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Computational Biochemistry

Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution
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  • Emile de Bruyn
    Emile de Bruyn
    Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
    Department of Physics, RWTH Aachen University, 52062 Aachen, Germany
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    Orcidhttps://orcid.org/0000-0002-8748-2553
  • Anton Emil Dorn
    Anton Emil Dorn
    Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
    Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
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  • Giulia Rossetti*
    Giulia Rossetti
    Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
    Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
    Department of Neurology, RWTH Aachen University, 52074 Aachen, Germany
    *E-mail: [email protected]
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    Orcidhttps://orcid.org/0000-0002-2032-4630
  • Claudio Fernandez
    Claudio Fernandez
    Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPINAT), Partner of the Max Planck Institute for Multidisciplinary Sciences (MPINAT, MPG), Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina
    Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
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    Orcidhttps://orcid.org/0000-0003-0454-7735
  • Tiago F. Outeiro
    Tiago F. Outeiro
    Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany
    Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
    Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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  • Jörg B. Schulz
    Jörg B. Schulz
    Department of Physics, RWTH Aachen University, 52062 Aachen, Germany
    Department of Neurology, RWTH Aachen University, 52074 Aachen, Germany
    JARA Brain Institute Molecular Neuroscience and Neuroimaging (INM-11), Research Centre Jülich and RWTH Aachen University, 52074 Aachen, Germany
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  • Paolo Carloni
    Paolo Carloni
    Department of Physics, RWTH Aachen University, 52062 Aachen, Germany
    Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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Journal of Chemical Information and Modeling

Cite this: J. Chem. Inf. Model. 2024, 64, 21, 8215–8226
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https://doi.org/10.1021/acs.jcim.4c01172
Published October 27, 2024

Copyright © 2024 The Authors. Published by American Chemical Society. This publication is licensed under

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Abstract

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Serine 129 can be phosphorylated in pathological inclusions formed by the intrinsically disordered protein human α-synuclein (AS), a key player in Parkinson’s disease and other synucleinopathies. Here, molecular simulations provide insight into the structural ensemble of phosphorylated AS. The simulations allow us to suggest that phosphorylation significantly impacts the structural content of the physiological AS conformational ensemble in aqueous solution, as the phosphate group is mostly solvated. The hydrophobic region of AS contains β-hairpin structures, which may increase the propensity of the protein to undergo amyloid formation, as seen in the nonphysiological (nonacetylated) form of the protein in a recent molecular simulation study. Our findings are consistent with existing experimental data with the caveat of the observed limitations of the force field for the phosphorylated moiety.

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Introduction

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Parkinson’s disease (PD) is the second most common neurodegenerative disease after Alzheimer’s disease, (1) affecting several million people worldwide. (2,3) The typical pathological hallmark is the accumulation of fibrillar protein inclusions, know as Lewy bodies (LBs) and Lewy neurites (LNs) in the brain. (4,5) The major component of LBs and LNs is fibrillar forms of the human α-synuclein (AS) protein. (3,6) AS is a 140 amino acid disordered conformational ensemble both in aqueous solution and in vivo. AS acquires some degree of structure when bound to the membrane or to cellular partners. (7,8)
The primary sequence of AS can be divided in three domains: the positively charged N-terminus (residues 1–60), the overall neutral hydrophobic region (residues 61–95)[We choose to use the more accurate term “hydrophobic region” instead of the historical but inaccurate term “non-amyloid component (NAC)”. (9)], and the negatively charged C-terminal domain (residues 96–140, Figure 1). We choose to use the more accurate term “hydrophobic region” instead of the historical but inaccurate term “non-amyloid component (NAC)”. (9) Under physiological conditions, the protein is acetylated on the first residue. N-Terminal acetylation does not significantly change the fibrillization propensity in vitro. (10) In LBs, a significant fraction of AS is phosphorylated on S129. (11) Another phosphorylation site of α-synuclein at T64 has also been described. (10) S129 phosphorylation may be regulated by neuronal activity, suggesting that the process may be part of the normal physiology of AS. (12,13) This post-translational modification (PTM) might play also a pathological role. (14−17) S129 phosphorylation may be regulated by neuronal activity, suggesting that the process may be part of the normal physiology of AS. (12,13)

