of reaching a given target site is a key determinant of efficacy and important for understanding the mechanisms of unfavorable potential side effects.

Other largely unexplored questions revolve around interactions with nucleic acids, membranes, and cytoskeletal components. Some studies are hinting at crowding effects altering the structure and dynamics of DNA and RNA,(103, 104) but how the presence of nucleic acids in the cellular interior affects proteins that do not specifically bind DNA or RNA is unclear. Chromosomal DNA fills a large part of bacterial cells(251-253) and most cytoplasmic proteins will not be able to avoid nonspecific interactions with the DNA, yet there is almost no insight, especially from simulation, how that may affect protein diffusion and/or stability. The major challenge in addressing such questions is the lack of realistic high-resolution molecular models of chromosomal DNA.

Membrane protein crowding has received some attention with limited insights from simulations.(148, 254, 255) However, interactions between membranes and crowded cellular interiors are unclear. For example, one may wonder how nonmembrane binding proteins that are pushed to interact with membranes simply by virtue of cellular crowding maintain their stability and whether they become kinetically trapped or gain fluidity by facing a membrane bilayer instead of a crowded cytoplasm. It is also possible that the structure and dynamics of membranes themselves are affected by the presence of a crowded cytoplasm, little of which has been explored so far. Clearly, this is a wide open area that is ripe for detailed atomistic simulations to generate insights and guide experiments.

The ultimate goal is a molecular-level understanding of entire cells. Fully atomistic whole-cell simulations, at least for bacterial cells, are not too far from reality. However, a larger impact will probably be realized by using the detailed insights from atomistic simulations of cellular environments to build more simplified models that capture the essential physics but scale to longer time scales and allow the exploration of biological questions by the broader community without requiring access to extreme high-performance computing environments. Computationally tractable, yet physically realistic in silico whole-cell models also offer much potential for transforming rational drug design protocols that up to now largely rely on single molecules and highly empirical approaches.(256, 257)

The authors declare no competing financial interest.

Acknowledgment

Funding was provided by the National Institute of Health Grants R01 GM084953 and GM103695 (to M.F.), the National Science Foundation Grant MCB 1330560 (to M.F.), the Fund from the High Performance Computing Infrastructure (HPCI) Strategic Program (hp120309, hp130003, hp140229, hp150233) and HPCI general trial use project (hp150145, hp160120) and FLAGSHIP 2020 project focused area 1 “Innovative drug discovery infrastructure through functional control of biomolecular systems” (hp160207, hp170254) of the Ministry of Education, Culture, Sports, Science and Technology (MEXT) (to Y.S.), a Grant-in-Aid for Scientific Research on Innovative Areas “Novel measurement techniques for visualizing “live” protein molecules at work” (No. 26119006) (to Y.S.), a grant from JST CREST on “Structural Life Science and Advanced Core Technologies for Innovative Life Science Research” (to Y.S.), RIKEN QBiC, iTHES, and Dynamic Structural Biology (to Y.S.), a Grant-in-Aid for Scientific Research (C) from MEXT (No. 25410025) (to I.Y.). Computer time was used at NSF XSEDE facilities (TG-MCB090003).

Reference QuickView

References

This article references 257 other publications.