Figure 1

Figure 1. Sequence of amino acid residues in AS; positively charged residues are highlighted in blue, and negatively charged ones are highlighted in red. Three domains can be identified: the positively charged N-terminus (residues 1–60), the overall neutral hydrophobic region (residues 61–95), and the negatively charged C-terminal domain (residues 96–104). In physiological conditions, the protein is acetylated on the first residue, although this post-translational modification does not significantly affect the fibrillization propensity in vitro. (18) In LBs, a significant fraction of AS is phosphorylated on S129. (11) A novel phosphorylation site at T64 has also been recently described. (10)

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The formation of the S129–O–PO32– group at the C-terminus of phosphorylated α synuclein (pAS) instead of one of the other two domains is intriguing, because it introduces as many as two negative charges at physiological pH (the pKa1 and pKa2 of phosphoserine are <2 and 5.6 (19)). The phosphate group is likely partially monoprotonated under physiological conditions. The effect of protonation is discussed in the Supporting Information.
The impact of phosphorylation on the structural ensemble and aggregation propensity of physiological AS is not known. Thus, far, Circular Dichroisim (CD) studies on the non-N-term acetylated form of the protein in solution show that the conformational ensemble does not change significantly upon S129 phosphorylation. (20,21) This contrasts with findings by CD studies for phosphorylation on protein variants. (20−22) These point to significant changes in the structural ensemble upon phosphorylation. On the detailed molecular level, replica exchange simulations based on the CHARMM36m force field (23) point to an increase of looped secondary structure close to a β -hairpin spread throughout the hydrophobic region upon phosphorylation. (24) However, the structure of the physiological form differs from that of the nonacetylated one (which does not exist in human cells), (25−27) so firm conclusions on the effect of phosphorylation on endogenous AS cannot be made from these studies.
Here we investigate the impact of phosphorylation on the physiological form of AS by molecular simulation. For this study, one may face several challenges. First, the force field must be adequate to describe IDPs such as AS. The DES-Amber ff99SB, (28) the Amber a99SB-disp, (29) and CHARMM36m (23) force fields have been tailored for IDPs; (29−31) the last two have been successfully used for the nonacetylated form of the proteins. (29,31,32) All of these force fields appear therefore to be well suited to study AS. Second, accurately describing a doubly charged group such as phosphate in pAS is nontrivial. Indeed, Amber (33−35) and CHARMM (36,37) based simulations of phosphorylated protein have at times shown artifacts. (38−41) Therefore, we have adapted phosphate parameters from the DES-AMBER DNA force field, (42) recently calibrated on osmotic coefficient calculations. Finally, the conformational space of the protein structural ensemble needs to be efficiently explored. Among the many methodologies used to investigate IDPs successfully, (43−52) our predictions based on Replica Exchange with Solute Tempering 2 (REST2) (53) enhanced sampling predictions of wild-type (54,55) and mutants of AS (55,56) and turned out to reproduce a variety of biophysical properties of the protein; and hence, they appear well suitable to study this problem.
Here, we present 600 ns REST2 simulations of AS and pAS based on the DES-Amber (42) and a99SB-disp force-fields. (29) We use TIP4P-D for DES-Amber, and the accompanying modified TIP4P-D water model was used for a99SB-disp. To the best of the authors’ knowledge, these simulations are the only ones so far (i) reporting on the physiological form of AS in explicit solvent and (ii) describing in detail the hydration properties of the phosphate, which has never been reported in previous simulation studies. (38−41,81−85) Many molecular simulation studies, besides those in refs (29) and, (32) focus on the nonacetylated protein. (31,57−80) Calculations of the protein in an implicit solvent are not reported here.