1.
Gershenson, A.; Gierasch, L. M. Protein Folding in the Cell: Challenges and Progress Curr. Opin. Struct. Biol. 2011, 21, 32– 41 DOI: 10.1016/j.sbi.2010.11.001
[Crossref], [PubMed], [CAS]
1.
Protein folding in the cell: challenges and progress
Gershenson, Anne; Gierasch, Lila M.
Current Opinion in Structural Biology (2011), 21 (1), 32-41CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)
It is hard to imagine a more extreme contrast than that between the dil. solns. used for in vitro studies of protein folding and the crowded, compartmentalized, sticky, spatially inhomogeneous interior of a cell. This review highlights recent research exploring protein folding in the cell with a focus on issues that are generally not relevant to in vitro studies of protein folding, such as macromol. crowding, hindered diffusion, cotranslational folding, mol. chaperones, and evolutionary pressures. The tech. obstacles that must be overcome to characterize protein folding in the cell are driving methodol. advances, and we draw attention to several examples, such as fluorescence imaging of folding in cells and genetic screens for in-cell stability.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhvFKhur4%253D&md5=77ecb5ca7410a80ce167c49c5186d89c
2.
Wirth, A. J.; Gruebele, M. Quinary Protein Structure and the Consequences of Crowding in Living Cells: Leaving the Test-Tube Behind BioEssays 2013, 35, 984– 993 DOI: 10.1002/bies.201300080
[Crossref], [PubMed], [CAS]
2.
Quinary protein structure and the consequences of crowding in living cells: Leaving the test-tube behind
Wirth, Anna Jean; Gruebele, Martin
BioEssays (2013), 35 (11), 984-993CODEN: BIOEEJ; ISSN:0265-9247. (Wiley-Blackwell)
A review. Although the importance of weak protein-protein interactions has been understood since the 1980s, scant attention has been paid to this "quinary structure". The transient nature of quinary structure facilitates dynamic sub-cellular organization through loose grouping of proteins with multiple binding partners. Despite our growing appreciation of the quinary structure paradigm in cell biol., we do not yet understand how the many forces inside the cell - the excluded vol. effect, the "stickiness" of the cytoplasm, and hydrodynamic interactions - perturb the weakest functional protein interactions. We discuss the unresolved problem of how the forces in the cell modulate quinary structure, and to what extent the cell has evolved to exert control over the weakest biomol. interactions. We conclude by highlighting the new exptl. and computational tools coming online for in vivo studies, which are a crit. next step if we are to understand quinary structure in its native environment.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhs1eltLfL&md5=16887cd981a6f37058d31ed4d08bae8a
3.
Mittal, S.; Chowhan, R. K.; Singh, L. R. Macromolecular Crowding: Macromolecules Friend or Foe Biochim. Biophys. Acta, Gen. Subj. 2015, 1850, 1822– 1831 DOI: 10.1016/j.bbagen.2015.05.002
[Crossref], [PubMed], [CAS]
3.
Macromolecular crowding: Macromolecules friend or foe
Mittal, Shruti; Chowhan, Rimpy Kaur; Singh, Laishram Rajendrakumar
Biochimica et Biophysica Acta, General Subjects (2015), 1850 (9), 1822-1831CODEN: BBGSB3; ISSN:0304-4165. (Elsevier B.V.)
A review. The cellular interior is known to be densely crowded due to the presence of sol. and insol. macromols., which altogether occupy ∼40% of the total cellular vol. This results in altered biol. properties of macromols. Macromol. crowding is obsd. to have both pos. and neg. effects on protein folding, structure, stability, and function. Significant data has been accumulated so far on both the aspects. However, most of the review articles so far have focused on the pos. aspects of macromol. crowding and not much attention has been paid on the deleterious aspects of crowding on macromols. In order to have a complete knowledge of the effect of macromol. crowding on proteins and enzymes, it is important to look into both aspects of crowding to det. its precise role under physiol. conditions. To fill the gap in the understanding of the effect of macromol. crowding on proteins and enzymes, the authors focus on the deleterious influence of crowding on macromols. Macromol. crowding is not always good but also has several deleterious effects on various macromol. properties. Taken together, the properties of biol. macromols. in vivo appears to be finely regulated by the nature and level of the intracellular crowdedness in order to perform their biol. functions appropriately. The information provided here gives an understanding of the role played by the nature and level of cellular crowdedness in intensifying and/or alleviating the burden of various proteopathies.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXotlGrs78%253D&md5=314e9d2494a9b78056ced86aaeccb6f9
4.
Spitzer, J.; Pielak, G. J.; Poolman, B. Emergence of Life: Physical Chemistry Changes the Paradigm Biol. Direct 2015, 10, 33 DOI: 10.1186/s13062-015-0060-y
[Crossref], [PubMed], [CAS]
4.
Emergence of life: Physical chemistry changes the paradigm
Spitzer Jan; Pielak Gary J; Poolman Bert
Biology direct (2015), 10 (), 33 ISSN:.
Origin of life research has been slow to advance not only because of its complex evolutionary nature (Franklin Harold: In Search of Cell History, 2014) but also because of the lack of agreement on fundamental concepts, including the question of 'what is life?'. To re-energize the research and define a new experimental paradigm, we advance four premises to better understand the physicochemical complexities of life's emergence: (1) Chemical and Darwinian (biological) evolutions are distinct, but become continuous with the appearance of heredity. (2) Earth's chemical evolution is driven by energies of cycling (diurnal) disequilibria and by energies of hydrothermal vents. (3) Earth's overall chemical complexity must be high at the origin of life for a subset of (complex) chemicals to phase separate and evolve into living states. (4) Macromolecular crowding in aqueous electrolytes under confined conditions enables evolution of molecular recognition and cellular self-organization. We discuss these premises in relation to current 'constructive' (non-evolutionary) paradigm of origins research - the process of complexification of chemical matter 'from the simple to the complex'. This paradigm artificially avoids planetary chemical complexity and the natural tendency of molecular compositions toward maximum disorder embodied in the second law of thermodynamics. Our four premises suggest an empirical program of experiments involving complex chemical compositions under cycling gradients of temperature, water activity and electromagnetic radiation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2Mbit1Cjtg%253D%253D&md5=45c877baf38074ac63aeaf90f518da27
5.
Heyden, M.; Ebbinghaus, S.; Winter, R. Das Innere der Zelle: Ein komplexes Lösungsmittel Chem. Unserer Zeit 2017, 51, 26– 33 DOI: 10.1002/ciuz.201700777
[Crossref], [CAS]
5.
The interior of the cell: a complex solvent, biochemical reactions under physiological and extreme conditions
Heyden, Matthias; Ebbinghaus, Simon; Winter, Roland
Chemie in Unserer Zeit (2017), 51 (1), 26-33CODEN: CUNZAW; ISSN:0009-2851. (Wiley-VCH Verlag GmbH & Co. KGaA)
The interior of a living cell is very distinct from dil. aq. solns. that are often used to study the function of proteins and enzymes exptl. Here, we discuss novel exptl. techniques and modeling approaches that provide a deeper understanding of the effects of crowding, intermol. interactions, and the influence of osmolytes in realistic biol. environments, including cells. Further, we discuss adaptation mechanisms involving in-cell solvation environments to extreme conditions, such as high pressure in the deep sea, and their relevance to biotechnol.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXitlCmsro%253D&md5=02b36643a803dcfca673667ffea6a432
6.
Gnutt, D.; Ebbinghaus, S. The Macromolecular Crowding Effect – From in vitro into the Cell Biol. Chem. 2016, 397, 37– 44 DOI: 10.1515/hsz-2015-0161
[Crossref], [PubMed], [CAS]
6.
The macromolecular crowding effect - from in vitro into the cell
Gnutt, David; Ebbinghaus, Simon
Biological Chemistry (2016), 397 (1), 37-44CODEN: BICHF3; ISSN:1431-6730. (Walter de Gruyter GmbH)
A review. The influence of the cellular milieu, a complex and crowded solvent, is often neglected when biomol. structure and function were studied in vitro. To mimic the cellular environment, crowding effects are commonly induced in vitro using artificial crowding agents like Ficoll or dextran. However, it is unclear if such effects are also obsd. in cellulo. Diverging results on protein stability in living cells point out the need for new quant. methods to study the contributions of excluded vol. and nonspecific interactions to the cellular crowding effect. New crowding sensitive probes may be used to directly study crowding effects in living cells. Moreover, processes where crowding effects could play a crucial role in mol. cell biol. are discussed.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhvFKjtbrO&md5=8b56225658ea332d61b4cdaca219a457
7.
Shahid, S.; Hassan, M. I.; Islam, A.; Ahmad, F. Size-Dependent Studies of Macromolecular Crowding on the Thermodynamic Stability, Structure and Functional Activity of Proteins: In vitro and in silico Approaches Biochim. Biophys. Acta, Gen. Subj. 2017, 1861, 178– 197 DOI: 10.1016/j.bbagen.2016.11.014
[Crossref], [PubMed], [CAS]
7.
Size-dependent studies of macromolecular crowding on the thermodynamic stability, structure and functional activity of proteins: in vitro and in silico approaches
Shahid, Sumra; Hassan, Md. Imtaiyaz; Islam, Asimul; Ahmad, Faizan
Biochimica et Biophysica Acta, General Subjects (2017), 1861 (2), 178-197CODEN: BBGSB3; ISSN:0304-4165. (Elsevier B.V.)
A review. The environment inside cells in which proteins fold and function are quite different from that of the dil. buffer solns. often used during in vitro expts. The presence of large amts. of macromols. of varying shapes, sizes and compns. makes the intracellular milieu extremely crowded. The overall concn. of macromols. ranges from 50 to 400 g l- 1, and they occupy 10-40% of the total cellular vol. These differences in solvent conditions and the level of crowdedness resulting in excluded vol. effects can have significant consequences on proteins' biophys. properties. A question that arises is: how important is it to examine the roles of shape, size and compn. of macromol. crowders in altering the biol. properties of proteins. This review article aims at focusing, gathering and summarizing all of the research investigations done by means of in vitro and in silico approaches taking into account the size-dependent influence of the crowders on proteins' properties. Altogether, the internal architecture of macromol. crowding environment including size, shape and concn. of crowders, appears to be playing an extremely important role in causing changes in the biol. processes. Most often the small sized crowders have been found more effective crowding agents. However, thermodn. stability, structure and functional activity of proteins have been governed by vol. exclusion as well as soft (chem.) interactions. The article provides an understanding of importance of internal architecture of the cellular environment in altering the biophys. properties of proteins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvVeqtLjP&md5=8a7c9832134a0e760ae0846ff8e721ff
8.
Minton, A. P. The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media J. Biol. Chem. 2001, 276, 10577– 10580 DOI: 10.1074/jbc.R100005200
[Crossref], [PubMed], [CAS]
8.
The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media
Minton, Allen P.
Journal of Biological Chemistry (2001), 276 (14), 10577-10580CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
A review, with 48 refs., on the influence of macromol. crowding and macromol. confinement on biochem. reactions in physiol. media.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXjvFCqtr8%253D&md5=719bbc7f7d4e18ba22fbf1c7d2ec65f8
9.
Minton, A. P. Models for Excluded Volume Interaction Between an Unfolded Protein and Rigid Macromolecular Cosolutes: Macromolecular Crowding and Protein Stability Revisited Biophys. J. 2005, 88, 971– 985 DOI: 10.1529/biophysj.104.050351
[Crossref], [PubMed], [CAS]
9.
Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: macromolecular crowding and protein stability revisited
Minton, Allen P.
Biophysical Journal (2005), 88 (2), 971-985CODEN: BIOJAU; ISSN:0006-3495. (Biophysical Society)
Statistical-thermodn. models for the excluded vol. interaction between an unfolded polypeptide chain and a hard sphere or hard rod cosolute are presented, permitting estn. of the free energy of transfer of a polypeptide chain with fixed radius of gyration from a dil. (ideal) soln. to a soln. contg. vol. fraction Φ of either cosolute. Also presented is a general thermodn. description of the equil. between a unique native state and a manifold of unfolded or partially unfolded states of a protein distinguished by their resp. radii of gyration. Together with results of a Monte Carlo calcn. of the distribution of radii of gyration of four different unfolded proteins published by Goldenberg in 2003, these models are used to est. the effect of intermol. excluded vol. upon an exptl. measurable apparent two-state const. for equil. between native and nonnative conformations of each of the four proteins, and upon the exptl. measurable root mean-square radius of gyration of the unfolded protein. Model calcns. predict that addn. of inert cosolutes at vol. fractions exceeding 0.1 stabilizes the native state relative to unfolded states by an amt. that increases strongly with Φ and with the size of the native protein relative to the size of inert cosolute, and results in significant compaction of the manifold of unfolded states. Predicted effects are in qual. and/or semiquant. accord with the results of several published exptl. studies.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXhtlyjsbw%253D&md5=bb58d024641a0599e6f210b19ed10066
10.
Zhou, H.-X.; Rivas, G.; Minton, A. P. Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences Annu. Rev. Biophys. 2008, 37, 375– 397 DOI: 10.1146/annurev.biophys.37.032807.125817
[Crossref], [PubMed], [CAS]
10.
Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences
Zhou, Huan-Xiang; Rivas, German; Minton, Allen P.
Annual Review of Biophysics (2008), 37 (), 375-397CODEN: ARBNCV ISSN:. (Annual Reviews Inc.)
A review. Expected and obsd. effects of vol. exclusion on the free energy of rigid and flexible macromols. in crowded and confined systems, and consequent effects of crowding and confinement on macromol. reaction rates and equil. are summarized. Findings from relevant theor./simulation and exptl. literature published from 2004 onward are reviewed. Addnl. complexity arising from the heterogeneity of local environments in biol. media, and the presence of nonspecific interactions between macromols. over and above steric repulsion, are discussed. Theor. and exptl. approaches to the characterization of crowding- and confinement-induced effects in systems approaching the complexity of living organisms are suggested.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXnsVGlurg%253D&md5=2e1fe7edb342b273b68868b02a8d137b
11.
Cheung, M. S.; Klimov, D.; Thirumalai, D. Molecular Crowding Enhances Native State Stability and Refolding Rates of Globular Proteins Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 4753– 4758 DOI: 10.1073/pnas.0409630102
[Crossref], [PubMed], [CAS]
11.
Molecular crowding enhances native state stability and refolding rates of globular proteins
Cheung, Margaret S.; Klimov, Dmitri; Thirumalai, D.
Proceedings of the National Academy of Sciences of the United States of America (2005), 102 (13), 4753-4758CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
The presence of macromols. in cells geometrically restricts the available space for polypeptide chains. To study the effects of macromol. crowding on folding thermodn. and kinetics, we used an off-lattice model of the all-β-sheet WW domain in the presence of large spherical particles whose interaction with the polypeptide chain is purely repulsive. At all vol. fractions, .vphi.c, of the crowding agents the stability of the native state is enhanced. Remarkably, the refolding rates, which are larger than the value at .vphi.c = 0, increase nonmonotonically as .vphi.c increases, reaching a max. at .vphi.c = .vphi.*c. At high values of .vphi.c, the depletion-induced intramol. attraction produces compact structures with considerable structure in the denatured state. Changes in native state stability and folding kinetics at .vphi.c can be quant. mapped onto confinement in a vol.-fraction-dependent spherical pore with radius Rs ≈ (4π/3.vphi.c)1/3 Rc (Rc is the radius of the crowding particles) as long as .vphi.c ≤ .vphi.*c. We show that the extent of native state stabilization at finite .vphi.c is comparable with that in a spherical pore. In both situations, rate enhancement is due to destabilization of the denatured states with respect to .vphi.c = 0.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXjt1Ohsr4%253D&md5=7a997f7688c11127d053b1973a6325e9
12.
Stagg, L.; Zhang, S. Q.; Cheung, M. S.; Wittung-Stafshede, P. Molecular Crowding Enhances Native Structure and Stability of α/β Protein Flavodoxin Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 18976– 18981 DOI: 10.1073/pnas.0705127104
[Crossref], [PubMed], [CAS]
12.
Molecular crowding enhances native structure and stability of α/β protein flavodoxin
Stagg, Loren; Zhang, Shao-Qing; Cheung, Margaret S.; Wittung-Stafshede, Pernilla
Proceedings of the National Academy of Sciences of the United States of America (2007), 104 (48), 18976-18981CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
To investigate the consequences of macromol. crowding on the behavior of a globular protein, the authors performed a combined exptl. and computational study on the 148-residue single-domain α/β protein, Desulfovibrio desulfuricans apoflavodoxin (I). In vitro thermal unfolding expts., as well as assessment of I native and denatured structures, were probed by using far-UV CD in the presence of various amts. of Ficoll 70, an inert spherical crowding agent. Ficoll 70 had a concn.-dependent effect on the thermostability of I (ΔTm of 20° at 400 mg/mL; pH 7). As judged by CD, the addn. of Ficoll 70 caused an increase in the amt. of secondary structure in the native state ensemble (pH 7, 20°), but only minor effects on the denatured state. Theor. calcns., based on an off-lattice model and hard-sphere particles, were in good agreement with the in vitro data. The simulations demonstrated that, in the presence of 25% vol. occupancy of spheres, native I was thermally stabilized, and the free energy landscape shifted to favor more compact structures in both the native and denatured states. The difference contact map revealed that the native state compaction originated in stronger interactions between the helixes and the central β-sheet, as well as by less fraying in the terminal helixes. Thus, this study demonstrates that macromol. crowding has structural effects on the folded ensemble of polypeptides.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhsVSru7nL&md5=5e78b0c1ff64e81f9eb3004d73b6d398
13.
Mukherjee, S. K.; Gautam, S.; Biswas, S.; Kundu, J.; Chowdhury, P. K. Do Macromolecular Crowding Agents Exert only an Excluded Volume Effect? A Protein Solvation Study J. Phys. Chem. B 2015, 119, 14145– 14156 DOI: 10.1021/acs.jpcb.5b09446
[ACS Full Text ], [CAS]
13.
Do macromolecular crowding agents exert only an excluded volume effect? A protein solvation study
Mukherjee, Sanjib K.; Gautam, Saurabh; Biswas, Saikat; Kundu, Jayanta; Chowdhury, Pramit K.
Journal of Physical Chemistry B (2015), 119 (44), 14145-14156CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
The effect of macromol. crowding on protein structure and dynamics has mostly been explained on the basis of the excluded vol. effect, its origin being entropic. In recent times a progressive shift in this view has been taking place with increasing emphasis on soft interactions that are enthalpic by nature. Here, using very low concns. (1-10 g/L) of both synthetic (dextran- and poly(ethylene glycol) (PEG)-based) and protein (α-synuclein and myoglobin)-based crowders, the authors showed that the solvation of the fluorescent probe mol., 1-anilinonaphthalene-8-sulfonate) (ANS) bound to bovine serum albumin (BSA) and human serum albumin (HSA) was significantly modulated in both a protein- and crowder-dependent fashion. Since under such conditions the effect of excluded vol. is appreciably low, the authors propose that their observations are direct evidence of soft interactions between the macromol. crowding agents used and the serum proteins. Moreover, the data revealed, that since at these low crowder concns. major perturbations to the protein structure are unlikely to take place while minor perturbations might not be readily visible, protein solvation provides a unique spectral signature for capturing such local dynamics, thereby allowing one to decouple hard-sphere interactions from soft sphere ones. Furthermore, since fast fluctuations are known to play a major role in detg. the functional characteristics of proteins and enzymes, these results suggest that such motions are prone to be modulated even when the cellular crowding conditions are quite relaxed. In other words, by the time the excluded vol. effects come into the picture in the physiol. milieu, modulations of functionally important protein motions that need a relatively lower activation energy have already taken place as a result of the aforementioned enthalpic (soft) interactions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhs1ejsL3J&md5=9ee9c9bbfc3ceac2fce4ced31022e352
14.
Luh, L. M.; Hänsel, R.; Löhr, F.; Kirchner, D. K.; Krauskopf, K.; Pitzius, S.; Schäfer, B.; Tufar, P.; Corbeski, I.; Güntert, P. Molecular Crowding Drives Active Pin1 into Nonspecific Complexes with Endogenous Proteins Prior to Substrate Recognition J. Am. Chem. Soc. 2013, 135, 13796– 13803 DOI: 10.1021/ja405244v
[ACS Full Text ], [CAS]
14.
Molecular Crowding Drives Active Pin1 into Nonspecific Complexes with Endogenous Proteins Prior to Substrate Recognition
Luh, Laura M.; Haensel, Robert; Loehr, Frank; Kirchner, Donata K.; Krauskopf, Katharina; Pitzius, Susanne; Schaefer, Birgit; Tufar, Peter; Corbeski, Ivan; Guentert, Peter; Doetsch, Volker
Journal of the American Chemical Society (2013), 135 (37), 13796-13803CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Proteins and nucleic acids maintain the crowded interior of a living cell and can reach concns. in the order of 200-400 g/L which affects the physicochem. parameters of the environment, such as viscosity and hydrodynamic as well as nonspecific strong repulsive and weak attractive interactions. Dynamics, structure, and activity of macromols. were demonstrated to be affected by these parameters. However, it remains controversially debated, which of these factors are the dominant cause for the obsd. alterations in vivo. In this study we investigated the globular folded peptidyl-prolyl isomerase Pin1 in Xenopus laevis oocytes and in native-like crowded oocyte ext. by in-cell NMR spectroscopy. We show that active Pin1 is driven into nonspecific weak attractive interactions with intracellular proteins prior to substrate recognition. The substrate recognition site of Pin1 performs specific and nonspecific attractive interactions. Phosphorylation of the WW domain at Ser16 by PKA abrogates both substrate recognition and the nonspecific interactions with the endogenous proteins. Our results validate the hypothesis formulated by McConkey that the majority of globular folded proteins with surface charge properties close to neutral under physiol. conditions reside in macromol. complexes with other sticky proteins due to mol. crowding. In addn., we demonstrate that commonly used synthetic crowding agents like Ficoll 70 are not suitable to mimic the intracellular environment due to their incapability to simulate biol. important weak attractive interactions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhtlWltbvJ&md5=204de3485971a3441a87fe796d8ba2bb
15.
Senske, M.; Tork, L.; Born, B.; Havenith, M.; Herrmann, C.; Ebbinghaus, S. Protein Stabilization by Macromolecular Crowding through Enthalpy rather than Entropy J. Am. Chem. Soc. 2014, 136, 9036– 9041 DOI: 10.1021/ja503205y
[ACS Full Text ], [CAS]
15.
Protein stabilization by macromolecular crowding through enthalpy rather than entropy
Senske, Michael; Toerk, Lisa; Born, Benjamin; Havenith, Martina; Herrmann, Christian; Ebbinghaus, Simon
Journal of the American Chemical Society (2014), 136 (25), 9036-9041CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The interior of the cell is a densely crowded environment in which protein stability is affected differently than in dil. soln. Macromol. crowding is commonly understood in terms of an entropic vol. exclusion effect based on hardcore repulsions among the macromols. Here, the authors studied the thermal unfolding of ubiquitin in the presence of different cosolutes (glucose, dextran, poly(ethylene glycol), KCl, and urea). The results showed that for a correct dissection of the cosolute-induced changes of the free energy into its enthalpic and entropic contributions, the temp. dependence of the heat capacity change needs to be explicitly taken into account. In contrast to the prediction by excluded vol. theory, the authors obsd. an enthalpic stabilization and an entropic destabilization for glucose, dextran, and poly(ethylene glycol). The enthalpic stabilization mechanism induced by the macromol. crowder, dextran, was similar to the enthalpic stabilization mechanism of its monomeric building block, glucose. In the case of poly(ethylene glycol), entropy was dominating over enthalpy leading to an overall destabilization. The authors propose a new model to classify cosolute effects in terms of their enthalpic contributions to protein stability.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXpt1Klsb0%253D&md5=d176e4869b69d1e442528c9bc1c1758a
16.
Cohen, R. D.; Pielak, G. J. Electrostatic Contributions to Protein Quinary Structure J. Am. Chem. Soc. 2016, 138, 13139– 13142 DOI: 10.1021/jacs.6b07323
[ACS Full Text ], [CAS]
16.
Electrostatic Contributions to Protein Quinary Structure
Cohen, Rachel D.; Pielak, Gary J.
Journal of the American Chemical Society (2016), 138 (40), 13139-13142CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
There are 4 well-known levels of protein structure: primary (amino acid sequence), secondary (helixes, sheets, and turns), tertiary (3-dimensional structure) and quaternary (specific protein-protein interactions). The 5th level remains largely undefined because characterization of quinary structure, the transient but essential macromol. interactions that organize the crowded cellular interior, requires the measurement of equil. thermodn. parameters in living cells. The authors have overcome this challenge by quantifying the pH-dependence of quinary interactions in living Escherichia coli cells using the B1 domain of protein G (GB1, 6.2 kDa). To accomplish this goal, the authors buffered the cellular interior and used NMR-detected amide proton exchange to quantify the free energy of unfolding in cells. At neutral pH, the unfolding free energy in cells was comparable to that in buffered soln. As the pH decreased, the increased no. of attractive interactions between E. coli proteins and GB1 destabilized the protein in cells relative to buffer alone. The data showed that electrostatic interactions contribute to quinary structure.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsFyntrnO&md5=411728f6ee44e3896bfc8eb670157390
17.
Monteith, W. B.; Cohen, R. D.; Smith, A. E.; Guzman-Cisneros, E.; Pielak, G. J. Quinary Structure Modulates Protein Stability in Cells Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 1739– 1742 DOI: 10.1073/pnas.1417415112
[Crossref], [PubMed], [CAS]
17.
Quinary structure modulates protein stability in cells
Monteith, William B.; Cohen, Rachel D.; Smith, Austin E.; Guzman-Cisneros, Emilio; Pielak, Gary J.
Proceedings of the National Academy of Sciences of the United States of America (2015), 112 (6), 1739-1742CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
Protein quinary interactions organize the cellular interior and its metab. Although the interactions stabilizing secondary, tertiary, and quaternary protein structure are well defined, details about the protein-matrix contacts that comprise quinary structure remain elusive. This gap exists because proteins function in a crowded cellular environment, but are traditionally studied in simple buffered solns. Here, the authors used NMR-detected H/D exchange to quantify quinary interactions between the B1 domain of protein G and the cytosol of Escherichia coli. The authors demonstrated that a surface mutation in this protein was 10-fold more destabilizing in cells than in buffer, a surprising result that firmly establishes the significance of quinary interactions. Remarkably, the energy involved in these interactions could be as large as the energies that stabilize specific protein complexes. These results will drive the crit. task of implementing quinary structure into models for understanding the proteome.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVeiu7c%253D&md5=54134a35a9130de2493af23ea0d0475d
18.
Sarkar, M.; Pielak, G. J. An Osmolyte Mitigates the Destabilizing Effect of Protein Crowding Protein Sci. 2014, 23, 1161– 1164 DOI: 10.1002/pro.2510
[Crossref], [PubMed], [CAS]
18.
An osmolyte mitigates the destabilizing effect of protein crowding
Sarkar, Mohona; Pielak, Gary J.
Protein Science (2014), 23 (9), 1161-1164CODEN: PRCIEI; ISSN:1469-896X. (Wiley-Blackwell)
Most theories predict that macromol. crowding stabilizes globular proteins, but recent studies show that weak attractive interactions can result in crowding-induced destabilization. Osmolytes are ubiquitous in biol. and help protect cells against stress. Given that dehydration stress adds to the crowded nature of the cytoplasm, we speculated that cells might use osmolytes to overcome the destabilization caused by the increased weak interactions that accompany desiccation. We used NMR-detected amide proton exchange expts. to measure the stability of the test protein chymotrypsin inhibitor 2 under physiol. relevant crowded conditions in the presence and absence of the osmolyte glycine betaine. The osmolyte overcame the destabilizing effect of the cytosol. This result provides a physiol. relevant explanation for the accumulation of osmolytes by dehydration-stressed cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtlaisrnI&md5=b967e1531dc5cc34ee6c5f414dc90787
19.
Sarkar, M.; Lu, J.; Pielak, G. J. Protein Crowder Charge and Protein Stability Biochemistry 2014, 53, 1601– 1606 DOI: 10.1021/bi4016346
[ACS Full Text ], [CAS]
19.
Protein crowder charge and protein stability
Sarkar, Mohona; Lu, Joe; Pielak, Gary J.
Biochemistry (2014), 53 (10), 1601-1606CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
Macromol. crowding effects arise from steric repulsions and weak, nonspecific, chem. interactions. Steric repulsions stabilize globular proteins, but the effect of chem. interactions depends on their nature. Repulsive interactions such as those between similarly charged species should reinforce the effect of steric repulsions, increasing the equil. thermodn. stability of a test protein. Attractive chem. interactions, on the other hand, counteract the effect of hard-core repulsions, decreasing stability. Here, the authors tested these ideas by using anionic proteins from Escherichia coli as crowding agents and assessing the stability of the anionic test protein, chymotrypsin inhibitor 2, at pH 7.0. The anionic protein crowders destabilized the test protein despite the similarity of their net charges. Thus, weak, nonspecific, attractive interactions between proteins can overcome the charge-charge repulsion and counterbalance the stabilizing effect of steric repulsion.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXislentbs%253D&md5=a0ad133826dea503051ed6785b7d372e
20.
Wang, Y.; Sarkar, M.; Smith, A. E.; Krois, A. S.; Pielak, G. J. Macromolecular Crowding and Protein Stability J. Am. Chem. Soc. 2012, 134, 16614– 16618 DOI: 10.1021/ja305300m
[ACS Full Text ], [CAS]
20.
Macromolecular Crowding and Protein Stability
Wang, Yaqiang; Sarkar, Mohona; Smith, Austin E.; Krois, Alexander S.; Pielak, Gary J.
Journal of the American Chemical Society (2012), 134 (40), 16614-16618CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
An understanding of cellular chem. requires knowledge of how crowded environments affect proteins. The influence of crowding on protein stability arises from two phenomena, hard-core repulsions and soft (i.e., chem.) interactions. Most efforts to understand crowding effects on protein stability, however, focus on hard-core repulsions, which are inherently entropic and stabilizing. We assessed these phenomena by measuring the temp. dependence of NMR-detected amide proton exchange and used these data to ext. the entropic and enthalpic contributions of crowding to the stability of ubiquitin. Contrary to expectations, the contribution of chem. interactions is large and in many cases dominates the contribution from hardcore repulsions. Our results show that both chem. interactions and hard-core repulsions must be considered when assessing the effects of crowding and help explain previous observations about protein stability and dynamics in cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xhtlaju7bJ&md5=1e353634324d951bf6b2131955a510d1
21.
Benton, L. A.; Smith, A. E.; Young, G. B.; Pielak, G. J. Unexpected Effects of Macromolecular Crowding on Protein Stability Biochemistry 2012, 51, 9773– 9775 DOI: 10.1021/bi300909q
[ACS Full Text ], [CAS]
21.
Unexpected effects of macromolecular crowding on protein stability
Benton, Laura A.; Smith, Austin E.; Young, Gregory B.; Pielak, Gary J.
Biochemistry (2012), 51 (49), 9773-9775CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
Most theories about macromol. crowding focus on 2 ideas: the macromol. nature of the crowder and entropy. For proteins, the vol. excluded by the crowder favors compact native states over expanded denatured states, enhancing protein stability by decreasing the entropy of unfolding. Here, the authors tested these ideas with the widely used crowding agent Ficoll-70 and its monomer, sucrose. Contrary to expectations, Ficoll and sucrose had approx. the same stabilizing effect on chymotrypsin inhibitor 2. Furthermore, the stabilization was driven by enthalpy, not entropy. These results point to the need for carefully controlled studies and more sophisticated theories for understanding crowding effects.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xhs12mt7fL&md5=6748b278f6206b1353d670ce1270588a
22.
Miklos, A. C.; Sarkar, M.; Wang, Y.; Pielak, G. J. Protein Crowding Tunes Protein Stability J. Am. Chem. Soc. 2011, 133, 7116– 7120 DOI: 10.1021/ja200067p
[ACS Full Text ], [CAS]
22.
Protein crowding tunes protein stability
Miklos, Andrew C.; Sarkar, Mohona; Wang, Yaqiang; Pielak, Gary J.
Journal of the American Chemical Society (2011), 133 (18), 7116-7120CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Thirty percent of a cell's vol. is filled with macromols., and protein chem. in a crowded environment is predicted to differ from that in dil. soln. Here, the authors quantified the effect of crowding by globular proteins on the equil. thermodn. stability of a small globular protein. Theory has long predicted that crowding should stabilize proteins, and expts. using synthetic polymers as crowders show such stabilizing effects. Here, the authors examd. the effects of 2 globular proteins, bovine serum albumin and hen egg-white lysozyme, as crowding agents of the small globular protein, chymotrypsin inhibitor 2 (CI2). The authors found that the protein crowders could be mildly destabilizing to CI2. The destabilization arose from a competition between stabilizing excluded-vol. effects and destabilizing nonspecific interactions, including electrostatic interactions. This competition resulted in tunable stability, which could impact the understanding of the spatial and temporal roles of proteins in living systems.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXkvFyktbk%253D&md5=cabe174bbbcc6d7aabe3d7a5d5aaf54d
23.
Inomata, K.; Ohno, A.; Tochio, H.; Isogai, S.; Tenno, T.; Nakase, I.; Takeuchi, T.; Futaki, S.; Ito, Y.; Hiroaki, H. High-Resolution Multi-Dimensional NMR Spectroscopy of Proteins in Human Cells Nature 2009, 458, 106– 111 DOI: 10.1038/nature07839
[Crossref], [PubMed], [CAS]
23.
High-resolution multi-dimensional NMR spectroscopy of proteins in human cells
Inomata, Kohsuke; Ohno, Ayako; Tochio, Hidehito; Isogai, Shin; Tenno, Takeshi; Nakase, Ikuhiko; Takeuchi, Toshihide; Futaki, Shiroh; Ito, Yutaka; Hiroaki, Hidekazu; Shirakawa, Masahiro
Nature (London, United Kingdom) (2009), 458 (7234), 106-109CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
In-cell NMR is an isotope-aided multi-dimensional NMR technique that enables observations of conformations and functions of proteins in living cells at the at. level. This method has been successfully applied to proteins overexpressed in bacteria, providing information on protein-ligand interactions and conformations. However, the application of in-cell NMR to eukaryotic cells has been limited to Xenopus laevis oocytes. Wider application of the technique is hampered by inefficient delivery of isotope-labeled proteins into eukaryote somatic cells. Here the authors describe a method to obtain high-resoln. two-dimensional (2D) heteronuclear NMR spectra of proteins inside living human cells. Proteins were delivered to the cytosol by the pyrenebutyrate-mediated action of cell-penetrating peptides linked covalently to the proteins. The proteins were subsequently released from cell-penetrating peptides by endogenous enzymic activity or by autonomous reductive cleavage. The heteronuclear 2D spectra of three different proteins inside human cells demonstrate the broad application of this technique to studying interactions and protein processing. The in-cell NMR spectra of FKBP12 (also known as FKBP1A) show the formation of specific complexes between the protein and extracellularly administered immunosuppressants, demonstrating the utility of this technique in drug screening programs. Moreover, in-cell NMR spectroscopy demonstrates that ubiquitin has much higher hydrogen exchange rates in the intracellular environment, possibly due to multiple interactions with endogenous proteins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXis1Kitrs%253D&md5=742caa2c1c1cea832f1aeed3754afa8d
24.
Sakakibara, D.; Sasaki, A.; Ikeya, T.; Hamatsu, J.; Hanashima, T.; Mishima, M.; Yoshimasu, M.; Hayashi, N.; Mikawa, T.; Walchli, M. Protein Structure Determination in Living Cells by In-Cell NMR Spectroscopy Nature 2009, 458, 102– 105 DOI: 10.1038/nature07814
[Crossref], [PubMed], [CAS]
24.
Protein structure determination in living cells by in-cell NMR spectroscopy
Sakakibara, Daisuke; Sasaki, Atsuko; Ikeya, Teppei; Hamatsu, Junpei; Hanashima, Tomomi; Mishima, Masaki; Yoshimasu, Masatoshi; Hayashi, Nobuhiro; Mikawa, Tsutomu; Waelchli, Markus; Smith, Brian O.; Shirakawa, Masahiro; Guentert, Peter; Ito, Yutaka
Nature (London, United Kingdom) (2009), 458 (7234), 102-105CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Investigating proteins at work in a living environment at at. resoln. is a major goal of mol. biol., which has not been achieved even though methods for the three-dimensional (3D) structure detn. of purified proteins in single crystals or in soln. are widely used. Recent developments in NMR hardware and methodol. have enabled the measurement of high-resoln. heteronuclear multi-dimensional NMR spectra of macromols. in living cells (in-cell NMR). Various intracellular events such as conformational changes, dynamics and binding events have been investigated by this method. However, the low sensitivity and the short lifetime of the samples have so far prevented the acquisition of sufficient structural information to det. protein structures by in-cell NMR. Here the authors show the first, to the authors' knowledge, 3D protein structure calcd. exclusively on the basis of information obtained in living cells. The structure of the putative heavy-metal binding protein TTHA1718 from Thermus thermophilus HB8 overexpressed in Escherichia coli cells was solved by in-cell NMR. Rapid measurement of the 3D NMR spectra by nonlinear sampling of the indirectly acquired dimensions was used to overcome problems caused by the instability and low sensitivity of living E. coli samples. Almost all of the expected backbone NMR resonances and most of the side-chain NMR resonances were obsd. and assigned, enabling high quality (0.96 Å backbone root mean squared deviation) structures to be calcd. that are very similar to the in vitro structure of TTHA1718 detd. independently. The in-cell NMR approach can thus provide accurate high-resoln. structures of proteins in living environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXis1Kisb8%253D&md5=30f991c0a2b04e3dc878c8c4229e50f5
25.
Gnutt, D.; Gao, M.; Brylski, O.; Heyden, M.; Ebbinghaus, S. Excluded-Volume Effects in Living Cells Angew. Chem., Int. Ed. 2015, 54, 2548– 2551 DOI: 10.1002/anie.201409847
[Crossref], [PubMed], [CAS]
25.
Excluded-Volume Effects in Living Cells
Gnutt, David; Gao, Mimi; Brylski, Oliver; Heyden, Matthias; Ebbinghaus, Simon
Angewandte Chemie, International Edition (2015), 54 (8), 2548-2551CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
Biomols. evolve and function in densely crowded and highly heterogeneous cellular environments. Such conditions are often mimicked in the test tube by the addn. of artificial macromol. crowding agents. Still, it is unclear if such cosolutes indeed reflect the physicochem. properties of the cellular environment as the in-cell crowding effect has not yet been quantified. The authors have developed a macromol. crowding sensor based on a FRET-labeled polymer to probe the macromol. crowding effect inside single living cells. Surprisingly, excluded-vol. effects, although obsd. in the presence of artificial crowding agents, do not lead to a compression of the sensor in the cell. The av. conformation of the sensor is similar to that in aq. buffer soln. and cell lysate. However, the in-cell crowding effect is distributed heterogeneously and changes significantly upon cell stress. The authors present a tool to systematically study the in-cell crowding effect as a modulator of biomol. reactions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXntFI%253D&md5=227ff92edaede60a345166c8be70fd91
26.
Harada, R.; Sugita, Y.; Feig, M. Protein Crowding Affects Hydration Structure and Dynamics J. Am. Chem. Soc. 2012, 134, 4842– 4849 DOI: 10.1021/ja211115q
[ACS Full Text ], [CAS]
26.
Protein Crowding Affects Hydration Structure and Dynamics
Harada, Ryuhei; Sugita, Yuji; Feig, Michael
Journal of the American Chemical Society (2012), 134 (10), 4842-4849CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The effect of protein crowding on the structure and dynamics of water was examd. from explicit solvent mol. dynamics simulations of a series of protein G and protein G/villin systems at different protein concns. Hydration structure was analyzed in terms of radial distribution functions, three-dimensional hydration sites, and preservation of tetrahedral coordination. Anal. of hydration dynamics focused on self-diffusion rates and dielec. consts. as a function of crowding. The results show significant changes in both structure and dynamics of water under highly crowded conditions. The structure of water is altered mostly beyond the first solvation shell. Diffusion rates and dielec. consts. are significantly reduced following linear trends as a function of crowding reflecting highly constrained water in crowded environments. The reduced dynamics of diffusion is expected to be strongly related to hydrodynamic properties of crowded cellular environments while the reduced dielec. const. under crowded conditions has implications for the stability of biomols. in crowded environments. The results from this study suggest a prescription for modeling solvation in simulations of cellular environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XisFShsrs%253D&md5=162711cda59bf02ed866f1ad8290edce
27.
Tanizaki, S.; Clifford, J.; Connelly, B. D.; Feig, M. Conformational Sampling of Peptides in Cellular Environments Biophys. J. 2008, 94, 747– 759 DOI: 10.1529/biophysj.107.116236
[Crossref], [PubMed], [CAS]
27.
Conformational sampling of peptides in cellular environments
Tanizaki, Seiichiro; Clifford, Jacob; Connelly, Brian D.; Feig, Michael
Biophysical Journal (2008), 94 (3), 747-759CODEN: BIOJAU; ISSN:0006-3495. (Biophysical Society)
Biol. systems provide a complex environment that can be understood in terms of its dielec. properties. High concns. of macromols. and cosolvents effectively reduce the dielec. const. of cellular environments, thereby affecting the conformational sampling of biomols. To examine this effect in more detail, the conformational preference of alanine dipeptide, poly-alanine, and melittin in different dielec. environments is studied with computer simulations based on recently developed generalized Born methodol. Results from these simulations suggest that extended conformations are favored over α-helical conformations at the dipeptide level at and below dielec. consts. of 5-10. Furthermore, lower-dielec. environments begin to significantly stabilize helical structures in poly-alanine at ε = 20. In the more complex peptide melittin, different dielec. environments shift the equil. between two main conformations: a nearly fully extended helix that is most stable in low dielecs. and a compact, V-shaped conformation consisting of two helixes that is preferred in higher dielec. environments. An addnl. conformation is only found to be significantly populated at intermediate dielec. consts. Good agreement with previous studies of different peptides in specific, less-polar solvent environments, suggest that helix stabilization and shifts in conformational preferences in such environments are primarily due to a reduced dielec. environment rather than specific mol. details. The findings presented here make predictions of how peptide sampling may be altered in dense cellular environments with reduced dielec. response.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhsVahs78%253D&md5=7be12fe4c095a68be64193e627230fa4
28.
King, J. T.; Arthur, E. J.; Brooks, C. L.; Kubarych, K. J. Crowding Induced Collective Hydration of Biological Macromolecules over Extended Distances J. Am. Chem. Soc. 2014, 136, 188– 194 DOI: 10.1021/ja407858c
[ACS Full Text ], [CAS]
28.
Crowding Induced Collective Hydration of Biological Macromolecules over Extended Distances
King, John T.; Arthur, Evan J.; Brooks, Charles L., III; Kubarych, Kevin J.
Journal of the American Chemical Society (2014), 136 (1), 188-194CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Ultrafast two-dimensional IR (2D-IR) spectroscopy reveals picosecond protein and hydration dynamics of crowded hen egg white lysozyme (HEWL) labeled with a metal-carbonyl vibrational probe covalently attached to a solvent accessible His residue. HEWL is systematically crowded alternatively with polyethylene glycol (PEG) or excess lysozyme in order to distinguish the chem. inert polymer from the complex electrostatic profile of the protein crowder. The results are threefold: (1) A sharp dynamical jamming-like transition is obsd. in the picosecond protein and hydration dynamics that is attributed to an independent-to-collective hydration transition induced by macromol. crowding that slows the hydration dynamics up to an order of magnitude relative to bulk water. (2) The interprotein distance at which the transition occurs suggests collective hydration of proteins over distances of 30-40 Å. (3) Comparing the crowding effects of PEG400 to our previously reported expts. using glycerol exposes fundamental differences between small and macromol. crowding agents.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvFegtr7I&md5=74a36e97894b85bead6e3e7a84134d71
29.
Lu, C.; Prada-Gracia, D.; Rao, F. Structure and Dynamics of Water in Crowded Environments Slows Down Peptide Conformational Changes J. Chem. Phys. 2014, 141, 045101 DOI: 10.1063/1.4891465
[Crossref], [PubMed], [CAS]
29.
Structure and dynamics of water in crowded environments slows down peptide conformational changes
Lu, Cheng; Prada-Gracia, Diego; Rao, Francesco
Journal of Chemical Physics (2014), 141 (4), 045101/1-045101/6CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
The concn. of macromols. inside the cell is high with respect to conventional in vitro expts. or simulations. In an effort to characterize the effects of crowding on the thermodn. and kinetics of disordered peptides, mol. dynamics simulations were run at different concns. by varying the no. of identical weakly interacting peptides inside the simulation box. The authors found that the presence of crowding did not influence very much the overall thermodn. On the other hand, peptide conformational dynamics was found to be strongly affected, resulting in a dramatic slowing down at larger concns. The observation of long-lived water bridges between peptides at higher concns. points to a nontrivial role of the solvent in the altered peptide kinetics. These results reinforce the idea for an active role of water in mol. crowding, an effect that is expected to be relevant for problems influenced by large solvent exposure areas like in intrinsically disordered proteins. (c) 2014 American Institute of Physics.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXht1ChtbzI&md5=89b5c9721c70df849a58d7bb14f65d26
30.
Qi, H. W.; Nakka, P.; Chen, C.; Radhakrishnan, M. L. The Effect of Macromolecular Crowding on the Electrostatic Component of Barnase–Barstar Binding: A Computational, Implicit Solvent-Based Study PLoS One 2014, 9, e98618 DOI: 10.1371/journal.pone.0098618
[Crossref], [PubMed], [CAS]
30.
The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study
Qi, Helena W.; Nakka, Priyanka; Chen, Connie; Radhakrishnan, Mala L.
PLoS One (2014), 9 (6), e98618/1-e98618/11, 11 pp.CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)
Macromol. crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded vol., entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder-protein interactions and changes in solvation properties. In this work, we explore the effects of macromol. crowding on the electrostatic desolvation and solvent-screened interaction components of protein-protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase-barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aq. environment. On av., we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a const. crowder d. (fraction of total available vol. occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the mol. surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qual. similar to those using a lowered "effective" solvent dielec. to account for crowding, although the "best" effective dielec. const. will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qual. intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhs1aru7nL&md5=873d8803cca9ba489db1efd87b533b53
31.
Kim, Y. C.; Mittal, J. Crowding Induced Entropy-Enthalpy Compensation in Protein Association Equilibria Phys. Rev. Lett. 2013, 110, 208102 DOI: 10.1103/PhysRevLett.110.208102
[Crossref], [PubMed], [CAS]
31.
Crowding induced entropy-enthalpy compensation in protein association equilibria
Kim, Young C.; Mittal, Jeetain
Physical Review Letters (2013), 110 (20), 208102/1-208102/5CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
A statistical mech. theory is presented to predict the effects of macromol. crowding on protein assocn. equil., accounting for both excluded vol. and attractive interactions between proteins and crowding mols. Predicted binding free energies are in excellent agreement with simulation data over a wide range of crowder sizes and packing fractions. It is shown that attractive interactions between proteins and crowding agents counteract the stabilizing effects of excluded vol. interactions. A crit. attraction strength, for which there is no net effect of crowding, is approx. independent of the crowder packing fraction.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXpsFWhu7k%253D&md5=69c69ca1eb19593938054797aca0a991
32.
Zhang, N.; An, L.; Li, J.; Liu, Z.; Yao, L. Quinary Interactions Weaken the Electric Field Generated by Protein Side-Chain Charges in the Cell-like Environment J. Am. Chem. Soc. 2017, 139, 647– 654 DOI: 10.1021/jacs.6b11058
[ACS Full Text ], [CAS]
32.
Quinary Interactions Weaken the Electric Field Generated by Protein Side-Chain Charges in the Cell-like Environment
Zhang, Ning; An, Liaoyuan; Li, Jingwen; Liu, Zhijun; Yao, Lishan
Journal of the American Chemical Society (2017), 139 (2), 647-654CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The intramol. elec. field (e-field) generated by the 56-residue third Ig domain of protein G - also known as protein GB3 - side chain charges K/E10, K/E19, and D/K40 was measured in the absence or presence of macromol. crowding. The e-field responds differently to different crowding agents, dextran, Ficoll, BSA, and E. coli cell lysate. Dextran and Ficoll have no effect on the e-field. The lysate generally weakens the e-field but the amplitude of weakening varies greatly. For example, the e-field by K19 is reduced by 67% in the presence of 90 g/L lysate, corresponding to a charge change from 0.9 to 0.3 e for K19, whereas the e-fields by D/K40 are weakened only by ∼7% under the same lysate concn. The extent of the e-field weakening by BSA is in between that by Ficoll (dextran) and lysate. Further investigations suggest that the e-field weakening mechanism by lysate is similar to that by NaCl. That is, the e-field generated by a protein surface charge affects the distribution of lysate which creates a reaction field and weakens the protein e-field. Our study indicates that the protein electrostatic property can be changed significantly due to quinary interaction with the cell environment.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXivVSitQ%253D%253D&md5=2d0d6e4ef31d0e63ad1d917c44c872cb
33.
Ando, T.; Yu, I.; Feig, M.; Sugita, Y. Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model J. Phys. Chem. B 2016, 120, 11856– 11865 DOI: 10.1021/acs.jpcb.6b06243
[ACS Full Text ], [CAS]
33.
Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model
Ando, Tadashi; Yu, Isseki; Feig, Michael; Sugita, Yuji
Journal of Physical Chemistry B (2016), 120 (46), 11856-11865CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
The cytoplasm of a cell is crowded with many different kinds of macromols. The macromol. crowding affects the thermodn. and kinetics of biol. reactions in a living cell, such as protein folding, assocn., and diffusion. Theor. and simulation studies using simplified models focus on the essential features of the crowding effects and provide a basis for analyzing exptl. data. In most of the previous studies on crowding effects, a uniform crowder size was assumed, which was in contrast to the inhomogeneous size distribution of macromols. in a living cell. Here, the authors evaluated free energy changes upon macromol. assocn. in a cell-like inhomogeneous crowding system via a theory of hard-sphere fluids and free energy calcns. using Brownian dynamics trajectories. The inhomogeneous crowding model based on 41 different types of macromols. represented by spheres with different radii mimicked the physiol. concns. of macromols. in the cytoplasm of Mycoplasma genitalium. The free energy changes of macromol. assocn. evaluated by the theory and simulations were in good agreement with each other. The crowder size distribution affected both specific and nonspecific mol. assocns., suggesting that not only the vol. fraction but also the size distribution of macromols. are important factors for evaluating in vivo crowding effects. This study related in vitro expts. on macromol. crowding to in vivo crowding effects by using the theory of hard-sphere fluids with crowder-size heterogeneity.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhslOhsbvM&md5=4536bc7a2aa68017abe86437d849d62f
34.
Kondrat, S.; Zimmermann, O.; Wiechert, W.; von Lieres, E. The Effect of Composition on Diffusion of Macromolecules in a Crowded Environment Phys. Biol. 2015, 12, 046003 DOI: 10.1088/1478-3975/12/4/046003
[Crossref], [PubMed], [CAS]
34.
The effect of composition on diffusion of macromolecules in a crowded environment
Kondrat, Svyatoslav; Zimmermann, Olav; Wiechert, Wolfgang; von Lieres, Eric
Physical Biology (2015), 12 (4), 046003/1-046003/6CODEN: PBHIAT; ISSN:1478-3975. (IOP Publishing Ltd.)
We study diffusion of macromols. in a crowded cytoplasm-like environment, focusing on its dependence on compn. and its crossover to the anomalous subdiffusion. The crossover and the diffusion itself depend on both the vol. fraction and the relative concn. of macromols. In accordance with previous theor. and exptl. studies, diffusion slows down when the vol. fraction increases. Contrary to expectations, however, the diffusion is also strongly dependent on the mol. compn. The crossover time decreases and diffusion slows down when the smaller macromols. start to dominate. Interestingly, diffusion is faster in a cytoplasm-like (more polydisperse) system than it is in a two-component system, at comparable packing fractions, or even when the cytoplasm packing fraction is larger.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhtl2isbjI&md5=8d99312b337b9c4e50b9f062da9d1f7d
35.
Ellis, R. J.; Minton, A. P. Cell Biology - Join the Crowd Nature 2003, 425, 27– 28 DOI: 10.1038/425027a
[Crossref], [PubMed], [CAS]
35.
Cell biology: Join the crowd
Ellis, R. John; Minton, Allen P.
Nature (London, United Kingdom) (2003), 425 (6953), 27-28CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
There is no expanded citation for this reference.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3sXmvFaguro%253D&md5=f026034ad6bcdb687c686778f5ddda80
36.
Gershenson, A. Deciphering Protein Stability in Cells J. Mol. Biol. 2014, 426, 4– 6 DOI: 10.1016/j.jmb.2013.10.004
[Crossref], [PubMed], [CAS]
36.
Deciphering Protein Stability in Cells
Gershenson, Anne
Journal of Molecular Biology (2014), 426 (1), 4-6CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)
A review. Recently developed methods allow to study relative roles of physiol. environment, protein interactions, protein localization, protein lifetime and other factors that help shape the in-cell energy landscape of proteins detg. in-cell conformational distributions, stabilities and folding kinetics. One method, FReI (fast relaxation imaging), developed by Dr. Gruebele and colleagues, allows real-time measurements of protein thermal stability and folding kinetics in living cells with high spatial resoln.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhs1yrurbF&md5=ab477146f0b20459a4cea98e603b8163
37.
Cedeño, C.; Pauwels, K.; Tompa, P. Protein Delivery into Plant Cells: Toward in vivo Structural Biology Front. Plant Sci. 2017, 8, 519 DOI: 10.3389/fpls.2017.00519
[Crossref], [PubMed], [CAS]
37.
Protein Delivery into Plant Cells: Toward In vivo Structural Biology
Cedeno Cesyen; Pauwels Kris; Tompa Peter; Cedeno Cesyen; Pauwels Kris; Tompa Peter; Tompa Peter
Frontiers in plant science (2017), 8 (), 519 ISSN:.
Understanding the biologically relevant structural and functional behavior of proteins inside living plant cells is only possible through the combination of structural biology and cell biology. The state-of-the-art structural biology techniques are typically applied to molecules that are isolated from their native context. Although most experimental conditions can be easily controlled while dealing with an isolated, purified protein, a serious shortcoming of such in vitro work is that we cannot mimic the extremely complex intracellular environment in which the protein exists and functions. Therefore, it is highly desirable to investigate proteins in their natural habitat, i.e., within live cells. This is the major ambition of in-cell NMR, which aims to approach structure-function relationship under true in vivo conditions following delivery of labeled proteins into cells under physiological conditions. With a multidisciplinary approach that includes recombinant protein production, confocal fluorescence microscopy, nuclear magnetic resonance (NMR) spectroscopy and different intracellular protein delivery strategies, we explore the possibility to develop in-cell NMR studies in living plant cells. While we provide a comprehensive framework to set-up in-cell NMR, we identified the efficient intracellular introduction of isotope-labeled proteins as the major bottleneck. Based on experiments with the paradigmatic intrinsically disordered proteins (IDPs) Early Response to Dehydration protein 10 and 14, we also established the subcellular localization of ERD14 under abiotic stress.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC1crjvVansA%253D%253D&md5=ddfea2064c066920a9aa51a364749c4b
38.
Pastore, A.; Temussi, P. A. The Emperor’s New Clothes: Myths and Truths of In-Cell NMR. Arch. Biochem. Biophys. 2017, in press. DOI: DOI: 10.1016/j.abb.2017.02.008 .
[Crossref], [PubMed]
There is no corresponding record for this reference.
39.
Hänsel, R.; Luh, L. M.; Corbeski, I.; Trantirek, L.; Dötsch, V. In-Cell NMR and EPR Spectroscopy of Biomacromolecules Angew. Chem., Int. Ed. 2014, 53, 10300– 10314 DOI: 10.1002/anie.201311320
[Crossref], [PubMed], [CAS]
39.
In-cell NMR and EPR spectroscopy of biomacromolecules
Hansel Robert; Luh Laura M; Corbeski Ivan; Trantirek Lukas; Dotsch Volker
Angewandte Chemie (International ed. in English) (2014), 53 (39), 10300-14 ISSN:.
The dream of cell biologists is to be able to watch biological macromolecules perform their duties in the intracellular environment of live cells. Ideally, the observation of both the location and the conformation of these macromolecules with biophysical techniques is desired. The development of many fluorescence techniques, including superresolution fluorescence microscopy, has significantly enhanced our ability to spot proteins and other molecules in the crowded cellular environment. However, the observation of their structure and conformational changes while they attend their business is still very challenging. In principle, NMR and EPR spectroscopy can be used to investigate the conformation and dynamics of biological macromolecules in living cells. The development of in-cell magnetic resonance techniques has demonstrated the feasibility of this approach. Herein we review the different techniques with a focus on liquid-state in-cell NMR spectroscopy, provide an overview of applications, and discuss the challenges that lie ahead.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2cbmslSjsg%253D%253D&md5=5322f96d50560e7ee1430c28b024e4af
40.
Ikeya, T.; Hanashima, T.; Hosoya, S.; Shimazaki, M.; Ikeda, S.; Mishima, M.; Güntert, P.; Ito, Y. Improved In-Cell Structure Determination of Proteins at Near-Physiological Concentration Sci. Rep. 2016, 6, 38312 DOI: 10.1038/srep38312
[Crossref], [PubMed], [CAS]
40.
Improved in-cell structure determination of proteins at near-physiological concentration
Ikeya, Teppei; Hanashima, Tomomi; Hosoya, Saori; Shimazaki, Manato; Ikeda, Shiro; Mishima, Masaki; Guntert, Peter; Ito, Yutaka
Scientific Reports (2016), 6 (), 38312CODEN: SRCEC3; ISSN:2045-2322. (Nature Publishing Group)
Investigating three-dimensional (3D) structures of proteins in living cells by in-cell NMR (NMR) spectroscopy opens an avenue towards understanding the structural basis of their functions and phys. properties under physiol. conditions inside cells. In-cell NMR provides data at at. resoln. non-invasively, and has been used to detect protein-protein interactions, thermodn. of protein stability, the behavior of intrinsically disordered proteins, etc. in cells. However, so far only a single de novo 3D protein structure could be detd. based on data derived only from in-cell NMR. Here we introduce methods that enable in-cell NMR protein structure detn. for a larger no. of proteins at concns. that approach physiol. ones. The new methods comprise (1) advances in the processing of non-uniformly sampled NMR data, which reduces the measurement time for the intrinsically short-lived in-cell NMR samples, (2) automatic chem. shift assignment for obtaining an optimal resonance assignment, and (3) structure refinement with Bayesian inference, which makes it possible to calc. accurate 3D protein structures from sparse data sets of conformational restraints. As an example application we detd. the structure of the B1 domain of protein G at about 250 μM concn. in living E. coli cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XitFWnsrbF&md5=cf4169cda5d50fb68c7a3da872870eda
41.
Li, C.; Liu, M. Protein Dynamics in Living Cells Studied by In-Cell NMR Spectroscopy FEBS Lett. 2013, 587, 1008– 1011 DOI: 10.1016/j.febslet.2012.12.023
[Crossref], [PubMed], [CAS]
41.
Protein dynamics in living cells studied by in-cell NMR spectroscopy
Li, Conggang; Liu, Maili
FEBS Letters (2013), 587 (8), 1008-1011CODEN: FEBLAL; ISSN:0014-5793. (Elsevier B.V.)
A review. Most proteins function in cells where protein concns. can reach 400 g/l. However, most quant. studies of protein properties are performed in idealized, dil. conditions. Recently developed in-cell NMR techniques can provide protein structure and other biophys. properties inside living cells at at. resoln. Here we review how protein dynamics, including global and internal motions have been characterized by in-cell NMR, and then discuss the remaining challenges and future directions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsFCrsLc%253D&md5=c879117586e64efde125ec44858e911a
42.
Luchinat, E.; Banci, L. In-Cell NMR: A Topical Review IUCrJ 2017, 4, 108– 118 DOI: 10.1107/S2052252516020625
[Crossref], [PubMed], [CAS]
42.
In-cell NMR: a topical review
Luchinat, Enrico; Banci, Lucia
IUCrJ (2017), 4 (2), 108-118CODEN: IUCRAJ; ISSN:2052-2525. (International Union of Crystallography)
Classical structural biol. approaches allow structural characterization of biol. macromols. in vitro, far from their physiol. context. Nowadays, thanks to the wealth of structural data available and to technol. and methodol. advances, the interest of the research community is gradually shifting from pure structural detn. towards the study of functional aspects of biomols. Therefore, a cellular structural approach is ideally needed to characterize biol. mols., such as proteins, in their native cellular environment and the functional processes that they are involved in. In-cell NMR is a new application of high-resoln. NMR spectroscopy that allows structural and dynamical features of proteins and other macromols. to be analyzed directly in living cells. Owing to its challenging nature, this methodol. has shown slow, but steady, development over the past 15 years. To date, several in-cell NMR approaches have been successfully applied to both bacterial and eukaryotic cells, including several human cell lines, and important structural and functional aspects have been elucidated. In this topical review, the major advances of in-cell NMR are summarized, with a special focus on recent developments in eukaryotic and mammalian cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXjsF2qsLs%253D&md5=6aad5db9292fa82e4490b7e01f7e8f42
43.
Majumder, S.; Xue, J.; DeMott, C. M.; Reverdatto, S.; Burz, D. S.; Shekhtman, A. Probing Protein Quinary Interactions by In-Cell Nuclear Magnetic Resonance Spectroscopy Biochemistry 2015, 54, 2727– 2738 DOI: 10.1021/acs.biochem.5b00036
[ACS Full Text ], [CAS]
43.
Probing Protein Quinary Interactions by In-Cell Nuclear Magnetic Resonance Spectroscopy
Majumder, Subhabrata; Xue, Jing; DeMott, Christopher M.; Reverdatto, Sergey; Burz, David S.; Shekhtman, Alexander
Biochemistry (2015), 54 (17), 2727-2738CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
Historically introduced by McConkey to explain the slow mutation rate of highly abundant proteins, weak protein (quinary) interactions are an emergent property of living cells. The protein complexes that result from quinary interactions are transient and thus difficult to study biochem. in vitro. Cross-correlated relaxation-induced polarization transfer-based in-cell NMR allows the characterization of protein quinary interactions with at. resoln. inside live prokaryotic and eukaryotic cells. RNAs are an important component of protein quinary interactions. Protein quinary interactions are unique to the target protein and may affect physicochem. properties, protein activity, and interactions with drugs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXmslWjtrY%253D&md5=fc071a6ae1234a2ec2182baba7963fc0
44.
Müntener, T.; Häussinger, D.; Selenko, P.; Theillet, F.-X. In-Cell Protein Structures from 2D NMR Experiments J. Phys. Chem. Lett. 2016, 7, 2821– 2825 DOI: 10.1021/acs.jpclett.6b01074
[ACS Full Text ]
There is no corresponding record for this reference.
45.
Ohno, A.; Inomata, K.; Tochio, H.; Shirakawa, M. In-Cell NMR Spectroscopy in Protein Chemistry and Drug Discovery Curr. Top. Med. Chem. 2011, 11, 68– 73 DOI: 10.2174/156802611793611878
[Crossref], [PubMed], [CAS]
45.
In-cell NMR spectroscopy in protein chemistry and drug discovery
Ohno, Ayako; Inomata, Kohsuke; Tochio, Hidehito; Shirakawa, Masahiro
Current Topics in Medicinal Chemistry (Sharjah, United Arab Emirates) (2011), 11 (1), 68-73CODEN: CTMCCL; ISSN:1568-0266. (Bentham Science Publishers Ltd.)
A review. "In-cell NMR" is a unique method for characterization of conformation, interaction and dynamics of proteins inside living cells at at. level. Since the method was proposed by Dotch and co-workers in 2001(1), its application had been limited to bacterial cells and oocytes of Xenopus laevis(2). Recently, we reported the method for efficient delivery of 15N-labeled proteins into human HeLa cells by using cell-penetrating peptides, and measured high-resoln. two-dimensional 1H-15N correlation spectra of proteins in the cells. The in-cell NMR spectroscopy in human cells is capable of analyzing structures, interactions, dynamics and stability of proteins inside cells. Of its possible applications, we propose that in-cell NMR spectroscopy can be utilized as an effective step in protein-targeted drug development process, by demonstrating that interaction of FKBP12 with immunosuppressants administered extracellularly was successfully obsd. in living cells. This observation suggests that drug delivery and capability of target proteins inside cells for interaction with drugs can be investigated by in-cell NMR spectroscopy. More recently, an alternative way for intracellular delivery of labeled proteins for in-cell NMR was reported on 293F cells by Shimada and co-workers. Here, we review recent tech. development of in-cell NMR spectroscopy, and discuss potential usefulness for protein chem. and drug screening process.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXkslaiur0%253D&md5=a2522ea497e4ae06fe2717a22402d9df
46.
Rahman, S.; Byun, Y.; Hassan, M. I.; Kim, J.; Kumar, V. Towards Understanding Cellular Structure Biology: In-cell NMR Biochim. Biophys. Acta, Proteins Proteomics 2017, 1865, 547– 557 DOI: 10.1016/j.bbapap.2017.02.018
[Crossref], [PubMed], [CAS]
46.
Towards understanding cellular structure biology: In-cell NMR
Rahman, Safikur; Byun, Younhwa; Hassan, Md. Imtaiyaz; Kim, Jihoe; Kumar, Vijay
Biochimica et Biophysica Acta, Proteins and Proteomics (2017), 1865 (5), 547-557CODEN: BBAPBW; ISSN:1570-9639. (Elsevier B.V.)
A review. To watch biol. macromols. perform their functions inside the living cells is the dream of any biologists. In-cell NMR is a branch of biomol. NMR spectroscopy that can be used to observe the structures, interactions and dynamics of these mols. in the living cells at at. level. In principle, in-cell NMR can be applied to different cellular systems to achieve biol. relevant structural and functional information. In this review, we summarize the existing approaches in this field and discuss its applications in protein interactions, folding, stability and post-translational modifications. We hope this review will emphasize the effectiveness of in-cell NMR for studies of intricate biol. processes and for structural anal. in cellular environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXlvFyltLs%253D&md5=1ead6b5934d16d43c3aaa78d1a087287
47.
Sharaf, N. G.; Barnes, C. O.; Charlton, L. M.; Young, G. B.; Pielak, G. J. A Bioreactor for In-Cell Protein NMR J. Magn. Reson. 2010, 202, 140– 146 DOI: 10.1016/j.jmr.2009.10.008
[Crossref], [PubMed], [CAS]
47.
A bioreactor for in-cell protein NMR
Sharaf, Naima G.; Barnes, Christopher O.; Charlton, Lisa M.; Young, Gregory B.; Pielak, Gary J.
Journal of Magnetic Resonance (2010), 202 (2), 140-146CODEN: JMARF3; ISSN:1090-7807. (Elsevier B.V.)
The inside of the cell is a complex environment that is difficult to simulate when studying proteins and other mols. in vitro. The authors have developed a device and system that provides a controlled environment for NMR expts. involving living cells. The authors' device comprises 2 main parts, an NMR detection region and a circulation system. The flow of medium from the bottom of the device pushes alginate encapsulated cells into the circulation chamber. In the chamber, the exchange of oxygen and nutrients occurs between the media and the encapsulated cells. When the media flow is stopped, the encapsulated cells fall back into the NMR detection region, and spectra can be acquired. The authors have utilized the bioreactor to study the expression of the natively disordered protein α-synuclein, inside Escherichia coli cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhs1WgtbbP&md5=83d0799d6401b183be4f1524b5b8cff8
48.
Smith, A. E.; Zhou, L. Z.; Gorensek, A. H.; Senske, M.; Pielak, G. J. In-Cell Thermodynamics and a New Role for Protein Surfaces Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 1725– 1730 DOI: 10.1073/pnas.1518620113
[Crossref], [PubMed], [CAS]
48.
In-cell thermodynamics and a new role for protein surfaces
Smith, Austin E.; Zhou, Larry Z.; Gorensek, Annelise H.; Senske, Michael; Pielak, Gary J.
Proceedings of the National Academy of Sciences of the United States of America (2016), 113 (7), 1725-1730CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
There is abundant, physiol. relevant knowledge about protein cores; they are hydrophobic, exquisitely well-packed, and nearly all H-bonds are satisfied. An equivalent understanding of protein surfaces has remained elusive because proteins are almost exclusively studied in vitro in simple aq. solns. Here, the authors established the essential physiol. roles played by protein surfaces by measuring the equil. thermodn. and kinetics of protein folding in the complex environment of living Escherichia coli cells, and under physiol. relevant in vitro conditions. Fluorine NMR data on the 7-kDa globular N-terminal SH3 domain of Drosophila signal transduction protein drk (SH3) showed that charge-charge interactions were fundamental to protein stability and folding kinetics in cells. These results contradicted predictions from accepted theories of macromol. crowding and showed that cosolutes commonly used to mimic the cellular interior did not yield physiol. relevant information. As such, the authors provide the foundation for a complete picture of protein chem. in cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XmtVaitA%253D%253D&md5=e2789ab2b11225195cf19456fca7480f
49.
Danielsson, J.; Mu, X.; Lang, L.; Wang, H.; Binolfi, A.; Theillet, F.-X.; Bekei, B.; Logan, D. T.; Selenko, P.; Wennerström, H. Thermodynamics of Protein Destabilization in Live Cells Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 12402– 12407 DOI: 10.1073/pnas.1511308112
[Crossref], [PubMed], [CAS]
49.
Thermodynamics of protein destabilization in live cells
Danielsson, Jens; Mu, Xin; Lang, Lisa; Wang, Huabing; Binolfi, Andres; Theillet, Francois-Xavier; Bekei, Beata; Logan, Derek T.; Selenko, Philipp; Wennerstroem, Haakan; Oliveberg, Mikael
Proceedings of the National Academy of Sciences of the United States of America (2015), 112 (40), 12402-12407CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
Although protein folding and stability have been well explored under simplified conditions in vitro, it is yet unclear how these basic self-organization events are modulated by the crowded interior of live cells. To find out, we use here in-cell NMR to follow at at. resoln. the thermal unfolding of a β-barrel protein inside mammalian and bacterial cells. Challenging the view from in vitro crowding effects, we find that the cells destabilize the protein at 37° but with a conspicuous twist: while the melting temp. goes down the cold unfolding moves into the physiol. regime, coupled to an augmented heat-capacity change. The effect seems induced by transient, sequence-specific, interactions with the cellular components, acting preferentially on the unfolded ensemble. This points to a model where the in vivo influence on protein behavior is case specific, detd. by the individual protein's interplay with the functionally optimized "interaction landscape" of the cellular interior.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsFamsL%252FF&md5=758e77f5f11357b8dc40c779c385e242
50.
Smith, M. J.; Marshall, C. B.; Theillet, F.-X.; Binolfi, A.; Selenko, P.; Ikura, M. Real-Time NMR Monitoring of Biological Activities in Complex Physiological Environments Curr. Opin. Struct. Biol. 2015, 32, 39– 47 DOI: 10.1016/j.sbi.2015.02.003
[Crossref], [PubMed], [CAS]
50.
Real-time NMR monitoring of biological activities in complex physiological environments
Smith, Matthew J.; Marshall, Christopher B.; Theillet, Francois-Xavier; Binolfi, Andres; Selenko, Philipp; Ikura, Mitsuhiko
Current Opinion in Structural Biology (2015), 32 (), 39-47CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)
A review. Biol. reactions occur in a highly organized spatiotemporal context and with kinetics that are modulated by multiple environmental factors. To integrate these variables in the exptl. studies of native biol. activities, quant. tools for time-resolved in situ analyses in physiol. relevant settings are required. Here, the authors outline the use of high-resoln. NMR spectroscopy to directly observe biol. reactions in complex environments and in real-time. Specifically, how real-time NMR (RT-NMR) methods have delineated insights into metabolic processes, post-translational protein modifications, activities of cellular GTPases and their regulators, and of protein folding events are discussed.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXivFKjtbg%253D&md5=62266f4ba515b3306d7c5f04a1ee0d31
51.
Li, C.; Zhao, J.; Cheng, K.; Ge, Y.; Wu, Q.; Ye, Y.; Xu, G.; Zhang, Z.; Zheng, W.; Zhang, X. Magnetic Resonance Spectroscopy As a Tool for Assessing Macromolecular Structure and Function in Living Cells Annu. Rev. Anal. Chem. 2017, 10, 157– 182 DOI: 10.1146/annurev-anchem-061516-045237
[Crossref], [CAS]
51.
Magnetic Resonance Spectroscopy as a Tool for Assessing Macromolecular Structure and Function in Living Cells
Li Conggang; Zhao Jiajing; Cheng Kai; Ge Yuwei; Wu Qiong; Ye Yansheng; Xu Guohua; Zhang Zeting; Zheng Wenwen; Zhang Xu; Zhou Xin; Liu Maili; Pielak Gary
Annual review of analytical chemistry (Palo Alto, Calif.) (2017), 10 (1), 157-182 ISSN:.
Investigating the structure, modification, interaction, and function of biomolecules in their native cellular environment leads to physiologically relevant knowledge about their mechanisms, which will benefit drug discovery and design. In recent years, nuclear and electron magnetic resonance (NMR) spectroscopy has emerged as a useful tool for elucidating the structure and function of biomacromolecules, including proteins, nucleic acids, and carbohydrates in living cells at atomic resolution. In this review, we summarize the progress and future of in-cell NMR as it is applied to proteins, nucleic acids, and carbohydrates.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC1czntVamtA%253D%253D&md5=17a746c5bef47bed0a2ad577c7ddf3bc
52.
Smith, A. E.; Zhang, Z.; Pielak, G. J.; Li, C. NMR Studies of Protein Folding and Binding in Cells and Cell-Like Environments Curr. Opin. Struct. Biol. 2015, 30, 7– 16 DOI: 10.1016/j.sbi.2014.10.004
[Crossref], [PubMed], [CAS]
52.
NMR studies of protein folding and binding in cells and cell-like environments
Smith, Austin E.; Zhang, Zeting; Pielak, Gary J.; Li, Conggang
Current Opinion in Structural Biology (2015), 30 (), 7-16CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)
A review. Proteins function in cells where the concn. of macromols. can exceed 300 g/L. The ways in which this crowded environment affects the phys. properties of proteins remain poorly understood. We summarize recent NMR-based studies of protein folding and binding conducted in cells and in vitro under crowded conditions. Many of the observations can be understood in terms of interactions between proteins and the rest of the intracellular environment (i.e. quinary interactions). Nevertheless, NMR studies of folding and binding in cells and cell-like environments remain in their infancy. The frontier involves investigations of larger proteins and further efforts in higher eukaryotic cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhvVOkt7fE&md5=25281950380651f94332492fa8f82d12
53.
Xu, G.; Ye, Y.; Liu, X.; Cao, S.; Wu, Q.; Cheng, K.; Liu, M.; Pielak, G. J.; Li, C. Strategies for Protein NMR in Escherichia coli Biochemistry 2014, 53, 1971– 1981 DOI: 10.1021/bi500079u
[ACS Full Text ], [CAS]
53.
Strategies for Protein NMR in Escherichia coli
Xu, Guohua; Ye, Yansheng; Liu, Xiaoli; Cao, Shufen; Wu, Qiong; Cheng, Kai; Liu, Maili; Pielak, Gary J.; Li, Conggang
Biochemistry (2014), 53 (12), 1971-1981CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
In-cell NMR spectroscopy provides insight into protein conformation, dynamics, and function at at. resoln. in living cells. Systematic evaluation of isotopic-labeling strategies is necessary to observe the target protein in the sea of other mols. in the cell. Here, the authors study the detectability, sensitivity, and resoln. of in-cell NMR spectra of the globular proteins GB1, ubiquitin, calmodulin, and bcl-xl-cutloop, resulting from uniform 15N enrichment (with and without deuteration), selective 15N-Leu enrichment, 13C-Me enrichment of isoleucine, leucine, valine, and alanine, fractional 13C enrichment, and 19F labeling. Most of the target proteins can be obsd. by 19F labeling and 13C enrichment with direct detection because selectively labeling suppresses background signals and because deuteration improves in-cell spectra. The authors' results demonstrate that the detectability of proteins is detd. by weak interactions with intercellular components and that choosing appropriate labeling strategies is crit. for the success of in-cell protein NMR studies.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXjsFCmu78%253D&md5=97b076ff60e4211843b824b2b0f975a5
54.
Kaplan, M.; Cukkemane, A.; van Zundert, G. C. P.; Narasimhan, S.; Daniels, M.; Mance, D.; Waksman, G.; Bonvin, A. M. J. J.; Fronzes, R.; Folkers, G. E. Probing a Cell-Embedded Megadalton Protein Complex by DNP-Supported Solid-State NMR Nat. Methods 2015, 12, 649– 652 DOI: 10.1038/nmeth.3406
[Crossref], [PubMed], [CAS]
54.
Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR
Kaplan, Mohammed; Cukkemane, Abhishek; van Zundert, Gydo C. P.; Narasimhan, Siddarth; Daniels, Mark; Mance, Deni; Waksman, Gabriel; Bonvin, Alexandre M. J. J.; Fronzes, Remi; Folkers, Gert E.; Baldus, Marc
Nature Methods (2015), 12 (7), 649-652CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)
Studying biomols. at at. resoln. in their native environment is the ultimate aim of structural biol. We investigated the bacterial type IV secretion system core complex (T4SScc) by cellular dynamic nuclear polarization-based solid-state NMR spectroscopy to validate a structural model previously generated by combining in vitro and in silico data. Our results indicate that T4SScc is well folded in the cellular setting, revealing protein regions that had been elusive when studied in vitro.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFWqtbbL&md5=7fb9fd63247cdadbb355c5b38bab47f8
55.
Kay, L. E. New Views of Functionally Dynamic Proteins by Solution NMR Spectroscopy J. Mol. Biol. 2016, 428, 323– 331 DOI: 10.1016/j.jmb.2015.11.028
[Crossref], [PubMed], [CAS]
55.
New Views of Functionally Dynamic Proteins by Solution NMR Spectroscopy
Kay, Lewis E.
Journal of Molecular Biology (2016), 428 (2_Part_A), 323-331CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)
A review. In the past several decades soln. NMR spectroscopy has emerged as a powerful technique for the study of the structure and dynamics of proteins, providing detailed insights into biomol. function. Herein, I provide a summary of two important areas of application, focusing on NMR studies of (I) supramol. systems with aggregate mol. masses in the hundreds of kilodaltons and of (II) sparsely populated and transiently formed protein states that are thermally accessible from populated ground-state conformers. The crit. role of mol. dynamics in function is emphasized, highlighting the utility of the NMR technique in providing such often elusive information.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXitVyqsLjO&md5=6566a002787b156a78c3949432d38aff
56.
König, I.; Zarrine-Afsar, A.; Aznauryan, M.; Soranno, A.; Wunderlich, B.; Dingfelder, F.; Stuber, J. C.; Plückthun, A.; Nettels, D.; Schuler, B. Single-Molecule Spectroscopy of Protein Conformational Dynamics in Live Eukaryotic Cells Nat. Methods 2015, 12, 773– 779 DOI: 10.1038/nmeth.3475
[Crossref], [PubMed], [CAS]
56.
Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells
Konig, Iwo; Zarrine-Afsar, Arash; Aznauryan, Mikayel; Soranno, Andrea; Wunderlich, Bengt; Dingfelder, Fabian; Stuber, Jakob C.; Pluckthun, Andreas; Nettels, Daniel; Schuler, Benjamin
Nature Methods (2015), 12 (8), 773-779CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)
Single-mol. methods have become widely used for quantifying the conformational heterogeneity and structural dynamics of biomols. in vitro. Their application in vivo, however, has remained challenging owing to shortcomings in the design and reproducible delivery of labeled mols., the range of applicable anal. methods, and suboptimal cell culture conditions. By addressing these limitations in an integrated approach, we demonstrate the feasibility of probing protein dynamics from milliseconds down to the nanosecond regime in live eukaryotic cells with confocal single-mol. Forster resonance energy transfer (FRET) spectroscopy. We illustrate the versatility of the approach by detg. the dimensions and submicrosecond chain dynamics of an intrinsically disordered protein; by detecting even subtle changes in the temp. dependence of protein stability, including in-cell cold denaturation; and by quantifying the folding dynamics of a small protein. The methodol. opens possibilities for assessing the effect of the cellular environment on biomol. conformation, dynamics and function.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1WrurzE&md5=b1325f97799e4edb482698964fcae2c9
57.
Sustarsic, M.; Kapanidis, A. N. Taking the Ruler to the Jungle: Single-Molecule FRET for Understanding Biomolecular Structure and Dynamics in Live Cells Curr. Opin. Struct. Biol. 2015, 34, 52– 59 DOI: 10.1016/j.sbi.2015.07.001
[Crossref], [PubMed], [CAS]
57.
Taking the ruler to the jungle: single-molecule FRET for understanding biomolecular structure and dynamics in live cells
Sustarsic, Marko; Kapanidis, Achillefs N.
Current Opinion in Structural Biology (2015), 34 (), 52-59CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)
A review. Single-mol. Forster resonance energy transfer (smFRET) serves as a mol. ruler that is ideally posed to study static and dynamic heterogeneity in living cells. Observing smFRET in cells requires appropriately integrated labeling, internalization and imaging strategies, and significant progress has been made towards that goal. Pioneering studies demonstrated smFRET detection in both prokaryotic and eukaryotic systems, using both wide-field and confocal microscopies, and have started to answer exciting biol. questions. The authors anticipate that future tech. developments will open the door to smFRET for the study of structure, conformational changes and kinetics of biomols. in living cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFOlu7fF&md5=07a74dec448d36ed9f4c11b4ee618ece
58.
Gelman, H.; Wirth, A. J.; Gruebele, M. ReAsH as a Quantitative Probe of In-Cell Protein Dynamics Biochemistry 2016, 55, 1968– 1976 DOI: 10.1021/acs.biochem.5b01336
[ACS Full Text ], [CAS]
58.
ReAsH as a Quantitative Probe of In-Cell Protein Dynamics
Gelman, Hannah; Wirth, Anna Jean; Gruebele, Martin
Biochemistry (2016), 55 (13), 1968-1976CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
The tetracysteine (tc) tag/biarsenical dye system (FlAsH or ReAsH) promises to combine the flexibility of fluorescent protein tags with the small size of dye labels, allowing in-cell study of target proteins that are perturbed by large protein tags. Quant. thermodn. and kinetic studies in-cell using FlAsH and ReAsH have been hampered by methodol. complexities presented by the fluorescence properties of the tag-dye complex probed by either F.ovrddot.orster resonance energy transfer (FRET) or direct excitation. We label the model protein phosphoglycerate kinase (PGK) with AcGFP1 and ReAsH for direct comparison with AcGFP1/mCherry-labeled PGK. We find that fast relaxation imaging (FReI), combining millisecond temp. jump kinetics with fluorescence microscopy detection, circumvents many of the difficulties encountered working with the ReAsH system, allowing us to obtain quant. FRET measurements of protein stability and kinetics both in vitro and in cells. We also demonstrate the to us surprising result that fluorescence from directly excited, unburied ReAsH at the C-terminus of the model protein also reports on folding in vitro and in cells. Comparing the ReAsH-labeled protein to a construct labeled with two fluorescent protein tags allows us to evaluate how a bulkier protein tag affects protein dynamics in cells and in vitro. We find that the av. folding rate in the cell is closer to the in vitro rate with the smaller tag, highlighting the effect of tags on quant. in-cell measurements.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XjvVGis70%253D&md5=025fdc542087b1b587ae385e3f7f7107
59.
Feig, M.; Sugita, Y. Reaching New Levels of Realism in Modeling Biological Macromolecules in Cellular Environments J. Mol. Graphics Modell. 2013, 45, 144– 156 DOI: 10.1016/j.jmgm.2013.08.017
[Crossref], [PubMed], [CAS]
59.
Reaching new levels of realism in modeling biological macromolecules in cellular environments
Feig, Michael; Sugita, Yuji
Journal of Molecular Graphics & Modelling (2013), 45 (), 144-156CODEN: JMGMFI; ISSN:1093-3263. (Elsevier Ltd.)
A review. An increasing no. of studies are aimed at modeling cellular environments in a comprehensive and realistic fashion. A major challenge in these efforts is how to bridge spatial and temporal scales over many orders of magnitude. Furthermore, there are addnl. challenges in integrating different aspects ranging from questions about biomol. stability in crowded environments to the description of reactive processes on cellular scales. In this review, recent studies with models of biomols. in cellular environments at different levels of detail are discussed in terms of their strengths and weaknesses. In particular, atomistic models, implicit representations of cellular environments, coarse-grained and spheroidal models of biomols., as well as the inclusion of reactive processes via reaction-diffusion models are described. Furthermore, strategies for integrating the different models into a comprehensive description of cellular environments are discussed.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhs1Wksr%252FE&md5=c56d5feaa6f0d3fde059ee3a3998a4e6
60.
Perilla, J. R.; Goh, B. C.; Cassidy, C. K.; Liu, B.; Bernardi, R. C.; Rudack, T.; Yu, H.; Wu, Z.; Schulten, K. Molecular Dynamics Simulations of Large Macromolecular Complexes Curr. Opin. Struct. Biol. 2015, 31, 64– 74 DOI: 10.1016/j.sbi.2015.03.007
[Crossref], [PubMed], [CAS]
60.
Molecular dynamics simulations of large macromolecular complexes
Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus
Current Opinion in Structural Biology (2015), 31 (), 64-74CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)
A review. Connecting dynamics to structural data from diverse exptl. sources, mol. dynamics simulations permit the exploration of biol. phenomena in unparalleled detail. Advances in simulations are moving the at. resoln. descriptions of biol. systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, the authors review the progress, driven by large-scale mol. dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of mol. dynamics simulations in the crit. task of relating at. detail to the function of supramol. complexes, a task that cannot be achieved by smaller-scale simulations or existing exptl. approaches alone.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXlsFemsb4%253D&md5=8fb981e606aabacf4b75ede88434ec6a
61.
Feig, M.; Chocholousova, J.; Tanizaki, S. Extending the Horizon: Towards the Efficient Modeling of Large Biomolecular Complexes in Atomic Detail Theor. Chem. Acc. 2006, 116, 194– 205 DOI: 10.1007/s00214-005-0062-4
[Crossref], [CAS]
61.
Extending the horizon: Towards the efficient modeling of large biomolecular complexes in atomic detail
Feig, Michael; Chocholousova, Jana; Tanizaki, Seiichiro
Theoretical Chemistry Accounts (2006), 116 (1-3), 194-205CODEN: TCACFW; ISSN:1432-881X. (Springer GmbH)
A review. The application of evaluation of implicit solvent methods for the simulation of biomols. is described. Detailed comparisons with explicit solvent are described for the modeling of peptide and proteins in continuum aq. solvent. In addn., we are presenting new data on the simulation of DNA with implicit solvent and describe the development of a heterogeneous dielec. model for the simulation of integral membranes. The performance of implicit solvent simulations based on the generalized Born using mol. vol. (GBMV) generalized Born method is compared with explicit solvent simulations, and implications for the simulation of very large biomol. complexes is discussed. We are anticipating that the work described herein will lead to new, efficient modeling tools that will allow the simulation of longer timescales and larger system sizes in order to meet current and future challenges by the exptl. community.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xns1Sqtrg%253D&md5=44693f3d3ab4d904a83597c57ba424b9
62.
Hospital, A.; Goñi, J. R.; Orozco, M.; Gelpi, J. L. Molecular Dynamics Simulations: Advances and Applications Adv. Appl. Bioinform. Chem. 2015, 8, 37– 47 DOI: 10.2147/AABC.S70333
[Crossref], [PubMed], [CAS]
62.
Molecular dynamics simulations: advances and applications
Hospital Adam; Goni Josep Ramon; Orozco Modesto; Gelpi Josep L
Advances and applications in bioinformatics and chemistry : AABC (2015), 8 (), 37-47 ISSN:1178-6949.
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC28rgs1ShtQ%253D%253D&md5=1b8c8639bd3356dfb4d700a3ec325729
63.
Gavin, A. C.; Aloy, P.; Grandi, P.; Krause, R.; Boesche, M.; Marzioch, M.; Rau, C.; Jensen, L. J.; Bastuck, S.; Dumpelfeld, B. Proteome Survey Reveals Modularity of the Yeast Cell Machinery Nature 2006, 440, 631– 636 DOI: 10.1038/nature04532
[Crossref], [PubMed], [CAS]
63.
Proteome survey reveals modularity of the yeast cell machinery
Gavin, Anne-Claude; Aloy, Patrick; Grandi, Paola; Krause, Roland; Boesche, Markus; Marzioch, Martina; Rau, Christina; Jensen, Lars Juhl; Bastuck, Sonja; Duempelfeld, Birgit; Edelmann, Angela; Heurtier, Marie-Anne; Hoffman, Verena; Hoefert, Christian; Klein, Karin; Hudak, Manuela; Michon, Anne-Marie; Schelder, Malgorzata; Schirle, Markus; Remor, Marita; Rudi, Tatjana; Hooper, Sean; Bauer, Andreas; Bouwmeester, Tewis; Casari, Georg; Drewes, Gerard; Neubauer, Gitte; Rick, Jens M.; Kuster, Bernhard; Bork, Peer; Russell, Robert B.; Superti-Furga, Giulio
Nature (London, United Kingdom) (2006), 440 (7084), 631-636CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Protein complexes are key mol. entities that integrate multiple gene products to perform cellular functions. Here, the authors report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purifn. and mass spectrometry. Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several times, suggesting screen satn. The richness of the data set enabled a de novo characterization of the compn. and organization of the cellular machinery. The ensemble of cellular proteins partitions into 491 complexes, of which 257 are novel, that differentially combine with addnl. attachment proteins or protein modules to enable a diversification of potential functions. Support for this modular organization of the proteome comes from integration with available data on expression, localization, function, evolutionary conservation, protein structure and binary interactions. This study provides the largest collection of phys. detd. eukaryotic cellular machines so far and a platform for biol. data integration and modeling.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XivFWgtbw%253D&md5=0dff47d04468285f5a66db6c37ee1212
64.
Guell, M.; van Noort, V.; Yus, E.; Chen, W. H.; Leigh-Bell, J.; Michalodimitrakis, K.; Yamada, T.; Arumugam, M.; Doerks, T.; Kuhner, S. Transcriptome Complexity in a Genome-Reduced Bacterium Science 2009, 326, 1268– 1271 DOI: 10.1126/science.1176951
[Crossref], [PubMed], [CAS]
64.
Transcriptome complexity in a genome-reduced bacterium
Guell Marc; van Noort Vera; Yus Eva; Chen Wei-Hua; Leigh-Bell Justine; Michalodimitrakis Konstantinos; Yamada Takuji; Arumugam Manimozhiyan; Doerks Tobias; Kuhner Sebastian; Rode Michaela; Suyama Mikita; Schmidt Sabine; Gavin Anne-Claude; Bork Peer; Serrano Luis
Science (New York, N.Y.) (2009), 326 (5957), 1268-71 ISSN:.
To study basic principles of transcriptome organization in bacteria, we analyzed one of the smallest self-replicating organisms, Mycoplasma pneumoniae. We combined strand-specific tiling arrays, complemented by transcriptome sequencing, with more than 252 spotted arrays. We detected 117 previously undescribed, mostly noncoding transcripts, 89 of them in antisense configuration to known genes. We identified 341 operons, of which 139 are polycistronic; almost half of the latter show decaying expression in a staircase-like manner. Under various conditions, operons could be divided into 447 smaller transcriptional units, resulting in many alternative transcripts. Frequent antisense transcripts, alternative transcripts, and multiple regulators per gene imply a highly dynamic transcriptome, more similar to that of eukaryotes than previously thought.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BD1MfgslymtQ%253D%253D&md5=3187787fa4bff211412d36a82bb13b9f
65.
Yus, E.; Maier, T.; Michalodimitrakis, K.; van Noort, V.; Yamada, T.; Chen, W. H.; Wodke, J. A. H.; Guell, M.; Martinez, S.; Bourgeois, R. Impact of Genome Reduction on Bacterial Metabolism and Its Regulation Science 2009, 326, 1263– 1268 DOI: 10.1126/science.1177263
[Crossref], [PubMed], [CAS]
65.
Impact of genome reduction on bacterial metabolism and its regulation
Yus, Eva; Maier, Tobias; Michalodimitrakis, Konstantinos; van Noort, Vera; Yamada, Takuji; Chen, Wei-Hua; Wodke, Judith A. H.; Gueell, Marc; Martinez, Sira; Bourgeois, Ronan; Kuehner, Sebastian; Raineri, Emanuele; Letunic, Ivica; Kalinina, Olga V.; Rode, Michaela; Herrmann, Richard; Gutierrez-Gallego, Ricardo; Russell, Robert B.; Gavin, Anne-Claude; Bork, Peer; Serrano, Luis
Science (Washington, DC, United States) (2009), 326 (5957), 1263-1268CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
To understand basic principles of bacterial metab. organization and regulation, but also the impact of genome size, we systematically studied one of the smallest bacteria, Mycoplasma pneumoniae. A manually curated metabolic network of 189 reactions catalyzed by 129 enzymes allowed the design of a defined, minimal medium with 19 essential nutrients. More than 1300 growth curves were recorded in the presence of various nutrient concns. Measurements of biomass indicators, metabolites, and 13C-glucose expts. provided information on directionality, fluxes, and energetics; integration with transcription profiling enabled the global anal. of metabolic regulation. Compared with more complex bacteria, the M. pneumoniae metabolic network has a more linear topol. and contains a higher fraction of multifunctional enzymes; general features such as metabolite concns., cellular energetics, adaptability, and global gene expression responses are similar, however.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhsVKhtbbF&md5=7e313ca17efd6bff2b365c2d70797e4b
66.
Ye, Y.; Liu, X.; Zhang, Z.; Wu, Q.; Jiang, B.; Jiang, L.; Zhang, X.; Liu, M.; Pielak, G. J.; Li, C. ¹⁹F NMR Spectroscopy as a Probe of Cytoplasmic Viscosity and Weak Protein Interactions in Living Cells Chem. - Eur. J. 2013, 19, 12705– 12710 DOI: 10.1002/chem.201301657
[Crossref], [PubMed], [CAS]
66.
19F NMR Spectroscopy as a Probe of Cytoplasmic Viscosity and Weak Protein Interactions in Living Cells
Ye, Yansheng; Liu, Xiaoli; Zhang, Zeting; Wu, Qiong; Jiang, Bin; Jiang, Ling; Zhang, Xu; Liu, Maili; Pielak, Gary J.; Li, Conggang
Chemistry - A European Journal (2013), 19 (38), 12705-12710CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
Protein mobility in living cells is vital for cell function. Both cytosolic viscosity and weak protein-protein interactions affect mobility, but examg. viscosity and weak interaction effects is challenging. Herein, we demonstrate the use of 19F NMR spectroscopy to measure cytoplasmic viscosity and to characterize nonspecific protein-protein interactions in living Escherichia coli cells. The origins of resonance broadening in Escherichia coli cells were also investigated. We found that sample inhomogeneity has a negligible effect on resonance broadening, the cytoplasmic viscosity is only about 2-3 times that of water, and ubiquitous transient weak protein-protein interactions in the cytosol play a significant role in governing the detection of proteins by using in-cell NMR spectroscopy.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXht1Wrt7bM&md5=b7839d1ddbca91fcf1794e54f246feb2
67.
Sarkar, M.; Smith, A. E.; Pielak, G. J. Impact of Reconstituted Cytosol on Protein Stability Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 19342– 19347 DOI: 10.1073/pnas.1312678110
[Crossref], [PubMed], [CAS]
67.
Impact of reconstituted cytosol on protein stability
Sarkar, Mohona; Smith, Austin E.; Pielak, Gary J.
Proceedings of the National Academy of Sciences of the United States of America (2013), 110 (48), 19342-19347,S19342/1-S19342/19CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
Protein stability is usually studied in simple buffered solns., but most proteins function inside cells, where the heterogeneous and crowded environment presents a complex, nonideal system. Proteins are expected to behave differently under cellular crowding owing to two types of contacts: hard-core repulsions and weak, chem. interactions. The effect of hard-core repulsions is purely entropic, resulting in vol. exclusion owing to the mere presence of the crowders. The weak interactions can be repulsive or attractive, thus enhancing or diminishing the excluded vol., resp. We used a reductionist approach to assess the effects of intracellular crowding. Escherichia coli cytoplasm was dialyzed, lyophilized, and resuspended at two concns. NMR-detected amide proton exchange was then used to quantify the stability of the globular protein chymotrypsin inhibitor 2 (CI2) in these crowded solns. The cytosol destabilizes CI2, and the destabilization increases with increasing cytosol concn. This observation shows that the cytoplasm interacts favorably, but nonspecifically, with CI2, and these interactions overcome the stabilizing hard-core repulsions. The effects of the cytosol are even stronger than those of homogeneous protein crowders, reinforcing the biol. significance of weak, nonspecific interactions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvFemtbfP&md5=7eea2c3708b142db94c8cdbd61c34a55
68.
Guseman, A. J.; Pielak, G. J. Cosolute and Crowding Effects on a Side-By-Side Protein Dimer Biochemistry 2017, 56, 971– 976 DOI: 10.1021/acs.biochem.6b01251
[ACS Full Text ], [CAS]
68.
Cosolute and Crowding Effects on a Side-By-Side Protein Dimer
Guseman, Alex J.; Pielak, Gary J.
Biochemistry (2017), 56 (7), 971-976CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
The effects of small (∼102 Da) and larger (>103 Da) cosolutes on protein stability are broadly understood: excluding vol. stabilizes proteins and chem. interactions are stabilizing when repulsive, but destabilizing when attractive. Proteins, however, rarely work alone. Here, the authors investigated the effects of small and larger cosolutes on the equil. stability of the simplest defined protein-protein interactions, the side-by-side homodimer formed by the A34F variant of the 56-residue B1 domain of protein G. 19F NMR spectroscopy expts. revealed that the stabilizing and destabilizing influences of common cosolutes (e.g., trimethylamine oxide and urea, resp.) on protein stability also occur for protein-protein interactions. The results with more physiol. relevant mols. such as bovine serum albumin and reconstituted cytosol also reflected the importance of chem. interactions between the cosolute and the test protein. This study serves as a stepping-stone for understanding the effects of crowding on protein-protein interactions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtFKltL8%253D&md5=10e457f22384c7d583a737815c141ec6
69.
Bai, J.; Liu, M.; Pielak, G. J.; Li, C. Macromolecular and Small Molecular Crowding Have Similar Effects on α-Synuclein Structure ChemPhysChem 2017, 18, 55– 58 DOI: 10.1002/cphc.201601097
[Crossref], [PubMed], [CAS]
69.
Macromolecular and Small Molecular Crowding Have Similar Effects on α-Synuclein Structure
Bai, Jia; Liu, Maili; Pielak, Gary J.; Li, Conggang
ChemPhysChem (2017), 18 (1), 55-58CODEN: CPCHFT; ISSN:1439-4235. (Wiley-VCH Verlag GmbH & Co. KGaA)
The intracellular milieu contains upwards of 400 g of macromols. per L. This crowding is thought to have a larger influence on intrinsically disordered proteins, whose chains are expanded, than on compact globular proteins. Classic theories of macromol. crowding predict that increasing excluded vol. effects will lead disordered proteins to compaction, and a great deal of data, from both simulation and expts. support this idea. We used NMR, CD, and fluorescence spectroscopies to characterize the structure and fibrillation of α-synuclein, an intrinsically disordered protein implicated in Parkinson's disease, using Ficoll70, its monomer sucrose and bovine serum albumin as crowding agents. Surprisingly, vol. exclusion induced by high concns. of macromols. may not be the main reason for the compaction of α-synuclein. Our results indicate that all aspects crowding must be considered to understand protein conformation under crowded conditions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvFOgsLjJ&md5=ad326fac5c6dd649bf4de965c873c5d3
70.
Cohen, R. D.; Guseman, A. J.; Pielak, G. J. Intracellular pH Modulates Quinary Structure Protein Sci. 2015, 24, 1748– 1755 DOI: 10.1002/pro.2765
[Crossref], [PubMed], [CAS]
70.
Intracellular pH modulates quinary structure
Cohen, Rachel D.; Guseman, Alex J.; Pielak, Gary J.
Protein Science (2015), 24 (11), 1748-1755CODEN: PRCIEI; ISSN:1469-896X. (Wiley-Blackwell)
NMR spectroscopy can provide information about proteins in living cells. pH is an important characteristic of the intracellular environment because it modulates key protein properties such as net charge and stability. Here, we show that pH modulates quinary interactions, the weak, ubiquitous interactions between proteins and other cellular macromols. We use the K10H variant of the B domain of protein G (GB1, 6.2 kDa) as a pH reporter in Escherichia coli cells. By controlling the intracellular pH, we show that quinary interactions influence the quality of in-cell 15N-1H HSQC NMR spectra. At low pH, the quality is degraded because the increase in attractive interactions between E. coli proteins and GB1 slows GB1 tumbling and broadens its crosspeaks. The results demonstrate the importance of quinary interactions for furthering our understanding of protein chem. in living cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhsVWgtrjM&md5=08bdaacd785ac1759ac217816f638073
71.
Monteith, W. B.; Pielak, G. J. Residue Level Quantification of Protein Stability in Living Cells Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 11335– 11340 DOI: 10.1073/pnas.1406845111
[Crossref], [PubMed], [CAS]
71.
Residue level quantification of protein stability in living cells
Monteith, William B.; Pielak, Gary J.
Proceedings of the National Academy of Sciences of the United States of America (2014), 111 (31), 11335-11340CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
The intracellular milieu differs from the dil. conditions in which most biophys. and biochem. studies are performed. This difference has led both experimentalists and theoreticians to tackle the challenging task of understanding how the intracellular environment affects the properties of biopolymers. Despite a growing no. of in-cell studies, there is a lack of quant., residue-level information about equil. thermodn. protein stability under nonperturbing conditions. We report the use of NMR-detected hydrogen-deuterium exchange of quenched cell lysates to measure individual opening free energies of the 56-aa B1 domain of protein G (GB1) in living Escherichia coli cells without adding destabilizing cosolutes or heat. Comparisons to dil. soln. data (pH 7.6 and 37 °C) show that opening free energies increase by as much as 1.14 ± 0.05 kcal/mol in cells. Importantly, we also show that homogeneous protein crowders destabilize GB1, highlighting the challenge of recreating the cellular interior. We discuss our findings in terms of hard-core excluded vol. effects, charge-charge GB1-crowder interactions, and other factors. The quenched lysate method identifies the residues most important for folding GB1 in cells, and should prove useful for quantifying the stability of other globular proteins in cells to gain a more complete understanding of the effects of the intracellular environment on protein chem.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtFyqtLvE&md5=94398803cb3981e17af008dfe03dd9ea
72.
Sarkar, M.; Li, C.; Pielak, G. J. Soft Interactions and Crowding Biophys. Rev. 2013, 5, 187– 194 DOI: 10.1007/s12551-013-0104-4
[Crossref], [PubMed], [CAS]
72.
Soft interactions and crowding
Sarkar Mohona; Pielak Gary J; Li Conggang; Pielak Gary J; Pielak Gary J
Biophysical reviews (2013), 5 (2), 187-194 ISSN:1867-2450.
The intracellular milieu is complex, heterogeneous and crowded-an environment vastly different from dilute solutions in which most biophysical studies are performed. The crowded cytoplasm excludes about a third of the volume available to macromolecules in dilute solution. This excluded volume is the sum of two parts: steric repulsions and chemical interactions, also called soft interactions. Until recently, most efforts to understand crowding have focused on steric repulsions. Here, we summarize the results and conclusions from recent studies on macromolecular crowding, emphasizing the contribution of soft interactions to the equilibrium thermodynamics of protein stability. Despite their non-specific and weak nature, the large number of soft interactions present under many crowded conditions can sometimes overcome the stabilizing steric, excluded volume effect.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC1crnvVOgtA%253D%253D&md5=4202238b6c18f268b4865b08468ae1de
73.
Schlesinger, A. P.; Wang, Y.; Tadeo, X.; Millet, O.; Pielak, G. J. Macromolecular Crowding Fails To Fold a Globular Protein in Cells J. Am. Chem. Soc. 2011, 133, 8082– 8085 DOI: 10.1021/ja201206t
[ACS Full Text ], [CAS]
73.
Macromolecular Crowding Fails To Fold a Globular Protein in Cells
Schlesinger, Alexander P.; Wang, Yaqiang; Tadeo, Xavier; Millet, Oscar; Pielak, Gary J.
Journal of the American Chemical Society (2011), 133 (21), 8082-8085CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Proteins perform their functions in cells where macromol. solutes reach concns. of >300 g/L and occupy >30% of the vol. The vol. excluded by these macromols. stabilizes globular proteins because the native state occupies less space than the denatured state. Theory predicts that crowding can increase the ratio of folded to unfolded protein by a factor of 100, amounting to 3 kcal/mol of stabilization at room temp. We tested the idea that vol. exclusion dominates the crowding effect in cells using a variant of protein L, a 7 kDa globular protein with seven lysine residues replaced by glutamic acids; 84% of the variant mols. populate the denatured state in dil. buffer at room temp., compared with 0.1% for the wild-type protein. We then used in-cell NMR spectroscopy to show that the cytoplasm of Escherichia coli does not overcome even this modest (∼1 kcal/mol) free-energy deficit. The data are consistent with the idea that nonspecific interactions between cytoplasmic components can overcome the excluded-vol. effect. Evidence for these interactions is provided by the observations that adding simple salts folds the variant in dil. soln. but increasing the salt concn. inside E. coli does not fold the protein. Our data are consistent with the results of other studies of protein stability in cells and suggest that stabilizing excluded-vol. effects, which must be present under crowded conditions, can be ameliorated by nonspecific interactions between cytoplasmic components.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXlvVSltLo%253D&md5=b4698d863b85f2b3ee40050f0c3c3263
74.
Stadmiller, S. S.; Gorensek-Benitez, A. H.; Guseman, A. J.; Pielak, G. J. Osmotic Shock Induced Protein Destabilization in Living Cells and Its Reversal by Glycine Betaine J. Mol. Biol. 2017, 429, 1155– 1161 DOI: 10.1016/j.jmb.2017.03.001
[Crossref], [PubMed], [CAS]
74.
Osmotic shock induced protein destabilization in living cells and its reversal by glycine betaine
Stadmiller, Samantha S.; Gorensek-Benitez, Annelise H.; Guseman, Alex J.; Pielak, Gary J.
Journal of Molecular Biology (2017), 429 (8), 1155-1161CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)
Many organisms can adapt to changes in the solute content of their surroundings (i.e., the osmolarity). Hyperosmotic shock causes water efflux and a concomitant redn. in cell vol., which is countered by the accumulation of osmolytes. This vol. redn. increases the crowded nature of the cytoplasm, which is expected to affect protein stability. In contrast to traditional theory, which predicts that more crowded conditions can only increase protein stability, recent work has shown that crowding can destabilize proteins through transient attractive interactions. Here, we quantified protein stability in living Escherichia coli cells before and after hyperosmotic shock in the presence and absence of the osmolyte, glycine betaine. The 7-kDa N-terminal src-homol. 3 (SH3) domain of Drosophila signal transduction protein drk was used as the test protein. We found that hyperosmotic shock decreased SH3 stability in cells, consistent with the idea that transient attractive interactions are important under physiol. relevant crowded conditions. The subsequent uptake of glycine betaine returned SH3 to the stability obsd. without osmotic shock. These results highlight the effect of transient attractive interactions on protein stability in cells and provide a new explanation for why stressed cells accumulate osmolytes.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXjvF2gsL4%253D&md5=a235779d51960e9090e682b40580e9c7
75.
Theillet, F.-X.; Binolfi, A.; Bekei, B.; Martorana, A.; Rose, H. M.; Stuiver, M.; Verzini, S.; Lorenz, D.; van Rossum, M.; Goldfarb, D. Structural Disorder of Monomeric α-Synuclein Persists in Mammalian Cells Nature 2016, 530, 45– 50 DOI: 10.1038/nature16531
[Crossref], [PubMed], [CAS]
75.
Structural disorder of monomeric α-synuclein persists in mammalian cells
Theillet, Francois-Xavier; Binolfi, Andres; Bekei, Beata; Martorana, Andrea; Rose, Honor May; Stuiver, Marchel; Verzini, Silvia; Lorenz, Dorothea; van Rossum, Marleen; Goldfarb, Daniella; Selenko, Philipp
Nature (London, United Kingdom) (2016), 530 (7588), 45-50CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)
Intracellular aggregation of the human amyloid protein, α-synuclein (I), is causally linked to Parkinson's disease. While the isolated protein is intrinsically disordered, its native structure in mammalian cells is not known. Here, the authors used NMR and ESR spectroscopy to derive at.-resoln. insights into the structure and dynamics of I in different mammalian cell types. The authors showed that the disordered nature of monomeric I was stably preserved in non-neuronal and neuronal cells. Under physiol. cell conditions, I was N-terminally acetylated and adopted conformations that were more compact than when in buffer, with residues of the aggregation-prone non-amyloid-β component (NAC) region shielded from exposure to the cytoplasm, which presumably counteracts spontaneous aggregation. These results established that different types of crowded intracellular environments do not inherently promote I oligomerization and, more generally, that intrinsic structural disorder is sustainable in mammalian cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsFyitLY%253D&md5=690fc45b24fef292a589e1ecc9bc70b9
76.
Soranno, A.; Koenig, I.; Borgia, M. B.; Hofmann, H.; Zosel, F.; Nettels, D.; Schuler, B. Single-Molecule Spectroscopy Reveals Polymer Effects of Disordered Proteins in Crowded Environments Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 4874– 4879 DOI: 10.1073/pnas.1322611111
[Crossref], [PubMed], [CAS]
76.
Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments
Soranno, Andrea; Koenig, Iwo; Borgia, Madeleine B.; Hofmann, Hagen; Zosel, Franziska; Nettels, Daniel; Schuler, Benjamin
Proceedings of the National Academy of Sciences of the United States of America (2014), 111 (13), 4874-4879CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
Intrinsically disordered proteins (IDPs) are involved in a wide range of regulatory processes in the cell. Owing to their flexibility, their conformations are expected to be particularly sensitive to the crowded cellular environment. Here we use single-mol. Foerster resonance energy transfer to quantify the effect of crowding as mimicked by commonly used biocompatible polymers. We observe a compaction of IDPs not only with increasing concn., but also with increasing size of the crowding agents, at variance with the predictions from scaled-particle theory, the prevalent paradigm in the field. However, the obsd. behavior can be explained quant. if the polymeric nature of both the IDPs and the crowding mols. is taken into account explicitly. Our results suggest that excluded vol. interactions between overlapping biopolymers and the resulting criticality of the system can be essential contributions to the physics governing the crowded cellular milieu.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXksVSnsLg%253D&md5=4d82db6b463802c5fe356bdd1874cfd6
77.
Anunciado, D. B.; Nyugen, V. P.; Hurst, G. B.; Doktycz, M. J.; Urban, V.; Langan, P.; Mamontov, E.; O’Neill, H. In vivo Protein Dynamics on the Nanometer Length Scale and Nanosecond Time Scale J. Phys. Chem. Lett. 2017, 8, 1899– 1904 DOI: 10.1021/acs.jpclett.7b00399
[ACS Full Text ], [CAS]
77.
In Vivo Protein Dynamics on the Nanometer Length Scale and Nanosecond Time Scale
Anunciado, Divina B.; Nyugen, Vyncent P.; Hurst, Gregory B.; Doktycz, Mitchel J.; Urban, Volker; Langan, Paul; Mamontov, Eugene; O'Neill, Hugh
Journal of Physical Chemistry Letters (2017), 8 (8), 1899-1904CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
Selectively labeled GroEL protein was produced in living deuterated bacterial cells to enhance its neutron scattering signal above that of the intracellular milieu. Quasi-elastic neutron scattering shows that the in-cell diffusion coeff. of GroEL was (4.7±0.3) × 10-12 m2/s, a factor of 4 slower than its diffusion coeff. in buffer soln. Internal protein dynamics showed a relaxation time of (65±6) ps, a factor of 2 slower compared to the protein in soln. Comparison to the literature suggests that the effective diffusivity of proteins depends on the length and time scale being probed. Retardation of in-cell diffusion compared to the buffer becomes more significant with the increasing probe length scale, suggesting that intracellular diffusion of biomols. is nonuniform over the cellular vol. The approach outlined here enables investigation of protein dynamics within living cells to open up new lines of research using "in-cell neutron scattering" to study the dynamics of complex biomol. systems.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXlslCjsbw%253D&md5=bce45d992ad5b00136ee44c7f43138fa
78.
Latham, M. P.; Kay, L. E. Is Buffer a Good Proxy for a Crowded Cell-Like Environment? A Comparative NMR Study of Calmodulin Side-Chain Dynamics in Buffer and E. coli Lysate PLoS One 2012, 7, e48226 DOI: 10.1371/journal.pone.0048226
[Crossref], [PubMed], [CAS]
78.
Is buffer a good proxy for a crowded cell-like environment? A comparative NMR study of calmodulin side-chain dynamics in buffer and E. coli lysate
Latham, Michael P.; Kay, Lewis E.
PLoS One (2012), 7 (10), e48226CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)
Biophys. studies of protein structure and dynamics are typically performed in a highly controlled manner involving only the protein(s) of interest. Comparatively fewer such studies have been carried out in the context of a cellular environment that typically involves many biomols., ions and metabolites. Recently, soln. NMR spectroscopy, focusing primarily on backbone amide groups as reporters, has emerged as a powerful technique for investigating protein structure and dynamics in vivo and in crowded "cell-like" environments. Here we extend these studies through a comparative anal. of Ile, Leu, Val and Met Me side-chain motions in apo, Ca2+-bound and Ca2+, peptide-bound calmodulin dissolved in aq. buffer or in E. coli lysate. Deuterium spin relaxation expts., sensitive to pico- to nano-second time-scale processes and Carr-Purcell-Meiboom-Gill relaxation dispersion expts., reporting on millisecond dynamics, have been recorded. Both similarities and differences in motional properties are noted for calmodulin dissolved in buffer or in lysate. These results emphasize that while significant insights can be obtained through detailed "test-tube" studies, expts. performed under conditions that are "cell-like" are crit. for obtaining a comprehensive understanding of protein motion in vivo and therefore for elucidating the relation between motion and function.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xhs12qs73F&md5=3fc018f9e97cf60274e4ab73ea850732
79.
Latham, M. P.; Kay, L. E. Probing Non-Specific Interactions of Ca²⁺-Calmodulin in E. coli Lysate J. Biomol. NMR 2013, 55, 239– 247 DOI: 10.1007/s10858-013-9705-2
[Crossref], [PubMed], [CAS]
79.
Probing non-specific interactions of Ca2+-calmodulin in E. coli lysate
Latham, Michael P.; Kay, Lewis E.
Journal of Biomolecular NMR (2013), 55 (3), 239-247CODEN: JBNME9; ISSN:0925-2738. (Springer)
The biol. environment in which a protein performs its function is a crowded milieu contg. millions of mols. that can potentially lead to a great many transient, non-specific interactions. NMR spectroscopy is esp. well suited to study these weak mol. contacts. Here, non-specific interactions between the Ca2+-bound form of calmodulin (CaM) and non-cognate proteins in Escherichia coli lysate are explored using Ile, Leu, Val and Met Me probes. Changes in CaM Me chem. shifts as a function of added E. coli lysate are measured to det. a min. av.' dissocn. const. for interactions between Ca2+-CaM and E. coli lysate proteins. 2H R2 and 13C R1 spin relaxation rates report on the binding reaction as well. Our results further highlight the power of Me contg. side-chains for characterizing biomol. interactions, even in complex in-cell like environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXltVCku70%253D&md5=abfcf2e3a294761d24c832c6e8856ddd
80.
Latham, M. P.; Kay, L. E. A Similar In Vitro and In Cell Lysate Folding Intermediate for the FF Domain J. Mol. Biol. 2014, 426, 3214– 3220 DOI: 10.1016/j.jmb.2014.07.019
[Crossref], [PubMed], [CAS]
80.
A Similar In Vitro and In Cell Lysate Folding Intermediate for the FF Domain
Latham, Michael P.; Kay, Lewis E.
Journal of Molecular Biology (2014), 426 (19), 3214-3220CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)
Understanding the mechanisms by which proteins fold into their three-dimensional structures, including a description of the intermediates that are formed during the folding process, remains a goal of protein science. Most studies are performed under carefully controlled conditions in which the folding reaction is monitored in a buffer soln. that is far from the natural milieu of the cell. Here, we have used 13C and 1H relaxation dispersion NMR spectroscopy to study folding of the FF domain in both Escherichia coli and Saccharomyces cerevisiae cellular lysates. We find that a conformationally excited state is populated in both lysates, which is very similar in structure to a folding intermediate obsd. in previous studies in buffer, with the kinetics and thermodn. of the interconversion between native and intermediate conformers somewhat changed. The results point to the importance of extending folding studies beyond the test tube yet emphasize that insights can be obtained through careful expts. recorded in controlled buffer solns.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXht1KlurrE&md5=a0cd3b4e61ad0807e721649d24b47f35
81.
Roos, M.; Ott, M.; Hofmann, M.; Link, S.; Rössler, E.; Balbach, J.; Kruschelnitsky, A.; Saalwächter, K. Coupling and Decoupling of Rotational and Translational Diffusion of Proteins under Crowding Conditions J. Am. Chem. Soc. 2016, 138, 10365– 10372 DOI: 10.1021/jacs.6b06615
[ACS Full Text ], [CAS]
81.
Coupling and Decoupling of Rotational and Translational Diffusion of Proteins under Crowding Conditions
Roos, Matthias; Ott, Maria; Hofmann, Marius; Link, Susanne; Roessler, Ernst; Balbach, Jochen; Krushelnitsky, Alexey; Saalwaechter, Kay
Journal of the American Chemical Society (2016), 138 (32), 10365-10372CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Mol. motion of biopolymers in vivo is known to be strongly influenced by the high concn. of org. matter inside cells, usually referred to as crowding conditions. To elucidate the effect of intermol. interactions on Brownian motion of proteins, we performed 1H pulsed-field gradient NMR and fluorescence correlation spectroscopy (FCS) expts. combined with small-angle X-ray scattering (SAXS) and viscosity measurements for three proteins, αB-cryst. (αBc), bovine serum albumin, and hen egg-white lysozyme (HEWL) in aq. soln. Our results demonstrate that long-time translational diffusion quant. follows the expected increase of macro-viscosity upon increasing the protein concn. in all cases, while rotational diffusion as assessed by polarized FCS and previous multi-frequency 1H NMR relaxometry expts. reveals protein-specific behavior spanning the full range between the limiting cases of full decoupling from (αBc) and full coupling to (HEWL) the macro-viscosity. SAXS was used to study the interactions between the proteins in soln., whereby it is shown that the three cases cover the range between a weakly interacting hard-sphere system (αBc) and screened Coulomb repulsion combined with short-range attraction (HEWL). Our results, as well as insights from the recent literature, suggest that the unusual rotational-translational coupling may be due to anisotropic interactions originating from hydrodynamic shape effects combined with high charge and possibly a patchy charge distribution.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtFyitLbK&md5=844a736917b46ee7208b64575b74296f
82.
Tai, J.; Dave, K.; Hahn, V.; Guzman, I.; Gruebele, M. Subcellular Modulation of Protein VlsE Stability and Folding Kinetics FEBS Lett. 2016, 590, 1409– 1416 DOI: 10.1002/1873-3468.12193
[Crossref], [PubMed], [CAS]
82.
Subcellular modulation of protein VlsE stability and folding kinetics
Tai, Jonathan; Dave, Kapil; Hahn, Vincent; Guzman, Irisbel; Gruebele, Martin
FEBS Letters (2016), 590 (10), 1409-1416CODEN: FEBLAL; ISSN:0014-5793. (Wiley-Blackwell)
The interior of a cell interacts differently with proteins than a dil. buffer because of a wide variety of macromols., chaperones, and osmolytes that crowd and interact with polypeptide chains. Here, the authors compare the folding of fluorescent constructs of protein VlsE among 3 environments inside cells. The nucleus increased the stability of VlsE relative to the cytoplasm, but slowed down the folding kinetics. VlsE was also more stable in the endoplasmic reticulum, but unlike phosphoglycerate kinase (PGK), tended to aggregate there. Thus, although fluorescent-tagged VlsE and PGK showed opposite stability trends from in vitro to the cytoplasm, their trends from cytoplasm to nucleus were similar.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xht1KrurfM&md5=aa4f0932e0e96a2b5bb6b71996146416
83.
Cino, E. A.; Karttunen, M.; Choy, W.-Y. Effects of Molecular Crowding on the Dynamics of Intrinsically Disordered Proteins PLoS One 2012, 7, e49876 DOI: 10.1371/journal.pone.0049876
[Crossref], [PubMed], [CAS]
83.
Effects of molecular crowding on the dynamics of intrinsically disordered proteins
Cino, Elio A.; Karttunen, Mikko; Choy, Wing-Yiu
PLoS One (2012), 7 (11), e49876CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)
Inside cells, the concn. of macromols. can reach up to 400 g/L. In such crowded environments, proteins are expected to behave differently than in vitro. It has been shown that the stability and the folding rate of a globular protein can be altered by the excluded vol. effect produced by a high d. of macromols. However, macromol. crowding effects on intrinsically disordered proteins (IDPs) are less explored. These proteins can be extremely dynamic and potentially sample a wide ensemble of conformations under non-denaturing conditions. The dynamic properties of IDPs are intimately related to the timescale of conformational exchange within the ensemble, which govern target recognition and how these proteins function. In this work, we investigated the macromol. crowding effects on the dynamics of several IDPs by measuring the NMR spin relaxation parameters of three disordered proteins (ProTα, TC1, and α-synuclein) with different extents of residual structures. To aid the interpretation of exptl. results, we also performed an MD simulation of ProTα. Based on the MD anal., a simple model to correlate the obsd. changes in relaxation rates to the alteration in protein motions under crowding conditions was proposed. Our results show that 1) IDPs remain at least partially disordered despite the presence of high concn. of other macromols., 2) the crowded environment has differential effects on the conformational propensity of distinct regions of an IDP, which may lead to selective stabilization of certain target-binding motifs, and 3) the segmental motions of IDPs on the nanosecond timescale are retained under crowded conditions. These findings strongly suggest that IDPs function as dynamic structural ensembles in cellular environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhvVCns7nO&md5=b0f501ffd3e1acdb8f190f37a1696f43
84.
Munari, F.; Bortot, A.; Zanzoni, S.; D’Onofrio, M.; Fushman, D.; Assfalg, M. Identification of Primary and Secondary UBA Footprints on the Surface of Ubiquitin in Cell-Mimicking Crowded Solution FEBS Lett. 2017, 591, 979– 990 DOI: 10.1002/1873-3468.12615
[Crossref], [PubMed], [CAS]
84.
Identification of primary and secondary UBA footprints on the surface of ubiquitin in cell-mimicking crowded solution
Munari, Francesca; Bortot, Andrea; Zanzoni, Serena; D'Onofrio, Mariapina; Fushman, David; Assfalg, Michael
FEBS Letters (2017), 591 (7), 979-990CODEN: FEBLAL; ISSN:0014-5793. (Wiley-Blackwell)
Despite significant advancements in our understanding of ubiquitin-mediated signaling, the influence of the intracellular environment on the formation of transient ubiquitin-partner complexes remains poorly explored. Here, we introduce macromol. crowding as a 1st level of complexity toward the imitation of a cellular environment in the study of such interactions. Using NMR spectroscopy, we found that the stereospecific complex of ubiquitin and the ubiquitin-assocd. domain (UBA) was minimally perturbed by crowding agent Ficoll. However, in addn. to the primary canonical recognition patch on ubiquitin, secondary patches were identified, indicating that in cell-mimicking crowded soln., UBA contacts ubiquitin at multiple sites.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXksV2ltLg%253D&md5=ac4088db66c26301a9c3c992c564b86e
85.
Ito, Y.; Selenko, P. Cellular Structural Biology Curr. Opin. Struct. Biol. 2010, 20, 640– 648 DOI: 10.1016/j.sbi.2010.07.006
[Crossref], [PubMed], [CAS]
85.
Cellular structural biology
Ito, Yutaka; Selenko, Philipp
Current Opinion in Structural Biology (2010), 20 (5), 640-648CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)
A review. While the complexity of the intracellular environment as a general property of every living organism is appreciated, there is a collectively lack of appropriate tools to analyze protein structures in a cellular context. In-cell NMR spectroscopy represents a novel biophys. tool to investigate the conformational and functional characteristics of biomols. at the at. level inside live cells. Here, the authors review recent in-cell NMR developments and provide an outlook towards future applications in prokaryotic and eukaryotic cells. The authors hope to thereby emphasize the usefulness of in-cell NMR techniques for cellular studies of complex biol. processes and for structural analyses in native environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtlKlsr7P&md5=0a8a26af4d70ce1f865330c8d07d878d
86.
Elcock, A. H. Models of Macromolecular Crowding Effects and the Need for Quantitative Comparisons with Experiment Curr. Opin. Struct. Biol. 2010, 20, 196– 206 DOI: 10.1016/j.sbi.2010.01.008
[Crossref], [PubMed], [CAS]
86.
Models of macromolecular crowding effects and the need for quantitative comparisons with experiment
Elcock, Adrian H.
Current Opinion in Structural Biology (2010), 20 (2), 196-206CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)
A review. In recent years significant effort has been devoted to exploring the potential effects of macromol. crowding on protein folding and assocn. phenomena. Theor. calcns. and mol. simulations have, in particular, been exploited to describe aspects of protein behavior in crowded and confined conditions and many aspects of the simulated behavior have reflected, at least at a qual. level, the behavior obsd. in expts. One major and immediate challenge for the theorists is to now produce models capable of making quant. accurate predictions of in vitro behavior. A second challenge is to derive models that explain results obtained from expts. performed in vivo, the results of which appear to call into question the assumed dominance of excluded-vol. effects in vivo.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXks1Sjsb4%253D&md5=b690fdf668cc2fdd575dc47aa567c00d
87.
Danielsson, J.; Oliveberg, M. Comparing Protein Behaviour in vitro and in vivo, What Does the Data Really Tell Us? Curr. Opin. Struct. Biol. 2017, 42, 129– 135 DOI: 10.1016/j.sbi.2017.01.002
[Crossref], [PubMed], [CAS]
87.
Comparing protein behaviour in vitro and in vivo, what does the data really tell us?
Danielsson, Jens; Oliveberg, Mikael
Current Opinion in Structural Biology (2017), 42 (), 129-135CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)
The recent advancement in moving 'biophys.' anal. of proteins in vivo has finally brought us to a position where we can start to make quant. comparisons with existing in-vitro data. A striking observation is that protein behavior in live cells seems, after all, not that different from in test tubes, not even at the level of complex mechanisms like protein aggregation. The example examd. in this review is the ALS assocd. protein SOD1 that apparently retains its in-vitro properties in vivo. Does this mean that the protocols for studying proteins in vivo are somehow oversimplified, or that the macromol. properties and interplay - despite being intrinsically malleable - are more evolutionary more 'streamlined' than previously anticipated. Whatever the answer may be the time is now right to put these data to crit. biol. test.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtFOis7k%253D&md5=446923616b7a3c5c27abe322f01433e8