Methods

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Molecular Simulations

System

The structure of the acetylated protein (AS) which best reproduced the chemical shifts in ref (86) was selected from the conformational ensemble previously reported in ref (54). The phosphorylated protein (pAS) was built by adding a phosphate group to S129 using PyMOL. (87)
AS and pAS were inserted in a water-filled dodecahedral simulation box with periodic boundary conditions and a minimum distance of 35 Å between the protein and the box edges. Na+ and Cl– ions were added to neutralize the system and achieve a concentration of 150 mmol L–1. Table 1 shows the composition of the systems.
Table 1. Number of Atoms in the Systems Simulated Here
 ProteinWaterSodiumChlorine
AS2,020190,533186176
pAS2,023172,359171159

Force Fields

The simulations were based on (i) the DES-Amber force field (28) and the standard TIP4P-D water model (88) (see Table S1 for a full list of the parameters used) and (ii) the a99SB-disp force field (29) and its accompanying modified TIP4P-D water model. (29)

Molecular Simulation Setup

Long range electrostatics were evaluated using the Particle-Mesh Ewald (PME) method, (89) using a cutoff distance of 12 Å in real space. The van der Waals interactions featured the same cutoff. Constant temperature conditions were achieved by coupling the systems with a Nosé–Hoover thermostat (90) at 300 K, with a time constant of 0.5 ps. Constant pressure was achieved with a Parrinello–Rahman barostat (91) at 1 bar, with a time constant of 2 ps (Table S1). The LINCS algorithm was used for all bonds involving hydrogen atoms. (92) The equations of motions were integrated using the md leapfrog algorithm, with a time step of 2 fs.

MD and REST Simulations

The proteins underwent energy minimization (Table S2) and subsequently 100 ps of MD in the NVT ensemble (Table S3). Then, they were heated up in 25 ps-long steps of 5 K in the same ensemble up to 300 K using simulated annealing (Tables S4 and S5). The systems were further equilibrated for 1 ns in the NPT ensemble (Table S6). Finally, they underwent 600 ns REST2 simulations (53) in the NPT ensemble, with a total of 32 replicas between 300 and 500 K exchanging every 1,000 simulation steps. The proteins were not found to be near their periodic images at distances of less than 12 Å during any of these simulations. The simulations converged after 100 ns (see the Results section).
Structurally similar conformational clusters were obtained following the method for clustering IDPs described in ref (93). For both AS and pAS, a total of 5,000 frames from the last 500 ns were clustered (Figures S7 and S8).

Calculated Properties

Based on the last 500 ns REST simulations, we obtained representative structures (using the method for clustering IDPs in ref (93), Figures S7 and S8), and we calculated the following properties: (i) The radius of gyration Rg, calculated using the MDTraj Python code. (94) (ii) The hydrodynamic radius, calculated from the radii of gyration using the linear fit of ref (67). (iii) The protein end-to-end distance between the N- and C-termini, using the MDTraj Python code. (94) (iv) The NMR chemical shifts of backbone nitrogen, hydrogen, Cα, Cβ, and backbone carbonyl carbon atoms, using the SPARTA+ code. (95) (v) The CD spectra of representative cluster structures, using the SESCA code. (96−98) (vi) The solvent accessible surface area (SASA) using the MDTraj code. (94) (vii) The contact map of protein residues using minimum pairwise distances between residues using the MDTraj code. (94) (viii) Radial distribution functions (RDFs) and time-resolved radial distribution functions (TRRDFs) using the SPEADI (99,100) code developed by the authors.
(ix) Hydrogen bonds were defined according to the scheme in ref (101). (x) Salt bridges were defined using a distance between two charged atoms in the protein at a distance below 3.25 Å as in ref (102). (xi) Secondary structure elements were identified using MDTraj (94) and DSSP. (103) (xii) Free energy profiles (or potentials of mean force, PMFs) were calculated according to ref (104) by constructing a 2-dimensional histogram of the radius of gyration and end-to-end distance of the protein along the converged part of the simulation and subsequently performing a Boltzmann inversion of the histogram
ΔGi=−kBTln(ρiρmin)
(1)
where ΔGi is the free energy at a point relative to the least dense part of the surface, and ρi is the density at that point.