88.
Roberts, E. Cellular and Molecular Structure as a Unifying Framework for Whole-Cell Modeling Curr. Opin. Struct. Biol. 2014, 25, 86– 91 DOI: 10.1016/j.sbi.2014.01.005
[Crossref], [PubMed], [CAS]
88.
Cellular and molecular structure as a unifying framework for whole-cell modeling
Roberts, Elijah
Current Opinion in Structural Biology (2014), 25 (), 86-91CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)
A review. Whole-cell modeling has the potential to play a major role in revolutionizing our understanding of cellular biol. over the next few decades. A computational model of the entire cell would allow cellular biologists to integrate data from many disparate sources in a single consistent framework. Such a comprehensive model would be useful both for hypothesis testing and in the discovery of new behaviors that emerge from complex biol. networks. Cellular and mol. structure can and should be a key organizing principle in a whole-cell model, connecting models across time and length scales in a multiscale approach. Here I present a summary of recent research centered around using mol. and cellular structure to model the behavior of cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXovFChu7g%253D&md5=60cdd0f066d6ff751dc3d5b7c5beb577
89.
Im, W.; Liang, J.; Olson, A.; Zhou, H.-X.; Vajda, S.; Vakser, I. A. Challenges in Structural Approaches to Cell Modeling J. Mol. Biol. 2016, 428, 2943– 2964 DOI: 10.1016/j.jmb.2016.05.024
[Crossref], [PubMed], [CAS]
89.
Challenges in structural approaches to cell modeling
Im, Wonpil; Liang, Jie; Olson, Arthur; Zhou, Huan-Xiang; Vajda, Sandor; Vakser, Ilya A.
Journal of Molecular Biology (2016), 428 (15), 2943-2964CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)
A review. Computational modeling is essential for structural characterization of biomol. mechanisms across the broad spectrum of scales. Adequate understanding of biomol. mechanisms inherently involves our ability to model them. Structural modeling of individual biomols. and their interactions has been rapidly progressing. However, in terms of the broader picture, the focus is shifting toward larger systems, up to the level of a cell. Such modeling involves a more dynamic and realistic representation of the interactomes in vivo, in a crowded cellular environment, as well as membranes and membrane proteins, and other cellular components. Structural modeling of a cell complements computational approaches to cellular mechanisms based on differential equations, graph models, and other techniques to model biol. networks, imaging data, etc. Structural modeling along with other computational and exptl. approaches will provide a fundamental understanding of life at the mol. level and lead to important applications to biol. and medicine. A cross section of diverse approaches presented in this review illustrates the developing shift from the structural modeling of individual mols. to that of cell biol. Studies in several related areas are covered: biol. networks; automated construction of three-dimensional cell models using exptl. data; modeling of protein complexes; prediction of non-specific and transient protein interactions; thermodn. and kinetic effects of crowding; cellular membrane modeling; and modeling of chromosomes. The review presents an expert opinion on the current state-of-the-art in these various aspects of structural modeling in cellular biol., and the prospects of future developments in this emerging field.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xptl2msrY%253D&md5=b5f04f79a203766d9fa90da604642f78
90.
Kyne, C.; Crowley, P. B. Grasping the Nature of the Cell Interior: From Physiological Chemistry to Chemical Biology FEBS J. 2016, 283, 3016– 3028 DOI: 10.1111/febs.13744
[Crossref], [PubMed], [CAS]
90.
Grasping the nature of the cell interior: from Physiological Chemistry to Chemical Biology
Kyne, Ciara; Crowley, Peter B.
FEBS Journal (2016), 283 (16), 3016-3028CODEN: FJEOAC; ISSN:1742-464X. (Wiley-Blackwell)
Current models of the cell interior emphasize its crowded, chem. complex and dynamically organised structure. Although the chem. compn. of cells is known, the cooperative intermol. interactions that govern cell ultrastructure are poorly understood. A major goal of biochem. is to capture these myriad interactions in vivo. We consider the landmark discoveries that have shaped this objective, starting from the vitalist framework established by early natural philosophers. Through this historical revisionism, we ext. important lessons for the bioinspired chemists of today. Scientific specialisation tends to insulate seminal ideas and hamper the unification of paradigms across biol. Therefore, we call for interdisciplinary collaboration in grappling with the complex cell interior. Recent successes in integrative structural biol. and chem. biol. demonstrate the power of hybrid approaches. The future roles of the (bio)chemist and model systems are also discussed as starting points for in vivo explorations.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XnsFahtb8%253D&md5=751684d06a300a768acdc97ba8c59d1b
91.
Zhou, H.-X. Polymer Crowders and Protein Crowders Act Similarly on Protein Folding Stability FEBS Lett. 2013, 587, 394– 397 DOI: 10.1016/j.febslet.2013.01.030
[Crossref], [PubMed], [CAS]
91.
Polymer crowders and protein crowders act similarly on protein folding stability
Zhou, Huan-Xiang
FEBS Letters (2013), 587 (5), 394-397CODEN: FEBLAL; ISSN:0014-5793. (Elsevier B.V.)
Recently, a polymer crowder and 2 protein crowders were found to have opposite effects on the folding stability of chymotrypsin inhibitor 2 (CI2), suggesting that they interact differently with CI2. Here, the authors propose that all of the macromol. crowders act similarly, with an entropic component favoring the folded state and an enthalpic component favoring the unfolded state. The net effect is destabilizing below a crossover temp., but stabilizing above it. This general trend is indeed obsd. in recent expts. and hints exptl. temp. as a reason for the opposite crowding effects of the polymer and protein crowders.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXit1yqur8%253D&md5=92373a326dfb445bc4e26e719ea11fd8
92.
Miklos, A. C.; Li, C.; Sharaf, N. G.; Pielak, G. J. Volume Exclusion and Soft Interaction Effects on Protein Stability under Crowded Conditions Biochemistry 2010, 49, 6984– 6991 DOI: 10.1021/bi100727y
[ACS Full Text ], [CAS]
92.
Volume Exclusion and Soft Interaction Effects on Protein Stability under Crowded Conditions
Miklos, Andrew C.; Li, Conggang; Sharaf, Naima G.; Pielak, Gary J.
Biochemistry (2010), 49 (33), 6984-6991CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
Most proteins function in nature under crowded conditions, and crowding can change protein properties. Quantification of crowding effects, however, is difficult because solns. contg. hundreds of grams of macromols. per L often interfere with the observation of the protein being studied. Models for macromol. crowding tend to focus on the steric effects of crowders, neglecting potential chem. interactions between the crowder and the test protein. Here, we report the first systematic, quant., residue-level study of crowding effects on the equil. stability of a globular protein. We used a system comprising poly(vinylpyrrolidone)s (PVPs) of varying mol. wts. as crowding agents and chymotrypsin inhibitor 2 (CI2) as a small globular test protein. Stability was quantified with NMR-detected amide 1H exchange. We analyzed the data in terms of hard particle exclusion, confinement, and soft interactions. For all crowded conditions, nearly every obsd. residue experiences a stabilizing effect. The exceptions are residues for which stabilities are unchanged. At a PVP concn. of 100 g/L, the data are consistent with theories of hard particle exclusion. At higher concns., the data are more consistent with confinement. The data show that the crowder also stabilizes the test protein by weakly binding its native state. We conclude that the role of native-state binding and other soft interactions needs to be seriously considered when applying both theory and expt. to studies of macromol. crowding.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXpsV2msb8%253D&md5=bd98a1a01664fe701d57c621f4f9fe94
93.
Ignatova, Z.; Krishnan, B.; Bombardier, J. P.; Marcelino, A. M. C.; Hong, J.; Gierasch, L. M. From the Test Tube to the Cell: Exploring the Folding and Aggregation of a β-Clam Protein Biopolymers 2007, 88, 157– 163 DOI: 10.1002/bip.20665
[Crossref], [PubMed], [CAS]
93.
From the test tube to the cell: exploring the folding and aggregation of a β-clam protein
Ignatova, Zoya; Krishnan, Beena; Bombardier, Jeffrey P.; Marcelino, Anna Marie C.; Hong, Jiang; Gierasch, Lila M.
Biopolymers (2007), 88 (2), 157-163CODEN: BIPMAA; ISSN:0006-3525. (John Wiley & Sons, Inc.)
A review. A crucial challenge in present biomedical research is the elucidation of how fundamental processes like protein folding and aggregation occur in the complex environment of the cell. Many new physico-chem. factors like crowding and confinement must be considered, and immense tech. hurdles must be overcome in order to explore these processes in vivo. Understanding protein misfolding and aggregation diseases and developing therapeutic strategies to these diseases demand that we gain mechanistic insight into behaviors and misbehaviors of proteins as they fold in vivo. We have developed a fluorescence approach using FlAsH labeling to study the thermodn. of folding of a model β-rich protein, cellular retinoic acid binding protein (CRABP) in Escherichia coli cells. The labeling approach has also enabled us to follow aggregation of a modified version of CRABP and chimeras between CRABP and huntingtin exon 1 with its glutamine repeat tract. In this article, we review our recent results using FlAsH labeling to study in-vivo folding and present new observations that hint at fundamental differences between the thermodn. and kinetics of protein folding in vivo and in vitro.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXksVWlt7c%253D&md5=729243dab8ab9cbab8bf24c8df4539ec
94.
Hong, J.; Gierasch, L. M. Macromolecular Crowding Remodels the Energy Landscape of a Protein by Favoring a More Compact Unfolded State J. Am. Chem. Soc. 2010, 132, 10445– 10452
[ACS Full Text ], [CAS]
94.
Macromolecular Crowding Remodels the Energy Landscape of a Protein by Favoring a More Compact Unfolded State
Hong, Jiang; Gierasch, Lila M.
Journal of the American Chemical Society (2010), 132 (30), 10445-10452CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The interior of cells is highly crowded with macromols., which impacts all physiol. processes. To explore how macromol. crowding may influence cellular protein folding, we interrogated the folding landscape of a model β-rich protein, cellular retinoic acid-binding protein I (CRABP I), in the presence of an inert crowding agent (Ficoll 70). Urea titrns. revealed a crowding-induced change in the water-accessible polar amide surface of its denatured state, based on an obsd. ca. 15% decrease in the change in unfolding free energy with respect to urea concn. (the m-value), and the effect of crowding on the equil. stability of CRABP I was less than our exptl. error (i.e., ≤1.2 kcal/mol). Consequently, we directly probed the effect of crowding on the denatured state of CRABP I by measuring side-chain accessibility using iodide quenching of tryptophan fluorescence and chem. modification of cysteines. We obsd. that the urea-denatured state is more compact under crowded conditions, and the obsd. extent of redn. of the m-value by crowding agent is fully consistent with the extent of redn. of the accessibility of the Trp and Cys probes, suggesting a random and nonspecific compaction of the unfolded state. The thermodn. consequences of crowding-induced compaction are discussed. In addn., over a wide range of Ficoll concn., crowding significantly retarded the unfolding kinetics of CRABP I without influencing the urea dependence of the unfolding rate, arguing for no appreciable change in the nature of the transition state. Our results demonstrate how macromol. crowding may influence protein folding by effects on both the unfolded state ensemble and unfolding kinetics.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXovVCitLs%253D&md5=3c4f883b8273c082a3db3636de21594e
95.
Macdonald, B.; McCarley, S.; Noeen, S.; van Giessen, A. E. Protein–Protein Interactions Affect α-Helix Stability in Crowded Environments J. Phys. Chem. B 2015, 119, 2956– 2967 DOI: 10.1021/jp512630s
[ACS Full Text ], [CAS]
95.
Protein-protein interactions affect alpha helix stability in crowded environments
Macdonald, Bryanne; McCarley, Shannon; Noeen, Sundus; van Giessen, Alan E.
Journal of Physical Chemistry B (2015), 119 (7), 2956-2967CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
The dense, heterogeneous cellular environment is known to affect protein stability through interactions with other biomacromols. The effect of excluded vol. due to these biomols., also known as crowding agents, on a protein of interest, or test protein, has long been known to increase the stability of the test protein. Recently, it has been recognized that attractive protein-crowder interactions play an important role. These interactions affect protein stability and can destabilize the test protein. However, most computational work investigating the role of attractive interactions has used spherical crowding agents and has neglected the specific roles of crowding agent hydrophobicity and H-bonding. Here, the authors used multicanonical mol. dynamics and a coarse-grained protein model to study the folding thermodn. of a small helical test protein [(AAQAA)3] in the presence of crowding agents that were themselves proteins. The results showed that the stability of the test protein depended on the hydrophobicity of the crowding agents. For low values of crowding agent hydrophobicity, the excluded vol. effect was dominant, and the test protein was stabilized relative to the dil. soln. For intermediate values of crowding agent hydrophobicity, the test protein was destabilized by favorable side-chain/side-chain interactions stabilizing the unfolded states. For high values of crowding agent hydrophobicity, the native state was stabilized by the strong intermol. attractions, causing the formation of a packed structure that increased the stability of the test protein through favorable side-chain/side-chain interactions. In addn., increasing crowding agent hydrophobicity increased the "foldability" of the test protein and altered the potential energy landscape by simultaneously deepening the basins corresponding to the folded and unfolded states and increasing the energy barrier between them.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXpvF2gtQ%253D%253D&md5=d98f70ce7a3a1931456e53691ded9921
96.
Macdonald, B.; McCarley, S.; Noeen, S.; van Giessen, A. E. β-Hairpin Crowding Agents Affect α-Helix Stability in Crowded Environments J. Phys. Chem. B 2016, 120, 650– 659 DOI: 10.1021/acs.jpcb.5b10575
[ACS Full Text ], [CAS]
96.
β-Hairpin Crowding Agents Affect α-Helix Stability in Crowded Environments
MacDonald, Bryanne; McCarley, Shannon; Noeen, Sundus; van Giessen, Alan E.
Journal of Physical Chemistry B (2016), 120 (4), 650-659CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
The dense, heterogeneous cellular environment is known to affect protein stability. It is now recognized that attractive "quinary" interactions with other biomacromols. in the cell, referred to as the crowding agents, play a significant role in detg. the stability of the protein of interest or test protein. These attractive interactions can reduce or overcome the stabilizing effect of the excluded vol. of the crowding agents. However, the roles of specific interactions, such as hydrogen bonding and side chain-side chain hydrophobic interactions, are still unclear. Here, we use mol. simulation to investigate the roles played by hydrophobic interactions and hydrogen bonding between a small helical test protein and equally sized crowding agent proteins in a fixed β-hairpin configuration. The test protein and crowding agents are represented by a coarse-grained protein model, and we use multicanonical mol. dynamics to study the folding thermodn. of the test protein. Our results confirm that the stability of the test protein depends on the hydrophobicity of the crowding agents and that the stability of the test protein is reduced through favorable side chain-side chain interactions that preferentially stabilize the unfolded states. In addn., we show that when the intermol. hydrophobic interactions are more favorable than the intramol. hydrophobic interactions, the β-rich crowding agents can completely destabilize the test protein, causing it to adopt configurations with increased β-content and preventing it from forming its native helical state. Similarities between our results and those seen in the formation of amyloid fibrils are also discussed.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XnvFelug%253D%253D&md5=89a780b8b7e27ee7a40f48b9fd82fa4b
97.
Bille, A.; Mohanty, S.; Irbäck, A. Peptide Folding in the Presence of Interacting Protein Crowders J. Chem. Phys. 2016, 144, 175105 DOI: 10.1063/1.4948462
[Crossref], [PubMed], [CAS]
97.
Peptide folding in the presence of interacting protein crowders
Bille, Anna; Mohanty, Sandipan; Irbaeck, Anders
Journal of Chemical Physics (2016), 144 (17), 175105/1-175105/9CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Using Monte Carlo methods, the authors explored and compared the effects of 2 protein crowders, bovine pancreatic trypsin inhibitor (BPTI) and streptococcal protein G B1 domain (GB1), on the folding thermodn. of 2 peptides, the compact helical Trp-cage and the β-hairpin-forming GB1 mutant (GB1m3). The thermally highly stable crowder proteins were modeled using a fixed backbone and rotatable side-chains, whereas the peptides were free to fold and unfold. In the simulations, the crowder proteins tended to distort the Trp-cage fold, while having a stabilizing effect on GB1m3. The extent of the effects on a given peptide depended on the crowder type. Due to a sticky patch on its surface, BPTI caused larger changes than GB1 in the melting properties of the peptides. The obsd. effects on the peptides stemmed largely from attractive and specific interactions with the crowder surfaces, and differed from those seen in ref. simulations with purely steric crowder particles. (c) 2016 American Institute of Physics.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XnsVajtLo%253D&md5=04272ff1a7d3a21719575bea09f494c9
98.
Bille, A.; Linse, B.; Mohanty, S.; Irbäck, A. Equilibrium Simulation of Trp-Cage in the Presence of Protein Crowders J. Chem. Phys. 2015, 143, 175102 DOI: 10.1063/1.4934997
[Crossref], [PubMed], [CAS]
98.
Equilibrium simulation of trp-cage in the presence of protein crowders
Bille, Anna; Linse, Bjoern; Mohanty, Sandipan; Irbaeck, Anders
Journal of Chemical Physics (2015), 143 (17), 175102/1-175102/7CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
While steric crowders tend to stabilize globular proteins, it has been found that protein crowders can have an either stabilizing or destabilizing effect, where a destabilization may arise from nonspecific attractive interactions between the test protein and the crowders. Here, the authors used Monte Carlo replica-exchange methods to explore the equil. behavior of Trp-cage miniprotein in the presence of protein crowders. The results suggested that the surrounding crowders prevented Trp-cage from adopting its global native fold, while giving rise to a stabilization of its main secondary structure element, an α-helix. With the crowding agent used (bovine pancreatic trypsin inhibitor), the Trp-cage-crowder interactions were found to be specific, involving a few key residues, most of which were Pro residues. The effects of these crowders were contrasted with those of hard-sphere crowders. (c) 2015 American Institute of Physics.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhslyhtrzE&md5=2f93080e098e183c7a53d77f6318fb88
99.
Kadumuri, R. V.; Gullipalli, J.; Subramanian, S.; Jaipuria, G.; Atreya, H. S.; Vadrevu, R. Crowding Interactions Perturb Structure and Stability by Destabilizing the Stable Core of the α-Subunit of Tryptophan Synthase FEBS Lett. 2016, 590, 2096– 2105 DOI: 10.1002/1873-3468.12259
[Crossref], [PubMed], [CAS]
99.
Crowding interactions perturb structure and stability by destabilizing the stable core of the α-subunit of tryptophan synthase
Kadumuri, Rajashekar Varma; Gullipalli, Jagadeesh; Subramanian, SriVidya; Jaipuria, Garima; Atreya, Hanudatta S.; Vadrevu, Ramakrishna
FEBS Letters (2016), 590 (14), 2096-2105CODEN: FEBLAL; ISSN:0014-5793. (Wiley-Blackwell)
The consequences of crowding derived from relatively small and intrinsically disordered proteins are not clear yet. We report the effect of ficoll-70 on the structure and stability of native and partially folded states of the 29 kDa alpha subunit of tryptophan synthase (αTS). Overall, combining the changes in the CD and fluorescence spectra, in conjunction with the gradual loss of cooperativity under urea denaturation in the presence of increasing amts. of ficoll, it may be concluded that the crowding agent perturbs not only the native state but also the partially folded state of αTS. Importantly, NMR data indicate that ficoll interacts with the residues that constitute the stable core of the protein thus shedding light on the origin of the obsd. perturbation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsFOrt77E&md5=d0be96a1f406068300c694a9eaa2c33c
100.
Qin, S.; Zhou, H.-X. Effects of Macromolecular Crowding on the Conformational Ensembles of Disordered Proteins J. Phys. Chem. Lett. 2013, 4, 3429– 3434 DOI: 10.1021/jz401817x
[ACS Full Text ], [CAS]
100.
Effects of Macromolecular Crowding on the Conformational Ensembles of Disordered Proteins
Qin, Sanbo; Zhou, Huan-Xiang
Journal of Physical Chemistry Letters (2013), 4 (20), 3429-3434CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
Due to their conformational malleability, intrinsically disordered proteins (IDPs) are particularly susceptible to influences of crowded cellular environments. Here we report a computational study of the effects of macromol. crowding on the conformational ensemble of a coarse-grained IDP model, by using two approaches. In one, the IDP is simulated along with the crowders; in the other, crowder-free simulations are postprocessed to predict the conformational ensembles under crowding. We found significant decreases in the radius of gyration of the IDP under crowding, and suggest repulsive interactions with crowders as a common cause for chain compaction in a no. of exptl. studies. The postprocessing approach accurately reproduced the conformational ensembles of the IDP in the direct simulations here, and holds enormous potential for realistic modeling of IDPs under crowding, by permitting thorough conformation sampling for the proteins even when they and the crowders are both represented at the all-atom level.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsFWlurbL&md5=32eb5f746de4d8b82f3df03c4b94e202
101.
Goldenberg, D. P.; Argyle, B. Minimal Effects of Macromolecular Crowding on an Intrinsically Disordered Protein: A Small-Angle Neutron Scattering Study Biophys. J. 2014, 106, 905– 914 DOI: 10.1016/j.bpj.2013.12.003
[Crossref], [PubMed], [CAS]
101.
Minimal Effects of Macromolecular Crowding on an Intrinsically Disordered Protein: A Small-Angle Neutron Scattering Study
Goldenberg, David P.; Argyle, Brian
Biophysical Journal (2014), 106 (4), 905-914CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
Small-angle neutron scattering was used to study the effects of macromol. crowding by two globular proteins, i.e., bovine pancreatic trypsin inhibitor and equine metmyoglobin, on the conformational ensemble of an intrinsically disordered protein, the N protein of bacteriophage λ. The λ N protein was uniformly labeled with 2H, and the concns. of D2O in the samples were adjusted to match the neutron scattering contrast of the unlabeled crowding proteins, thereby masking their contribution to the scattering profiles. Scattering from the deuterated λ N was recorded for samples contg. up to 0.12 g/mL bovine pancreatic trypsin inhibitor or 0.2 g/mL metmyoglobin. The radius of gyration of the uncrowded protein was estd. to be 30 Å and was found to be remarkably insensitive to the presence of crowders, varying by <2 Å for the highest crowder concns. The scattering profiles were also used to est. the fractal dimension of λ N, which was found to be ∼1.8 in the absence or presence of crowders, indicative of a well-solvated and expanded random coil under all of the conditions examd. These results are contrary to the predictions of theor. treatments and previous exptl. studies demonstrating compaction of unfolded proteins by crowding with polymers such as dextran and Ficoll. A computational simulation suggests that some previous treatments may have overestimated the effective vols. of disordered proteins and the variation of these vols. within an ensemble. The apparent insensitivity of λ N to crowding may also be due in part to weak attractive interactions with the crowding proteins, which may compensate for the effects of steric exclusion.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXislKru7o%253D&md5=8e4e10f1667e3d81d882f97b07fa8a1a
102.
Nakano, S.-i.; Sugimoto, N. Model Studies of the Effects of Intracellular Crowding on Nucleic Acid Interactions Mol. BioSyst. 2017, 13, 32– 41 DOI: 10.1039/C6MB00654J
[Crossref], [CAS]
102.
Model studies of the effects of intracellular crowding on nucleic acid interactions
Nakano, Shu-ichi; Sugimoto, Naoki
Molecular BioSystems (2017), 13 (1), 32-41CODEN: MBOIBW; ISSN:1742-2051. (Royal Society of Chemistry)
Mol. interactions and reactions in living cells occur with high concns. of background mols. and ions. Many research studies have shown that intracellular mols. have characteristics different from those obtained using simple aq. solns. To better understand the behavior of biomols. in intracellular environments, biophys. expts. were conducted under cell-mimicking conditions in a test tube. It has been shown that the mol. environments at the physiol. level of macromol. crowding, spatial confinement, water activity and dielec. const., have significant effects on the interactions of DNA and RNA for hybridization, higher-order folding, and catalytic activity. The exptl. approaches using in vitro model systems are useful to reveal the origin of the environmental effects and to bridge the gap between the behaviors of nucleic acids in vitro and in vivo. This paper highlights the model expts. used to evaluate the influences of intracellular environment on nucleic acid interactions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhsl2gt7jK&md5=ae6c8745bed06a6d3de70304a4ca06ea
103.
Yildirim, A.; Sharma, M.; Varner, B. M.; Fang, L.; Feig, M. Conformational Preferences of DNA in Reduced Dielectric Environments J. Phys. Chem. B 2014, 118, 10874– 10881 DOI: 10.1021/jp505727w
[ACS Full Text ], [CAS]
103.
Conformational preferences of DNA in reduced dielectric environments
Yildirim, Asli; Sharma, Monika; Varner, Bradley Michael; Fang, Liang; Feig, Michael
Journal of Physical Chemistry B (2014), 118 (37), 10874-10881CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
The effect of reduced dielec. environments on the conformational sampling of DNA was examd. through mol. dynamics (MD) simulations. Different dielec. environments were used to model one aspect of cellular environments. Implicit solvent based on the Generalized Born methodol. was used to reflect different dielec. environments in the MD simulations. The MD simulation results showed a tendency of DNA structures to favor noncanonical A-like conformations rather than canonical A- and B-forms as a result of the reduced dielec. environments. The results suggested that the reduced dielec. response in cellular environments may be sufficient to enhance the sampling of A-like DNA structures compared to dil. solvent conditions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsVekt7vN&md5=58a5d0a7fc0842d4edaaae82b7a015a2
104.
Nakano, S.-i.; Miyoshi, D.; Sugimoto, N. Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids Chem. Rev. 2014, 114, 2733– 2758 DOI: 10.1021/cr400113m
[ACS Full Text ], [CAS]
104.
Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids
Nakano, Shu-ichi; Miyoshi, Daisuke; Sugimoto, Naoki
Chemical Reviews (Washington, DC, United States) (2014), 114 (5), 2733-2758CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
A review. Recent progresses in microscopy and spectroscopy technologies for intracellular measurements, quant. studies using exptl. model systems, and computer simulations have led to an improved understanding of the interactions and reactions of nucleic acids under the macromol. crowding and small-mol. crowding conditions, which are the central theme of this review.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvFOntLjF&md5=289fa514fecb5ac40b5adfc1eab34256
105.
Gao, M.; Gnutt, D.; Orban, A.; Appel, B.; Righetti, F.; Winter, R.; Narberhaus, F.; Müller, S.; Ebbinghaus, S. RNA Hairpin Folding in the Crowded Cell Angew. Chem., Int. Ed. 2016, 55, 3224– 3228 DOI: 10.1002/anie.201510847
[Crossref], [CAS]
105.
RNA Hairpin Folding in the Crowded Cell
Gao, Mimi; Gnutt, David; Orban, Axel; Appel, Bettina; Righetti, Francesco; Winter, Roland; Narberhaus, Franz; Mueller, Sabine; Ebbinghaus, Simon
Angewandte Chemie, International Edition (2016), 55 (9), 3224-3228CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
Precise secondary and tertiary structure formation is critically important for the cellular functionality of ribonucleic acids (RNAs). RNA folding studies were mainly conducted in vitro, without the possibility of validating these expts. inside cells. Here, we directly resolve the folding stability of a hairpin-structured RNA inside live mammalian cells. We find that the stability inside the cell is comparable to that in dil. physiol. buffer. On the contrary, the addn. of in vitro artificial crowding agents, with the exception of high-mol.-wt. PEG, leads to a destabilization of the hairpin structure through surface interactions and redn. in water activity. We further show that RNA stability is highly variable within cell populations as well as within subcellular regions of the cytosol and nucleus. We conclude that inside cells the RNA is subject to (localized) stabilizing and destabilizing effects that lead to an on av. only marginal modulation compared to dild. buffer.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhslWlu7c%253D&md5=d46acc5faa8ee36b0d12c482abace3ec
106.
Baltierra-Jasso, L. E.; Morten, M. J.; Laflör, L.; Quinn, S. D.; Magennis, S. W. Crowding-Induced Hybridization of Single DNA Hairpins J. Am. Chem. Soc. 2015, 137, 16020– 16023 DOI: 10.1021/jacs.5b11829
[ACS Full Text ], [CAS]
106.
Crowding-Induced Hybridization of Single DNA Hairpins
Baltierra-Jasso, Laura E.; Morten, Michael J.; Laflor, Linda; Quinn, Steven D.; Magennis, Steven W.
Journal of the American Chemical Society (2015), 137 (51), 16020-16023CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
It is clear that a crowded environment influences the structure, dynamics, and interactions of biol. mols., but the complexity of this phenomenon demands the development of new exptl. and theor. approaches. Here we use two complementary single-mol. FRET techniques to show that the kinetics of DNA base pairing and unpairing, which are fundamental to both the biol. role of DNA and its technol. applications, are strongly modulated by a crowded environment. We directly obsd. single DNA hairpins, which are excellent model systems for studying hybridization, either freely diffusing in soln. or immobilized on a surface under crowding conditions. The hairpins followed two-state folding dynamics with a closing rate increasing by 4-fold and the opening rate decreasing 2-fold, for only modest concns. of crowder [10% (wt./wt.) polyethylene glycol (PEG)]. These expts. serve both to unambiguously highlight the impact of a crowded environment on a fundamental biol. process, DNA base pairing, and to illustrate the benefits of single-mol. approaches to probing the structure and dynamics of complex biomol. systems.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhvF2ltL7N&md5=41090b083fa05da3dffcf7e608be31b4
107.
Kilburn, D.; Roh, J. H.; Guo, L.; Briber, R. M.; Woodson, S. A. Molecular Crowding Stabilizes Folded RNA Structure by the Excluded Volume Effect J. Am. Chem. Soc. 2010, 132, 8690– 8696 DOI: 10.1021/ja101500g
[ACS Full Text ], [CAS]
107.
Molecular Crowding Stabilizes Folded RNA Structure by the Excluded Volume Effect
Kilburn, Duncan; Roh, Joon Ho; Guo, Liang; Briber, Robert M.; Woodson, Sarah A.
Journal of the American Chemical Society (2010), 132 (25), 8690-8696CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Crowder mols. in soln. alter the equil. between folded and unfolded states of biol. macromols. It is therefore crit. to account for the influence of these other mols. when describing the folding of RNA inside the cell. Small angle X-ray scattering expts. are reported on a 64 kDa bacterial group I ribozyme in the presence of polyethylene-glycol 1000 (PEG-1000), a mol. crowder with an av. mol. wt. of 1000 Da. In agreement with expected excluded vol. effects, PEG favors more compact RNA structures. First, the transition from the unfolded to the folded (more compact) state occurs at lower MgCl2 concns. in PEG. Second, the radius of gyration of the unfolded RNA decreases from 76 to 64 Å as the PEG concn. increases from 0 to 20% wt/vol. Changes to water and ion activities were measured exptl., and theor. models were used to evaluate the excluded vol. We conclude that the dominant influence of the PEG crowder on the folding process is the excluded vol. effect.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXmvFarsr4%253D&md5=bf937c83d949d83e93b1740f660323ca
108.
Tyrrell, J.; McGinnis, J. L.; Weeks, K. M.; Pielak, G. J. The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure Biochemistry 2013, 52, 8777– 8785 DOI: 10.1021/bi401207q
[ACS Full Text ], [CAS]
108.
The cellular environment stabilizes adenine riboswitch RNA structure
Tyrrell, Jillian; McGinnis, Jennifer L.; Weeks, Kevin M.; Pielak, Gary J.
Biochemistry (2013), 52 (48), 8777-8785CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
There are large differences between the intracellular environment and the conditions widely used to study RNA structure and function in vitro. To assess the effects of the crowded cellular environment on RNA, the authors examd. the structure and ligand binding function of the adenine riboswitch aptamer domain in healthy, growing Escherichia coli cells at single-nucleotide resoln. on the minute time scale using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension). The ligand-bound aptamer structure was essentially the same in cells and in buffer at 1 mM Mg2+, the approx. Mg2+ concn. that was measured in cells. In contrast, the in-cell conformation of the ligand-free aptamer was much more similar to the fully folded ligand-bound state. Even adding high Mg2+ concns. to the buffer used for in vitro analyses did not yield the conformation obsd. for the free aptamer in cells. The cellular environment thus stabilized the aptamer significantly more than did Mg2+ alone. The results showed that the intracellular environment has a large effect on RNA structure that ultimately favors highly organized conformations.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhslCrsrzF&md5=52621510e56eec589ac75ed430a42c36
109.
Tyrrell, J.; Weeks, K. M.; Pielak, G. J. Challenge of Mimicking the Influences of the Cellular Environment on RNA Structure by PEG-Induced Macromolecular Crowding Biochemistry 2015, 54, 6447– 6453 DOI: 10.1021/acs.biochem.5b00767
[ACS Full Text ], [CAS]
109.
Challenge of Mimicking the Influences of the Cellular Environment on RNA Structure by PEG-Induced Macromolecular Crowding
Tyrrell, Jillian; Weeks, Kevin M.; Pielak, Gary J.
Biochemistry (2015), 54 (42), 6447-6453CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
There are large differences between the cellular environment and the conditions widely used to study RNA in vitro. SHAPE RNA structure probing in Escherichia coli cells has shown that the cellular environment stabilizes both long-range and local tertiary interactions in the adenine riboswitch aptamer domain. Synthetic crowding agents are widely used to understand the forces that stabilize RNA structure and in efforts to recapitulate the cellular environment under simplified exptl. conditions. Here, we studied the structure and ligand binding ability of the adenine riboswitch in the presence of the macromol. crowding agent, polyethylene glycol (PEG). Ethylene glycol and low-mol. mass PEGs destabilized RNA structure and caused the riboswitch to sample secondary structures different from those obsd. in simple buffered solns. or in cells. In the presence of larger PEGs, longer-range loop-loop interactions were more similar to those in cells than in buffer alone, consistent with prior work showing that larger PEGs stabilize compact RNA states. Ligand affinity was weakened by low-mol. mass PEGs but increased with high-mol. mass PEGs, indicating that PEG cosolvents exert complex chem. and steric effects on RNA structure. Regardless of polymer size, however, nucleotide-resoln. structural characteristics obsd. in cells were not recapitulated in PEG solns. Our results reveal that the cellular environment is difficult to recapitulate in vitro; mimicking the cellular state will likely require a combination of crowding agents and other chem. species.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhs1SisLvJ&md5=f05d626a03594f92606a0ed48c00b97a
110.
Bryant, J. E.; Lecomte, J. T. J.; Lee, A. L.; Young, G. B.; Pielak, G. J. Protein Dynamics in Living Cells Biochemistry 2005, 44, 9275– 9279 DOI: 10.1021/bi050786j
[ACS Full Text ], [CAS]
110.
Protein Dynamics in Living Cells
Bryant, Julie E.; Lecomte, Juliette T. J.; Lee, Andrew L.; Young, Gregory B.; Pielak, Gary J.
Biochemistry (2005), 44 (26), 9275-9279CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
A protein's structure is most often used to explain its function, but function also depends on dynamics. To date, protein dynamics have been studied only in vitro under dil. soln. conditions where solute concns. are typically less than 10 g/L, yet proteins function in a crowded environment where the solute concn. can exceed 400 g/L. Does the intracellular environment affect protein dynamics The answer will help in assessing the biol. significance of the NMR-derived dynamics data collected to date. We investigated fast protein dynamics inside living Escherichia coli by using in-cell NMR. The backbone dynamics of apocytochrome b5 were quantified using {1H}-15N nuclear Overhauser effect (nOe) measurements, which characterize motions on the pico- to nanosecond time scale. The overall trend of backbone dynamics remains the same in cells. Some of the nOe values differ, but most of the differences track the increased intracellular viscosity rather than a change in dynamics. Therefore, it appears that dil. soln. steady-state {1H}-15N nOe measurements provide biol. relevant information about pico- to nanosecond backbone motion in proteins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXkvFSmtrY%253D&md5=8eb8493ab26d8f4ea1ecd346bf8beec6
111.
Bryant, J. E.; Lecomte, J. T. J.; Lee, A. L.; Young, G. B.; Pielak, G. J. Cytosol Has a Small Effect on Protein Backbone Dynamics Biochemistry 2006, 45, 10085– 10091 DOI: 10.1021/bi060547b
[ACS Full Text ], [CAS]
111.
Cytosol Has a Small Effect on Protein Backbone Dynamics
Bryant, Julie E.; Lecomte, Juliette T. J.; Lee, Andrew L.; Young, Gregory B.; Pielak, Gary J.
Biochemistry (2006), 45 (33), 10085-10091CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
Cells are crowded with macromols., yet most biophys. information about proteins is obtained in dil. soln. To det. the impact of this dichotomy, the authors used NMR spectroscopy to measure the backbone 15N T1 and T2 relaxation times and the {1H}-15N nuclear Overhauser enhancement (nOe) of uniformly 15N-enriched apocytochrome b5 in living Escherichia coli and in dil. soln. These data allowed the authors to assess the backbone dynamics of this partially folded protein in cells and in dil. soln. The two data sets were analyzed by using the model-free approach. Transfer from dil. soln. to the cytosol has a quant. effect on T1, T2, and nOe values. Most of the effects are attributed to an increase in the overall correlation time, caused by the increased viscosity of the cytosol compared to that of the dil. soln. The authors' main conclusion is that the cytosol does not alter the pattern of backbone dynamics of apocytochrome b5. Increases in the time scale of both the picosecond and millisecond motions are obsd., but the increases are less than ∼30%.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XnsFWlsrs%253D&md5=f73767599f2ae4005bdd38d25e12362b
112.
Abriata, L.; Spiga, E.; Dal Peraro, M. All-Atom Simulations of Crowding Effects on Ubiquitin Dynamics Phys. Biol. 2013, 10, 045006 DOI: 10.1088/1478-3975/10/4/045006
[Crossref], [PubMed], [CAS]
112.
All-atom simulations of crowding effects on ubiquitin dynamics
Abriata, Luciano A.; Spiga, Enrico; Dal Peraro, Matteo
Physical Biology (2013), 10 (4), 045006/1-045006/8, 8 pp.CODEN: PBHIAT; ISSN:1478-3975. (IOP Publishing Ltd.)
It is well-known that crowded environments affect the stability of proteins, with strong biol. and biotechnol. implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to probe exptl. Here we report on a simulation study aimed at evaluating the effects of crowding on internal protein dynamics, based on fully all-atom descriptions of the protein, the solvent and the crowder. Our model system consists of ubiquitin, a protein whose dynamic features are closely related to its ability to bind to multiple partners, in a 325 g L-1 soln. of glucose in water, a condition widely employed in in vitro studies of crowding effects. We observe a slight redn. in loop flexibility accompanied by a dramatic restriction of the conformational space explored in the timescale of the simulations (∼0.5 μs), indicating that crowding slows down collective motions and the rate of exploration of the conformational space. This effect is attributed to the extensive and long-lasting interactions obsd. between protein residues and glucose mols. throughout the entire protein surface. Potential implications of the obsd. effects are discussed.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhvFWntbY%253D&md5=29f3cea1e33cfc54b504e5a0840a2753
113.
Minh, D. D. L.; Chang, C.-e.; Trylska, J.; Tozzini, V.; McCammon, J. A. The Influence of Macromolecular Crowding on HIV-1 Protease Internal Dynamics J. Am. Chem. Soc. 2006, 128, 6006– 6007 DOI: 10.1021/ja060483s
[ACS Full Text ], [CAS]
113.
The Influence of Macromolecular Crowding on HIV-1 Protease Internal Dynamics
Minh, David D. L.; Chang, Chia-En; Trylska, Joanna; Tozzini, Valentina; McCammon, J. Andrew
Journal of the American Chemical Society (2006), 128 (18), 6006-6007CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
High macromol. concns., or crowded conditions, have been shown to affect a wide variety of mol. processes, including diffusion, assocn. and dissocn., and protein folding and stability. Here, the authors model the effect of macromol. crowding on the internal dynamics of a protein, HIV-1 protease, using Brownian dynamics simulations. HIV-1 protease possesses a pair of flaps which are postulated to open in the early stages of its catalytic mechanism. Compared to low concns., close-packed concns. of repulsive crowding agents are found to significantly reduce the fraction of time that the protease flaps are open. Macromol. crowding is likely to have a major effect on in vivo enzyme activity, and may play an important regulatory role in the viral life cycle.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XjtleqsLk%253D&md5=85008ac40803eb9b72f8fd1aca09c383
114.
Makowski, L.; Rodi, D. J.; Mandava, S.; Minh, D. D. L.; Gore, D. B.; Fischetti, R. F. Molecular Crowding Inhibits Intramolecular Breathing Motions in Proteins J. Mol. Biol. 2008, 375, 529– 546 DOI: 10.1016/j.jmb.2007.07.075
[Crossref], [PubMed], [CAS]
114.
Molecular Crowding Inhibits Intramolecular Breathing Motions in Proteins
Makowski, Lee; Rodi, Diane J.; Mandava, Suneeta; Minh, David D. L.; Gore, David B.; Fischetti, Robert F.
Journal of Molecular Biology (2008), 375 (2), 529-546CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)
In aq. soln. some proteins undergo large-scale movements of secondary structures, subunits or domains, referred to as protein "breathing", that define a native-state ensemble of structures. These fluctuations are sensitive to the nature and concn. of solutes and other proteins and are thereby expected to be different in the crowded interior of a cell than in dil. soln. Here the authors use a combination of wide angle x-ray scattering (WAXS) and computational modeling to derive a quant. measure of the spatial scale of conformational fluctuations in a protein soln. Concn.-dependent changes in the obsd. scattering intensities are consistent with a model of structural fluctuations in which secondary structures undergo rigid-body motions relative to one another. This motion increases with decreasing protein concn. or increasing temp. Anal. of a set of five structurally and functionally diverse proteins reveals a diversity of kinetic behaviors. Proteins with multiple disulfide bonds exhibit little or no increase in breathing in dil. solns. The spatial extent of structural fluctuations appears highly dependent on both protein structure and concn. and is universally suppressed at very high protein concns.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhsVWjsrjE&md5=06f625ce102f3584df348ee0ba56edc9
115.
Li, C.; Charlton, L. M.; Lakkavaram, A.; Seagle, C.; Wang, G.; Young, G. B.; Macdonald, J. M.; Pielak, G. J. Differential Dynamical Effects of Macromolecular Crowding on an Intrinsically Disordered Protein and a Globular Protein: Implications for In-Cell NMR Spectroscopy J. Am. Chem. Soc. 2008, 130, 6310– 6311 DOI: 10.1021/ja801020z
[ACS Full Text ], [CAS]
115.
Differential Dynamical Effects of Macromolecular Crowding on an Intrinsically Disordered Protein and a Globular Protein: Implications for In-Cell NMR Spectroscopy
Li, Conggang; Charlton, Lisa M.; Lakkavaram, Asha; Seagle, Christopher; Wang, Guifang; Young, Gregory B.; Macdonald, Jeffrey M.; Pielak, Gary J.
Journal of the American Chemical Society (2008), 130 (20), 6310-6311CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
In-cell NMR provides a valuable means to assess how macromols., with concns. up to 300 g/L in the cytoplasm, affect the structure and dynamics of proteins at at. resoln. Here an intrinsically disordered protein, α-synuclein (αSN), and a globular protein, chymotrypsin inhibitor 2 (CI2) were examd. by using in-cell NMR. High-resoln. in-cell spectra of αSN can be obtained, but CI2 leaks from the cell and the remaining intracellular CI2 is not detectable. Even after stabilizing the cells from leakage by using alginate encapsulation, no CI2 signal is detected. From in vitro studies the authors conclude that this difference in detectability is the result of the differential dynamical response of disordered and ordered proteins to the changes of motion caused by the increased viscosity in cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXkvVChurs%253D&md5=7232018e3ce7701dd37153d5697525e9
116.
Schreiber, G. Kinetic Studies of Protein–Protein Interactions Curr. Opin. Struct. Biol. 2002, 12, 41– 47 DOI: 10.1016/S0959-440X(02)00287-7
[Crossref], [PubMed], [CAS]
116.
Kinetic studies of protein-protein interactions
Schreiber, Gideon
Current Opinion in Structural Biology (2002), 12 (1), 41-47CODEN: COSBEF; ISSN:0959-440X. (Elsevier Science Ltd.)
A review with 52 refs. The structure of a protein-protein interaction, and its affinity and thermodn. characteristics depict a 'frozen' state of a complex. This picture ignores the kinetic nature of complex formation and dissocn., which are of major biol. and biophys. interest. This review highlights recent advances in deciphering the kinetic pathway of protein-protein complexation, the nature of the encounter complex, transition state, and intermediate along the reaction, and the effects of mutation, viscosity, pH, and salt on assocn. Kinetic studies are revealing how protein complexes form in a specific and rapid manner that allows them to carry out their often highly dynamic cellular functions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XhtF2it7k%253D&md5=b11fc40889f2128f80c7f185d1192f3e
117.
Northrup, S. H.; Erickson, H. P. Kinetics of Protein-Protein Association Explained by Brownian Dynamics Computer Simulation Proc. Natl. Acad. Sci. U. S. A. 1992, 89, 3338– 3342 DOI: 10.1073/pnas.89.8.3338
[Crossref], [PubMed], [CAS]
117.
Kinetics of protein-protein association explained by Brownian dynamics computer simulation
Northrup, Scott H.; Erickson, H. P.
Proceedings of the National Academy of Sciences of the United States of America (1992), 89 (8), 3338-42CODEN: PNASA6; ISSN:0027-8424.
Protein-protein bond formations, such as antibody-antigen complexation or aggregation of protein monomers into dimers and larger aggregates, occur with bimol. rate consts. on the order of 106 M-1·s-1, which is only 3 orders of magnitude slower than the diffusion-limited Smoluchowski rate. However, since the protein-protein bond requires rotational alignment to within a few angstroms of tolerance, purely geometric ests. would suggest that the obsd. rates might be 6 orders of magnitude below the Smoluchowski rate. Previous theor. treatments have not been solved for the highly specific docking criteria of protein-protein assocn.-the entire subunit interface must be aligned within 2 Å of the correct position. Several studies have suggested that diffusion alone could not produce the rapid assocn. kinetics and have postulated lengthy collisions and/or the operation of electrostatic or hydrophobic steering forces to accelerate the assocn. In the present study, the Brownian dynamics simulation method is used to compute the rate of assocn. of neutral spherical model proteins with the stated docking criteria. The Brownian simulation predicts a rate of 2 × 106 M-1·s-1 for this generic protein-protein assocn., a rate that is 2000 times faster than that predicted by the simplest geometric calcn. and is essentially equal to the rates obsd. for protein-protein assocn. in aq. soln. This high rate is obtained by simple diffusive processes and does not require any attractive or steering forces beyond those achieved for a partially formed bond. The rate enhancement is attributed to a diffusive entrapment effect, in which a protein pair surrounded and trapped by water undergoes multiple collisions with rotational reorientation during each encounter.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK38XkvVGntL0%253D&md5=e2707ca663625bfaf3d1bb147595f0da
118.
Zhou, H. X. Brownian Dynamics Study of the Influences of Electrostatic Interaction and Diffusion on Protein-Protein Association Kinetics Biophys. J. 1993, 64, 1711– 1726 DOI: 10.1016/S0006-3495(93)81543-1
[Crossref], [PubMed], [CAS]
118.
Brownian dynamics study of the influences of electrostatic interaction and diffusion on protein-protein association kinetics
Zhou, Huan Xiang
Biophysical Journal (1993), 64 (6), 1711-26CODEN: BIOJAU; ISSN:0006-3495.
A unified model is presented for protein-protein assocn. processes that are under the influences of electrostatic interaction and diffusion (e.g., protein oligomerization, enzyme catalysis, electron and energy transfer). The proteins are modeled as spheres that bear point charges and undergo translational and rotational Brownian motion. Before assocn. can occur the two spheres have to be aligned properly to form a reaction complex via diffusion. The reaction complex can either go on to form the product or it can dissoc. into the sep. reactants through diffusion. The electrostatic interaction, like diffusion, influences every step except the one that brings the reaction complex into the product. The interaction potential is obtained by extending the Kirkwood-Tanford protein model (Tanford, C.; Kirkwood, J. G., 1957) to two charge-embedded spheres and solving the consequent equations under a particular basis set. The time-dependent assocn. rate coeff. is then obtained through Brownian dynamics simulations according an algorithm developed earlier. This method is applied to a model system of the cytochrome c and cytochrome c peroxidase assocn. process and the results confirm the exptl. dependence of the assocn. rate const. on the soln. ionic strength. An important conclusion drawn from this study is that when the product is formed by very specific alignment of the reactants, as is often the case, the effect of the interaction potential is simply to scale the assocn. rate const. by a Boltzmann factor. This explains why mutations in the interface of the reaction complex have strong influences on the assocn. rate const. whereas those away from the interface have minimal effects. It comes about because the former mutations change the interaction potential of the reaction complex significantly and the latter ones do not.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK3sXks1Kjtbs%253D&md5=2ba2c9644db678694ce26b65349879ac
119.
Slutsky, M.; Mirny, L. A. Kinetics of Protein-DNA Interaction: Facilitated Target Location in Sequence-Dependent Potential Biophys. J. 2004, 87, 4021– 4035 DOI: 10.1529/biophysj.104.050765
[Crossref], [PubMed], [CAS]
119.
Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential
Slutsky, Michael; Mirny, Leonid A.
Biophysical Journal (2004), 87 (6), 4021-4035CODEN: BIOJAU; ISSN:0006-3495. (Biophysical Society)
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a long DNA mol. and then strongly binds this site. Here we aim to find a mechanism that can provide both a fast search (1-10 s) and high stability of the specific protein-DNA complex (Kd = 10-15-10-8 M). Earlier studies have suggested that rapid search involves sliding of the protein along the DNA. Here we consider sliding as a one-dimensional diffusion in a sequence-dependent rough energy landscape. We demonstrate that, despite the landscape's roughness, rapid search can be achieved if one-dimensional sliding is accompanied by three-dimensional diffusion. We est. the range of the specific and nonspecific DNA-binding energy required for rapid search and suggest expts. that can test our mechanism. We show that optimal search requires a protein to spend half of its time sliding along the DNA and the other half diffusing in three dimensions. We also establish that, paradoxically, realistic energy functions cannot provide both rapid search and strong binding of a rigid protein. To reconcile these two fundamental requirements we propose a search-and-fold mechanism that involves the coupling of protein binding and partial protein folding. The proposed mechanism has several important biol. implications for search in the presence of other proteins and nucleosomes, simultaneous search by several proteins, etc. The proposed mechanism also provides a new framework for interpretation of exptl. and structural data on protein-DNA interactions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhtVOmtbbI&md5=cb4686768d74075f9b2c94c031b8a030
120.
Berg, O. G.; Winter, R. B.; Von Hippel, P. H. Diffusion-Driven Mechanisms of Protein Translocation on Nucleic Acids. 1. Models and Theory Biochemistry 1981, 20, 6929– 6948 DOI: 10.1021/bi00527a028
[ACS Full Text ], [CAS]
120.
Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory
Berg, Otto G.; Winter, Robert B.; Von Hippel, Peter H.
Biochemistry (1981), 20 (24), 6929-48CODEN: BICHAW; ISSN:0006-2960.
Genome regulatory proteins (e.g., repressors or polymerases) which function by binding to specific chromosomal target base pair sequences (e.g., operators or promoters) can appear to arrive at their targets at faster than diffusion-controlled rates. These proteins also exhibit appreciable affinity for nonspecific DNA, and thus this apparently facilitated binding rate must be interpreted in terms of a 2-step binding mechanism. The 1st step involves free diffusion to any nonspecific binding site on the DNA, and the 2nd step comprises a series of protein translocation events which are also driven by thermal fluctuations. Because of nonspecific binding, the search process in the 2nd step is of reduced dimensionality (or vol.); this results in an accelerated apparent rate of target location. The 4 types of processes are defined which may be involved in these protein translocation events between DNA sites. These are (1) macroscopic dissocn.-reassocn. processes within the domain of the DNA mol., (2) microscopic dissocn.-reassocn. events between closely spaced sites in the DNA mol., (3) intersegment transfer (via ring-closure) processes between different segments of the DNA mol., and (4) sliding along the DNA mol. Math. and phys. descriptions of each of these processes is presented, and the consequences of each for the overall rate of target location are worked out as a function of both the nonspecific binding affinity between protein and DNA and the length of the DNA mol. contg. the target sequence. The theory is developed in terms of the Escherichia coli lac repressor-operator interaction. However, this approach is general for the anal. of mechanisms of biol. target location involving facilitated transfer processes via nonspecific binding to the general system of which the target forms a small part.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3MXlvF2nt7c%253D&md5=1db2f5018f3ab6356d5827d30da3a5b3
121.
Li, C.; Wang, Y.; Pielak, G. J. Translational and Rotational Diffusion of a Small Globular Protein under Crowded Conditions J. Phys. Chem. B 2009, 113, 13390– 13392 DOI: 10.1021/jp907744m
[ACS Full Text ], [CAS]
121.
Translational and rotational diffusion of a small globular protein under crowded conditions
Li, Conggang; Wang, Yaqiang; Pielak, Gary J.
Journal of Physical Chemistry B (2009), 113 (40), 13390-13392CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
Protein-protein interaction is the fundamental step of biol. signal transduction. Interacting proteins find each other by diffusion. To gain insight into diffusion under the crowded conditions found in cells, the authors used NMR spectroscopy to measure the effects of solvent additives on the translational and rotational diffusion of the 7.4-kDa globular protein, chymotrypsin inhibitor 2. The additives were glycerol and the macromol. crowding agent, polyvinyl pyrrolidone (PVP). Both translational diffusion and rotational diffusion decreased with increasing soln. viscosity. For glycerol, the decrease obeyed the Stokes-Einstein and Stokes-Einstein Debye laws. Three types of deviation were obsd. for PVP: (1) the decrease in diffusion with increased viscosity was less than predicted; (2) this neg. deviation was greater for rotational diffusion; and (3) the neg. deviation increased with increasing PVP mol. wt. The results were discussed in terms of other studies on the effects of macromols. on globular protein diffusion.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtFCjtrjO&md5=6bc5ca69e9ab9771f450fe5662c8f33f
122.
Wang, Y.; Benton, L. A.; Singh, V.; Pielak, G. J. Disordered Protein Diffusion under Crowded Conditions J. Phys. Chem. Lett. 2012, 3, 2703– 2706 DOI: 10.1021/jz3010915
[ACS Full Text ], [CAS]
122.
Disordered protein diffusion under crowded conditions
Wang, Yaqiang; Benton, Laura A.; Singh, Vishavpreet; Pielak, Gary J.
Journal of Physical Chemistry Letters (2012), 3 (18), 2703-2706CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
Intrinsically disordered proteins (IDPs) are important in signaling, regulation, and translocation. Understanding their diffusion under physiol. relevant conditions will yield insight into their functions. Here, the authors used NMR spectroscopy to quantify the translational diffusion of a globular and an IDP in dil. soln. and under crowded conditions. In dil. soln., the globular protein, chymotrypsin inhibitor 2 (CI2; 7.4 kDa) diffused faster than the IDP, α-synuclein (α-syn; 14 kDa). Surprisingly, the opposite occurred under crowded conditions; α-syn diffused faster than CI2, even though α-syn was larger than CI2. These data showed that shape is a key parameter detg. protein diffusion under crowded conditions, adding to the properties known to be affected by macromol. crowding. The results also offer a clue about why many signaling proteins are disordered.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtlSks77L&md5=8f79cc3d6d06cdf3169ce421c09406b6
123.
Wang, Y.; Li, C.; Pielak, G. J. Effects of Proteins on Protein Diffusion J. Am. Chem. Soc. 2010, 132, 9392– 9397 DOI: 10.1021/ja102296k
[ACS Full Text ], [CAS]
123.
Effects of Proteins on Protein Diffusion
Wang, Yaqiang; Li, Conggang; Pielak, Gary J.
Journal of the American Chemical Society (2010), 132 (27), 9392-9397CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Despite increased attention, little is known about how the crowded intracellular environment affects basic phenomena like protein diffusion. Here, we use NMR to quantify the rotational and translational diffusion of a 7.4-kDa test protein, chymotrypsin inhibitor 2 (CI2), in solns. of glycerol, synthetic polymers, proteins, and cell lysates. As expected, translational diffusion and rotational diffusion decrease with increasing viscosity. In glycerol, for example, the decrease follows the Stokes-Einstein and Stokes-Einstein-Debye laws. Synthetic polymers cause neg. deviation from the Stokes laws and affect translation more than rotation. Surprisingly, however, protein crowders have the opposite effect, causing pos. deviation and reducing rotational diffusion more than translational diffusion. Indeed, bulk proteins severely attenuate the rotational diffusion of CI2 in crowded protein solns. Similarly, CI2 diffusion in cell lysates is comparable to its diffusion in crowded protein solns., supporting the biol. relevance of the results. The rotational attenuation is independent of the size and total charge of the crowding protein, suggesting that the effect is general. The difference between the behavior of synthetic polymers and protein crowders suggests that synthetic polymers may not be suitable mimics of the intracellular environment. NMR relaxation data reveal that the source of the difference between synthetic polymers and proteins is the presence of weak interactions between the proteins and CI2. In summary, weak but nonspecific, noncovalent chem. interactions between proteins appear to fundamentally impact protein diffusion in cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXns1Wru7o%253D&md5=17766105ef7a622c8159e83cc90763dc
124.
Li, C.; Pielak, G. J. Using NMR to Distinguish Viscosity Effects from Nonspecific Protein Binding under Crowded Conditions J. Am. Chem. Soc. 2009, 131, 1368– 1369 DOI: 10.1021/ja808428d
[ACS Full Text ], [CAS]
124.
Using NMR to Distinguish Viscosity Effects from Nonspecific Protein Binding under Crowded Conditions
Li, Conggang; Pielak, Gary J.
Journal of the American Chemical Society (2009), 131 (4), 1368-1369CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Conventional NMR approaches to detect weak protein binding and aggregation are hindered by the increased viscosity brought about by crowding. The authors describe a simple and reliable NMR method to distinguish viscosity effects from binding and aggregation under crowded conditions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXlt1Siuw%253D%253D&md5=8e0f3e985c2a971f14679347a91f351c
125.
Geyer, T. Mixing Normal and Anomalous Diffusion J. Chem. Phys. 2012, 137, 115101 DOI: 10.1063/1.4753804
[Crossref], [PubMed], [CAS]
125.
Mixing normal and anomalous diffusion
Geyer, Tihamer
Journal of Chemical Physics (2012), 137 (11), 115101/1-115101/5CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
In the densely filled biol. cells often subdiffusion is obsd., where the av. squared displacement increases slower than linear with the length of the observation interval. One reason for such subdiffusive behavior is attractive interactions between the diffusing particles that lead to temporary complex formation. Here, we show that such transient binding is not an av. state of the particles but that intervals of free diffusion alternate with slower displacement when bound to neighboring particles. The obsd. macroscopic behavior is then the weighted av. of these two contributions. Interestingly, even at very high concns., the unbound fraction still exhibits essentially normal diffusion. (c) 2012 American Institute of Physics.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtlOis7bO&md5=cc1c728e746c9ef9a3be6b1be4ae3033
126.
Banks, D. S.; Fradin, C. Anomalous Diffusion of Proteins due to Molecular Crowding Biophys. J. 2005, 89, 2960– 2971 DOI: 10.1529/biophysj.104.051078
[Crossref], [PubMed], [CAS]
126.
Anomalous diffusion of proteins due to molecular crowding
Banks, Daniel S.; Fradin, Cecile
Biophysical Journal (2005), 89 (5), 2960-2971CODEN: BIOJAU; ISSN:0006-3495. (Biophysical Society)
We have studied the diffusion of tracer proteins in highly concd. random-coil polymer and globular protein solns. imitating the crowded conditions encountered in cellular environments. Using fluorescence correlation spectroscopy, we measured the anomalous diffusion exponent α characterizing the dependence of the mean square displacement of the tracer proteins on time, 〈R2(t)〉 ∼ tα. We obsd. that the diffusion of proteins in dextran solns. with concns. up to 400 g/l is subdiffusive (α < 1) even at low obstacle concn. The anomalous diffusion exponent α decreases continuously with increasing obstacle concn. and mol. wt., but does not depend on buffer ionic strength, neither does it depend strongly on soln. temp. At very high random-coil polymer concns., α reaches a limit value of α1 ≈ 3/4, which we take to be the signature of a coupling between the motions of the tracer proteins and the segments of the dextran chains. A similar, although less pronounced, subdiffusive behavior is obsd. for the diffusion of streptavidin in concd. globular protein solns. These observations indicate that protein diffusion in the cell cytoplasm and nucleus should be anomalous as well, with consequences for measurements of solute diffusion coeffs. in cells and for the modeling of cellular processes relying on diffusion.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXht1WmurjE&md5=744ff30c81166c3394c5b5ea43792706
127.
Hasnain, S.; McClendon, C. L.; Hsu, M. T.; Jacobson, M. P.; Bandyopadhyay, P. A New Coarse-Grained Model for E. coli Cytoplasm: Accurate Calculation of the Diffusion Coefficient of Proteins and Observation of Anomalous Diffusion PLoS One 2014, 9, e106466 DOI: 10.1371/journal.pone.0106466
[Crossref], [PubMed], [CAS]
127.
A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion
Hasnain, Sabeeha; McClendon, Christopher L.; Hsu, Monica T.; Jacobson, Matthew P.; Bandyopadhyay, Pradipta
PLoS One (2014), 9 (9), e106466/1-e106466/12, 12 pp.CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)
A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean-field approach. Extensive BD simulations were performed to calc. the diffusion coeffs. of three different proteins in the cellular environment. The results are in close agreement with exptl. or previously simulated values, where available. Control simulations without HI showed that use of HI is essential to obtain accurate diffusion coeffs. Anomalous diffusion inside the crowded cellular medium was investigated with Fractional Brownian motion anal., and found to be present in this model. By running a series of control simulations in which various forces were removed systematically, it was found that repulsive interactions (vol. exclusion) are the main cause for anomalous diffusion, with a secondary contribution from HI.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhs12ht7%252FI&md5=f274730e7572e411658fbd6276c13d6d
128.
Galanti, M.; Fanelli, D.; Maritan, A.; Piazza, F. Diffusion of Tagged Particles in a Crowded Medium Europhys. Lett. 2014, 107, 20006 DOI: 10.1209/0295-5075/107/20006
[Crossref]
There is no corresponding record for this reference.
129.