Validation of the REST2 Setup

To investigate the impact of our REST2 setup parameters on our results, we performed additional 60 ns simulations with higher replicas (64) and temperatures ranging between 300 and 600 K. Comparison with 60 ns with our setup (32 replicas and temperatures ranging from 300 and 500 K) shows that these new simulations explore less efficiently the protein conformational space. Thus, increasing the number of replicas and the maximum temperature does not lead to an improvement of the results. A rationale for this result is provided in the SI on p 8 and with Figures S1 and S2.

Results and Discussion

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We performed REST2 simulations (53) for 600 ns, using 32 replicas, for both AS and pAS in aqueous solution. Figures S3 and S4 provide details of the exchange between replicas. The root mean-square deviation (RMSD) of the simulations demonstrates that the lowest temperature replica was not trapped in local minima (Figure S5). The calculations were based on the DES-Amber (42) and the a99SB-disp force fields; (29) both were already used for IDPs. We report results at length for calculations using the former, while we provide a summary for the latter here and details in the Supporting Information.

Convergence

We calculated two quantities as a function of simulated time to investigate the convergence of the systems (Figure S6): (i) the running averages of the percentage of secondary structures. In particular, helix structures reached a plateau after 100 ns; (ii) the running averages of the Cα chemical shifts which converge closely to the experimental values within 100 ns. Because of the limitations of the standard usage of RMSD with IDPs such as AS, (105) the running RMSD of atomic positions was not taken into account beyond monitoring the simulations. Based on this analysis, we calculated all properties in the interval 100–600 ns.

Comparison with Experiment

Experimental data was compared to properties calculated from the trajectories after the determined convergence of 100 ns.
For each residue in the protein, the chemical shifts of backbone nitrogen, hydrogen, Cα, Cβ, and backbone carbonyl carbon atoms were calculated where present in the structure. Comparison was made with the experimental values published in ref (86) (Figure 2).

Figure 2

Figure 2. Calculated chemical shifts of (a) N, (b) Cα, (c) Cβ, (d) C, and (e) H atoms and in AS and pAS against the experimental data from Roche et al. (86) Correlation coefficients are given for AS (blue) and pAS (orange), respectively.

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The calculated chemical shifts of 15N, as well as the 13C NMR chemical shifts of Cα and Cβ are in excellent agreement with the experimental values, both for AS and pAS. The calculated shifts for the backbone carbonyl carbon atoms correlate less well with those obtained through experiment yet are still broadly comparable. The calculated shifts for heavy atoms overall are in better agreement than those reported previously by some of the authors in ref (54), possibly because a much longer exploration of the conformational ensemble has been covered here (a total of 90 ns of REST2 simulations in ref (54) and 500 ns REST2 simulations here). The predicted shifts for 1H NMR are generally less accurate, a well-known weakness of current chemical shift prediction methods, (106) and was previously observed in calculated values from MD simulations of AS in ref (54).
The calculated CD spectra of AS and pAS are in fair accord with experimentally measured spectra (27) (Figure 3). The minima of the calculated spectra are shifted 6 nm higher than the experimentally obtained values (204 and 198 nm, respectively), similar to what was found in ref (54).

Figure 3

Figure 3. Circular Dichroism spectra of the AS and pAS cluster midpoint structures obtained during the converged part of the simulations. Shading indicates the standard error.

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The minima of the calculated spectra range up to −15 × 10–3° cm2 dmol–1 for specific conformations, similar to what was found by the authors previously. As to be expected given the improvement in force fields, these minima average to −14 × 10–3°cm2 dmol–1 for both AS and pAS, in much better agreement with the experimental results compared to previous results using the Amber ff99SB-ildn force field and TIP3P water model. (54) The minima in the experimental spectra of Maltsev et al. are found at −19 × 10–3°cm2 dmol–1.

Effect of Phosphorylation on the Protein

The AS ensemble, on average, is less compact than the pAS ensemble (Figure 4). In AS, the C-terminal domain is further from the N-terminal domain, with the hydrophobic region situated between them. Phosphorylation increases the number of contacts between the C- and N-terminal domains, causing the hydrophobic region to shift to the side of the protein.