Wilcox, A. E.; LoConte, M. A.; Slade, K. M. Effects of Macromolecular Crowding on Alcohol Dehydrogenase Activity Are Substrate-Dependent Biochemistry 2016, 55, 3550– 3558 DOI: 10.1021/acs.biochem.6b00257
[ACS Full Text ], [CAS]
129.
Effects of macromolecular crowding on alcohol dehydrogenase activity are substrate-dependent
Wilcox, A. E.; LoConte, Micaela A.; Slade, Kristin M.
Biochemistry (2016), 55 (25), 3550-3558CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
Enzymes operate in a densely packed cellular environment that rarely matches the dil. conditions under which they are studied. To better understand the ramifications of this crowding, the Michaelis-Menten kinetics of yeast alc. dehydrogenase (YADH) were monitored spectrophotometrically in the presence of high concns. of dextran. Crowding decreased the maximal rate of the reaction by 40% for assays with ethanol, the primary substrate of YADH. This observation was attributed to slowed release of the reduced β-NAD product, which is rate-limiting. In contrast, when larger alcs. were used as the YADH substrate, the rate-limiting step becomes hydride transfer and crowding instead increased the maximal rate of the reaction by 20-40%. This work reveals the importance of considering enzyme mechanism when evaluating the ways in which crowding can alter kinetics.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XpsVCmu7k%253D&md5=36a035f811e5162ea28be74f0877e4d7
130.
Johansson, H.; Jensen, M. R.; Gesmar, H.; Meier, S.; Vinther, J. M.; Keeler, C.; Hodsdon, M. E.; Led, J. J. Specific and Nonspecific Interactions in Ultraweak Protein–Protein Associations Revealed by Solvent Paramagnetic Relaxation Enhancements J. Am. Chem. Soc. 2014, 136, 10277– 10286 DOI: 10.1021/ja503546j
[ACS Full Text ], [CAS]
130.
Specific and Nonspecific Interactions in Ultraweak Protein-Protein Associations Revealed by Solvent Paramagnetic Relaxation Enhancements
Johansson, Helle; Jensen, Malene Ringkjoebing; Gesmar, Henrik; Meier, Sebastian; Vinther, Joachim M.; Keeler, Camille; Hodsdon, Michael E.; Led, Jens J.
Journal of the American Chemical Society (2014), 136 (29), 10277-10286CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Weak and transient protein-protein interactions underlie numerous biol. processes. However, the location of the interaction sites of the specific complexes and the effect of transient, nonspecific protein-protein interactions often remain elusive. The authors have investigated the weak self-assocn. of human growth hormone (hGH, KD = 0.90±0.03 mM) at neutral pH by the paramagnetic relaxation enhancement (PRE) of the amide protons induced by the sol. paramagnetic relaxation agent, gadodiamide (Gd(DTPA-BMA)). Primarily, the PREs are in agreement with the general Hwang-Freed model for relaxation by translational diffusion, only if crowding effects on the diffusion in the protein soln. are taken into account. Second, by measuring the PREs of the amide protons at increasing hGH concns. and a const. concn. of the relaxation agent, it is shown that a distinction can be made between residues that are affected only by transient, nonspecific protein-protein interactions and residues that are involved in specific protein-protein assocns. Thus, the PREs of the former residues increase linearly with the hGH concn. in the entire concn. range because of a redn. of the diffusion caused by the transient, nonspecific protein-protein interactions, while the PREs of the latter residues increase only at the lower hGH concns. but decrease at the higher concns. because of specific protein-protein assocns. that impede the access of gadodiamide to the residues of the interaction surface. Finally, it is found that the ultraweak aggregation of hGH involves several interaction sites that are located in patches covering a large part of the protein surface.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtVKnsb%252FP&md5=d967ee04ece7e60fc505b6f9ef4ded6a
131.
Cohen, R. D.; Pielak, G. J. A Cell is More than the Sum of Its (Dilute) Parts: A Brief History of Quinary Structure Protein Sci. 2017, 26, 403– 413 DOI: 10.1002/pro.3092
[Crossref], [PubMed], [CAS]
131.
A cell is more than the sum of its (dilute) parts: A brief history of quinary structure
Cohen, Rachel D.; Pielak, Gary J.
Protein Science (2017), 26 (3), 403-413CODEN: PRCIEI; ISSN:1469-896X. (Wiley-Blackwell)
A review. Most knowledge of protein structure and function is derived from expts. performed with purified protein resuspended in dil., buffered solns. However, proteins function in the crowded, complex cellular environment. Although the first four levels of protein structure provide important information, a complete understanding requires consideration of quinary structure. Quinary structure comprises the transient interactions between macromols. that provides organization and compartmentalization inside cells. We review the history of quinary structure in the context of several metabolic pathways, and the technol. advances that have yielded recent insight into protein behavior in living cells. The evidence demonstrates that protein behavior in isolated solns. deviates from behavior in the physiol. environment.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXisV2rurc%253D&md5=aa1e25ba6330967f1c2ade942accefdf
132.
Pérez Santero, S.; Favretto, F.; Zanzoni, S.; Chignola, R.; Assfalg, M.; D’Onofrio, M. Effects of Macromolecular Crowding on a Small Lipid Binding Protein Probed at the Single-Amino Acid Level Arch. Biochem. Biophys. 2016, 606, 99– 110 DOI: 10.1016/j.abb.2016.07.017
[Crossref], [PubMed], [CAS]
132.
Effects of macromolecular crowding on a small lipid binding protein probed at the single-amino acid level
Perez Santero, Silvia; Favretto, Filippo; Zanzoni, Serena; Chignola, Roberto; Assfalg, Michael; D'Onofrio, Mariapina
Archives of Biochemistry and Biophysics (2016), 606 (), 99-110CODEN: ABBIA4; ISSN:0003-9861. (Elsevier B.V.)
Macromol. crowding is a distinctive feature of the cellular interior, influencing the behavior of biomacromols. Despite significant advancements in the description of the effects of crowding on global protein properties, the influence of cellular components on local protein attributes has received limited attention. Here, we describe a residue-level systematic interrogation of the structural, dynamic, and binding properties of the liver fatty acid binding protein (LFABP) in crowded solns. Two-dimensional NMR spectral fingerprints and relaxation data were collected on LFABP in the presence of polymeric and biomol. crowders. Non-interacting crowders produced minimal site-specific spectral perturbations on ligand-free and lipid-bound LFABP. Conformational adaptations upon ligand binding reproduced those obsd. in dil. soln., but a perturbation of the free oleate state resulted in less favorable uptake. When LFABP engaged in direct interactions with background mols., changes in local chem. environments were detected for residues of the internal binding pocket and of the external surface. Enhanced complexity was introduced by investigating LFABP in cell lysates, and in membrane-bounded compartments. LFABP was able to capture ligands from prokaryotic and eukaryotic cell lysates, and from artificial cells (water-in-oil emulsion droplets). The data suggest that promiscuous interactions are a major factor influencing protein function in the cell.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xht1Kltr%252FE&md5=4ae84b2238a1044f1bdc476db9546f45
133.
Kim, Y. C.; Bhattacharya, A.; Mittal, J. Macromolecular Crowding Effects on Coupled Folding and Binding J. Phys. Chem. B 2014, 118, 12621– 12629 DOI: 10.1021/jp508046y
[ACS Full Text ], [CAS]
133.
Macromolecular crowding effects on coupled folding and binding
Kim, Young C.; Bhattacharya, Apratim; Mittal, Jeetain
Journal of Physical Chemistry B (2014), 118 (44), 12621-12629CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
Replica-exchange mol. dynamics simulations were performed on the protein complex pKID-KIX to understand the effects of macromol. crowding on coupled folding and binding events. A structure-based protein model at the residue level was adopted for the 2 proteins to include intramol. conformational flexibility, while crowding macromols. were represented as spherical particles. The interactions between the crowders and protein residues could be either purely repulsive or a combination of short-range repulsion and intermediate-range attraction. Consistent with previous studies on rigid-body protein binding in the presence of spherical crowders, the authors found that the complex formation was stabilized by repulsive protein-crowder interactions and destabilized by sufficiently strong attractive protein-crowder interactions. Competition between stabilizing repulsive and destabilizing attractive interactions was quant. captured by a previous theor. model developed for describing the change in the binding free energy of rigid proteins in a crowded environment. The authors found that protein flexibility had little effect on the thermodn. of pKID-KIX binding (with respect to bulk) for repulsive and weakly attractive protein-crowder interactions. For strong protein-crowder attractive interactions, the destabilizing effect due to crowding was attenuated by protein flexibility. Interestingly, the mechanism of coupled folding and binding obsd. in bulk remained unchanged under highly crowded conditions over a broad range of protein-crowder interaction strengths. Also, strong protein-crowder attractive interactions could significantly stabilize intermediate states involving partial contact between pKID and KIX domains.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhslCjtL%252FN&md5=d99d90cc29ce2d2b04b3684b4484d87e
134.
Kim, Y. C.; Best, R. B.; Mittal, J. Macromolecular Crowding Effects on Protein-Protein Binding Affinity and Specificity J. Chem. Phys. 2010, 133, 205101 DOI: 10.1063/1.3516589
[Crossref], [PubMed], [CAS]
134.
Macromolecular crowding effects on protein-protein binding affinity and specificity
Kim, Young C.; Best, Robert B.; Mittal, Jeetain
Journal of Chemical Physics (2010), 133 (20), 205101/1-205101/7CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Macromol. crowding in cells is recognized to have a significant impact on biol. function, yet quant. models for its effects are relatively undeveloped. The influence of crowding on protein-protein interactions is of particular interest, since these mediate many processes in the cell, including the self-assembly of larger complexes, recognition, and signaling. Here, the authors used a residue-level coarse-grained model to investigate the effects of macromol. crowding on the assembly of protein-protein complexes. Interactions between the proteins were treated using a fully transferable energy function, and interactions of protein residues with the spherical crowders were repulsive. The authors showed that the binding free energy for 2 protein complexes, ubiquitin/UIM1 peptide and cytochrome c/cytochrome c peroxidase, decreased modestly as the concn. of crowding agents increased. To obtain a quant. description of the stabilizing effect, the authors mapped the aspherical individual proteins and protein complexes onto spheres whose radii were calcd. from the crowder-excluded protein vols. With this correspondence, it was found that the change in the binding free energy due to crowding could be quant. described by the scaled particle theory model without any fitting parameters. The effects of a mixt. of different-size crowders, as would be found in a real cell, were predicted by the same model with an additivity ansatz. The authors also obtained the remarkable result that crowding increased the fraction of specific complexes at the expense of nonspecific transient encounter complexes in a crowded environment. This result, due to the greater excluded vol. of the nonspecific complexes, demonstrated that macromol. crowding can have subtle functional effects beyond the relative stability of bound and unbound complexes. (c) 2010 American Institute of Physics.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhsVGnu7%252FO&md5=30188826be54a1983e6ce98ec73aad2d
135.
Qin, S. B.; Cai, L.; Zhou, H. X. A Method for Computing Association Rate Constants of Atomistically Represented Proteins under Macromolecular Crowding Phys. Biol. 2012, 9, 066008 DOI: 10.1088/1478-3975/9/6/066008
[Crossref], [PubMed], [CAS]
135.
A method for computing association rate constants of atomistically represented proteins under macromolecular crowding
Qin, Sanbo; Cai, Lu; Zhou, Huan-Xiang
Physical Biology (2012), 9 (6), 066008, 11 pp.CODEN: PBHIAT; ISSN:1478-3975. (IOP Publishing Ltd.)
In cellular environments, two protein mols. on their way to form a specific complex encounter many bystander macromols. The latter mols., or crowders, affect both the energetics of the interaction between the test mols. and the dynamics of their relative motion. In earlier work, it has been shown that, in modeling the assocn. kinetics of the test mols., the presence of crowders can be accounted for by their energetic and dynamic effects. The recent development of the transient-complex theory for protein assocn. in dil. solns. makes it possible to easily incorporate the energetic and dynamic effects of crowders. The transient complex refers to a late on-pathway intermediate, in which the two protein mols. have near-native relative sepn. and orientation, but have yet to form the many short-range specific interactions of the native complex. The transient-complex theory predicts the assocn. rate const. as ka = ka0exp(-ΔG*el/kBT), where ka0 is the 'basal' rate const. for reaching the transient complex by unbiased diffusion, and the Boltzmann factors captures the influence of long-range electrostatic interactions between the protein mols. Crowders slow down the diffusion, therefore reducing the basal rate const. (to kac0), and induce an effective interaction energy ΔGc. We show that the latter interaction energy for atomistic proteins in the presence of spherical crowders is 'long'-ranged, allowing the assocn. rate const. under crowding to be computed as kac = kac0exp[-(ΔG*el + ΔG*c)/kBT]. Applications demonstrate that this computational method allows for realistic modeling of protein assocn. kinetics under crowding.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsFWru7jI&md5=f7e18cf271eeaa494768cc4d1ac6606c
136.
Musiani, F.; Giorgetti, A. Protein Aggregation and Molecular Crowding: Perspectives from Multiscale Simulations Int. Rev. Cell Mol. Biol. 2017, 329, 49– 77 DOI: 10.1016/bs.ircmb.2016.08.009
[Crossref], [PubMed], [CAS]
136.
Protein Aggregation and Molecular Crowding: Perspectives From Multiscale Simulations
Musiani F; Giorgetti A
International review of cell and molecular biology (2017), 329 (), 49-77 ISSN:1937-6448.
Cells are extremely crowded environments, thus the use of diluted salted aqueous solutions containing a single protein is too simplistic to mimic the real situation. Macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, interactions with cognate biomolecules, and pathological aggregation. The latter phenomenon typically leads to the formation of amyloid fibrils that are linked to several lethal neurodegenerative diseases, but that can also play a functional role in certain organisms. The majority of molecular simulations performed before the last few years were conducted in diluted solutions and were restricted both in the timescales and in the system dimensions by the available computational resources. In recent years, several computational solutions were developed to get close to physiological conditions. In this review we summarize the main computational techniques used to tackle the issue of protein aggregation both in a diluted and in a crowded environment.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC1c7nvFeisA%253D%253D&md5=2eb5d366003a680335be2ed6c6c2b987
137.
White, D. A.; Buell, A. K.; Knowles, T. P. J.; Welland, M. E.; Dobson, C. M. Protein Aggregation in Crowded Environments J. Am. Chem. Soc. 2010, 132, 5170– 5175 DOI: 10.1021/ja909997e
[ACS Full Text ], [CAS]
137.
Protein Aggregation in Crowded Environments
White, Duncan A.; Buell, Alexander K.; Knowles, Tuomas P. J.; Welland, Mark E.; Dobson, Christopher M.
Journal of the American Chemical Society (2010), 132 (14), 5170-5175CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The physicochem. parameters of biomols. are the key determinants of the multitude of processes that govern the normal and aberrant behavior of living systems. A particularly important aspect of such behavior is the role it plays in the self-assocn. of proteins to form organized aggregates such as the amyloid or amyloid-like fibrils that are assocd. with pathol. conditions including Alzheimer's disease and Type II diabetes. In this study we describe quant. quartz crystal microbalance measurements of the kinetics of the growth of amyloid fibrils in a range of crowded environments and in conjunction with theor. predictions demonstrate the existence of general relationships that link the propensities of protein mols. to aggregate with fundamental parameters that describe their specific structures and local environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXjvVaqurg%253D&md5=07158f4ed877fbc54aaa9013d8c904fb
138.
Ellis, R. J.; Minton, A. P. Protein Aggregation in Crowded Environments Biol. Chem. 2006, 387, 485– 497 DOI: 10.1515/BC.2006.064
[Crossref], [PubMed], [CAS]
138.
Protein aggregation in crowded environments
Ellis, R. John; Minton, Allen P.
Biological Chemistry (2006), 387 (5), 485-497CODEN: BICHF3; ISSN:1431-6730. (Walter de Gruyter GmbH & Co. KG)
A review. The generic tendency of proteins to aggregate into non-functional, and sometimes cytotoxic, structures poses a universal problem for all types of cell. This tendency is greatly exacerbated by the high total concn. of macromols. found within most intracellular compartments, a phenomenon referred to as macromol. crowding. Here, the authors discuss the quant. effects of crowding on protein aggregation and the role of mol. chaperones in combating this problem.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XlsFWnsLo%253D&md5=db7a30bf16fc75dbd2424bc7fa3fdfca
139.
Qin, S.; Zhou, H.-X. Protein Folding, Binding, and Droplet Formation in Cell-Like Conditions Curr. Opin. Struct. Biol. 2017, 43, 28– 37 DOI: 10.1016/j.sbi.2016.10.006
[Crossref], [PubMed], [CAS]
139.
Protein folding, binding, and droplet formation in cell-like conditions
Qin, Sanbo; Zhou, Huan-Xiang
Current Opinion in Structural Biology (2017), 43 (), 28-37CODEN: COSBEF; ISSN:0959-440X. (Elsevier Ltd.)
The many bystander macromols. in the crowded cellular environments present both steric repulsion and weak attraction to proteins undergoing folding or binding and hence impact the thermodn. and kinetic properties of these processes. The weak but nonrandom binding with bystander macromols. may facilitate subcellular localization and biol. function. Weak binding also leads to the emergence of a protein-rich droplet phase, which has been implicated in regulating a variety of cellular functions. All these important problems can now be addressed by realistic modeling of intermol. interactions. Configurational sampling of concd. protein solns. is an ongoing challenge.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhslSit7fI&md5=cb941e44b073e07cf793241e39889003
140.
Spitzer, J.; Poolman, B. How Crowded is the Prokaryotic Cytoplasm? FEBS Lett. 2013, 587, 2094– 2098 DOI: 10.1016/j.febslet.2013.05.051
[Crossref], [PubMed], [CAS]
140.
How crowded is the prokaryotic cytoplasm?
Spitzer, Jan; Poolman, Bert
FEBS Letters (2013), 587 (14), 2094-2098CODEN: FEBLAL; ISSN:0014-5793. (Elsevier B.V.)
The authors consider biomacromol. crowding within the cytoplasm of prokaryotic cells as a 2-phase system of 'supercrowded' cytogel and 'dil.' cytosol; they simplify and quantify this model for a coccoid cell over a wide range of biomacromol. crowding. The key result showed that the supercrowded cytogel extended the vectorial character of the plasma membrane deeper into the cytoplasm by about 20-70 nm. The authors discuss useful physiol. insights that this model provides into the functioning of a prokaryotic cell on the micrometer scale.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXpvVGltL0%253D&md5=1bacdff3e1d2a520e3f53a123951b637
141.
Duff, M. R., Jr.; Grubbs, J.; Serpersu, E.; Howell, E. E. Weak Interactions between Folate and Osmolytes in Solution Biochemistry 2012, 51, 2309– 2318 DOI: 10.1021/bi3000947
[ACS Full Text ], [CAS]
141.
Weak Interactions between Folate and Osmolytes in Solution
Duff, Michael R.; Grubbs, Jordan; Serpersu, Engin; Howell, Elizabeth E.
Biochemistry (2012), 51 (11), 2309-2318CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
Previous osmotic stress studies on the role of solvent in two structurally unrelated dihydrofolate reductases (DHFRs) found weaker binding of dihydrofolate (DHF) to either enzyme in the presence of osmolytes. To explain these unusual results, weak interactions between DHF and osmolytes were proposed, with a competition between osmolyte and DHFR for DHF. High osmolyte concns. will inhibit binding of the cognate pair. To evaluate this hypothesis, we devised a small mol. approach. Dimerization of folate, monitored by NMR, was weakened 2-3-fold upon addn. of betaine or DMSO, supporting preferential interaction of either osmolyte with the monomer (as it possesses a larger surface area). Nuclear Overhauser effect (NOE) spectroscopy expts. found a pos. NOE for the interaction of the C3'/C5' benzoyl ring protons with the C9 proton in buffer; however, a neg. NOE was obsd. upon addn. of betaine or DMSO. This change indicated a decreased tumbling rate, consistent with osmolyte interaction. Osmotic stress expts. also showed that betaine, DMSO, and sucrose preferentially interact with folate. Further, studies with the folate fragments, p-aminobenzoic acid and pterin 6-carboxylate, revealed interactions for both model compds. with betaine and sucrose. In contrast, DMSO was strongly excluded from the pterin ring but preferentially interacted with the p-aminobenzoyl moiety. These interactions are likely to be important in vivo because of the crowded conditions of the cell where weak contacts can more readily compete with specific binding interactions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XivVCmtLk%253D&md5=ba0de0c05f8b72588d17e143a47fce1c
142.
Miklos, A. C.; Sumpter, M.; Zhou, H.-X. Competitive Interactions of Ligands and Macromolecular Crowders with Maltose Binding Protein PLoS One 2013, 8, e74969 DOI: 10.1371/journal.pone.0074969
[Crossref], [PubMed], [CAS]
142.
Competitive interactions of ligands and macromolecular crowders with maltose binding protein
Miklos, Andrew C.; Sumpter, Matthew; Zhou, Huan-Xiang
PLoS One (2013), 8 (10), e74969CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)
Cellular signaling involves a cascade of recognition events occurring in a complex environment with high concns. of proteins, polysaccharides, and other macromols. The influence of macromol. crowders on protein binding affinity through hard-core repulsion is well studied, and possible contributions of protein-crowder soft attraction have been implicated recently. Here we present direct evidence for weak assocn. of maltose binding protein (MBP) with a polysaccharide crowder Ficoll, and that this assocn. effectively competes with the binding of the natural ligand, maltose. Titrn. data over wide ranges of maltose and Ficoll concns. fit well with a three-state competitive binding model. Broadening of MBP 1H-15N TROSY spectra by the addn. of Ficoll indicates weak protein-crowder assocn., and subsequent recovery of sharp NMR peaks upon addn. of maltose indicates that the interactions of the crowder and the ligand with MBP are competitive. We hypothesize that, in the Escherichia coli periplasm, the competitive interactions of polysaccharides and maltose with MBP could allow MBP to shuttle between the peptidoglycan attached to the outer membrane and the ATP-binding cassette transporter in the inner membrane.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsF2ku7bK&md5=330df13a2666ae384624c91aebeeab7d
143.
Abriata, L. A.; Spiga, E.; Dal Peraro, M. Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics Biophys. J. 2016, 111, 743– 755 DOI: 10.1016/j.bpj.2016.07.011
[Crossref], [PubMed], [CAS]
143.
Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics
Abriata, Luciano A.; Spiga, Enrico; Peraro, Matteo Dal
Biophysical Journal (2016), 111 (4), 743-755CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
Most studies of protein structure and function are performed in dil. conditions, but proteins typically experience high solute concns. in their physiol. scenarios and biotechnol. applications. High solute concns. have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and at. levels. Here, NMR and mol. dynamics investigations on ubiquitin disclose variable interactions with concd. solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chem. properties. Most strikingly, small polar uncharged mols. are sticky on the protein surface, whereas charged small mols. are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromol. crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromol. crowders do not exert such strong perturbation. Finally, mol. dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the phys. chem. of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xht12nsbnM&md5=a99d2402fef4705ebd921091f6f02799
144.
Heinen, M.; Zanini, F.; Roosen-Runge, F.; Fedunova, D.; Zhang, F. J.; Hennig, M.; Seydel, T.; Schweins, R.; Sztucki, M.; Antalik, M. Viscosity and Diffusion: Crowding and Salt Effects in Protein Solutions Soft Matter 2012, 8, 1404– 1419 DOI: 10.1039/C1SM06242E
[Crossref], [CAS]
144.
Viscosity and diffusion: crowding and salt effects in protein solutions
Heinen, Marco; Zanini, Fabio; Roosen-Runge, Felix; Fedunova, Diana; Zhang, Fajun; Hennig, Marcus; Seydel, Tilo; Schweins, Ralf; Sztucki, Michael; Antalik, Marian; Schreiber, Frank; Naegele, Gerhard
Soft Matter (2012), 8 (5), 1404-1419CODEN: SMOABF; ISSN:1744-683X. (Royal Society of Chemistry)
We report on a joint exptl.-theor. study of collective diffusion in, and static shear viscosity of solns. of bovine serum albumin (BSA) proteins, focusing on the dependence on protein and salt concn. Data obtained from dynamic light scattering and rheometric measurements are compared to theor. calcns. based on an anal. treatable spheroid model of BSA with isotropic screened Coulomb plus hard-sphere interactions. The only input to the dynamics calcns. is the static structure factor obtained from a consistent theor. fit to a concn. series of small-angle X-ray scattering (SAXS) data. This fit is based on an integral equation scheme that combines high accuracy with low computational cost. All exptl. probed dynamic and static properties are reproduced theor. with an at least semi-quant. accuracy. For lower protein concn. and low salinity, both theory and expt. show a max. in the reduced viscosity, caused by the electrostatic repulsion of proteins. On employing our theor. and exptl. results, the applicability range of a generalized Stokes-Einstein (GSE) relation connecting viscosity, collective diffusion coeff., and osmotic compressibility, proposed by Kholodenko and Douglas is examd. Significant violation of the GSE relation is found, both in exptl. data and in theor. models, in concd. systems at physiol. salinity, and under low-salt conditions for arbitrary protein concns.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XlvVGqtA%253D%253D&md5=8b4a1f8e7c8e2b24bae427c367e8dfda
145.
Szymanski, J.; Patkowski, A.; Wilk, A.; Garstecki, P.; Holyst, R. Diffusion and Viscosity in a Crowded Environment: From Nano- to Macroscale J. Phys. Chem. B 2006, 110, 25593– 25597 DOI: 10.1021/jp0666784
[ACS Full Text ], [CAS]
145.
Diffusion and Viscosity in a Crowded Environment: from Nano- to Macroscale
Szymanski, Jedrzej; Patkowski, Adam; Wilk, Agnieszka; Garstecki, Piotr; Holyst, Robert
Journal of Physical Chemistry B (2006), 110 (51), 25593-25597CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
Although water is the chief component of living cells, food, and personal care products, the supramol. components make their viscosity larger than that of water by several orders of magnitude. Using fluorescence correlation spectroscopy (FCS), photon correlation spectroscopy (PCS), NMR, and rheol. data, we show how the viscosity changes from the value for water at the mol. scale to the large macroviscosity. We detd. the viscosity experienced by nanoprobes (of sizes from 0.28 to 190 nm) in aq. micellar soln. of hexaethylene-glycol-monododecyl-ether (in a range of concn. from 0.1% wt./wt. to 35% wt./wt.) and identified a clear crossover at the length scale of 17 ± 2 nm (slightly larger than persistence length of micelles) at which viscosity acquires its macroscopic value. The sharp dependence of the viscosity coeffs. on the size of the probe in the nanoregime has important consequences for diffusion-limited reactions in crowded environments (e.g., living cells).
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xht1anur3I&md5=ee932d092a3f894fb370f79d78d811b4
146.
Despa, F.; Fernandez, A.; Berry, R. S. Dielectric Modulation of Biological Water Phys. Rev. Lett. 2004, 93, 228104 DOI: 10.1103/PhysRevLett.93.228104
[Crossref], [PubMed], [CAS]
146.
Dielectric Modulation of Biological Water
Despa, Florin; Fernandez, Ariel; Berry, R. Stephen
Physical Review Letters (2004), 93 (22), 228104/1-228104/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)
We show that water constrained by vicinal hydrophobes undergoes a librational dynamics that lowers the dielec. susceptibility and induces a "red shift" of the relaxation frequency in the hydration shell. The results shed light on the way proteins enhance their intramol. interactions as they fold or assoc.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhtVejtbnP&md5=27402124fb4bb4241416a0347d66cd04
147.
Huang, K.-Y.; Kingsley, C. N.; Sheil, R.; Cheng, C.-Y.; Bierma, J. C.; Roskamp, K. W.; Khago, D.; Martin, R. W.; Han, S. Stability of Protein-Specific Hydration Shell on Crowding J. Am. Chem. Soc. 2016, 138, 5392– 5402 DOI: 10.1021/jacs.6b01989
[ACS Full Text ], [CAS]
147.
Stability of Protein-Specific Hydration Shell on Crowding
Huang, Kuo-Ying; Kingsley, Carolyn N.; Sheil, Ryan; Cheng, Chi-Yuan; Bierma, Jan C.; Roskamp, Kyle W.; Khago, Domarin; Martin, Rachel W.; Han, Songi
Journal of the American Chemical Society (2016), 138 (16), 5392-5402CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
We demonstrate that the effect of protein crowding is critically dependent on the stability of the protein's hydration shell, which can dramatically vary between different proteins. In the human eye lens, γS-crystallin (γS-WT) forms a densely packed transparent hydrogel with a high refractive index, making it an ideal system for studying the effects of protein crowding. A single point mutation generates the cataract-related variant γS-G18V, dramatically altering the optical properties of the eye lens. This system offers an opportunity to explore fundamental questions regarding the effect of protein crowding, using γS-WT and γS-G18V: (i) how do the diffusion dynamics of hydration water change as a function of protein crowding; and (ii) upon hydrogel formation of γS-WT, has a dynamic transition occurred generating a single population of hydration water, or do populations of bulk and hydration water coexist. Using localized spin probes, we sep. probe the local translational diffusivity of both surface hydration and interstitial water of γS-WT and γS-G18V in soln. Surprisingly, we find that under the influence of hydrogel formation at highly crowded γS-WT concns. up to 500 mg/mL, the protein hydration shell remains remarkably dynamic, slowing by less than a factor of 2, if at all, compared to that in dil. protein solns. of ∼5 mg/mL. Upon self-crowding, the population of this robust surface hydration water increases, while a significant bulk-like water population coexists even at ∼500 mg/mL protein concns. In contrast, surface water of γS-G18V irreversibly dehydrates with moderate concn. increases or subtle alterations to the soln. conditions, demonstrating that the effect of protein crowding is highly dependent on the stability of the protein-specific hydration shell. The core function of γS-crystallin in the eye lens may be precisely its capacity to preserve a robust hydration shell, whose stability is abolished by a single G18V mutation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XlsFOjsrk%253D&md5=bd7bdf22ced8bf18904611bdbbb991c9
148.
Guigas, G.; Weiss, M. Effects of Protein Crowding on Membrane Systems Biochim. Biophys. Acta, Biomembr. 2016, 1858, 2441– 2450 DOI: 10.1016/j.bbamem.2015.12.021
[Crossref], [PubMed], [CAS]
148.
Effects of protein crowding on membrane systems
Guigas, Gernot; Weiss, Matthias
Biochimica et Biophysica Acta, Biomembranes (2016), 1858 (10), 2441-2450CODEN: BBBMBS; ISSN:0005-2736. (Elsevier B.V.)
A review. Cellular membranes are typically decorated with a plethora of embedded and adsorbed macromols., e.g. proteins, that participate in numerous vital processes. With typical surface densities of 30,000 proteins per μm2 cellular membranes are indeed crowded places that leave only few nanometers of private space for individual proteins. Here, the authors review recent advances in the authors' understanding of protein crowding in membrane systems. The authors first give a brief overview on state-of-the-art approaches in expt. and simulation that are frequently used to study crowded membranes. After that, the authors review how crowding can affect diffusive transport of proteins and lipids in membrane systems. Next, lipid and protein sorting in crowded membrane systems, including effects like protein cluster formation, phase segregation, and lipid droplet formation are discussed. Subsequently, the authors highlight recent progress in uncovering crowding-induced conformational changes of membranes, e.g. membrane budding and vesicle formation. Finally, the authors give a short outlook on potential future developments in the field of crowded membrane systems. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz R´og.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28Xhtlaqsw%253D%253D&md5=f73618ebe102ad6211d5b63928435f16
149.
Wang, Q.; Cheung; Margaret, S. A Physics-Based Approach of Coarse-Graining the Cytoplasm of Escherichia coli (CGCYTO) Biophys. J. 2012, 102, 2353– 2361 DOI: 10.1016/j.bpj.2012.04.010
[Crossref], [PubMed], [CAS]
149.
A Physics-Based Approach of Coarse-Graining the Cytoplasm of Escherichia coli (CGCYTO)
Wang, Qian; Cheung, Margaret S.
Biophysical Journal (2012), 102 (10), 2353-2361CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
We have investigated protein stability in an environment of Escherichia coli cytoplasm using coarse-grained computer simulations. To coarse-grain a small slide of E. coli's cytoplasm consisting of over 16 million atoms, we have developed a self-assembled clustering algorithm (CGCYTO). CGCYTO uses the shape parameter and asphericity as well as a parameter λ (ranging from 0 to 1) that measures the covolume of a test protein and a macromol. against the covolume of a test protein and a sphere of equal vol. as that of a macromol. for the criteria of coarse-graining a cytoplasmic model. A cutoff λc = 0.8 was chosen based on the size of a test protein and computational resources and it detd. the resoln. of a coarse-grained cytoplasm. We compared the results from a polydisperse cytoplasmic model (PD model) produced by CGCYTO with two other coarse-grained hard-sphere cytoplasmic models: 1), F70 model, macromols. in the cytoplasm were modeled by homogeneous hard spheres with a radius of 55 Å, the size of Ficoll70 and 2), HS model, each macromol. in the cytoplasm was modeled by a hard sphere of equal vol. It was found that the folding temp. Tf of a test protein (apoazurin) in a PD model is ∼5° greater than that in a F70 model. In addn., the deviation of Tf in a PD model is twice as much as that in a HS model when an apoazurin is randomly placed at different voids formed by particle fluctuations in PD models.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XntFamtrs%253D&md5=dc86125ac718ac640fea7bc49e2de2d9
150.
Sterpone, F.; Derreumaux, P.; Melchionna, S. Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics J. Chem. Theory Comput. 2015, 11, 1843– 1853 DOI: 10.1021/ct501015h
[ACS Full Text ], [CAS]
150.
Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics
Sterpone, Fabio; Derreumaux, Philippe; Melchionna, Simone
Journal of Chemical Theory and Computation (2015), 11 (4), 1843-1853CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
A novel simulation framework that integrates the OPEP coarse-grained (CG) model for proteins with the Lattice Boltzmann (LB) methodol. to account for the fluid solvent at mesoscale level is presented. OPEP is a very efficient, water-free and electrostatic-free force field that reproduces at quasi-atomistic detail processes like peptide folding, structural rearrangements, and aggregation dynamics. The LB method is based on the kinetic description of the solvent to solve the fluid mechanics under a wide range of conditions, with the further advantage of being highly scalable on parallel architectures. The capabilities of the approach are presented, and the strategy is effective in exploring the role of hydrodynamics on protein relaxation and peptide aggregation. The end result is a strategy for modeling systems of thousands of proteins, such as in the case of dense protein suspensions. The future perspectives of the multiscale approach are also discussed.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXkvVelsrw%253D&md5=88e635a720d6431800027baed091b35c
151.
Blanco, P.; Via, M.; Garcés, J.; Madurga, S.; Mas, F. Brownian Dynamics Computational Model of Protein Diffusion in Crowded Media with Dextran Macromolecules as Obstacles Entropy 2017, 19, 105 DOI: 10.3390/e19030105
[Crossref]
There is no corresponding record for this reference.
152.
Feig, M.; Tanizaki, S.; Sayadi, M. Implicit Solvent Simulations of Biomolecules in Cellular Environments. Annual Reviews in Computational Chemistry; Elsevier: Oxford, U.K., 2008; Vol. 4, pp 107– 121.
[Crossref]
There is no corresponding record for this reference.
153.
Starzyk, A.; Wojciechowski, M.; Cieplak, M. Structural Fluctuations and Thermal Stability of Proteins in Crowded Environments: Effects of the Excluded Volume Phys. Biol. 2016, 13, 066002 DOI: 10.1088/1478-3975/13/6/066002
[Crossref], [PubMed], [CAS]
153.
Structural fluctuations and thermal stability of proteins in crowded environments: effects of the excluded volume
Starzyk Anna; Wojciechowski Michal; Cieplak Marek
Physical biology (2016), 13 (6), 066002 ISSN:.
We perform molecular dynamics simulations for a simple coarse-grained model of a protein placed inside of a softly repulsive sphere of radius R. The protein is surrounded either by a number of same molecules or a number of spherical crowding particles that immitate other biomolecules such as the osmolytes. The two descriptions are shown to lead to distinct results when testing thermal stability as assessed by studying the unfolding times as a function of temperature. We consider three examples of proteins and show that crowding increases the thermal stability provided the inter-protein or protein-crowder interactions are repulsive. On the other hand, an introduction of attraction between the proteins is found to destabilize the proteins. Crowding by repulsive crowder particles is seen to enhance the RMSF in certain exposed regions. The effect grows on decreasing the size of the crowding particles. In the absence of crowding the RMSF anticorrelates with the coordination number related to the residue-residue interaction.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2srpsVKhtA%253D%253D&md5=a2a2c753a302c85a10a937f4b4454d4d
154.
McGuffee, S. R.; Elcock, A. H. Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm PLoS Comput. Biol. 2010, 6, e1000694 DOI: 10.1371/journal.pcbi.1000694
[Crossref], [PubMed], [CAS]
154.
Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm
McGuffee Sean R; Elcock Adrian H
PLoS computational biology (2010), 6 (3), e1000694 ISSN:.
A longstanding question in molecular biology is the extent to which the behavior of macromolecules observed in vitro accurately reflects their behavior in vivo. A number of sophisticated experimental techniques now allow the behavior of individual types of macromolecule to be studied directly in vivo; none, however, allow a wide range of molecule types to be observed simultaneously. In order to tackle this issue we have adopted a computational perspective, and, having selected the model prokaryote Escherichia coli as a test system, have assembled an atomically detailed model of its cytoplasmic environment that includes 50 of the most abundant types of macromolecules at experimentally measured concentrations. Brownian dynamics (BD) simulations of the cytoplasm model have been calibrated to reproduce the translational diffusion coefficients of Green Fluorescent Protein (GFP) observed in vivo, and "snapshots" of the simulation trajectories have been used to compute the cytoplasm's effects on the thermodynamics of protein folding, association and aggregation events. The simulation model successfully describes the relative thermodynamic stabilities of proteins measured in E. coli, and shows that effects additional to the commonly cited "crowding" effect must be included in attempts to understand macromolecular behavior in vivo.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC3c7nsV2mtg%253D%253D&md5=4f91d65ce6896c286ab894e87354426a
155.
Ando, T.; Skolnick, J. Crowding and Hydrodynamic Interactions Likely Dominate in vivo Macromolecular Motion Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 18457– 18462 DOI: 10.1073/pnas.1011354107
[Crossref], [PubMed], [CAS]
155.
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion
Ando, Tadashi; Skolnick, Jeffrey
Proceedings of the National Academy of Sciences of the United States of America (2010), 107 (43), 18457-18462, S18457/1-S18457/11CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
To begin to elucidate the principles of intermol. dynamics in the crowded environment of cells, employing Brownian dynamics (BD) simulations, we examd. possible mechanism(s) responsible for the great redn. in diffusion consts. of macromols. in vivo from that at infinite diln. In an Escherichia coli cytoplasm model comprised of 15 different macromol. types at physiol. concns., BD simulations of mol.-shaped and equiv. sphere representations were performed with a soft repulsive potential. At cellular concns., the calcd. diffusion const. of GFP is much larger than expt., with no significant shape dependence. Next, using the equiv. sphere system, hydrodynamic interactions (HI) were considered. Without adjustable parameters, the in vivo exptl. GFP diffusion const. was reproduced. Finally, the effects of nonspecific attractive interactions were examd. The redn. in diffusivity is very sensitive to macromol. radius with the motion of the largest macromols. dramatically slowed down; this is not seen if HI dominate. In addn., long-lived clusters involving the largest macromols. form if attractions dominate, whereas HI give rise to significant, size independent intermol. dynamic correlations. These qual. differences provide a testable means of differentiating the importance of HI vs. nonspecific attractive interactions on macromol. motion in cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtl2ktr3F&md5=9943a7992940ef23b1f8d8602dbb262d
156.
Mereghetti, P.; Wade, R. C. Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions J. Phys. Chem. B 2012, 116, 8523– 8533 DOI: 10.1021/jp212532h
[ACS Full Text ], [CAS]
156.
Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions
Mereghetti, Paolo; Wade, Rebecca C.
Journal of Physical Chemistry B (2012), 116 (29), 8523-8533CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
High macromol. concns. are a distinguishing feature of living organisms. Understanding how the high concn. of solutes affects the dynamic properties of biol. macromols. is fundamental for the comprehension of biol. processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein Brownian dynamics simulation method. Concd. solns. (30-40% vol. fraction) of myoglobin, Hb A, and sickle cell Hb S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coeffs. were computed. Good agreement of computed properties with available exptl. data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the assocn. properties of concd. protein solns. Specifically, they show a qual. difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coeff. is controlled by macromol. shape and hydrodynamic interactions, the rotational diffusion coeff. is affected by macromol. shape, direct intermol. interactions, and both translational and rotational hydrodynamic interactions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38Xnt1WrtLs%253D&md5=c0b0851b5f44089bfa5e9be998afefd6
157.
Mereghetti, P.; Gabdoulline, R. R.; Wade, R. C. Brownian Dynamics Simulation of Protein Solutions Structural and Dynamical Properties Biophys. J. 2010, 99, 3782– 3791 DOI: 10.1016/j.bpj.2010.10.035
[Crossref], [PubMed], [CAS]
157.
Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties
Mereghetti, Paolo; Gabdoulline, Razif R.; Wade, Rebecca C.
Biophysical Journal (2010), 99 (11), 3782-3791CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
The study of solns. of biomacromols. provides an important basis for understanding the behavior of many fundamental cellular processes, such as protein folding, self-assembly, biochem. reactions, and signal transduction. Here, we describe a Brownian dynamics simulation procedure and its validation for the study of the dynamic and structural properties of protein solns. In the model used, the proteins are treated as atomically detailed rigid bodies moving in a continuum solvent. The protein-protein interaction forces are described by the sum of electrostatic interaction, electrostatic desolvation, nonpolar desolvation, and soft-core repulsion terms. The linearized Poisson-Boltzmann equation is solved to compute electrostatic terms. Simulations of homogeneous solns. of three different proteins with varying concns., pH, and ionic strength were performed. The results were compared to exptl. data and theor. values in terms of long-time self-diffusion coeffs., second virial coeffs., and structure factors. The results agree with the exptl. trends and, in many cases, exptl. values are reproduced quant. There are no parameters specific to certain protein types in the interaction model, and hence the model should be applicable to the simulation of the behavior of mixts. of macromols. in cell-like crowded environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhsV2js7bK&md5=edd47d8e7987df13aadcb07685412b22
158.
Trovato, F.; Tozzini, V. Diffusion within the Cytoplasm: A Mesoscale Model of Interacting Macromolecules Biophys. J. 2014, 107, 2579– 2591 DOI: 10.1016/j.bpj.2014.09.043
[Crossref], [PubMed], [CAS]
158.
Diffusion within the Cytoplasm: A Mesoscale Model of Interacting Macromolecules
Trovato, Fabio; Tozzini, Valentina
Biophysical Journal (2014), 107 (11), 2579-2591CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
Recent expts. carried out in the dense cytoplasm of living cells have highlighted the importance of proteome compn. and nonspecific intermol. interactions in regulating macromol. diffusion and organization. Despite this, the dependence of diffusion-interaction on physicochem. properties such as the degree of poly-dispersity and the balance between steric repulsion and nonspecific attraction among macromols. was not systematically addressed. In this work, we study the problem of diffusion-interaction in the bacterial cytoplasm, combining theory and exptl. data to build a minimal coarse-grained representation of the cytoplasm, which also includes, for the first time to our knowledge, the nucleoid. With stochastic mol.-dynamics simulations of a virtual cytoplasm we are able to track the single biomol. motion, sizing from 3 to 80 nm, on submillisecond-long trajectories. We demonstrate that the size dependence of diffusion coeffs., anomalous exponents, and the effective viscosity experienced by biomols. in the cytoplasm is fine-tuned by the intermol. interactions. Accounting only for excluded vol. in these potentials gives a weaker size-dependence than that expected from exptl. data. On the contrary, adding nonspecific attraction in the range of 1-10 thermal energy units produces a stronger variation of the transport properties at growing biopolymer sizes. Normal and anomalous diffusive regimes emerge straightforwardly from the combination of high macromol. concn., poly-dispersity, stochasticity, and weak nonspecific interactions. As a result, small biopolymers experience a viscous cytoplasm, while the motion of big ones is jammed because the entanglements produced by the network of interactions and the entropic effects caused by poly-dispersity are stronger.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhvFGisrrJ&md5=3778c54c82981a65d21c6fc15983be95
159.
Qin, S. B.; Minh, D. D. L.; McCammon, J. A.; Zhou, H. X. Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease J. Phys. Chem. Lett. 2010, 1, 107– 110 DOI: 10.1021/jz900023w
[ACS Full Text ], [CAS]
159.
Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease
Qin, Sanbo; Minh, David D. L.; McCammon, J. Andrew; Zhou, Huan-Xiang
Journal of Physical Chemistry Letters (2010), 1 (1), 107-110CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
The internal dynamics of proteins inside of cells may be affected by the crowded intracellular environments. Here, the authors test a novel approach to simulations of crowding, in which simulations in the absence of crowders are postprocessed to predict crowding effects, against the direct approach of simulations in the presence of crowders. The effects of crowding on the flap dynamics of HIV-1 protease predicted by the postprocessing approach are found to agree well with those calcd. by the direct approach. The postprocessing approach presents distinct advantages over the direct approach in terms of accuracy and speed and is expected to have broad impact on atomistic simulations of macromol. crowding.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXhtl2qtbvP&md5=53edcc91c57e42ae946631f9c312313c
160.
Cheung, M. S.; Thirumalai, D. Effects of crowding and confinement on the structures of the transition state ensemble in proteins J. Phys. Chem. B 2007, 111, 8250– 8257 DOI: 10.1021/jp068201y
[ACS Full Text ], [CAS]
160.
Effects of crowding and confinement on the structures of the transition state ensemble in proteins
Cheung, Margaret S.; Thirumalai, D.
Journal of Physical Chemistry B (2007), 111 (28), 8250-8257CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
The characterization of the structures of the transition state ensemble is a key step in describing the folding reaction. Using 2 variants of a coarse-grained model of the 3-stranded β-sheet WW domain and a fully automated progress variable clustering (PVC) algorithm, the authors dissected the effect of macromol. crowding and confinement on changes in the transition state structures in comparison to bulk. Each amino acid was represented using a Cα atom and a side-chain. The distance between the Cα atom and center of mass of the side-chain was taken to be its effective van der Waals radius. For the bulk case, the authors predicted using the PVC algorithm, which does not assume knowledge of the underlying folding reaction coordinate, that there were 2 classes of structures in the transition state ensemble (TSE). The structures in both of the classes were compact. The dominant cluster was more structured than the structures in the less populated class. In accord with bulk expts., the residues in strands β2 and β3 and the interactions at the β2-β3 interface were structured. When only excluded vol. interactions between the crowding particles and the WW domain were taken into account or when the protein was confined to an inert spherical pore, the overall structure of the TSE did not change dramatically. However, in this entropy-dominated regime, the width of the TSE decreased and the structures became more oblate and less spherical as the vol. fraction of crowding particle increased or when the pore radius decreased. It suggested that the shape changes, which are computed using the moment of inertia tensor, may represent the slow degrees of freedom during the folding process. When non-native interactions between side-chains and interactions with the cavity of the pores were taken into account, the TSE became considerably broader. Although the topol. in the transition had a fold similar to the native state, the structures were far more plastic than in the bulk. The TSE was sensitive to the size of the pore as well as interactions between the pore and the protein. The differences between the 2 cases (confinement in an inert pore and when pore-protein interactions were considered) arose due to the increased importance of enthalpic interactions in the transition state as the strength of the protein-pore interaction increased.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXmslyrt7Y%253D&md5=16cfa63f347c362f7180b483424f8232
161.
Homouz, D.; Perham, M.; Samiotakis, A.; Cheung, M. S.; Wittung-Stafshede, P. Crowded, Cell-Like Environment Induces Shape Changes in Aspherical Protein Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 11754– 11759 DOI: 10.1073/pnas.0803672105
[Crossref], [PubMed], [CAS]
161.
Crowded, cell-like environment induces shape changes in aspherical protein
Homouz, Dirar; Perham, Michael; Samiotakis, Antonios; Cheung, Margaret S.; Wittung-Stafshede, Pernilla
Proceedings of the National Academy of Sciences of the United States of America (2008), 105 (33), 11754-11759CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
How the crowded environment inside cells affects the structures of proteins with aspherical shapes is a vital question because many proteins and protein-protein complexes in vivo adopt anisotropic shapes. Here we address this question by combining computational and exptl. studies of a football-shaped protein (i.e., Borrelia burgdorferi VlsE) in crowded, cell-like conditions. The results show that macromol. crowding affects protein-folding dynamics as well as overall protein shape. In crowded milieus, distinct conformational changes in VlsE are accompanied by secondary structure alterations that lead to exposure of a hidden antigenic region. Our work demonstrates the malleability of "native" proteins and implies that crowding-induced shape changes may be important for protein function and malfunction in vivo.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhtVCnur3E&md5=3ae077a224e35597da119407693d4ad6
162.
Homouz, D.; Stagg, L.; Wittung-Stafshede, P.; Cheung, M. S. Macromolecular Crowding Modulates Folding Mechanism of alpha/beta Protein Apoflavodoxin Biophys. J. 2009, 96, 671– 680 DOI: 10.1016/j.bpj.2008.10.014
[Crossref], [PubMed], [CAS]
162.
Macromolecular crowding modulates folding mechanism of α/β protein apoflavodoxin
Homouz, Dirar; Stagg, Loren; Wittung-Stafshede, Pernilla; Cheung, Margaret S.
Biophysical Journal (2009), 96 (2), 671-680CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
Protein dynamics in cells may be different from those in dil. solns. in vitro, because the environment in cells is highly concd. with other macromols. This vol. exclusion because of macromol. crowding is predicted to affect both equil. and kinetic processes involving protein conformational changes. Here, to quantify macromol. crowding effects on protein folding mechanisms, the authors investigated the folding energy landscape of an α/β protein, apoflavodoxin, in the presence of inert macromol. crowding agents, using in silico and in vitro approaches. By means of coarse-grained mol. simulations and topol.-based potential interactions, the authors probed the effects of increased vol. fractions of crowding agents (.vphi.c) as well as of crowding agent geometry (sphere or spherocylinder) at high .vphi.c. Parallel kinetic folding expts. with purified Desulfovibrio desulfuricans apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and dextran (spherocylinder) synthetic crowding agents. In conclusion, the authors identified the in silico crowding conditions that best enhanced protein stability, and discovered that upon manipulation of the crowding conditions, folding routes experiencing topol. frustrations could be either enhanced or relieved. The authors' test-tube expts. confirmed that apoflavodoxin's time-resolved folding path is modulated by crowding agent geometry. Macromol. crowding effects may be a tool for the manipulation of protein folding and function in living cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXht12ktrY%253D&md5=67d9150d847b71155e3a731ee83bb805
163.
McGuffee, S. R.; Elcock, A. H. Atomically Detailed Simulations of Concentrated Protein Solutions: The Effects of Salt, pH, Point Mutations, and Protein Concentration in Simulations of 1000-Molecule Systems J. Am. Chem. Soc. 2006, 128, 12098– 12110 DOI: 10.1021/ja0614058
[ACS Full Text ], [CAS]
163.
Atomically Detailed Simulations of Concentrated Protein Solutions: The Effects of Salt, pH, Point Mutations, and Protein Concentration in Simulations of 1000-Molecule Systems
McGuffee, Sean R.; Elcock, Adrian H.
Journal of the American Chemical Society (2006), 128 (37), 12098-12110CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
An ability to accurately simulate the dynamic behavior of concd. macromol. solns. would be of considerable utility in studies of a wide range of biol. systems. With this goal in mind, a Brownian dynamics (BD) simulation method is reported here that allows systems to be modeled that comprise in excess of 1000 protein mols., all of which are treated in at. detail. Intermol. forces are described in the method using an energy function that incorporates electrostatic and hydrophobic interactions and that is calibrated to reproduce exptl. thermodn. information with a single adjustable parameter. Using the method, BD simulations have been performed over a wide range of pH and ionic strengths for three proteins: hen egg white lysozyme (HEWL), chymotrypsinogen, and T4 lysozyme. The simulations reproduce exptl. trends in second virial coeffs. (B22) and translational diffusion coeffs., correctly capture changes in B22 values due to single amino acid substitutions, and reveal a new explanation for the difficulties reported previously in the literature in reproducing B22 values for protein solns. of very low ionic strength. In addn., a strong correlation is found between a residue's probability of being involved in a protein-protein contact in the simulations and its probability of being involved in an exptl. crystal contact. Finally, exploratory simulations of HEWL indicate that the simulation model also gives a promising description of behavior at very high protein concns. (∼250 g/L), suggesting that it may provide a suitable computational framework for modeling the complex behavior exhibited by macromols. in cellular conditions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xos1Sgt74%253D&md5=efe7dc75c317564852061f9fc13e33f3
164.
Gabdoulline, R. R.; Wade, R. C. Protein-Protein Association: Investigation of Factors Influencing Association Rates by Brownian Dynamics Simulations J. Mol. Biol. 2001, 306, 1139– 1155 DOI: 10.1006/jmbi.2000.4404
[Crossref], [PubMed], [CAS]
164.
Protein-Protein Association: Investigation of Factors Influencing Association Rates by Brownian Dynamics Simulations
Gabdoulline, Razif R.; Wade, Rebecca C.
Journal of Molecular Biology (2001), 306 (5), 1139-1155CODEN: JMOBAK; ISSN:0022-2836. (Academic Press)
The rate of protein-protein assocn. limits the response time due to protein-protein interactions. The bimol. assocn. rate may be diffusion-controlled or influenced, and in such cases, Brownian dynamics simulations of protein-protein diffusional assocn. may be used to compute assocn. rates. Here, we report Brownian dynamics simulations of the diffusional assocn. of five different protein-protein pairs: barnase and barstar, acetylcholinesterase and fasciculin-2, cytochrome c peroxidase and cytochrome c, the HyHEL-5 antibody and hen egg lysozyme (HEL), and the HyHEL-10 antibody and HEL. The same protocol was used to compute the diffusional assocn. rates for all the protein pairs in order to assess, by comparison to exptl. measured rates, whether the assocn. of these proteins can be explained solely on the basis of diffusional encounter. The simulation protocol is similar to those previously derived for simulation of the assocn. of barnase and barstar, and of acetylcholinesterase and fasciculin-2; these produced results in excellent agreement with exptl. data for these protein pairs, with changes in assocn. rate due to mutations reproduced within the limits of expected computational and modeling errors. Here, we find that for all protein pairs, the effects of mutations can be well reproduced by the simulations, even though the degree of the electrostatic translational and orientational steering varies widely between the cases. However, the abs. values of assocn. rates for the acetylcholinesterase: fasciculin-2 and HyHEL-10 antibody: HEL pairs are overestimated. Comparison of bound and unbound protein structures shows that this may be due to gating resulting from protein flexibility in some of the proteins. This may lower the assocn. rates compared to their bimol. diffusional encounter rates. (c) 2001 Academic Press.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXhsFOhu70%253D&md5=bcbb9688ff2da041de412d7a5fe8eeb3
165.
Kar, P.; Feig, M. Recent Advances in Transferable Coarse-Grained Modeling of Proteins Adv. Protein Chem. Struct. Biol. 2014, 96, 143– 180 DOI: 10.1016/bs.apcsb.2014.06.005
[Crossref], [PubMed], [CAS]
165.
Recent advances in transferable coarse-grained modeling of proteins
Kar Parimal; Feig Michael
Advances in protein chemistry and structural biology (2014), 96 (), 143-80 ISSN:.
Computer simulations are indispensable tools for studying the structure and dynamics of biological macromolecules. Biochemical processes occur on different scales of length and time. Atomistic simulations cannot cover the relevant spatiotemporal scales at which the cellular processes occur. To address this challenge, coarse-grained (CG) modeling of the biological systems is employed. Over the last few years, many CG models for proteins continue to be developed. However, many of them are not transferable with respect to different systems and different environments. In this review, we discuss those CG protein models that are transferable and that retain chemical specificity. We restrict ourselves to CG models of soluble proteins only. We also briefly review recent progress made in the multiscale hybrid all-atom/CG simulations of proteins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2MzktVGnsA%253D%253D&md5=07a9b4ea06c6ead31bdd6dfdf71515ff
166.
Kar, P.; Gopal, S. M.; Cheng, Y. M.; Predeus, A. V.; Feig, M. PRIMO: A Transferable Coarse-Grained Force Field for Proteins J. Chem. Theory Comput. 2013, 9, 3769– 3788 DOI: 10.1021/ct400230y
[ACS Full Text ], [CAS]
166.
PRIMO: A Transferable Coarse-Grained Force Field for Proteins
Kar, Parimal; Gopal, Srinivasa Murthy; Cheng, Yi-Ming; Predeus, Alexander; Feig, Michael
Journal of Chemical Theory and Computation (2013), 9 (8), 3769-3788CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
The authors describe here the PRIMO (protein intermediate model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multiscale simulations. The energy function consists of std. mol. dynamics energy terms plus a hydrogen-bonding potential term and is mainly parametrized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent was treated implicitly via the generalized Born model. The bonded interactions are either harmonic or distance-based spline interpolated potentials. These potentials are defined on the basis of all-atom mol. dynamics (MD) simulations of dipeptides with the CHARMM22/CMAP force field. The nonbonded parameters are tuned by matching conformational free energies of diverse set of conformations with that of CHARMM all-atom results. PRIMO is designed to provide a correct description of conformational distribution of the backbone (φ/ψ) and side chains (χ1) for all amino acids with a CMAP correction term. The CMAP potential in PRIMO is optimized based on the new CHARMM C36 CMAP. The resulting optimized force field has been applied in MD simulations of several proteins of 36-155 amino acids and showed that the root-mean-squared-deviation of the av. structure from the corresponding crystallog. structure varies between 1.80 and 4.03 Å. PRIMO is shown to fold several small peptides to their native-like structures from extended conformations. These results suggest the applicability of the PRIMO force field in the study of protein structures in aq. soln., structure predictions, as well as ab initio folding of small peptides.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhtVWht7rM&md5=7fd81d83f708b223a00d0bfb707bd5d0
167.
Andrews, C. T.; Elcock, A. H. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids J. Chem. Theory Comput. 2014, 10, 5178– 5194 DOI: 10.1021/ct5006328
[ACS Full Text ], [CAS]
167.
COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids
Andrews, Casey T.; Elcock, Adrian H.
Journal of Chemical Theory and Computation (2014), 10 (11), 5178-5194CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
The authors describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent mol. dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions--which the authors term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)--quant. reproduced all of the "target" MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concd. amino acid solns.; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and are in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concns. that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic. The anomalously strong intermol. interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP's nonbonded parameters, however, produced results in better accordance with expt. Overall, the authors' results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be esp. useful for modeling unfolded or intrinsically disordered proteins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhslSku7fE&md5=0a8791fb16ac2575780826d55739a0f2
168.
Chiricotto, M.; Sterpone, F.; Derreumaux, P.; Melchionna, S. Multiscale Simulation of Molecular Processes in Cellular Environments Philos. Trans. R. Soc., A 2016, 374, 20160225 DOI: 10.1098/rsta.2016.0225
[Crossref], [CAS]
168.
Multiscale simulation of molecular processes in cellular environments
Chiricotto, Mara; Sterpone, Fabio; Derreumaux, Philippe; Melchionna, Simone
Philosophical Transactions of the Royal Society, A: Mathematical, Physical & Engineering Sciences (2016), 374 (2080), 20160225/1-20160225/13CODEN: PTRMAD; ISSN:1364-503X. (Royal Society)
We describe the recent advances in studying biol. systems via multiscale simulations. Our scheme is based on a coarse-grained representation of the macromols. and a mesoscopic description of the solvent. The dual technique handles particles, the aq. solvent and their mutual exchange of forces resulting in a stable and accurate methodol. allowing biosystems of unprecedented size to be simulated.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvFOrurzP&md5=ba5fe7265d0f77ba5d2a72bc73fe0b54
169.
Predeus, A. V.; Gul, S.; Gopal, S. M.; Feig, M. Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations J. Phys. Chem. B 2012, 116, 8610– 8620 DOI: 10.1021/jp300129u
[ACS Full Text ], [CAS]
169.
Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations
Predeus, Alexander V.; Gul, Seref; Gopal, Srinivasa M.; Feig, Michael
Journal of Physical Chemistry B (2012), 116 (29), 8610-8620CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
Macromol. crowding is recognized as an important factor influencing folding and conformational dynamics of proteins and nucleic acids. Previous views of crowding have focused on the mostly entropic vol. exclusion effect of crowding, but recent studies are indicating the importance of enthalpic effects, in particular, changes in electrostatic interactions due to crowding. Here, temp. replica exchange mol. dynamics simulations of trp-cage and melittin in the presence of explicit protein crowders are presented to further examine the effect of protein crowders on peptide dynamics. The simulations involve a three-component multiscale modeling scheme where the peptides are represented at an atomistic level, the crowder proteins at a coarse-grained level, and the surrounding aq. solvent as implicit solvent. This scheme optimally balances a phys. realistic description for the peptide with computational efficiency. The multiscale simulations were compared with simulations of the same peptides in different dielec. environments with dielec. consts. ranging from 5 to 80. It is found that the sampling in the presence of the crowders resembles sampling with reduced dielec. consts. between 10 and 40. Furthermore, diverse conformational ensembles are generated in the presence of crowders including partially unfolded states for trp-cage. These findings emphasize the importance of enthalpic interactions over vol. exclusion effects in describing the effects of cellular crowding.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XktVynsb8%253D&md5=1422e75e835e493a2d9a6c2cdb266a1c
170.
Feig, M.; Sugita, Y. Variable Interactions between Protein Crowders and Biomolecular Solutes are Important in Understanding Cellular Crowding J. Phys. Chem. B 2012, 116, 599– 605 DOI: 10.1021/jp209302e
[ACS Full Text ], [CAS]
170.
Variable Interactions between Protein Crowders and Biomolecular Solutes Are Important in Understanding Cellular Crowding
Feig, Michael; Sugita, Yuji
Journal of Physical Chemistry B (2012), 116 (1), 599-605CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
The effect of cellular crowding was examd. from mol. dynamics simulations of chymotrypsin inhibitor 2 (CI2) in the presence of either lysozyme or bovine serum albumin (BSA) crowder mols. as a complement to recent exptl. studies of the same systems. The simulations confirm a destabilization and significantly slowed diffusion of CI2 in the presence of lysozyme and indicate that this observation is a result of extensive, nonspecific protein-protein interactions between CI2 and lysozyme. CI2 interacts much less with BSA crowders corresponding to a weak effect of crowding. Energetic anal. suggests an overall favorable crowding free energy in the presence of lysozyme, while weaker interactions with BSA appear to be unfavorable.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhsFansbrL&md5=5c687a06491efcc7d2d4e8e7e1557efe
171.
Harada, R.; Tochio, N.; Kigawa, T.; Sugita, Y.; Feig, M. Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions J. Am. Chem. Soc. 2013, 135, 3696– 3701 DOI: 10.1021/ja3126992
[ACS Full Text ], [CAS]
171.
Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions
Harada, Ryuhei; Tochio, Naoya; Kigawa, Takanori; Sugita, Yuji; Feig, Michael
Journal of the American Chemical Society (2013), 135 (9), 3696-3701CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The effect of cellular crowding environments on protein structure and stability is a key issue in mol. and cellular biol. The classical view of crowding emphasizes the vol. exclusion effect that generally favors compact, native states. Here, results from mol. dynamics simulations and NMR expts. show that protein crowders may destabilize native states via protein-protein interactions. In the model system considered here, mixts. of villin head piece and protein G at high concns., villin structures become increasingly destabilized upon increasing crowder concns. The denatured states obsd. in the simulation involve partial unfolding as well as more subtle conformational shifts. The unfolded states remain overall compact and only partially overlap with unfolded ensembles at high temp. and in the presence of urea. NMR measurements on the same systems confirm structural changes upon crowding based on changes of chem. shifts relative to dil. conditions. An anal. of protein-protein interactions and energetic aspects suggests the importance of enthalpic and solvation contributions to the crowding free energies that challenge an entropic-centered view of crowding effects.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXisVCrtrk%253D&md5=f0962a89262ca0fe54bcd357e460e145
172.
Wang, P.-h.; Yu, I.; Feig, M.; Sugita, Y. Influence of Protein Crowder Size on Hydration Structure and Dynamics in Macromolecular Crowding Chem. Phys. Lett. 2017, 671, 63– 70 DOI: 10.1016/j.cplett.2017.01.012
[Crossref], [CAS]
172.
Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding
Wang, Po-hung; Yu, Isseki; Feig, Michael; Sugita, Yuji
Chemical Physics Letters (2017), 671 (), 63-70CODEN: CHPLBC; ISSN:0009-2614. (Elsevier B.V.)
We investigate the effects of protein crowder sizes on hydration structure and dynamics in macromol. crowded systems by all-atom MD simulations. The crowded systems consisting of only small proteins showed larger total surface areas than those of large proteins at the same vol. fractions. As a result, more water mols. were trapped within the hydration shells, slowing down water diffusion. The simulation results suggest that the protein crowder size is another factor to det. the effect of macromol. crowding and to explain the exptl. kinetic data of proteins and DNAs in the presence of crowding agents.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtFOgsrs%253D&md5=51ed477927672704b8ad7a2fbbf2de07
173.
Yu, I.; Mori, T.; Ando, T.; Harada, R.; Jung, J.; Sugita, Y.; Feig, M. Biomolecular Interactions Modulate Macromolecular Structure and Dynamics in Atomistic Model of a Bacterial Cytoplasm eLife 2016, 5, e19274 DOI: 10.7554/eLife.19274
[Crossref], [PubMed]
There is no corresponding record for this reference.
174.
Candotti, M.; Orozco, M. The Differential Response of Proteins to Macromolecular Crowding PLoS Comput. Biol. 2016, 12, e1005040 DOI: 10.1371/journal.pcbi.1005040
[Crossref], [PubMed], [CAS]
174.
The differential response of proteins to macromolecular crowding
Candotti, Michela; Orozco, Modesto
PLoS Computational Biology (2016), 12 (7), e1005040/1-e1005040/18CODEN: PCBLBG; ISSN:1553-7358. (Public Library of Science)
The habitat in which proteins exert their function contains up to 400 g/L of macromols., most of which are proteins. The repercussions of this dense environment on protein behavior are often overlooked or addressed using synthetic agents such as poly(ethylene glycol), whose ability to mimic protein crowders has not been demonstrated. Here we performed a comprehensive atomistic mol. dynamic anal. of the effect of protein crowders on the structure and dynamics of three proteins, namely an intrinsically disordered protein (ACTR), a molten globule conformation (NCBD), and a one-fold structure (IRF-3) protein. We found that crowding does not stabilize the native compact structure, and, in fact, often prevents structural collapse. Poly(ethylene glycol) PEG500 failed to reproduce many aspects of the physiol.-relevant protein crowders, thus indicating its unsuitability to mimic the cell interior. Instead, the impact of protein crowding on the structure and dynamics of a protein depends on its degree of disorder and results from two competing effects: the excluded vol., which favors compact states, and quinary interactions, which favor extended conformers. Such a viscous environment slows down protein flexibility and restricts the conformational landscape, often biasing it towards bioactive conformations but hindering biol. relevant protein-protein contacts. Overall, the protein crowders used here act as unspecific chaperons that modulate the protein conformational space, thus having relevant consequences for disordered proteins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvVWltL%252FM&md5=82c9d43f0e83f4145dd441c88f02884f
175.
Virk, A. S.; Stait-Gardner, T.; Willis, S. A.; Torres, A. M.; Price, W. S. Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations Front. Phys. 2015, 3, 1 DOI: 10.3389/fphy.2015.00001
[Crossref]
There is no corresponding record for this reference.
176.
Karandur, D.; Wong, K.-Y.; Pettitt, B. M. Solubility and Aggregation of Gly₅ in Water J. Phys. Chem. B 2014, 118, 9565– 9572 DOI: 10.1021/jp503358n
[ACS Full Text ], [CAS]
176.
Solubility and Aggregation of Gly5 in Water
Karandur, Deepti; Wong, Ka-Yiu; Pettitt, B. Montgomery
Journal of Physical Chemistry B (2014), 118 (32), 9565-9572CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
Exptl., the soly. of oligoglycines in water decreases as its length increases. Computationally, the free energy of solvation becomes more favorable with chain length for short (n = 1-5) oligoglycines. We present results of large scale simulations with over 600 pentaglycines at varying concns. in explicit solvent to consider the mechanism of aggregation. The soly. limit of Gly5 for the force field used was calcd. and compared with exptl. values. We find that intermol. interactions between pentaglycines are favored over interactions between glycine and water, leading to their aggregation. However, the interaction driving peptide assocns., liq.-liq. phase sepn., are not predominantly hydrogen bonding. Instead, non-hydrogen bonding interactions between partially charged atoms on the peptide backbone allow the formation of dipole-dipole and charge layering correlations that mechanistically stabilize the formation of large, stable peptide clusters.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtFKms7vP&md5=bab58ae00c6a26a8049f7ae6a92a5fba
177.
Petrov, D.; Zagrovic, B. Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments? PLoS Comput. Biol. 2014, 10, e1003638 DOI: 10.1371/journal.pcbi.1003638
[Crossref], [PubMed], [CAS]
177.
Are current atomistic force fields accurate enough to study proteins in crowded environments?
Petrov, Drazen; Zagrovic, Bojan
PLoS Computational Biology (2014), 10 (5), e1003638/1-e1003638/11, 11 pp.CODEN: PCBLBG; ISSN:1553-7358. (Public Library of Science)
The high concn. of macromols. in the crowded cellular interior influences different thermodn. and kinetic properties of proteins, including their structural stabilities, intermol. binding affinities and enzymic rates. Moreover, various structural biol. methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concn. Due to large sampling requirements, however, the accuracy of classical mol. dynamics (MD) simulations in capturing protein behavior at high concn. still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 μs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concn. We first perform an exhaustive set of simulations with multiple protein mols. in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and soln. ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estd. aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is exptl. known to be sol. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly obsd. for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for addnl. two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the picture of protein behavior in biol. relevant crowded environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsVGktb%252FK&md5=8632da9facdaa7ee1bca01e89a9119dc
178.
Andrews, C. T.; Elcock, A. H. Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other J. Chem. Theory Comput. 2013, 9, 4585– 4602 DOI: 10.1021/ct400371h
[ACS Full Text ], [CAS]
178.
Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other
Andrews, Casey T.; Elcock, Adrian H.
Journal of Chemical Theory and Computation (2013), 9 (10), 4585-4602CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Although it is now commonly accepted that the highly crowded conditions encountered inside biol. cells have the potential to significantly alter the thermodn. properties of biomols., it is not known to what extent the thermodn. of fundamental types of interactions such as salt bridges and hydrophobic interactions are strengthened or weakened by high biomol. concns. As one way of addressing this question the authors have performed a series of all-atom explicit solvent mol. dynamics (MD) simulations to study the effect of increasing solute concn. on the behavior of four types of zwitterionic amino acids in aq. soln. The authors have simulated systems contg. glycine, valine, phenylalanine, or asparagine at concns. of 50, 100, 200, and 300 mg/mL. Each mol. system has been simulated for 1 μs to obtain statistically converged ests. of thermodn. parameters, and each has been conducted with 8 different force fields and water models; the combined simulation time is 128 μs. The d., viscosity, and dielec. increments of the four amino acids calcd. from the simulations have been compared to corresponding exptl. measurements. While all of the force fields perform well at reproducing the d. increments, discrepancies for the viscosity and dielec. increments raise questions both about the accuracy of the simulation force fields and, in certain cases, the exptl. data. The authors also observe large differences between the various force fields' descriptions of the interaction thermodn. of salt bridges and, surprisingly, these differences also lead to qual. different predictions of their dependences on solute concn. For the aliph. interactions of valine side chains, fewer differences are obsd. between the force fields, but significant differences are again obsd. for arom. interactions of phenylalanine side chains. Taken together, the results highlight the potential power of using explicit-solvent simulation methods to understand behavior in concd. systems but also hint at potential difficulties in using these methods to obtain consistent views of behavior in intracellular environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXht12htrfE&md5=edb0031f09d38ae73c5d946d07645faa
179.
Abriata, L. A.; Dal Peraro, M. Assessing the Potential of Atomistic Molecular Dynamics Simulations to Probe Reversible Protein-Protein Recognition and Binding Sci. Rep. 2015, 5, 10549 DOI: 10.1038/srep10549
[Crossref], [PubMed], [CAS]
179.
Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
Abriata Luciano A; Dal Peraro Matteo
Scientific reports (2015), 5 (), 10549 ISSN:.
Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements, and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50 Å distances; that conformational selection can take place within surface-to-surface distances of 10 to 40 Å i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2MfosFGmsA%253D%253D&md5=59145b657d08e4ae29d7443e0906e1c9
180.
Piana, S.; Donchev, A. G.; Robustelli, P.; Shaw, D. E. Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States J. Phys. Chem. B 2015, 119, 5113– 5123 DOI: 10.1021/jp508971m
[ACS Full Text ], [CAS]
180.
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States
Piana, Stefano; Donchev, Alexander G.; Robustelli, Paul; Shaw, David E.
Journal of Physical Chemistry B (2015), 119 (16), 5113-5123CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
Many proteins can be partially or completely disordered under physiol. conditions. Structural characterization of these disordered states using exptl. methods can be challenging, since they are composed of a structurally heterogeneous ensemble of conformations rather than a single dominant conformation. Mol. dynamics (MD) simulations should in principle provide an ideal tool for elucidating the compn. and behavior of disordered states at an at. level of detail. Unfortunately, MD simulations using current physics-based models tend to produce disordered-state ensembles that are structurally too compact relative to expts. We find that the water models typically used in MD simulations significantly underestimate London dispersion interactions, and speculate that this may be a possible reason for these erroneous results. To test this hypothesis, we create a new water model, TIP4P-D, that approx. corrects for these deficiencies in modeling water dispersion interactions while maintaining compatibility with existing physics-based models. We show that simulations of solvated proteins using this new water model typically result in disordered states that are substantially more expanded and in better agreement with expt. These results represent a significant step toward extending the range of applicability of MD simulations to include the study of (partially or fully) disordered protein states.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXksVOrt7s%253D&md5=45a16c7288d70415451190d71e7cd233
181.
Best, R. B.; Mittal, J. Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse J. Phys. Chem. B 2010, 114, 14916– 14923 DOI: 10.1021/jp108618d
[ACS Full Text ], [CAS]
181.
Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse
Best, Robert B.; Mittal, Jeetain
Journal of Physical Chemistry B (2010), 114 (46), 14916-14923CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
A recognized shortcoming in current protein simulations is that most force fields are parametrized with relatively primitive three-site water models. Since the deficiencies of the common three-site water models in reproducing the phase diagram of water are well-known, an improved description of the solvent will be required, for example, to study proteins in mol. simulations at thermodn. conditions other than std. temp. and pressure. Here, we combine a protein force field derived from Amber ff03 together with the highly optimized TIP4P/2005 water model, with a small backbone modification to match the population of helical states obtained with the new water model to expt. Remarkably, we find that the resulting force field, Amber ff03w, produces a more cooperative helix-coil transition, compared with the similarly "backbone-cor." Amber ff03* model with TIP3P water, with calcd. helix propagation parameters in good agreement with the expt. The radius of gyration for nonhelical conformations is significantly larger for Amber ff03w than for Amber ff03* and shows a collapse with increasing temp. as found in single-mol. expts. on longer proteins. The origin of the collapse appears to be a more favorable enthalpic component of the peptide-solvent interaction and is correlated with increasing turn formation, in accord with the expt. In addn. to this enhanced cooperativity, we verify that, with the new force field, replica exchange folding simulations of the GB1 hairpin and Trp cage result in folded structures, starting from completely unfolded initial conditions; simulations of folded proteins are also stable. These results together suggest that Amber ff03w (with TIP4P/2005) will be well suited for studying protein folding and properties of unfolded state and intrinsically disordered proteins over a wide range of thermodn. conditions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtlKjsbnN&md5=f6f532d7b002a5c54cbdc3125a005b44
182.
Hermans, J.; Berendsen, H. J. C.; van Gunsteren, W. F.; Postma, J. P. M. A Consistent Empirical Potential for Water-Protein Interactions Biopolymers 1984, 23, 1513– 1518 DOI: 10.1002/bip.360230807
[Crossref], [CAS]
182.
A consistent empirical potential for water-protein interactions
Hermans, Jan; Berendsen, Herman J. C.; Van Gunsteren, Wilfred F.; Postma, Johan P. M.
Biopolymers (1984), 23 (8), 1513-18CODEN: BIPMAA; ISSN:0006-3525.
A simple point-charge potential, developed earlier for the calcn. of intermol. forces in mol.-dynamics simulations of liq. H2O, has been extended to include interactions between H2O mols. and polar groups of proteins. A complete potential for use in the simulation of protein dynamics in H2O is reported.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2cXltVKjs7c%253D&md5=5521167d8da8b5511c522ebf5cbac2ba
183.
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926– 935 DOI: 10.1063/1.445869
[Crossref], [CAS]
183.
Comparison of simple potential functions for simulating liquid water
Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.; Impey, Roger W.; Klein, Michael L.
Journal of Chemical Physics (1983), 79 (2), 926-35CODEN: JCPSA6; ISSN:0021-9606.
Classical Monte Carlo simulations were carried out for liq. H2O in the NPT ensemble at 25° and 1 atm using 6 of the simpler intermol. potential functions for the dimer. Comparisons were made with exptl. thermodn. and structural data including the neutron diffraction results of Thiessen and Narten (1982). The computed densities and potential energies agree with expt. except for the original Bernal-Fowler model, which yields an 18% overest. of the d. and poor structural results. The discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons were made for the self-diffusion coeffs. obtained from mol. dynamics simulations.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3sXksF2htL4%253D&md5=a1161334e381746be8c9b15a5e56f704
184.
Yeh, I. C.; Hummer, G. System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics Simulations with Periodic Boundary Conditions J. Phys. Chem. B 2004, 108, 15873– 15879 DOI: 10.1021/jp0477147
[ACS Full Text ], [CAS]
184.
System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics Simulations with Periodic Boundary Conditions
Yeh, In-Chul; Hummer, Gerhard
Journal of Physical Chemistry B (2004), 108 (40), 15873-15879CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
We study the system-size dependence of translational diffusion coeffs. and viscosities in mol. dynamics simulations under periodic boundary conditions. Simulations of water under ambient conditions and a Lennard-Jones (LJ) fluid show that the diffusion coeffs. increase strongly as the system size increases. We test a simple analytic correction for the system-size effects that is based on hydrodynamic arguments. This correction scales as N-1/3, where N is the no. of particles. For a cubic simulation box of length L, the diffusion coeff. cor. for system-size effects is D0 = DPBC + 2.837297kBT/(6πηL), where DPBC is the diffusion coeff. calcd. in the simulation, kB the Boltzmann const., T the abs. temp., and η the shear viscosity of the solvent. For water, LJ fluids, and hard-sphere fluids, this correction quant. accounts for the system-size dependence of the calcd. self-diffusion coeffs. In contrast to diffusion coeffs., the shear viscosities of water and the LJ fluid show no significant system-size dependences.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXnsV2iurk%253D&md5=e333a4ea27b4451db997737f0e3f6a4f
185.
Venable, R. M.; Hatcher, E.; Guvench, O.; MacKerell, A. D.; Pastor, R. W. Comparing Simulated and Experimental Translation and Rotation Constants: Range of Validity for Viscosity Scaling J. Phys. Chem. B 2010, 114, 12501– 12507 DOI: 10.1021/jp105549s
[ACS Full Text ], [CAS]
185.
Comparing Simulated and Experimental Translation and Rotation Constants: Range of Validity for Viscosity Scaling
Venable, Richard M.; Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D., Jr.; Pastor, Richard W.
Journal of Physical Chemistry B (2010), 114 (39), 12501-12507CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
Proper simulation of dynamic properties, including mol. diffusion, is an important goal of empirical force fields. However, the widely used TIP3P water model does not reproduce the exptl. viscosity of water. Consequently, scaling of simulated diffusion consts. of solutes in aq. solns. is required to effectively compare them with expt. It is proposed that scaling by the ratio of viscosities of model and real water is appropriate in the regime where the concn. dependence of simulated and exptl. soln. viscosities is parallel. With this ansatz, viscosity scaling can be carried out for glucose and trehalose up to 20 wt % for simulations carried out with the CHARMM additive carbohydrate force field C35 and TIP3P water; above this value, the concn. dependence of simulated viscosities lags that of expt., and scaling is not advised. Scaled translational diffusion consts. for glucose and the disaccharides trehalose, maltose, and melibiose at low concn. agree nearly quant. with expt., as do NMR 13C T1's for glucose, trehalose, and maltose; these results support the use of C35 for simulations of sugar transport properties at low concn. At high concns. the scaled diffusion consts. for glucose and trehalose underestimate and overestimate expt., resp. Hydrodynamic bead model calcns. indicate a hydration level of approx. 1 water/hydroxyl for glucose. Patterns for the disaccharides are more complicated, though trehalose binds 0.5 to 1 more water than does maltose depending on the anal.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtFelsbjP&md5=c834d788808476d184c733c427996379
186.
Huang, J.; Rauscher, S.; Nawrocki, G.; Ran, T.; Feig, M.; de Groot, B. L.; Grubmüller, H.; MacKerell, A. D., Jr. CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins Nat. Methods 2017, 14, 71– 73 DOI: 10.1038/nmeth.4067
[Crossref], [PubMed], [CAS]
186.
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Huang, Jing; Rauscher, Sarah; Nawrocki, Grzegorz; Ran, Ting; Feig, Michael; de Groot, Bert L.; Grubmuller, Helmut; MacKerell, Alexander D. Jr
Nature Methods (2017), 14 (1), 71-73CODEN: NMAEA3; ISSN:1548-7091. (Nature Publishing Group)
The all-atom additive CHARMM36 protein force field is widely used in mol. modeling and simulations. We present its refinement, CHARMM36m (http://mackerell.umaryland.edu/charmm_ff.shtml), with improved accuracy in generating polypeptide backbone conformational ensembles for intrinsically disordered peptides and proteins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvVSiu77I&md5=0aa151fbef2ee0b5e2cfb593c54330c2
187.
Best, R. B.; Zhu, X.; Shim, J.; Lopes, P.; Mittal, J.; Feig, M.; MacKerell, A. D., Jr Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles J. Chem. Theory Comput. 2012, 8, 3257– 3273 DOI: 10.1021/ct300400x
[ACS Full Text ], [CAS]
187.
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone .vphi., ψ and Side-Chain χ1 and χ2 Dihedral Angles
Best, Robert B.; Zhu, Xiao; Shim, Jihyun; Lopes, Pedro E. M.; Mittal, Jeetain; Feig, Michael; MacKerell, Alexander D.
Journal of Chemical Theory and Computation (2012), 8 (9), 3257-3273CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
While the quality of the current CHARMM22/CMAP additive force field for proteins has been demonstrated in a large no. of applications, limitations in the model with respect to the equil. between the sampling of helical and extended conformations in folding simulations have been noted. To overcome this, as well as make other improvements in the model, we present a combination of refinements that should result in enhanced accuracy in simulations of proteins. The common (non-Gly, -Pro) backbone CMAP potential has been refined against exptl. soln. NMR data for weakly structured peptides, resulting in a rebalancing of the energies of the α-helix and extended regions of the Ramachandran map, correcting the α-helical bias of CHARMM22/CMAP. The Gly and Pro CMAPs have been refitted to more accurate quantum-mech. energy surfaces. Side-chain torsion parameters have been optimized by fitting to backbone-dependent quantum-mech. energy surfaces, followed by addnl. empirical optimization targeting NMR scalar couplings for unfolded proteins. A comprehensive validation of the revised force field was then performed against a collection of exptl. data: (i) comparison of simulations of eight proteins in their crystal environments with crystal structures; (ii) comparison with backbone scalar couplings for weakly structured peptides; (iii) comparison with NMR residual dipolar couplings and scalar couplings for both backbone and side-chains in folded proteins; (iv) equil. folding of mini-proteins. The results indicate that the revised CHARMM 36 parameters represent an improved model for modeling and simulation studies of proteins, including studies of protein folding, assembly, and functionally relevant conformational changes.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtVKqurfP&md5=9a48a0c5770fb1e887c3bb34d45b1354
188.
Best, R. B.; Mittal, J.; Feig, M.; MacKerell, A. D. Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α-Helix and β-Hairpin Formation Biophys. J. 2012, 103, 1045– 1051 DOI: 10.1016/j.bpj.2012.07.042
[Crossref], [PubMed], [CAS]
188.
Inclusion of Many-Body Effects in the Additive CHARMM Protein CMAP Potential Results in Enhanced Cooperativity of α-Helix and β-Hairpin Formation
Best, Robert B.; Mittal, Jeetain; Feig, Michael; MacKerell, Alexander D.
Biophysical Journal (2012), 103 (5), 1045-1051CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
Folding simulations on peptides and proteins using empirical force fields have demonstrated the sensitivity of the results to details of the backbone potential. A recently revised version of the additive CHARMM protein force field, which includes optimization of the backbone CMAP potential to achieve good balance between different types of secondary structure, correcting the α-helical bias present in the former CHARMM22/CMAP energy function, is shown to result in improved cooperativity for the helix-coil transition. This is due to retention of the empirical corrections introduced in the original CMAP to reproduce folded protein structures-corrections that capture many-body effects missing from an energy surface fitted to gas phase calcns. on dipeptides. The exptl. temp. dependence of helix formation in (AAQAA)3 and parameters for helix nucleation and elongation are in much better agreement with expt. than those obtained with other recent force fields. In contrast, CMAP parameters derived by fitting to a vacuum quantum mech. surface for the alanine dipeptide do not reproduce the enhanced cooperativity, showing that the empirical backbone corrections, and not some other feature of the force field, are responsible. It is also found that the cooperativity of β-hairpin formation is much improved relative to other force fields studied. Comparison with (.vphi.,ψ) distributions from the Protein Data Bank further justifies the inclusion of many-body effects in the CMAP. These results suggest that the revised energy function will be suitable for both simulations of unfolded or intrinsically disordered proteins and for investigating protein-folding mechanisms.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtlWktr7P&md5=5e3d3b458670e34bdc0bafc3fc7bdeaa
189.
Harder, E.; Damm, W.; Maple, J.; Wu, C.; Reboul, M.; Xiang, J. Y.; Wang, L.; Lupyan, D.; Dahlgren, M. K.; Knight, J. L. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins J. Chem. Theory Comput. 2016, 12, 281– 296 DOI: 10.1021/acs.jctc.5b00864
[ACS Full Text ], [CAS]
189.
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins
Harder, Edward; Damm, Wolfgang; Maple, Jon; Wu, Chuanjie; Reboul, Mark; Xiang, Jin Yu; Wang, Lingle; Lupyan, Dmitry; Dahlgren, Markus K.; Knight, Jennifer L.; Kaus, Joseph W.; Cerutti, David S.; Krilov, Goran; Jorgensen, William L.; Abel, Robert; Friesner, Richard A.
Journal of Chemical Theory and Computation (2016), 12 (1), 281-296CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
The parametrization and validation of the OPLS3 force field for small mols. and proteins are reported. Enhancements with respect to the previous version (OPLS2.1) include the addn. of off-atom charge sites to represent halogen bonding and aryl nitrogen lone pairs as well as a complete refit of peptide dihedral parameters to better model the native structure of proteins. To adequately cover medicinal chem. space, OPLS3 employs over an order of magnitude more ref. data and assocd. parameter types relative to other commonly used small mol. force fields (e.g., MMFF and OPLS_2005). As a consequence, OPLS3 achieves a high level of accuracy across performance benchmarks that assess small mol. conformational propensities and solvation. The newly fitted peptide dihedrals lead to significant improvements in the representation of secondary structure elements in simulated peptides and native structure stability over a no. of proteins. Together, the improvements made to both the small mol. and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhvVCjtbfE&md5=42663f8cfa84b80a67132bbb13b9b7ce
190.
Margreitter, C.; Reif, M. M.; Oostenbrink, C. Update on Phosphate and Charged Post-Translationally Modified Amino Acid Parameters in the GROMOS Force Field J. Comput. Chem. 2017, 38, 714– 720 DOI: 10.1002/jcc.24733
[Crossref], [PubMed], [CAS]
190.
Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field
Margreitter, Christian; Reif, Maria M.; Oostenbrink, Chris
Journal of Computational Chemistry (2017), 38 (10), 714-720CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
In this study, we propose newly derived parameters for phosphate ions in the context of the GROMOS force field parameter sets. The non-bonded parameters used up to now lead to a hydration free energy, which renders the dihydrogen phosphate ion too hydrophobic when compared to exptl. derived values, making a reparametrization of the phosphate moiety necessary. Phosphate species are of great importance in biomol. simulations not only because of their crucial role in the backbone of nucleic acids but also as they represent one of the most important types of post-translational modifications to protein side-chains and are an integral part in many lipids. Our re-parametrization of the free dihydrogen phosphate (H2PO4-) and three derivs. (Me phosphate, di-Me phosphate, and Ph phosphate) leads, in conjunction with the previously updated charged side-chains in the GROMOS parameter set 54A8, to new nucleic acid backbone parameters and a 54A8 version of the widely used GROMOS protein post-translational modification parameter set.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhs1emtL8%253D&md5=1a38523b570278727b0a44a9c8fa5916
191.
Best, R. B.; Zheng, W.; Mittal, J. Balanced Protein-Water Interactions Improve Properties of Disorderd Proteins and Non-Specific Protein Association J. Chem. Theory Comput. 2014, 10, 5113– 5124 DOI: 10.1021/ct500569b
[ACS Full Text ], [CAS]
191.
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
Best, Robert B.; Zheng, Wenwei; Mittal, Jeetain
Journal of Chemical Theory and Computation (2014), 10 (11), 5113-5124CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Some frequently encountered deficiencies in all-atom mol. simulations, such as nonspecific protein-protein interactions being too strong, and unfolded or disordered states being too collapsed, suggest that proteins are insufficiently well solvated in simulations using current state-of-the-art force fields. To address these issues, we make the simplest possible change, by modifying the short-range protein-water pair interactions, and leaving all the water-water and protein-protein parameters unchanged. We find that a modest strengthening of protein-water interactions is sufficient to recover the correct dimensions of intrinsically disordered or unfolded proteins, as detd. by direct comparison with small-angle x-ray scattering (SAXS) and Forster resonance energy transfer (FRET) data. The modification also results in more realistic protein-protein affinities, and av. solvation free energies of model compds. which are more consistent with expt. Most importantly, we show that this scaling is small enough not to affect adversely the stability of the folded state, with only a modest effect on the stability of model peptides forming α-helix and β-sheet structures. The proposed adjustment opens the way to more accurate atomistic simulations of proteins, particularly for intrinsically disordered proteins, protein-protein assocn., and crowded cellular environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhslKktrrO&md5=415ef7c31ab1b11d8494e38ec559ca09
192.
Maier, J. A.; Martinez, C.; Kasavajhala, K.; Wickstrom, L.; Hauser, K. E.; Simmerling, C. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB J. Chem. Theory Comput. 2015, 11, 3696– 3713 DOI: 10.1021/acs.jctc.5b00255
[ACS Full Text ], [CAS]
192.
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
Maier, James A.; Martinez, Carmenza; Kasavajhala, Koushik; Wickstrom, Lauren; Hauser, Kevin E.; Simmerling, Carlos
Journal of Chemical Theory and Computation (2015), 11 (8), 3696-3713CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Mol. mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Av. errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a phys. motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reprodn. of NMR χ1 scalar coupling measurements for proteins in soln. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtFequ7rN&md5=7b803577b3b6912cc6750cfbd356596e
193.
Jung, J.; Mori, T.; Kobayashi, C.; Matsunaga, Y.; Yoda, T.; Feig, M.; Sugita, Y. GENESIS: A Hybrid-Parallel and Multi-Scale Molecular Dynamics Simulator with Enhanced Sampling Algorithms for Biomolecular and Cellular Simulations Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2015, 5, 310– 323 DOI: 10.1002/wcms.1220
[Crossref], [PubMed], [CAS]
193.
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji
Wiley Interdisciplinary Reviews: Computational Molecular Science (2015), 5 (4), 310-323CODEN: WIRCAH; ISSN:1759-0884. (Wiley-Blackwell)
GENESIS (Generalized-Ensemble Simulation System) is a new software package for mol. dynamics (MD) simulations of macromols. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an at. decompn. algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decompn. scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biol. systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decompn. space is shared in real-space and reciprocal-space calcns. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and mol. models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220 For further resources related to this article, please visit the . Conflict of interest: The authors have declared no conflicts of interest for this article.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXps12msbg%253D&md5=ee259553b1d0e6c12a7e1f009015d31a
194.
Jung, J.; Naurse, A.; Kobayashi, C.; Sugita, Y. Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations J. Chem. Theory Comput. 2016, 12, 4947– 4958 DOI: 10.1021/acs.jctc.6b00241
[ACS Full Text ], [CAS]
194.
Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations
Jung, Jaewoon; Naurse, Akira; Kobayashi, Chigusa; Sugita, Yuji
Journal of Chemical Theory and Computation (2016), 12 (10), 4947-4958CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Graphics processing unit (GPU) has become a popular computational platform for mol. dynamics (MD) simulations of biomols. A significant speedup in the simulations of small- or medium-size systems using only a few computer nodes with a single or multiple GPUs has been reported. Due to GPU memory limitation and slow communication between GPUs on different computer nodes, it is not straightforward to accelerate MD simulations of large biol. systems that contain a few million or more atoms on massively parallel supercomputers with GPUs. The authors develop a new scheme in their MD software, GENESIS, to reduce the total computational time on such computers. Computationally intensive real-space non-bonded interactions are computed mainly on GPUs in the scheme, while less intensive bonded interactions and communication-intensive reciprocal-space interactions were performed on CPUs. Based on the midpoint cell method as a domain decompn. scheme, the authors invent the single particle interaction list for reducing the GPU memory usage. Since total computational time is limited by the reciprocal-space computation, the authors use the RESPA multiple time-step integration and reduce the CPU resting time by assigning a subset of non-bonded interactions on CPUs as well as on GPUs when the reciprocal-space computation is skipped. The authors validated their GPU implementations in GENESIS on BPTI and a membrane protein, porin, by MD simulations and an alanine-tripeptide by REMD simulations. Benchmark calcns. on TSUBAME supercomputer showed that an MD simulation of a million atoms system was scalable up to 256 computer nodes with GPUs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhsFWqsbjK&md5=1018f5ac59110ab75a0d90dedb7cc01f
195.
Friedrichs, M. S.; Eastman, P.; Vaidyanathan, V.; Houston, M.; Legrand, S.; Beberg, A. L.; Ensign, D. L.; Bruns, C. M.; Pande, V. S. Accelerating Molecular Dynamic Simulation on Graphics Processing Units J. Comput. Chem. 2009, 30, 864– 872 DOI: 10.1002/jcc.21209
[Crossref], [PubMed], [CAS]
195.
Accelerating molecular dynamic simulation on graphics processing units
Friedrichs, Mark S.; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L.; Ensign, Daniel L.; Bruns, Christopher M.; Pande, Vijay S.
Journal of Computational Chemistry (2009), 30 (6), 864-872CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
The authors describe a complete implementation of all-atom protein mol. dynamics running entirely on a graphics processing unit (GPU), including all std. force field terms, integration, constraints, and implicit solvent. The authors discuss the design of their algorithms and important optimizations needed to fully take advantage of a GPU. The authors evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXjvFantro%253D&md5=9d8d059c70f7282951636c98bdd521b7
196.
Krieger, E.; Vriend, G. New Ways to Boost Molecular Dynamics Simulations J. Comput. Chem. 2015, 36, 996– 1007 DOI: 10.1002/jcc.23899
[Crossref], [PubMed], [CAS]
196.
New ways to boost molecular dynamics simulations
Krieger, Elmar; Vriend, Gert
Journal of Computational Chemistry (2015), 36 (13), 996-1007CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all-atom force field at 160 ns/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 Å cutoff, correct atom masses, reproducible trajectory, CPU with 3.6 GHz, no turbo boost, 8 AVX registers). The new features include a mixed multiple time-step algorithm (reaching 5 fs), a tuned version of LINCS to constrain bond angles, the fusion of pair list creation and force calcn., pressure coupling with a "densostat," and exploitation of new CPU instruction sets like AVX2. The impact of Intel's new transactional memory, at. instructions, and sloppy pair lists is also analyzed. The algorithms map well to GPUs and can automatically handle most Protein Data Bank (PDB) files including ligands. An implementation is available as part of the YASARA mol. modeling and simulation program.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXlsVOgsbo%253D&md5=5b3cd97c67fa308b9333d016cf31e0b7
197.
Abraham, M. J.; Murtola, T.; Schulz, R.; Páll, S.; Smith, J. C.; Hess, B.; Lindahl, E. GROMACS: High Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers SoftwareX 2015, 1–2, 19– 25 DOI: 10.1016/j.softx.2015.06.001
[Crossref]
There is no corresponding record for this reference.
198.
Salomon-Ferrer, R.; Götz, A. W.; Poole, D.; Le Grand, S.; Walker, R. C. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald J. Chem. Theory Comput. 2013, 9, 3878– 3888 DOI: 10.1021/ct400314y
[ACS Full Text ], [CAS]
198.
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
Salomon-Ferrer, Romelia; Gotz, Andreas W.; Poole, Duncan; Le Grand, Scott; Walker, Ross C.
Journal of Chemical Theory and Computation (2013), 9 (9), 3878-3888CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
We present an implementation of explicit solvent all atom classical mol. dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled GPUs. First released publicly in Apr. 2010 as part of version 11 of the AMBER MD package and further improved and optimized over the last two years, this implementation supports the three most widely used statistical mech. ensembles (NVE, NVT, and NPT), uses particle mesh Ewald (PME) for the long-range electrostatics, and runs entirely on CUDA-enabled NVIDIA graphics processing units (GPUs), providing results that are statistically indistinguishable from the traditional CPU version of the software and with performance that exceeds that achievable by the CPU version of AMBER software running on all conventional CPU-based clusters and supercomputers. We briefly discuss three different precision models developed specifically for this work (SPDP, SPFP, and DPDP) and highlight the tech. details of the approach as it extends beyond previously reported work [Goetz et al., J. Chem. Theory Comput.2012, DOI: 10.1021/ct200909j; Le Grand et al., Comp. Phys. Comm.2013, DOI: 10.1016/j.cpc.2012.09.022].We highlight the substantial improvements in performance that are seen over traditional CPU-only machines and provide validation of our implementation and precision models. We also provide evidence supporting our decision to deprecate the previously described fully single precision (SPSP) model from the latest release of the AMBER software package.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXht1arsrzP&md5=57e18d35e8b81e9a79788ef5af17d19f
199.
Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Eastwood, M. P.; Bank, J. A.; Jumper, J. M.; Salmon, J. K.; Shan, Y. B. Atomic-Level Characterization of the Structural Dynamics of Proteins Science 2010, 330, 341– 346 DOI: 10.1126/science.1187409
[Crossref], [PubMed], [CAS]
199.
Atomic-Level Characterization of the Structural Dynamics of Proteins
Shaw, David E.; Maragakis, Paul; Lindorff-Larsen, Kresten; Piana, Stefano; Dror, Ron O.; Eastwood, Michael P.; Bank, Joseph A.; Jumper, John M.; Salmon, John K.; Shan, Yibing; Wriggers, Willy
Science (Washington, DC, United States) (2010), 330 (6002), 341-346CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
Mol. dynamics (MD) simulations are widely used to study protein motions at an at. level of detail, but they have been limited to time scales shorter than those of many biol. crit. conformational changes. We examd. two fundamental processes in protein dynamics-protein folding and conformational change within the folded state-by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equil. simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; sep. simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-ms simulation of the folded protein BPTI reveals a small no. of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXht1OisL%252FN&md5=85c9d897881e8684fc39d69b2b6b2fad
200.
Abrams, C.; Bussi, G. Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration Entropy 2014, 16, 163– 199 DOI: 10.3390/e16010163
[Crossref], [CAS]
200.
Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration
Abrams, Cameron; Bussi, Giovanni
Entropy (2014), 16 (1), 163-199, 37 pp.CODEN: ENTRFG; ISSN:1099-4300. (MDPI AG)
We review a selection of methods for performing enhanced sampling in mol. dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodn. integration that use mean force biasing, including the adaptive biasing force algorithm and temp. acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We conclude with a brief presentation of some combination methods.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXptV2htbg%253D&md5=7e27e14ffdacdd6de1e89f512b0f96ce
201.
Torrie, G. M.; Valleau, J. P. Monte-Carlo Free-Energy Estimates using Non-Boltzmann Sampling - Application to Subcritical Lennard-Jones Fluid Chem. Phys. Lett. 1974, 28, 578– 581 DOI: 10.1016/0009-2614(74)80109-0
[Crossref], [CAS]
201.
Monte-Carlo free energy estimates using non-Boltzmann sampling. Application to the subcritical Lennard-Jones fluid
Torrie, Glenn M.; Valleau, John P.
Chemical Physics Letters (1974), 28 (4), 578-81CODEN: CHPLBC; ISSN:0009-2614.
A Monte Carlo technique is presented for estn. of the free energies of fluids by sampling on distributions designed for this purpose, rather than on the usual Boltzmann distribution. As an illustration of its use, the free energy of a Lennard-Jones fluid in the liq.-vapour coexistence region was estd. by relating it to that of the inverse-12 (soft sphere) fluid, which itself shows no condensation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaE2MXnslyjtQ%253D%253D&md5=4cdfeafc8c3bfc6bf08e50d8448b75f4
202.
Sugita, Y.; Okamoto, Y. Replica-Exchange Molecular Dynamics Method for Protein Folding Chem. Phys. Lett. 1999, 314, 141– 151 DOI: 10.1016/S0009-2614(99)01123-9
[Crossref], [CAS]
202.
Replica-exchange molecular dynamics method for protein folding
Sugita, Y.; Okamoto, Y.
Chemical Physics Letters (1999), 314 (1,2), 141-151CODEN: CHPLBC; ISSN:0009-2614. (Elsevier Science B.V.)
We have developed a formulation for mol. dynamics algorithm for the replica-exchange method. The effectiveness of the method for the protein-folding problem is tested with the penta-peptide Met-enkephalin. The method can overcome the multiple-min. problem by exchanging non-interacting replicas of the system at several temps. From only one simulation run, one can obtain probability distributions in canonical ensemble for a wide temp. range using multiple-histogram re-weighting techniques, which allows the calcn. of any thermodn. quantity as a function of temp. in that range.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1MXotVKrsLc%253D&md5=0fec0ff81ca7806c1e1ac29e5f50ce19
203.
Okamoto, Y. Generalized-Ensemble Algorithms: Enhanced Sampling Techniques for Monte Carlo and Molecular Dynamics Simulations J. Mol. Graphics Modell. 2004, 22, 425– 439 DOI: 10.1016/j.jmgm.2003.12.009
[Crossref], [PubMed], [CAS]
203.
Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations
Okamoto, Yuko
Journal of Molecular Graphics & Modelling (2004), 22 (5), 425-439CODEN: JMGMFI; ISSN:1093-3263. (Elsevier Science Inc.)
A review. In complex systems with many degrees of freedom such as spin glass and biomol. systems, conventional simulations in canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble performs a random walk in potential energy space and overcomes this difficulty. From only one simulation run, one can obtain canonical ensemble avs. of phys. quantities as functions of temp. by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review the generalized ensemble algorithms. Three well-known methods, namely, multicanonical algorithm (MUCA), simulated tempering (ST), and replica-exchange method (REM), are described first. Both Monte Carlo (MC) and mol. dynamics (MD) versions of the algorithms are given. We then present five new generalized-ensemble algorithms which are extensions of the above methods.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXjt1Shurs%253D&md5=9b42db9b7c7ac532c2d4ac2fea2ab574
204.
Micheletti, C.; Laio, A.; Parrinello, M. Reconstructing the Density of States by History-Dependent Metadynamics Phys. Rev. Lett. 2004, 92, 92 DOI: 10.1103/PhysRevLett.92.170601
[Crossref]
There is no corresponding record for this reference.
205.
Guo, Z.; Brooks, C. L., III Rapid Screening of Binding Affinities: Application of the λ-Dynamics Method to a Trypsin-Inhibitor System J. Am. Chem. Soc. 1998, 120, 1920– 1921 DOI: 10.1021/ja973418e
[ACS Full Text ], [CAS]
205.
Rapid screening of binding affinities: Application of the λ-dynamics method to a trypsin-inhibitor system
Guo, Zhuyan; Brooks, Charles L., III
Journal of the American Chemical Society (1998), 120 (8), 1920-1921CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
The rapid assessment of potential ligands as putative leads in the design of new therapeutics is a growing interest given the recent emergence of combinatorial approaches to compd. synthesis. A computational approach that rapidly evaluates the relative binding affinities of a set of ligands to a common protein receptor is a key component in such design. In this work, the λ-dynamics methodol. developed recently by Brooks and co-workers is used in a novel way to screen a set of benzamidine derivs. for their relative ability to bind to trypsin. The particular inhibitors studied are benzamidine, p-amino-benzamidine, p-methyl-benzamidine, and p-chlorobenzamidine. The method gives the correct ranking of binding affinities with <100 ps of simulation, even though the binding affinity between some of the inhibitors differs by ∼0.5 kcal/mol. The resulted are validated by comparison to conventional free energy perturbation (FEP) calcns.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXhsVeku7g%253D&md5=6af1b023f7187a6e6a96ab3c3f7348da
206.
Hamelberg, D.; Mongan, J.; McCammon, J. A. Accelerated Molecular Dynamics: A Promising and Efficient Simulation Method for Biomolecules J. Chem. Phys. 2004, 120, 11919– 11929 DOI: 10.1063/1.1755656
[Crossref], [PubMed], [CAS]
206.
Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules
Hamelberg, Donald; Mongan, John; McCammon, J. Andrew
Journal of Chemical Physics (2004), 120 (24), 11919-11929CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
Many interesting dynamic properties of biol. mols. cannot be simulated directly using mol. dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy min. with high free energy barriers for large nos. of computational steps. The dynamic evolution of many mol. systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated mol. dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in mol. dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy min. to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomols., samples the conformational space more efficiently than normal mol. dynamics simulations, and converges to the correct canonical distribution.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXkvVant7w%253D&md5=f7ee967e10493f27a944bed8cd17c640
207.
Cossins, B. P.; Jacobson, M. P.; Guallar, V. A New View of the Bacterial Cytosol Environment PLoS Comput. Biol. 2011, 7, e1002066 DOI: 10.1371/journal.pcbi.1002066
[Crossref], [PubMed], [CAS]
207.
A new view of the bacterial cytosol environment
Cossins, Benjamin P.; Jacobson, Matthew P.; Guallar, Victor
PLoS Computational Biology (2011), 7 (6), e1002066CODEN: PCBLBG; ISSN:1553-7358. (Public Library of Science)
The cytosol is the major environment in all bacterial cells. The true phys. and dynamical nature of the cytosol soln. is not fully understood and here a modeling approach is applied. Using recent and detailed data on metabolite concns., we have created a mol. mech. model of the prokaryotic cytosol environment of Escherichia coli, contg. proteins, metabolites and monat. ions. The authors use 200 ns mol. dynamics simulations to compute diffusion rates, the extent of contact between mols. and dielec. consts. Large metabolites spend ∼80% of their time in contact with other mols. while small metabolites vary with some only spending 20% of time in contact. Large non-covalently interacting metabolite structures mediated by hydrogen-bonds, ionic and π stacking interactions are common and often assoc. with proteins. Mg2+ ions were prominent in NIMS and almost absent free in soln. K+ is generally not involved in NIMSs and populates the solvent fairly uniformly, hence its important role as an osmolyte. In simulations contg. ubiquitin, to represent a protein component, metabolite diffusion was reduced owing to long lasting protein-metabolite interactions. Hence, it is likely that with larger proteins metabolites would diffuse even more slowly. The dielec. const. of these simulations was found to differ from that of pure water only through a large contribution from ubiquitin as metabolite and monat. ion effects cancel. These findings suggest regions of influence specific to particular proteins affecting metabolite diffusion and electrostatics. Also, some proteins may have a higher propensity for assocns. with metabolites owing to their larger electrostatic fields. Future studies may be able to accurately predict how binding interactions differ in the cytosol relative to dil. aq. soln.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXnslCns7c%253D&md5=4a32306a71dac9faa202499006c70931
208.
Spiga, E.; Abriata, L. A.; Piazza, F.; Dal Peraro, M. Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics J. Phys. Chem. B 2014, 118, 5310– 5321 DOI: 10.1021/jp4126705
[ACS Full Text ], [CAS]
208.
Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics
Spiga, Enrico; Abriata, Luciano A.; Piazza, Francesco; Dal Peraro, Matteo
Journal of Physical Chemistry B (2014), 118 (20), 5310-5321CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
We present herein a thorough description of the effects of high glucose concns. on the diffusion, hydration and internal dynamics of ubiquitin, as predicted from extensive mol. dynamics simulations on several systems described at fully atomistic level. We observe that the protein acts as a seed that speeds up the natural propensity of glucose to cluster at high concn.; the sugar mols. thus aggregate around the protein trapping it inside a dynamic cage. This process extensively dehydrates the protein surface, restricts the motions of the remaining water mols., and drags the large-scale, collective motions of protein atoms slowing down the rate of exploration of the conformational space despite only a slight dampening of fast, local dynamics. We discuss how these effects could be relevant to the function of sugars as preservation agents in biol. materials, and how crowding by small sticky mols. could modulate proteins across different reaction coordinates inside the cellular cytosol.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXmvFCjt74%253D&md5=913ec5f55758c7a1e10d20469588abe9
209.
Zhou, H.-X. Influences of Crowded Cellular Environments on Protein Folding, Binding, and Oligomerization: Biological Consequences and Potentials of Atomistic Modeling FEBS Lett. 2013, 587, 1053– 1061 DOI: 10.1016/j.febslet.2013.01.064
[Crossref], [PubMed], [CAS]
209.
Influence of crowded cellular environments on protein folding, binding, and oligomerization: Biological consequences and potentials of atomistic modeling
Zhou, Huan-Xiang
FEBS Letters (2013), 587 (8), 1053-1061CODEN: FEBLAL; ISSN:0014-5793. (Elsevier B.V.)
A review. Recent expts. inside cells and in cytomimetic conditions have demonstrated that the crowded environments found therein can significantly reshape the energy landscapes of individual protein mols. and their oligomers. The resulting shifts in populations of conformational and oligomeric states have numerous biol. consequences, e.g., concerning the efficiency of replication and transcription, the development of aggregation-related diseases, and the efficacy of small-mol. drugs. Some of the effects of crowding can be anticipated from hard-particle theor. models, but the in vitro and in vivo measurements indicate that these effects are often subtle and complex. These observations, coupled with recent computational studies at the atomistic level, suggest that the latter detailed modeling may be required to yield a quant. understanding on the influence of crowded cellular environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXislyqtb4%253D&md5=7bda3b264918f7cd30511dcd28ba95c5
210.
Qin, S.; Zhou, H.-X. Further Development of the FFT-based Method for Atomistic Modeling of Protein Folding and Binding under Crowding: Optimization of Accuracy and Speed J. Chem. Theory Comput. 2014, 10, 2824– 2835 DOI: 10.1021/ct5001878
[ACS Full Text ], [CAS]
210.
Further Development of the FFT-based Method for Atomistic Modeling of Protein Folding and Binding under Crowding: Optimization of Accuracy and Speed
Qin, Sanbo; Zhou, Huan-Xiang
Journal of Chemical Theory and Computation (2014), 10 (7), 2824-2835CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Recently, the authors (Qin, S.; Zhou, H. X., J. Chem. Theory Comput.2013, 9, 4633-4643) developed the FFT-based method for Modeling Atomistic Proteins-crowder interactions, henceforth FMAP. Given its potential wide use for calcg. effects of crowding on protein folding and binding free energies, here the authors aimed to optimize the accuracy and speed of FMAP. FMAP is based on expressing protein-crowder interactions as correlation functions and evaluating the latter via fast Fourier transform (FFT). The numerical accuracy of FFT improves as the grid spacing for discretizing space is reduced, but at increasing computational cost. The authors sought to speed up FMAP calcns. by using a relatively coarse grid spacing of 0.6 Å and then correcting for discretization errors. This strategy was tested for different types of interactions (hard-core repulsion, nonpolar attraction, and electrostatic interaction) and over a wide range of protein-crowder systems. The authors were able to correct for the numerical errors on hard-core repulsion and nonpolar attraction by an 8% inflation of at. hard-core radii and on electrostatic interaction by a 5% inflation of the magnitudes of protein at. charges. The cor. results have higher accuracy and enjoy a speedup of >100-fold over those obtained using a fine grid spacing of 0.15 Å. With this optimization of accuracy and speed, FMAP may become a practical tool for realistic modeling of protein folding and binding in cell-like environments.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXnsVegs74%253D&md5=e29937e8e898fab53abcae23ca5015d4
211.
Qin, S.; Zhou, H.-X. Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding and Binding Stability Biophys. J. 2009, 97, 12– 19 DOI: 10.1016/j.bpj.2009.03.066
[Crossref], [PubMed], [CAS]
211.
Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability
Qin, Sanbo; Zhou, Huan-Xiang
Biophysical Journal (2009), 97 (1), 12-19CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
Theor. models predict that macromol. crowding can increase protein folding stability, but depending on details of the models (e.g., how the denatured state is represented), the level of stabilization predicted can be very different. In this study, we represented the native and denatured states atomistically, with conformations sampled from explicit-solvent mol. dynamics simulations at room temp. and high temp., resp. We then designed an efficient algorithm to calc. the allowed fraction, f, when the protein mol. is placed inside a box of crowders. That a fraction of placements of the protein mol. is disallowed because of vol. exclusion by the crowders to an increase in chem. potential, given by Δμ = -kBT Inf. The difference in Δμ between the native and denatured states predicts the effect of crowding on the folding free energy. Even when the crowders occupied 35% of the soln. vol., the stabilization reached only 1.5 kcal/mol for cytochrome b562. The modest stabilization predicted is consistent with exptl. studies. Interestingly, a mixt. of different sized crowders was found to exert a greater effect than the sum of the individual species of crowders. The stabilization of crowding on the binding stability of bamase and barstar, based on atomistic modeling of the proteins, was similarly modest. These findings have profound implications for macromol. crowding inside cells.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXpsFOmt70%253D&md5=d858d5606abb61416c97d45d34482707
212.
Drake, J. A.; Pettitt, B. M. Force Field-Dependent Solution Properties of Glycine Oligomers J. Comput. Chem. 2015, 36, 1275– 1285 DOI: 10.1002/jcc.23934
[Crossref], [PubMed], [CAS]
212.
Force field-dependent solution properties of glycine oligomers
Drake, Justin A.; Pettitt, B. Montgomery
Journal of Computational Chemistry (2015), 36 (17), 1275-1285CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
Mol. simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodn. mechanisms that govern their function. As the no. of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in soln. To this end, we performed a comparative structural anal. of Gly3 and Gly10 in aq. soln. from all atom, microsecond mol. dynamics (MD) simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly3 and Gly10 were simulated for at least 300 ns and 1 μs, resp. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g., end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in soln. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. © 2015 Wiley Periodicals, Inc.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXnvFSqs7g%253D&md5=d0629ad0346c5ff212cec15d7a6ce7f8
213.
Kuroda, Y.; Suenaga, A.; Sato, Y.; Kosuda, S.; Taiji, M. All-Atom Molecular Dynamics Analysis of Multi-Peptide Systems Reproduces Peptide Solubility In Line with Experimental Observations Sci. Rep. 2016, 6, 19479 DOI: 10.1038/srep19479
[Crossref], [PubMed], [CAS]
213.
All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations
Kuroda, Yutaka; Suenaga, Atsushi; Sato, Yuji; Kosuda, Satoshi; Taiji, Makoto
Scientific Reports (2016), 6 (), 19479CODEN: SRCEC3; ISSN:2045-2322. (Nature Publishing Group)
In order to investigate the contribution of individual amino acids to protein and peptide soly., we carried out 100 ns mol. dynamics (MD) simulations of 106 Å3 cubic boxes contg. ∼3 × 104 water mols. and 27 tetra-peptides regularly positioned at 23 Å from each other and composed of a single amino acid type for all natural amino acids but cysteine and glycine. The calcns. were performed using Amber with a std. force field on a special purpose MDGRAPE-3 computer, without introducing any "artificial" hydrophobic interactions. Tetra-peptides composed of I, V, L, M, N, Q, F, W, Y, and H formed large amorphous clusters, and those contg. A, P, S, and T formed smaller ones. Tetra-peptides made of D, E, K, and R did not cluster at all. These observations correlated well with exptl. soly. tendencies as well as hydrophobicity scales with correlation coeffs. of 0.5 to > 0.9. Repulsive Coulomb interactions were dominant in ensuring high soly., whereas both Coulomb and van der Waals (vdW) energies contributed to the aggregations of low soly. amino acids. Overall, this very first all-atom mol. dynamics simulation of a multi-peptide system appears to reproduce the basic properties of peptide soly., essentially in line with exptl. observations.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhslOgtr8%253D&md5=9519f4569d07cdbeb2298f88f6d9cdf7
214.
Feig, M.; Harada, R.; Mori, T.; Yu, I.; Takahashi, K.; Sugita, Y. Complete Atomistic Model of a Bacterial Cytoplasm Integrates Physics, Biochemistry, and Systems Biology J. Mol. Graphics Modell. 2015, 58, 1– 9 DOI: 10.1016/j.jmgm.2015.02.004
[Crossref], [PubMed], [CAS]
214.
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology
Feig, Michael; Harada, Ryuhei; Mori, Takaharu; Yu, Isseki; Takahashi, Koichi; Sugita, Yuji
Journal of Molecular Graphics & Modelling (2015), 58 (), 1-9CODEN: JMGMFI; ISSN:1093-3263. (Elsevier Ltd.)
A model for the cytoplasm of Mycoplasma genitalium is presented that integrates data from a variety of sources into a phys. and biochem. consistent model. Based on gene annotations, core genes expected to be present in the cytoplasm were detd. and a metabolic reaction network was reconstructed. The set of cytoplasmic genes and metabolites from the predicted reactions were assembled into a comprehensive atomistic model consisting of proteins with predicted structures, RNA, protein/RNA complexes, metabolites, ions, and solvent. The resulting model bridges between atomistic and cellular scales, between phys. and biochem. aspects, and between structural and systems views of cellular systems and is meant as a starting point for a variety of simulation studies.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXjvVGgsbs%253D&md5=010a6dcb260ada5d23df6fe05343e8bf
215.
Kurniawan, N. A.; Enemark, S.; Rajagopalan, R. Crowding Alters the Folding Kinetics of a β-Hairpin by Modulating the Stability of Intermediates J. Am. Chem. Soc. 2012, 134, 10200– 10208 DOI: 10.1021/ja302943m
[ACS Full Text ], [CAS]
215.
Crowding Alters the Folding Kinetics of a β-Hairpin by Modulating the Stability of Intermediates
Kurniawan, Nicholas A.; Enemark, Soeren; Rajagopalan, Raj
Journal of the American Chemical Society (2012), 134 (24), 10200-10208CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
Crowded environments inside cells exert significant effects on protein structure, stability, and function, but their effects on (pre)folding dynamics and kinetics, esp. at mol. levels, remain ill-understood. Here, we examine the latter for, as an initial candidate, a small de novo β-hairpin using extensive all-atom mol. dynamics simulations for crowder vol. fractions .vphi. up to 40%. We find that crowding does not introduce new folding intermediates or misfolded structures, although, as expected, it promotes compact structures and reduces the accessible conformational space. Furthermore, while hydrophobic-collapse-mediated folding is slightly enhanced, the turn-directed zipper mechanism (dominant in crowder-free situations) increases many-fold, becoming even more dominant. Interestingly, .vphi. influences the stability of the folding intermediates (FI1 and FI2) in an apparently counterintuitive manner, which can be understood only by considering specific intrachain interactions and intermediate (and hierarchical) structural transitions. For .vphi. values <20%, native-turn formation is enhanced, and FI1, characterized by a hairpin structure but slightly mismatched hydrophobic contacts, increases in frequency, thus enhancing eventual folding. However, higher .vphi. values impede native-turn formation, and FI2, which lacks native turns, re-emerges and increasingly acts as a kinetic trap. The change in the stability of these intermediates with .vphi. strongly correlates with the hierarchical folding stages and their kinetics. The results show that crowding assists intermediate structural changes more by impeding backward transitions than by promoting forward transitions and that a delicate competition between redn. in configuration space and introduction of kinetic traps along the folding route is key to understanding folding kinetics under crowded conditions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XnslGru7g%253D&md5=30d111229b87a32bde41641a8f741b63
216.
Carballo-Pacheco, M.; Strodel, B. Advances in the Simulation of Protein Aggregation at the Atomistic Scale J. Phys. Chem. B 2016, 120, 2991– 2999 DOI: 10.1021/acs.jpcb.6b00059
[ACS Full Text ], [CAS]
216.
Advances in the Simulation of Protein Aggregation at the Atomistic Scale
Carballo-Pacheco, Martin; Strodel, Birgit
Journal of Physical Chemistry B (2016), 120 (12), 2991-2999CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
Protein aggregation into highly structured amyloid fibrils is assocd. with various diseases including Alzheimer's disease, Parkinson's disease, and type II diabetes. Amyloids can also have normal biol. functions and, in the future, could be used as the basis for novel nanoscale materials. However, a full understanding of the physicochem. forces that drive protein aggregation is still lacking. Such understanding is crucial for the development of drugs that can effectively inhibit aberrant amyloid aggregation and for the directed design of functional amyloids. Atomistic simulations can help understand protein aggregation. In particular, atomistic simulations can be used to study the initial formation of toxic oligomers which are hard to characterize exptl. and to understand the difference in aggregation behavior between different amyloidogenic peptides. Here, we review the latest atomistic simulations of protein aggregation, concg. on amyloidogenic protein fragments, and provide an outlook for the future in this field.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XjvFyku7s%253D&md5=1fff9267bd13969d4df66f16478ab7d7
217.
Maffeo, C.; Luan, B.; Aksimentiev, A. End-To-End Attraction of Duplex DNA Nucleic Acids Res. 2012, 40, 3812– 3821 DOI: 10.1093/nar/gkr1220
[Crossref], [PubMed], [CAS]
217.
End-to-end attraction of duplex DNA
Maffeo, Christopher; Luan, Binquan; Aksimentiev, Aleksei
Nucleic Acids Research (2012), 40 (9), 3812-3821CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)
Recent expts. have demonstrated spontaneous end-to-end assocn. of short duplex DNA fragments into long rod-like structures. By means of extensive all-atom mol. dynamic simulations, we characterized end-to-end interactions of duplex DNA, quant. describing the forces, free energy and kinetics of the end-to-end assocn. process. We found short DNA duplexes to spontaneously aggregate end-to-end when axially aligned in a small vol. of monovalent electrolyte. It was obsd. that electrostatic repulsion of 5'-phosphoryl groups promoted the formation of aggregates in a conformation similar to the B-form DNA double helix. Application of an external force revealed that rupture of the end-to-end assembly occurs by the shearing of the terminal base pairs. The std. binding free energy and the kinetic rates of end-to-end assocn. and dissocn. processes were estd. using two complementary methods: umbrella sampling simulations of two DNA fragments and direct observation of the aggregation process in a system contg. 458 DNA fragments. We found the end-to-end force to be short range, attractive, hydrophobic and only weakly dependent on the ion concn. The relation between the stacking free energy and end-to-end attraction is discussed as well as possible roles of the end-to-end interaction in biol. and nanotechnol. systems.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XmvF2mtL0%253D&md5=640a1832a505439bc63d0927313f2b5c
218.
Hajnic, M.; Osorio, J. I.; Zagrovic, B. Interaction Preferences between Nucleobase Mimetics and Amino Acids in Aqueous Solutions Phys. Chem. Chem. Phys. 2015, 17, 21414– 21422 DOI: 10.1039/C5CP01486G
[Crossref], [PubMed], [CAS]
218.
Interaction preferences between nucleobase mimetics and amino acids in aqueous solutions
Hajnic, Matea; Osorio, Juan I.; Zagrovic, Bojan
Physical Chemistry Chemical Physics (2015), 17 (33), 21414-21422CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
Despite the paramount importance of protein-nucleic acid interactions in different cellular processes, our understanding of such interactions at the atomistic level remains incomplete. We have used mol. dynamics (MD) simulations and 15 μs of sampling time to study the behavior of amino acids and amino acid sidechain analogs in aq. solns. of different mimetics of naturally occurring nucleobases, including dimethylpyridine (DMP) and unsubstituted purine and pyrimidine rings. By using structural and energetic anal., we have derived preference scales for the interaction of amino acids and their sidechain analogs with different nucleobase mimetics and have exhaustively compared them with each other. A close correspondence with a std. hydrophobicity measure in the case of the pyrimidine mimetic DMP and purines suggests that the hydrophobic effect is the main defining factor behind such interactions. We analyze our findings in the context of the origin of the genetic code and the recently proposed cognate mRNA-protein complementarity hypothesis. Most importantly, we show that unsubstituted purine and pyrimidine rings alone cannot differentiate between predominantly purine- and pyrimidine-coded amino acids, suggesting that for such specificity to exist, it must primarily reside in ring substituents.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtF2mtLvP&md5=f07b836261a35e8186765d1e325a713f
219.
Hajnic, M.; Osorio, J. I.; Zagrovic, B. Computational Analysis of Amino Acids and their Sidechain Analogs in Crowded Solutions of RNA Nucleobases with Implications for the mRNA–Protein Complementarity Hypothesis Nucleic Acids Res. 2014, 42, 12984– 12994 DOI: 10.1093/nar/gku1035
[Crossref], [PubMed], [CAS]
219.
Computational analysis of amino acids and their sidechain analogs in crowded solutions of RNA nucleobases with implications for the mRNA-protein complementarity hypothesis
Hajnic, Matea; Osorio, Juan Iregui; Zagrovic, Bojan
Nucleic Acids Research (2014), 42 (21), 12984-12994CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)
Many crit. processes in the cell involve direct binding between RNAs and proteins, making it imperative to fully understand the physicochem. principles behind such interactions at the atomistic level. Here, we use mol. dynamics simulations and 15 μs of sampling to study the behavior of amino acids and amino acid sidechain analogs in high-concn. aq. solns. of std. RNA nucleobases. Structural and energetic anal. of simulated systems allows us to derive interaction propensity scales for different amino acid/nucleobase combinations. The derived scales closely match and greatly extend the available exptl. data, providing a comprehensive foundation for studying RNA-protein interactions in different contexts. By using these scales, we demonstrate a statistically significant connection between nucleobase compn. of human mRNA coding sequences and nucleobase interaction propensities of their cognate protein sequences. For example, pyrimidine d. profiles of mRNAs match uracil propensity profiles of their cognate proteins with a median Pearson correlation coeff. of R = -0.70. Our results provide support for the recently proposed hypotheses that mRNAs and their cognate proteins may be physicochem. complementary to each other and bind, esp. if unstructured, with the complementarity level being neg. influenced by mRNA adenine content. Finally, we utilize the derived scales to refine the complementarity hypothesis and closely examine its physicochem. underpinnings.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtVCrtb7I&md5=92f57157ac25acc1a1307438a5ac6744
220.
Palazzesi, F.; Prakash, M. K.; Bonomi, M.; Barducci, A. Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States J. Chem. Theory Comput. 2015, 11, 2– 7 DOI: 10.1021/ct500718s
[ACS Full Text ], [CAS]
220.
Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States
Palazzesi, Ferruccio; Prakash, Meher K.; Bonomi, Massimiliano; Barducci, Alessandro
Journal of Chemical Theory and Computation (2015), 11 (1), 2-7CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Mol. Dynamics (MD) plays a fundamental role in characterizing protein disordered states that are emerging as crucial actors in many biol. processes. Here the authors assess the accuracy of three current force-fields in modeling disordered peptides by combining enhanced-sampling MD simulations with NMR data. These force-fields generate significantly different conformational ensembles, and AMBER03w provides the best agreement with expts., which is further improved by adding the ILDN corrections.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXitFeit7bO&md5=997c50dda2779cd92286484bd4d3b951
221.
Henriques, J.; Cragnell, C.; Skepö, M. Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment J. Chem. Theory Comput. 2015, 11, 3420– 3431 DOI: 10.1021/ct501178z
[ACS Full Text ], [CAS]
221.
Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment
Henriques, Joao; Cragnell, Carolina; Skepoe, Marie
Journal of Chemical Theory and Computation (2015), 11 (7), 3420-3431CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
An increasing no. of studies using mol. dynamics (MD) simulations of unfolded and intrinsically disordered proteins (IDPs) suggest that current force fields sample conformations that are overly collapsed. Here, we study the applicability of several state-of-the-art MD force fields, of the AMBER and GROMOS variety, for the simulation of Histatin 5, a short (24 residues) cationic salivary IDP with antimicrobial and antifungal properties. The quality of the simulations is assessed in three complementary analyses: (i) protein shape and size comparison with recent exptl. small-angle X-ray scattering data; (ii) secondary structure prediction; (iii) energy landscape exploration and conformational class anal. Our results show that, indeed, std. force fields sample conformations that are too compact, being systematically unable to reproduce exptl. evidence such as the scattering function, the shape of the protein as compared with the Kratky plot, and intrapeptide distances obtained through the pair distance distribution function, p(r). The consistency of this deviation suggests that the problem is not mainly due to protein-protein or water-water interactions, whose parametrization varies the most between force fields and water models. In fact, as originally proposed in [Best et al. J. Chem. Theory Comput. 2014, 10, 5113-5124.], balanced protein-water interactions may be the key to solving this problem. Our simulations using this approach produce results in very good agreement with expt.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtVakur7E&md5=0a48d58b55bbef2cfcfad189a05aa117
222.
Rauscher, S.; Gapsys, V.; Gajda, M. J.; Zweckstetter, M.; de Groot, B. L.; Grubmüller, H. Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment J. Chem. Theory Comput. 2015, 11, 5513– 5524 DOI: 10.1021/acs.jctc.5b00736
[ACS Full Text ], [CAS]
222.
Structural ensembles of intrinsically disordered proteins depend strongly on force field: A comparison to experiment
Rauscher, Sarah; Gapsys, Vytautas; Gajda, Michal J.; Zweckstetter, Markus; de Groot, Bert L.; Grubmueller, Helmut
Journal of Chemical Theory and Computation (2015), 11 (11), 5513-5524CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
Intrinsically disordered proteins (IDPs) are notoriously challenging to study both exptl. and computationally. The structure of IDPs cannot be described by a single conformation but must instead be described as an ensemble of interconverting conformations. Atomistic simulations are increasingly used to obtain such IDP conformational ensembles. Here, the authors compared the IDP ensembles generated by 8 all-atom empirical force fields against primary SAXS and NMR data. Ensembles obtained with different force fields exhibited marked differences in chain dimensions, H-bonding, and secondary structure content. These differences were unexpectedly large: changing the force field was found to have a stronger effect on secondary structure content than changing the entire peptide sequence. The CHARMM 22* ensemble performed best in this force field comparison: it had the lowest error in chem. shifts and J-couplings and agreed well with the SAXS data. A high population of left-handed α-helix was present in the CHARMM 36 ensemble, which was inconsistent with measured scalar couplings. To eliminate inadequate sampling as a reason for differences between force fields, extensive simulations were carried out (0.964 ms in total); the remaining small sampling uncertainty was shown to be much smaller than the obsd. differences. The findings highlighted how IDPs, with their rugged energy landscapes, are highly sensitive test systems that are capable of revealing force field deficiencies and, therefore, contributing to force field development.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhs1ChsbvM&md5=0c38ce869b7b2bb569f59f9a77c19bed
223.
Cho, S. S.; Reddy, G.; Straub, J. E.; Thirumalai, D. Entropic Stabilization of Proteins by TMAO J. Phys. Chem. B 2011, 115, 13401– 13407 DOI: 10.1021/jp207289b
[ACS Full Text ], [CAS]
223.
Entropic Stabilization of Proteins by TMAO
Cho, Samuel S.; Reddy, Govardhan; Straub, John E.; Thirumalai, D.
Journal of Physical Chemistry B (2011), 115 (45), 13401-13407CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
The osmolyte trimethylamine N-oxide (TMAO) accumulates in the cell in response to osmotic stress and increases the thermodn. stability of folded proteins. To understand the mechanism of TMAO induced stabilization of folded protein states, we systematically investigated the action of TMAO on several model dipeptides (leucine, L2, serine, S2, glutamine, Q2, lysine, K2, and glycine, G2) in order to elucidate the effect of residue-specific TMAO interactions on small fragments of solvent-exposed conformations of the denatured states of proteins. We find that TMAO preferentially hydrogen bonds with the exposed dipeptide backbone but generally not with nonpolar or polar side chains. However, interactions with the pos. charged Lys are substantially greater than with the backbone. The dipeptide G2 is a useful model of the pure amide backbone; interacts with TMAO by forming a hydrogen bond between the amide nitrogen and the oxygen in TMAO. In contrast, TMAO is depleted from the protein backbone in the hexapeptide G6, which shows that the length of the polypeptide chain is relevant in aq. TMAO solns. These simulations lead to the hypothesis that TMAO-induced stabilization of proteins and peptides is a consequence of depletion of the solute from the protein surface provided intramol. interactions are more favorable than those between TMAO and the backbone. To test our hypothesis, we performed addnl. simulations of the action of TMAO on an intrinsically disordered Aβ16-22 (KLVFFAE) monomer. In the absence of TMAO, Aβ16-22 is a disordered random coil. However, in aq. TMAO soln., Aβ16-22 monomer samples compact conformations. A transition from random coil to α-helical secondary structure is obsd. at high TMAO concns. The coil to α-helix transition is highly cooperative esp. considering the small no. of residues in Aβ16-22. Our work highlights the potential similarities between the action of TMAO on long polypeptide chains and entropic stabilization of proteins in a crowded environment due to excluded vol. interactions. In this sense, the chem. chaperone TMAO is a nanocrowding particle.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXht12jsrvF&md5=cff0d37c05c2830121feb667bf3fecad
224.
Auton, M.; Bolen, D. W.; Rosgen, J. Structural Thermodynamics of Protein Preferential Solvation: Osmolyte Solvation of Proteins, Aminoacids, and Peptides Proteins: Struct., Funct., Genet. 2008, 73, 802– 813 DOI: 10.1002/prot.22103
[Crossref], [PubMed], [CAS]
224.
Structural thermodynamics of protein preferential solvation: osmolyte solvation of proteins, aminoacids, and peptides
Auton, Matthew; Bolen, D. Wayne; Rosgen, Jorg
Proteins: Structure, Function, and Bioinformatics (2008), 73 (4), 802-813CODEN: PSFBAF ISSN:. (Wiley-Liss, Inc.)
Protein stability and soly. depend strongly on the presence of osmolytes, because of the protein preference to be solvated by either water or osmolyte. It has traditionally been assumed that only this relative preference can be measured, and that the individual solvation contributions of water and osmolyte are inaccessible. However, it is possible to det. hydration and osmolyte solvation (osmolation) sep. using Kirkwood-Buff theory, and this fact has recently been utilized by several researchers. Here, we provide a thermodn. assessment of how each surface group on proteins contributes to the overall hydration and osmolation. Our anal. is based on transfer free energy measurements with model-compds. that were previously demonstrated to allow for a very successful prediction of osmolyte-dependent protein stability. When combined with Kirkwood-Buff theory, the Transfer Model provides a space-resolved solvation pattern of the peptide unit, amino acids, and the folding/unfolding equil. of proteins in the presence of osmolytes. We find that the major solvation effects on protein side-chains originate from the osmolytes, and that the hydration mostly depends on the size of the side-chain. The peptide backbone unit displays a much more variable hydration in the different osmolyte solns. Interestingly, the presence of sucrose leads to simultaneous accumulation of both the sugar and water in the vicinity of peptide groups, resulting from a saccharide accumulation that is less than the accumulation of water, a net preferential exclusion. Only the denaturing osmolyte, urea, obeys the classical solvent exchange mechanism in which the preferential interaction with the peptide unit excludes water.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhsVCls7jN&md5=1b2fbb0c4ce76d12e490d8412e442f69
225.
Record, M. T.; Anderson, C. F. Interpretation of Preferential Interaction Coefficients of Nonelectrolytes and of Electrolyte Ions in Terms of a Two-Domain Model Biophys. J. 1995, 68, 786– 794 DOI: 10.1016/S0006-3495(95)80254-7
[Crossref], [PubMed], [CAS]
225.
Interpretation of preferential interaction coefficients of nonelectrolytes and of electrolyte ions in terms of a two-domain model
Record, M. Thomas, Jr.; Anderson, Charles F.
Biophysical Journal (1995), 68 (3), 786-94CODEN: BIOJAU; ISSN:0006-3495. (Biophysical Society)
For a three-component system consisting of solvent (1), polymer of polyelectrolyte (2J), and a nonelectrolyte or electrolyte solute (3), a two-domain description is developed to describe thermodn. effects of interactions between solute components (2J) and (3). Equil. dialysis, which for an electrolyte solute produces the Donnan distribution of ions across a semipermeable membrane, provides a fundamental basis for this two-domain description whose applicability is not restricted, however, to systems where dialysis equil. is established. Explicit expressions are obtained for the solute-polymer preferential interaction coeff. Γ3.2J (nonelectrolyte case) and for Γ+,2J and Γ-,2J, which are corresponding coeffs. defined Γ+,2J = |ZJ| + Γ-,2J = 0.5(|ZJ| + B-,2J + B+,2J) - B1,2Jm3/m1. Here B+,2J, B-,2J, and B1,2J are defined per mol of species J, resp., as the no. of moles of cation, anion, and water included within the local domains that surround isolated mols. of J; ZJ is the charge on J; m3 is the molal concn. of uniunivalent electrolyte, and m1 = 55.5 mol/kg for water. Incorporating this result into a general thermodn. description (derived by us elsewhere) of the effects of the activity a± of excess uniunivalent salt on an equil. involving two or more charged species J (each of which is dil. in comparison with the salt) yields: SaKobs = d ln kobs/d ln a± = Δ(Γ+,2J + Γ-,2J) = Δ(B+,2J + B-,2J - 2B1,2Jm3/m1) where Kobs is an equil. quotient defined in terms of the molar concns. of the participants, J, and Δ denotes a stoichiometrically weighted combination of terms pertaining to the reactant(s) product(s). The derivation presented here does not depend on any particular mol. model for salt-polyelectrolyte (or solute-polymer) interactions; it therefore generalizes our earlier (1978) derivation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2MXjvFChtLY%253D&md5=80ae24e73b115e2bf35bc8dd122868ab
226.
Canchi, D. R.; García, A. E. Cosolvent Effects on Protein Stability Annu. Rev. Phys. Chem. 2013, 64, 273– 293 DOI: 10.1146/annurev-physchem-040412-110156
[Crossref], [PubMed], [CAS]
226.
Cosolvent effects on protein stability
Canchi, Deepak R.; Garcia, Angel E.
Annual Review of Physical Chemistry (2013), 64 (), 273-293CODEN: ARPLAP; ISSN:0066-426X. (Annual Reviews Inc.)
A review. Proteins are marginally stable, and the folding/unfolding equil. of proteins in aq. soln. can easily be altered by the addn. of small org. mols. known as cosolvents. Cosolvents that shift the equil. toward the unfolded ensemble are termed denaturants, whereas those that favor the folded ensemble are known as protecting osmolytes. Urea is a widely used denaturant in protein folding studies, and the mol. mechanism of its action has been vigorously debated in the literature. Here we review recent exptl. as well as computational studies that show an emerging consensus in this problem. Urea has been shown to denature proteins through a direct mechanism, by interacting favorably with the peptide backbone as well as the amino acid side chains. In contrast, the mol. mechanism by which the naturally occurring protecting osmolyte trimethylamine N-oxide (TMAO) stabilizes proteins is not clear. Recent studies have established the strong interaction of TMAO with water. Detailed mol. simulations, when used with force fields that incorporate these interactions, can provide insight into this problem. We present the development of a model for TMAO that is consistent with exptl. observations and that provides phys. insight into the role of cosolvent-cosolvent interaction in detg. its preferential interaction with proteins.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXntVCrsro%253D&md5=36cabc8dfbcc8547d82166a2b45956e8
227.
Arakawa, T.; Timasheff, S. N. The Stabilization of Proteins by Osmolytes Biophys. J. 1985, 47, 411– 414 DOI: 10.1016/S0006-3495(85)83932-1
[Crossref], [PubMed], [CAS]
227.
The stabilization of proteins by osmolytes
Arakawa, T.; Timasheff, S. N.
Biophysical Journal (1985), 47 (3), 411-14CODEN: BIOJAU; ISSN:0006-3495.
The preferential interactions of lysozyme with solvent components and the effects of solvent additives on its stability were examd. for several neutral osmolytes: L-proline, L-serine, γ-aminobutyric acid, sarcosine, taurine, α-alanine, β-alanine, glycine, betaine, and trimethylamine N-oxide. All of these substances stabilized the protein structure against thermal denaturation and (except for trimethylamine N-oxide, for which interaction measurements could not be made) were strongly excluded from the protein domain, rendering unlikely their direct binding to proteins. On the other hand, valine, not known as an osmolyte, had no stabilizing effect, although it induced a large protein-preferential hydration. A possible explanation is given for the use of these substances as osmotic-pressure-regulating agents in organisms living under high osmotic pressure.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2MXhs1antb4%253D&md5=c148d5282cdc3482732bcbf20673f9a9
228.
Yu, I.; Jindo, Y.; Nagaoka, M. Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Direct Interaction and Hydration Alteration J. Phys. Chem. B 2007, 111, 10231– 10238 DOI: 10.1021/jp068367z
[ACS Full Text ], [CAS]
228.
Microscopic Understanding of Preferential Exclusion of Compatible Solute Ectoine: Direct Interaction and Hydration Alteration
Yu, Isseki; Jindo, Yoichi; Nagaoka, Masataka
Journal of Physical Chemistry B (2007), 111 (34), 10231-10238CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
Ectoine, a zwitterionic compatible solute (CS), acts as an effective stabilizer of protein function. Using mol. dynamics simulation, solvent spatial distributions around both Met-enkephalin (M-Enk) and chymotrypsin inhibitor 2 (CI2) were investigated at the mol. level in ectoine aq. soln. An unexpected finding was that ectoine exhibits preferential binding, as an overall tendency, around both peptides. However, with the aid of the surficial Kirkwood-Buff parameter, it was clearly shown that the preferential exclusion of ectoine from the peptide surface was weaker in the smaller M-Enk than in the larger CI2. It is concluded that a denser and more structured hydration layer, such as that developed on the surface of CI2, is an important factor in the exclusion of ectoine.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXosVCktbk%253D&md5=293a68b74b53000f2dc1299c6b9f1d73
229.
Kokubo, H.; Pettitt, B. M. Preferential Solvation in Urea Solutions at Different Concentrations: Properties from Simulation Studies J. Phys. Chem. B 2007, 111, 5233– 5242 DOI: 10.1021/jp067659x
[ACS Full Text ], [CAS]
229.
Preferential Solvation in Urea Solutions at Different Concentrations: Properties from Simulation Studies
Kokubo, Hironori; Pettitt, B. Montgomery
Journal of Physical Chemistry B (2007), 111 (19), 5233-5242CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
The authors performed mol. dynamics simulations of urea solns. at different concns. with two urea models (OPLS and KBFF) to examine the structures responsible for the thermodn. soln. properties. The simulation results showed that hydrogen-bonding properties such as the av. no. of hydrogen bonds and their lifetime distributions were nearly const. at all concns. between infinite diln. and the soly. limit. This implies that the characterization of urea-water solns. in the molarity concn. scale as nearly ideal is a result of facile local hydrogen bonding rather than a global property. Thus, urea concn. does not influence the local propensity for hydrogen bonds, only how they are satisfied. By comparison, the KBFF model of urea donated fewer hydrogen bonds than OPLS. The KBFF urea model in TIP3P water better reproduced the exptl. d. and diffusion const. data. Preferential solvation anal. showed that there were weak urea-urea and water-water assocns. in OPLS soln. at short distances, but there were no strong assocns. The authors divided urea mols. into large, medium, and small clusters to examine fluctuation properties and found that any particular urea mol. did not stay in the same cluster for a long time. Neither persistent nor large clusters were found.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXksVWgtb8%253D&md5=12eff7bd45ac177dfc0172b7081a677a
230.
Aburi, M.; Smith, P. E. A Combined Simulation and Kirkwood-Buff Approach to Quantify Cosolvent Effects on the Conformational Preferences of Peptides in Solution J. Phys. Chem. B 2004, 108, 7382– 7388 DOI: 10.1021/jp036582z
[ACS Full Text ], [CAS]
230.
A combined simulation and Kirkwood-Buff approach to quantify cosolvent effects on the conformational preferences of peptides in solution
Aburi, Mahalaxmi; Smith, Paul E.
Journal of Physical Chemistry B (2004), 108 (22), 7382-7388CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
A mol. dynamics study of the effects of salt on the conformational preferences of leucine enkephalin (LE) in water has been performed to outline a general approach for quantifying the effects of a cosolvent on a biomol. equil. in soln. using mol. simulation. The simulations of LE suggest that the peptide exists as a mixt. of folded and unfolded conformations in pure water, and a potential of mean force calcn. indicates the population of the folded form to be 53±3%. The addn. of 2 M salt reduces the population of the folded form to 12±5%. A combination of the simulation data and Kirkwood-Buff theory is used to det. the preferential interactions of the cosolvent with the peptide and to reproduce the population changes indicated by the potential of mean force calcns. The results demonstrate the potential of a combined simulation and Kirkwood-Buff approach for quantifying simulation data in an effort to understand the effects of cosolvents on the thermodn. of biomols. in soln., esp. for systems where potential of mean force calcns. are unfeasible.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXjsV2rsr0%253D&md5=34c4768c7b780eb79357ab8720503be0
231.
Shimizu, S.; Matubayasi, N. Preferential Hydration of Proteins: A Kirkwood-Buff Approach Chem. Phys. Lett. 2006, 420, 518– 522 DOI: 10.1016/j.cplett.2006.01.034
[Crossref], [CAS]
231.
Preferential hydration of proteins: A Kirkwood-Buff approach
Shimizu, Seishi; Matubayasi, Nobuyuki
Chemical Physics Letters (2006), 420 (4-6), 518-522CODEN: CHPLBC; ISSN:0009-2614. (Elsevier B.V.)
The presence of cosolvents affects the stability of proteins in aq. solns. Some (such as trehalose and polyethelene glycol) enhances the stability of proteins, whereas others (such as urea) denatures the proteins. We explain different actions of cosolvents based upon the recent theor. developments in the application of Kirkwood-Buff theory.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XitVegsLk%253D&md5=28112198f9738306e7002abb9f2612eb
232.
Yu, I.; Nakada, K.; Nagaoka, M. Spatio-Temporal Characteristics of Transfer Free Energy of Apomyoglobin into the Crowding Condition with Trimethylamine N-oxide: A Study with Three Types of the Kirkwood-Buff Integral J. Phys. Chem. B 2012, 116, 4080– 4088 DOI: 10.1021/jp300380p
[ACS Full Text ], [CAS]
232.
Spatio-Temporal Characteristics of the Transfer Free Energy of Apomyoglobin into the Molecular Crowding Condition with Trimethylamine N-oxide: A Study with Three Types of the Kirkwood-Buff Integral
Yu, Isseki; Nakada, Kyoko; Nagaoka, Masataka
Journal of Physical Chemistry B (2012), 116 (13), 4080-4088CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
The transfer free energy (TFE) of apomyoglobin (AMb) from pure water into aq. soln. with trimethylamine N-oxide (TMAO) was investigated by all-atom mol. dynamics (MD) simulation combined with the Kirkwood-Buff (KB) integral method. The simulated TFE and the preferential interaction parameter correlated favorably with exptl. values. In addn., the time-resolved KB integral revealed that a significant fluctuation in the TFE arose from the alteration in TMAO solvation around AMb. Furthermore, spatial decompn. of the KB integrals revealed how the local elements of the TFE are spatially distributed around AMb. These results revealed the spatio-temporal characteristics of the protein TFE into the mol. crowding condition with TMAO.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XjtVCqtLc%253D&md5=f3e0249df31a7c9ac5af6e337e63525c
233.
Minton, A. P. Excluded Volume as a Determinant of Macromolecular Structure and Reactivity Biopolymers 1981, 20, 2093– 2120 DOI: 10.1002/bip.1981.360201006
[Crossref], [CAS]
233.
Excluded volume as a determinant of macromolecular structure and reactivity
Minton, Allen P.
Biopolymers (1981), 20 (10), 2093-120CODEN: BIPMAA; ISSN:0006-3525.
The effect of excluded vol. on the thermodn. activity of globular macromols. and macromol. complexes in soln. is studied with the hard-particle approxn. Activity coeffs. are calcd. as a function of the fraction of total vol. occupied by macromols. using relations obtained from scaled particle and lattice models. Significant and readily observable effects are predicted to occur as the fraction of vol. occupied by globular macromols. increases. Compact quasi-spherical macromol. conformations become increasingly energetically favored over extended anisometric conformations. Self-assocn. and heteroassocn. processes are enhanced, particularly those leading to the formation of compact quasi-spherical aggregates. Depending on the details of the reaction mechanism, the rate of an enzyme-catalyzed reaction may monotonically decrease, go through a max., or exhibit more complex behavior. A given degree of vol. occupancy by larger macromols. is predicted to have less effect on the structure and self-assocn. of smaller macromols. than the same degree of vol. occupancy by smaller macromols. has on the structure and self-assocn. of larger macromols.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3MXlvVaktb8%253D&md5=68ad47405f14f6f927eceb86284a9cba
234.
Koshland, D. E. The Key–Lock Theory and the Induced Fit Theory Angew. Chem., Int. Ed. Engl. 1995, 33, 2375– 2378 DOI: 10.1002/anie.199423751
[Crossref]
There is no corresponding record for this reference.
235.
Ebbinghaus, S.; Gruebele, M. Protein Folding Landscapes in the Living Cell J. Phys. Chem. Lett. 2011, 2, 314– 319 DOI: 10.1021/jz101729z
[ACS Full Text ], [CAS]
235.
Protein Folding Landscapes in the Living Cell
Ebbinghaus, Simon; Gruebele, Martin
Journal of Physical Chemistry Letters (2011), 2 (4), 314-319CODEN: JPCLCD; ISSN:1948-7185. (American Chemical Society)
A review. This Perspective highlights studies of protein structure, stability, and folding kinetics that can now be carried out in prokaryotic and eukaryotic cells. The general features of cooperative folding transitions and kinetics remain the same as those in vitro, but the folding free energy landscape and local viscosity vary according to microenvironments in the cellular landscape. Expts. in vitro provide a basis for comparing crowding and chem. effects with expts. inside of the cell. Perhaps cells even evolved to post-translationally modulate protein folding and binding through chem. patterns or by crowding.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtlClt74%253D&md5=cd11f0ac1c66756b8f883f6c9af27c85
236.
Miklos, A. C.; Li, C.; Sorrell, C. D.; Lyon, L. A.; Pielak, G. J. An Upper Limit for Macromolecular Crowding Effects BMC Biophys. 2011, 4, 13 DOI: 10.1186/2046-1682-4-13
[Crossref], [PubMed], [CAS]
236.
An upper limit for macromolecular crowding effects
Miklos, Andrew C.; Li, Conggang; Sorrell, Courtney D.; Lyon, L. Andrew; Pielak, Gary J.
BMC Biophysics (2011), 4 (), 13CODEN: BBMIG8; ISSN:2046-1682. (BioMed Central Ltd.)
Background: Solns. contg. high macromol. concns. are predicted to affect a no. of protein properties compared to those properties in dil. soln. In cells, these macromol. crowders have a large range of sizes and can occupy 30% or more of the available vol. We chose to study the stability and ps-ns internal dynamics of a globular protein whose radius is ∼2 nm when crowded by a synthetic microgel composed of poly(N-isopropylacrylamide-co-acrylic acid) with particle radii of ∼300 nm. Results: Our studies revealed no change in protein rotational or ps-ns backbone dynamics and only mild (∼0.5 kcal/mol at 37°C, pH 5.4) stabilization at a vol. occupancy of 70%, which approaches the occupancy of closely packing spheres. The lack of change in rotational dynamics indicates the absence of strong crowder-protein interactions. Conclusions: Our observations are explained by the large size discrepancy between the protein and crowders and by the internal structure of the microgels, which provide interstitial spaces and internal pores where the protein can exist in a dil. soln.-like environment. In summary, microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXpvFGlsbs%253D&md5=732c2dff8c636bb9bc847ccbe0382284
237.
Roosen-Runge, F.; Hennig, M.; Zhang, F. J.; Jacobs, R. M. J.; Sztucki, M.; Schober, H.; Seydel, T.; Schreiber, F. Protein Self-Diffusion in Crowded Solutions Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 11815– 11820 DOI: 10.1073/pnas.1107287108
[Crossref], [PubMed], [CAS]
237.
Protein self-diffusion in crowded solutions
Roosen-Runge, Felix; Hennig, Marcus; Zhang, Fajun; Jacobs, Robert M. J.; Sztucki, Michael; Schober, Helmut; Seydel, Tilo; Schreiber, Frank
Proceedings of the National Academy of Sciences of the United States of America (2011), 108 (29), 11815-11820CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
Macromol. crowding in biol. media is an essential factor for cellular function. The interplay of intermol. interactions at multiple time and length scales governs a fine-tuned system of reaction and transport processes, including particularly protein diffusion as a limiting or driving factor. Using quasielastic neutron backscattering, we probe the protein self-diffusion in crowded aq. solns. of bovine serum albumin on nanosecond time and nanometer length scales employing the same protein as crowding agent. The measured diffusion coeff. D(φ) strongly decreases with increasing protein vol. fraction φ explored within 7% ≤ φ ≤ 30%. With an ellipsoidal protein model and an anal. framework involving colloid diffusion theory, we sep. the rotational Dr(φ) and translational Dt(φ) contributions to D(φ). The resulting Dt(φ) is described by short-time self-diffusion of effective spheres. Protein self-diffusion at biol. vol. fractions is found to be slowed down to 20% of the dil. limit solely due to hydrodynamic interactions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXps1eksbY%253D&md5=e15311a1c35d3719ae67891c83b9befe
238.
Dix, J. A.; Verkman, A. S. Crowding Effects on Diffusion in Solutions and Cells Annu. Rev. Biophys. 2008, 37, 247– 263 DOI: 10.1146/annurev.biophys.37.032807.125824
[Crossref], [PubMed], [CAS]
238.
Crowding effects on diffusion in solutions and cells
Dix, James A.; Verkman, A. S.
Annual Review of Biophysics (2008), 37 (), 247-263CODEN: ARBNCV ISSN:. (Annual Reviews Inc.)
A review. Here, the authors review the effects of mol. crowding on solute diffusion in soln. and in cellular aq. compartments and membranes. Anomalous diffusion, in which mean squared displacement does not increase linearly with time, is predicted in simulations of solute diffusion in media crowed with fixed or mobile obstacles, or when solute diffusion is restricted or accelerated by a variety of geometric or active transport processes. Exptl. measurements of solute diffusion in solns. and cellular aq. compartments, however, generally show Brownian diffusion. In cell membranes, there are examples of both Brownian and anomalous diffusion, with the latter likely produced by lipid-protein and protein-protein interactions. It is concluded that the notion of universally anomalous diffusion in cells as a consequence of mol. crowding is not correct and that slowing of diffusion in cells is less marked than has been generally assumed.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXnsVGlur4%253D&md5=e8d69b369bb3e15421828cc9f336a034
239.
Dauty, E.; Verkman, A. S. Molecular Crowding Reduces to a Similar Extent the Diffusion of Small Solutes and Macromolecules: Measurement by Fluorescence Correlation Spectroscopy J. Mol. Recognit. 2004, 17, 441– 447 DOI: 10.1002/jmr.709
[Crossref], [PubMed], [CAS]
239.
Molecular crowding reduces to a similar extent the diffusion of small solutes and macromolecules: Measurement by fluorescence correlation spectroscopy
Dauty, Emmanuel; Verkman, A. S.
Journal of Molecular Recognition (2004), 17 (5), 441-447CODEN: JMORE4; ISSN:0952-3499. (John Wiley & Sons Ltd.)
Aq. environments in living cells are crowded, with up to >50% small and macromol.-size solutes. We investigated quant. one important consequence of mol. crowding-reduced diffusion of biol. important solutes. Fluorescence correlation spectroscopy (FCS) was used to measure the diffusion of a series of fluorescent small solutes and macromols. In water, diffusion coeffs. (Dwo) were (in cm2/s × 10-8): rhodamine green (270), albumin (52), dextrans (75, 10 kDa; 10, 500 kDa), double-stranded DNAs (96, 20 bp; 10, 1 kb; 3.4, 4.5 kb) and polystyrene nanospheres (5.4, 20 nm diam.; 2.3, 100 nm). Aq.-phase diffusion (Dw) in solns. crowded with Ficoll-70 (0-60%) was reduced by up to 650-fold in an exponential manner: Dw = Dwoexp(-[C]/[C]exp), where [C]exp is the concn. (in%) of crowding agent reducing Dwo by 63%. FCS data for all solutes and Ficoll-70 concns. fitted well to a model of single-component, simple (non-anomalous) diffusion. Interestingly [C]exp were nearly identical (11±2%, SD) for diffusion of the very different types of macromols. in Ficoll-70 solns. However, [C]exp was dependent on the nature of the crowding agent: for example, [C]exp for diffusion of rhodamine green was 30% for glycerol and 16% for 500 kDa dextran. Our results indicate that mol. crowding can greatly reduce aq.-phase diffusion of biol. important macromols., and demonstrate a previously unrecognized insensitivity of crowding effects on the size and characteristics of the diffusing species.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXnvVWnsL8%253D&md5=0fa0bdc67790f6e25c6e3ddfdb2fef9c
240.
Höfling, F.; Franosch, T. Anomalous Transport in the Crowded World of Biological Cells Rep. Prog. Phys. 2013, 76, 046602 DOI: 10.1088/0034-4885/76/4/046602
[Crossref], [PubMed], [CAS]
240.
Anomalous transport in the crowded world of biological cells
Hofling Felix; Franosch Thomas
Reports on progress in physics. Physical Society (Great Britain) (2013), 76 (4), 046602 ISSN:.
A ubiquitous observation in cell biology is that the diffusive motion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarizing their densely packed and heterogeneous structures. The most familiar phenomenon is a sublinear, power-law increase of the mean-square displacement (MSD) as a function of the lag time, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations in time, non-Gaussian distributions of spatial displacements, heterogeneous diffusion and a fraction of immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarize some widely used theoretical models: Gaussian models like fractional Brownian motion and Langevin equations for visco-elastic media, the continuous-time random walk model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Particular emphasis is put on the spatio-temporal properties of the transport in terms of two-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even if the MSDs are identical. Then, we review the theory underlying commonly applied experimental techniques in the presence of anomalous transport like single-particle tracking, fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where a variety of model systems mimic physiological crowding conditions. Finally, computer simulations are discussed which play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC3svltlSjtg%253D%253D&md5=29950a5746b2a1df52632f5d4eb9ce7d
241.
Ridgway, D.; Broderick, G.; Lopez-Campistrous, A.; Ru’aini, M.; Winter, P.; Hamilton, M.; Boulanger, P.; Kovalenko, A.; Ellison, M. J. Coarse-Grained Molecular Simulation of Diffusion and Reaction Kinetics in a Crowded Virtual Cytoplasm Biophys. J. 2008, 94, 3748– 3759 DOI: 10.1529/biophysj.107.116053
[Crossref], [PubMed], [CAS]
241.
Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm
Ridgway, Douglas; Broderick, Gordon; Lopez-Campistrous, Ana; Ru'aini, Melania; Winter, Philip; Hamilton, Matthew; Boulanger, Pierre; Kovalenko, Andriy; Ellison, Michael J.
Biophysical Journal (2008), 94 (10), 3748-3759CODEN: BIOJAU; ISSN:0006-3495. (Biophysical Society)
The authors present a general-purpose model for biomol. simulations at the mol. level that incorporates stochasticity, spatial dependence, and vol. exclusion, using diffusing and reacting particles with phys. dimensions. To validate the model, the authors first established the formal relationship between the microscopic model parameters (timestep, move length, and reaction probabilities) and the macroscopic coeffs. for diffusion and reaction rate. The authors then compared simulation results with Smoluchowski theory for diffusion-limited irreversible reactions and the best available approxn. for diffusion-influenced reversible reactions. To simulate the volumetric effects of a crowded intracellular environment, the authors created a virtual cytoplasm composed of a heterogeneous population of particles diffusion at rates appropriate to their size. The particle-size distribution was estd. from the relative abundance, mass, and stoichiometries of protein complexes using an exptl. derived proteome catalog from Escherichia coli K12. Simulated diffusion consts. exhibited anomalous behavior as a function of time and crowding. Although significant, the volumetric impact of crowding on diffusion cannot fully account for retarded protein mobility in vivo, suggesting that other biophys. factors are at play. The simulated effect of crowding on barnase-barstar dimerization, an exptl. characterized example of a biomol. assocn. reaction, reveals a biphasic time course, indicating that crowding exerts different effects over different timescales. These observations illustrate that quant. realism in biosimulation will depend to some extent on mesoscale phenomena that are not currently well understood.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXlsF2htLk%253D&md5=43fa92c0b355aecae75aa0d0d45702d3
242.
Shaw, D. E.; Grossman, J. P.; Bank, J. A.; Batson, B.; Butts, J. A.; Chao, J. C.; Deneroff, M. M.; Dror, R. O.; Even, A.; Fenton, C. H.; Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer. Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis; IEEE Press: New Orleans, LA, 2014; pp 41– 53.
[Crossref]
There is no corresponding record for this reference.
243.
Schutz, C. N.; Warshel, A. What are the Dielectric ″Constants″ of Proteins and How to Validate Electrostatic Models? Proteins: Struct., Funct., Genet. 2001, 44, 400– 417 DOI: 10.1002/prot.1106
[Crossref], [PubMed], [CAS]
243.
What are the dielectric "constants" of proteins and how to validate electrostatic models?
Schutz, Claudia N.; Warshel, Arieh
Proteins: Structure, Function, and Genetics (2001), 44 (4), 400-417CODEN: PSFGEY; ISSN:0887-3585. (Wiley-Liss, Inc.)
A review, with refs. Implicit models for evaluation of electrostatic energies in proteins include dielec. consts. that represent effect of the protein environment. Unfortunately, the results obtained by such models are very sensitive to the value used for the dielec. const. Furthermore, the factors that det. the optimal value of these consts. are far from being obvious. This review considers the meaning of the protein dielec. consts. and the ways to det. their optimal values. It is pointed out that typical benchmarks for validation of electrostatic models cannot discriminate between consistent and inconsistent models. In particular, the obsd. pKa values of surface groups can be reproduced correctly by models with entirely incorrect phys. features. Thus, the authors introduce a discriminative benchmark that only includes residues whose pKa values are shifted significantly from their values in water. The authors also use the semimacroscopic version of the protein dipole Langevin dipole (PDLD/S) formulation to generate a series of models that move gradually from microscopic to fully macroscopic models. These include the linear response version of the PDLD/S models, Poisson Boltzmann (PB)-type models, and Tanford Kirkwood (TK)-type models. Using the authors' different models and the discriminative benchmark, the authors show that the protein dielec. const., εp, is not a universal const. but simply a parameter that depends on the model used. It is also shown in agreement with the authors' previous works that εp represents the factors that are not considered explicitly. The use of a discriminative benchmark appears to help not only in identifying nonphys. models but also in analyzing effects that are not reproduced in an accurate way by consistent models. These include the effect of water penetration and the effect of the protein reorganization. Finally, the authors show that the optimal dielec. const. for self-energies is not the optimal const. for charge-charge interactions.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXmt1SjtLo%253D&md5=b23d735d9eb4b8817f4024c390935a3b
244.
Gilson, M. K.; Honig, B. H. The Dielectric-Constant of a Folded Protein Biopolymers 1986, 25, 2097– 2119 DOI: 10.1002/bip.360251106
[Crossref], [PubMed], [CAS]
244.
The dielectric constant of a folded protein
Gilson, Michael K.; Honig, Barry H.
Biopolymers (1986), 25 (11), 2097-119CODEN: BIPMAA; ISSN:0006-3525.
To obtain a theor. est. of the dielec. const. of a folded protein, a form of the Kirkwood-Froehlich dielec. theory was developed that applied to polar solids and folded proteins. The resulting theory incorporated a factor expressing the degree to which dipolar groups are constrained within the structure of the material, as well as a generalized form of Kirkwood's correlation factor. The theory was applied to a hypothetical isotropic protein composed of randomly oriented α-helixes and having a no. d. of dipolar groups equal to that found in actual proteins. The factor of constraint and the generalized dipole correlation factor were calcd. by using normal mode anal. Temp. factors were also computed by normal mode anal. and were in reasonable agreement with those found exptl. The computed dielec. const. was low; the best est. was 2.5-4.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2sXksF2msQ%253D%253D&md5=d0891f56bf002e2a6efb232ef7787512
245.
Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew J. Chem. Phys. 2004, 120, 9665– 9678 DOI: 10.1063/1.1683075
[Crossref], [PubMed], [CAS]
245.
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
Horn, Hans W.; Swope, William C.; Pitera, Jed W.; Madura, Jeffry D.; Dick, Thomas J.; Hura, Greg L.; Head-Gordon, Teresa
Journal of Chemical Physics (2004), 120 (20), 9665-9678CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
A re-parameterization of the std. TIP4P water model for use with Ewald techniques is introduced, providing an overall global improvement in water properties relative to several popular nonpolarizable and polarizable water potentials. Using high precision simulations, and careful application of std. anal. corrections, we show that the new TIP4P-Ew potential has a d. max. at ∼1°, and reproduces exptl. bulk-densities and the enthalpy of vaporization, ΔHvap, from -37.5 to 127° at 1 atm with an abs. av. error of less than 1%. Structural properties are in very good agreement with X-ray scattering intensities at temps. between 0 and 77° and dynamical properties such as self-diffusion coeff. are in excellent agreement with expt. The parameterization approach used can be easily generalized to rehabilitate any water force field using available exptl. data over a range of thermodn. points.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXjvVSqsb4%253D&md5=ef0e8aa3e0297ea6827f2d883261c649
246.
Paschek, D.; Day, R.; Garcia, A. E. Influence of Water-Protein Hydrogen Bonding on the Stability of Trp-Cage Miniprotein. A Comparison between the TIP3P and TIP4P-Ew Water Models Phys. Chem. Chem. Phys. 2011, 13, 19840– 19847 DOI: 10.1039/c1cp22110h
[Crossref], [PubMed], [CAS]
246.
Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models
Paschek, Dietmar; Day, Ryan; Garcia, Angel E.
Physical Chemistry Chemical Physics (2011), 13 (44), 19840-19847CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
Here, the authors report extensive replica exchange mol. dynamics (REMD) simulations on the folding/unfolding equil. of Trp-cage miniprotein using the Amber ff99SB all-atom force field and TIP3P and TIP4P-Ew explicit water solvent models. REMD simulation-lengths in the 500 ns to the microsecond regime per replica were required to adequately sample the folding/unfolding equil. The authors obsd. that this equil. was significantly affected by the choice of the water model. Compared with exptl. data, simulations using the TIP3P solvent described the stability of the Trp-cage quite realistically, providing a m.p. which was just a few Kelvins above the exptl. transition temp. of 317 K. The TIP4P-Ew model shifted the equil. toward the unfolded state and lowered the free energy of unfolding by ∼3 kJ/mol at 280 K, demonstrating the need to fine-tune the protein-force field depending on the chosen water model. The authors reported evidence that the main difference between the 2 water models was mostly due to the different solvation of polar groups of the peptide. The unfolded state of the Trp-cage miniprotein was stabilized by an increasing no. of H-bonds, destabilizing the α-helical part of the mol. and opening the R-D salt bridge. By reweighting the strength of solvent-peptide H-bonds by adding a H-bond square well potential, the authors could fully recover the effect of the different water models and est. the shift in population as due to a difference in H-bond-strength of ∼0.4 kJ/mol per H-bond.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXhtl2htr%252FO&md5=fdf609e2a5a69dc62cb8e5bb709644a8
247.
Freedberg, D. I.; Selenko, P. Live Cell NMR Annu. Rev. Biophys. 2014, 43, 171– 192 DOI: 10.1146/annurev-biophys-051013-023136
[Crossref], [PubMed], [CAS]
247.
Live cell NMR
Freedberg, Daron I.; Selenko, Philipp
Annual Review of Biophysics (2014), 43 (), 171-192CODEN: ARBNCV; ISSN:1936-122X. (Annual Reviews)
Ever since scientists realized that cells are the basic building blocks of all life, they have been developing tools to look inside them to reveal the architectures and mechanisms that define their biol. functions. Whereas "looking into cells" is typically said in ref. to optical microscopy, high-resoln. in-cell and on-cell NMR (NMR) spectroscopy is a powerful method that offers exciting new possibilities for structural and functional studies in and on live cells. In contrast to conventional imaging techniques, in- and on-cell NMR methods do not provide spatial information on cellular biomols. Instead, they enable at.-resoln. insights into the native cell states of proteins, nucleic acids, glycans, and lipids. Here we review recent advances and developments in both fields and discuss emerging concepts that have been delineated with these methods.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtFOht7rK&md5=e594ddc4f200cb0689ddb0f8a0f0b4c8
248.
Gruebele, M.; Dave, K.; Sukenik, S. Globular Protein Folding in vitro and in vivo Annu. Rev. Biophys. 2016, 45, 233– 251 DOI: 10.1146/annurev-biophys-062215-011236
[Crossref], [PubMed], [CAS]
248.
Globular Protein Folding In Vitro and In Vivo
Gruebele, Martin; Dave, Kapil; Sukenik, Shahar
Annual Review of Biophysics (2016), 45 (), 233-251CODEN: ARBNCV; ISSN:1936-122X. (Annual Reviews)
A review. In vitro, computational, and theor. studies of protein folding have converged to paint a rich and complex energy landscape. This landscape is sensitively modulated by environmental conditions and subject to evolutionary pressure on protein function. Of these environments, none is more complex than the cell itself, where proteins function in the cytosol, in membranes, and in different compartments. A wide variety of kinetic and thermodn. expts., ranging from single-mol. studies to jump kinetics and from NMR to imaging on the microscope, have elucidated how protein energy landscapes facilitate folding and how they are subject to evolutionary constraints and environmental perturbation. Here we review some recent developments in the field and refer the reader to some original work and addnl. reviews that cover this broad topic in protein science.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhtFCrtrjM&md5=ab8805b9fe60c7e178b2eb897390d21a
249.
Shtengel, G.; Galbraith, J. A.; Galbraith, C. G.; Lippincott-Schwartz, J.; Gillette, J. M.; Manley, S.; Sougrat, R.; Waterman, C. M.; Kanchanawong, P.; Davidson, M. W. Interferometric Fluorescent Super-Resolution Microscopy Resolves 3D Cellular Ultrastructure Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 3125– 3130 DOI: 10.1073/pnas.0813131106
[Crossref], [PubMed], [CAS]
249.
Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure
Shtengel, Gleb; Galbraith, James A.; Galbraith, Catherine G.; Lippincott-Schwartz, Jennifer; Gillette, Jennifer M.; Manley, Suliana; Sougrat, Rachid; Waterman, Clare M.; Kanchanawong, Pakorn; Davidson, Michael W.; Fetter, Richard D.; Hess, Harald F.
Proceedings of the National Academy of Sciences of the United States of America (2009), 106 (9), 3125-3130CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
Understanding mol.-scale architecture of cells requires detn. of 3D locations of specific proteins with accuracy matching their nanometer-length scale. Existing electron and light microscopy techniques are limited either in mol. specificity or resoln. Here, we introduce interferometric photoactivated localization microscopy (iPALM), the combination of photoactivated localization microscopy with single-photon, simultaneous multiphase interferometry that provides sub-20-nm 3D protein localization with optimal mol. specificity. We demonstrate measurement of the 25-nm microtubule diam., resolve the dorsal and ventral plasma membranes, and visualize the arrangement of integrin receptors within endoplasmic reticulum and adhesion complexes, 3D protein organization previously resolved only by electron microscopy. IPALM thus closes the gap between electron tomog. and light microscopy, enabling both mol. specification and resoln. of cellular nanoarchitecture.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXivFyqu7w%253D&md5=efdee152b32d07dcd78f5c31f2babf4c
250.
Cheng, Y.; Grigorieff, N.; Penczek; Pawel, A.; Walz, T. A Primer to Single-Particle Cryo-Electron Microscopy Cell 2015, 161, 438– 449 DOI: 10.1016/j.cell.2015.03.050
[Crossref], [PubMed], [CAS]
250.
A Primer to Single-Particle Cryo-Electron Microscopy
Cheng, Yifan; Grigorieff, Nikolaus; Penczek, Pawel A.; Walz, Thomas
Cell (Cambridge, MA, United States) (2015), 161 (3), 438-449CODEN: CELLB5; ISSN:0092-8674. (Cell Press)
A review. Cryo-electron microscopy (cryo-EM) of single-particle specimens was used to det. the structure of proteins and macromol. complexes without the need for crystals. Recent advances in detector technol. and software algorithms now allow images of unprecedented quality to be recorded and structures to be detd. at near-at. resoln. However, compared with x-ray crystallog., cryo-EM is a young technique with distinct challenges. This primer explains the different steps and considerations involved in structure detn. by single-particle cryo-EM to provide an overview for scientists wishing to understand more about this technique and the interpretation of data obtained with it, as well as a starting guide for new practitioners.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXnt1eru7c%253D&md5=f63f750d997e4487cf22ab6d930e0ea5
251.
Lee, S. F.; Thompson; Michael, A.; Schwartz, M. A.; Shapiro, L.; Moerner, W. E. Super-Resolution Imaging of the Nucleoid-Associated Protein HU in Caulobacter crescentus Biophys. J. 2011, 100, L31– L33 DOI: 10.1016/j.bpj.2011.02.022
[Crossref], [PubMed], [CAS]
251.
Super-Resolution Imaging of the Nucleoid-Associated Protein HU in Caulobacter crescentus
Lee, Steven F.; Thompson, Michael A.; Schwartz, Monica A.; Shapiro, Lucy; Moerner, W. E.
Biophysical Journal (2011), 100 (7), L31-L33CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
Little is known about the structure and function of most nucleoid-assocd. proteins (NAPs) in bacteria. One reason for this is that the distribution and structure of the proteins is obfuscated by the diffraction limit in std. wide-field and confocal fluorescence imaging. In particular, the distribution of HU, which is the most abundant NAP, has received little attention. In this study, we investigate the distribution of HU in Caulobacter crescentus using a combination of super-resoln. fluorescence imaging and spatial point statistics. By simply increasing the laser power, single mols. of the fluorescent protein fusion HU2-eYFP can be made to blink on and off to achieve super-resoln. imaging with a single excitation source. Through quantification by Ripley's K-test and comparison with Monte Carlo simulations, we find the protein is slightly clustered within a mostly uniform distribution throughout the swarmer and stalked stages of the cell cycle but more highly clustered in predivisional cells. The methods presented in this letter should be of broad applicability in the future study of prokaryotic NAPs.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXktF2htrc%253D&md5=ebad4b7067a810630931594b02e2bce9
252.
Bakshi, S.; Choi, H.; Weisshaar, J. C. The Spatial Biology of Transcription and Translation in Rapidly Growing Escherichia coli Front. Microbiol. 2015, 6, 636 DOI: 10.3389/fmicb.2015.00636
[Crossref], [PubMed], [CAS]
252.
The spatial biology of transcription and translation in rapidly growing Escherichia coli
Bakshi Somenath; Choi Heejun; Weisshaar James C
Frontiers in microbiology (2015), 6 (), 636 ISSN:.
Single-molecule fluorescence provides high resolution spatial distributions of ribosomes and RNA polymerase (RNAP) in live, rapidly growing Escherichia coli. Ribosomes are more strongly segregated from the nucleoids (chromosomal DNA) than previous widefield fluorescence studies suggested. While most transcription may be co-translational, the evidence indicates that most translation occurs on free mRNA copies that have diffused from the nucleoids to a ribosome-rich region. Analysis of time-resolved images of the nucleoid spatial distribution after treatment with the transcription-halting drug rifampicin and the translation-halting drug chloramphenicol shows that both drugs cause nucleoid contraction on the 0-3 min timescale. This is consistent with the transertion hypothesis. We suggest that the longer-term (20-30 min) nucleoid expansion after Rif treatment arises from conversion of 70S-polysomes to 30S and 50S subunits, which readily penetrate the nucleoids. Monte Carlo simulations of a polymer bead model built to mimic the chromosomal DNA and ribosomes (either 70S-polysomes or 30S and 50S subunits) explain spatial segregation or mixing of ribosomes and nucleoids in terms of excluded volume and entropic effects alone. A comprehensive model of the transcription-translation-transertion system incorporates this new information about the spatial organization of the E. coli cytoplasm. We propose that transertion, which radially expands the nucleoids, is essential for recycling of 30S and 50S subunits from ribosome-rich regions back into the nucleoids. There they initiate co-transcriptional translation, which is an important mechanism for maintaining RNAP forward progress and protecting the nascent mRNA chain. Segregation of 70S-polysomes from the nucleoid may facilitate rapid growth by shortening the search time for ribosomes to find free mRNA concentrated outside the nucleoid and the search time for RNAP concentrated within the nucleoid to find transcription initiation sites.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC28%252FkslGmtA%253D%253D&md5=5214d19e6d21de72077a103a0aa12122
253.
Wang, X.; Llopis, P. M.; Rudner, D. Z. Organization and Segregation of Bacterial Chromosomes Nat. Rev. Genet. 2013, 14, 191– 203 DOI: 10.1038/nrg3375
[Crossref], [PubMed], [CAS]
253.
Organization and segregation of bacterial chromosomes
Wang, Xindan; Llopis, Paula Montero; Rudner, David Z.
Nature Reviews Genetics (2013), 14 (3), 191-203CODEN: NRGAAM; ISSN:1471-0056. (Nature Publishing Group)
A review. The bacterial chromosome must be compacted more than 1,000-fold to fit into the compartment in which it resides. How it is condensed, organized and ultimately segregated has been a puzzle for over half a century. Recent advances in live-cell imaging and genome-scale analyses have led to new insights into these problems. We argue that the key feature of compaction is the orderly folding of DNA along adjacent segments and that this organization provides easy and efficient access for protein-DNA transactions and has a central role in driving segregation. Similar principles and common proteins are used in eukaryotes to condense and to resolve sister chromatids at metaphase.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXitlaitb4%253D&md5=38da5ea0992345dd13e6b2141f2a2c95
254.
Zhou, H. X. Crowding Effects of Membrane Proteins J. Phys. Chem. B 2009, 113, 7995– 8005 DOI: 10.1021/jp8107446
[ACS Full Text ], [CAS]
254.
Crowding Effects of Membrane Proteins
Zhou, Huan-Xiang
Journal of Physical Chemistry B (2009), 113 (23), 7995-8005CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
In cell membranes, membrane proteins occupy ∼30% of the total surface area. Crowding effects similar to those in the soln. phase are thus to be expected. In addn., there are crowding effects unique to proteins bound to the two-dimensional membranes, such as those exerted on the equilibration of a protein between two membrane orientations and on the redistribution of proteins between different locations in a cell membrane. This article aims to present a theor. framework for understanding the various crowding effects within membranes. For illustration, the theory is used to analyze previously published exptl. and simulation data. It is hoped that the article will encourage quant. analyses in future expts. and spur systematic investigation of membrane crowding effects.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXjvVegur0%253D&md5=0152e70585c6e9a10c9df80ab69e3d88
255.
Kim, J. S.; Yethiraj, A. Crowding Effects on Association Reactions at Membranes Biophys. J. 2010, 98, 951– 958 DOI: 10.1016/j.bpj.2009.11.022
[Crossref], [PubMed], [CAS]
255.
Crowding effects on association reactions at membranes
Kim, Jun Soo; Yethiraj, Arun
Biophysical Journal (2010), 98 (6), 951-958CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
The effect of macromol. crowding on the binding of ligands to a receptor near membranes is studied using Brownian dynamics simulations. The receptor is modeled as a reactive patch on a hard surface and the ligands and crowding agents are modeled as spheres that interact via a steep repulsive interaction potential. When a ligand collides with the patch, it reacts with probability prxn. The assocn. rate const. (k∞) can be decompd. into contributions from diffusion-limited (kD) and reaction-limited (kR) rates, i.e., 1/k∞ = 1/kD + 1/kR. The simulations show that kD is a nonmonotonic function of the vol. fraction of crowding agents for receptors of small sizes. KR is always an increasing function of the vol. fraction of crowding agents, and the assocn. rate const. k∞ detd. from both contributions has a qual. different dependence on the macromol. crowding for high and low values of the reaction probability prxn. The simulation results are used to predict the velocity of the membrane protrusion driven by actin filament elongation. Based on the simple model where the protrusive force on the membrane is generated by the intercalation of actin monomers between the membrane and actin filament ends, the authors predict that crowding increases the local concn. of actin monomers near the filament ends and hence accelerates the membrane protrusion.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXmtVWnt70%253D&md5=8a8ee3e6e7f792bc6b7700d124056cfb
256.
Gane, P. J.; Dean, P. M. Recent Advances in Structure-Based Rational Drug Design Curr. Opin. Struct. Biol. 2000, 10, 401– 404 DOI: 10.1016/S0959-440X(00)00105-6
[Crossref], [PubMed], [CAS]
256.
Recent advances in structure-based rational drug design
Gane, Paul J.; Dean, Philip M.
Current Opinion in Structural Biology (2000), 10 (4), 401-404CODEN: COSBEF; ISSN:0959-440X. (Elsevier Science Ltd.)
A review with 33 refs. Two approaches to structure-based drug design, i.e., the docking of known compds. into a target protein and mol. assembly in situ, are seen to be merging technologies. The need for structural information about drug-protein complexes is now fundamental for drug discovery.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3cXlvFOmtrs%253D&md5=7cd3881e867d9151557dcdd5f7f0e4bb
257.
Taft, C. A.; Da Silva, V. B.; Da Silva, C. Current Topics in Computer-Aided Drug Design J. Pharm. Sci. 2008, 97, 1089– 1098 DOI: 10.1002/jps.21293
[Crossref], [PubMed], [CAS]
257.
Current topics in computer-aided drug design
Taft, Carlton A.; Da Silva, Vinicius Barreto; Da Silva, Carlos Henrique Tomich De Paula
Journal of Pharmaceutical Sciences (2007), 97 (3), 1089-1098CODEN: JPMSAE; ISSN:0022-3549. (Wiley-Liss, Inc.)
A review. The addn. of computer-aided drug design (CADD) technologies to the research and drug discovery approaches could lead to a redn. of up to 50% in the cost of drug design. Designing a drug is the process of finding or creating a mol. which has a specific activity on a biol. organism. Development and drug discovery is a time-consuming, expensive, and interdisciplinary process whereas scientific advancements during the past two decades have altered the way pharmaceutical research produces new bioactive mols. Advances in computational techniques and hardware solns. have enabled in silico methods to speed up lead optimization and identification. We will review current topics in computer-aided mol. design underscoring some of the most recent approaches and interdisciplinary processes. We will discuss some of the most efficient pathways and design.
>> More from SciFinder ^®
https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXivFentb0%253D&md5=d1f694bd076172871b3c9b90caaf1ddc

Feature Article

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

Abstract

Introduction

Key Questions

Cellular Environments in Computer Simulations

Atomistic Simulations of Cellular Crowding

Connections with Experiment

Next Steps

Acknowledgment

References

Atomistic Modeling of Intrinsically Disordered Proteins Under Polyethylene Glycol Crowding: Quantitative Comparison with Experimental Data and Implication of Protein–Crowder Attraction

Grafting through Method for Implanting of Lysozyme Enzyme in Molecular Brush for Improved Biocatalytic Activity and Thermal Stability

Designing Highly Thermostable Lysozyme–Copolymer Conjugates: Focus on Effect of Polymer Concentration

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

Thermal Stabilization of Enzymes with Molecular Brushes

Solvent Composition Drives the Rebinding Kinetics of Nitric Oxide to Microperoxidase

Insights into Noncovalent Binding Obtained from Molecular Dynamics Simulations

Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size

Recent advances in carrier mediated nose-to-brain delivery of pharmaceutics

A reactive, scalable, and transferable model for molecular energies from a neural network approach based on local information

Macromolecular crowding effects in flexible polymer solutions

Markov modeling of peptide folding in the presence of protein crowders

How does solvation in the cell affect protein folding and binding?

Macromolecular crowding and the importance of proper hydration for the structure and dynamics of protein solutions

Molecular simulations of cellular processes

Related Content:

Metrics

Products

User Resources

Support

Partners

Feature Article

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

Abstract

Introduction

Key Questions

Cellular Environments in Computer Simulations

Atomistic Simulations of Cellular Crowding

Connections with Experiment

Next Steps

Acknowledgment

References

Related Content:

Explore by:

Metrics

This website uses cookies to improve your user experience. By continuing to use the site, you are accepting our use of cookies. Read the ACS privacy policy.

Products

User Resources

Support

Partners