Figure 4

Figure 4. Structures of cluster midpoints representing the structural ensembles of AS (a-c) and pAS (d-f), from (a) 6.80% to (b) 48.85%, (c) 100%, (d) 5.80%, (e) 49.63%, and (f) 100%. See Table S7 for details.

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The ten largest conformational clusters of AS and pAS (from I to X in Figure 4) represent a total of 48.85% and 49.63% of the converged simulation trajectories, respectively (Table S7). The single conformational clusters are displayed in Figures S9 and S10.
The calculated mean hydrodynamic radius (RH) and the mean radii of gyration (Rg) decrease significantly upon phosphorylation. The distribution of Rg of AS is broader than that of pAS (Figure 5(a)). The first properties (within the standard deviation) agree with experiment (28.2 and 35.3 Å for AS and pAS, (22) respectively, Table 2).
Table 2. Calculated Properties of AS and pAS with Standard Deviation: (i) Hydrodynamic RH and Gyration (Rg) Radii of the Protein, (ii) Average Number of Hydrogen Bonds, and (iii) Average Number of Salt Bridges
ProteinRH [Å]Rg [Å]NSBNHB
AS43.9  ± 21.261.3 ± 15.23.13 ± 2.2319.52 ± 4.28
pAS34.0 ± 19.033.5 ± 12.83.78 ± 2.6420.67 ± 4.32
Mean change–9.9–27.80.651.15

Figure 5

Figure 5. AS (blue) and pAS (orange) Rg distributions (a) and corresponding approximate free energy landscapes over the distance between the protein termini and radii of gyration (b-c).

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An approximate estimate of the potential of mean force (PMF, see Methods), as a function of the radius of gyration and end-to-end distance of the protein, provides qualitative insights into the change in the free energy landscape of the protein upon phosphorylation. Figure 5(b-c) shows that the system passes from the shallow multibasin landscape of AS (Figure 5(b)), to the bivariate-like basin distribution for pAS (Figure 5(c)). This qualitative comparison suggests that phosphorylation induces a clear-cut separation between extended and compact ensembles of conformations for AS.
The intramolecular interactions between the hydrophobic region and the C-terminus decrease upon phosphorylation; the C-terminus instead interacts with the N-terminal domain (Figure 6). The first dozen residues interact with the hydrophobic region in AS, while they interact with the N-terminal region in pAS (Figure 6(b)).

Figure 6

Figure 6. (a) Contact maps of AS (triangle above) and pAS (triangle below) and (b) their differences. Brighter values correspond to closer distances in the corresponding triangle compared to the opposite triangle.

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The number of hydrogen bonds and salt bridges within their standard deviations does not change significantly upon phosphorylation (Figure 7, Table 2). While the first are almost exclusively formed within every single domain (Figure 7(a-b)), persistent salt bridges are formed for both proteins between the N-term and hydrophobic regions (K23–E20 and K58-E61, respectively; Figure 7(c)). Few salt bridges are formed between the C-terminal domain and one of the two other domains, such as E130–K80 in AS. The absence of the E130–K80 salt bridge in pAS might be caused by the presence of sodium counterions close to the pS129 residue (Figures 8 and 9).

Figure 7

Figure 7. Distribution of the total number of salt bridges (a) and hydrogen bonds (b) in AS (blue) and pAS (orange). Frequency with which intradomain (black labels) and interdomain (red labels) salt bridges (c) and hydrogen bonds (d) are found in AS and pAS. Salt bridges and hydrogen bonds are displayed that occur during at least 2 and 25% of the converged trajectory, respectively, in either the AS or pAS simulation.

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Figure 8

Figure 8. RDFs (g(r)) of (a-e) water oxygen atoms surrounding (a-b) backbone carbon atoms, (c) side-chain carbon, and (d-e) side-chain oxygen atoms. (f-g) RDFs of sodium ions surrounding side-chain oxygen atoms. (h) Integral of the TRRDF (n(r,t)) of sodium ions over 1 ns time windows. Insets show the integral of g(r) up to 5 Å.

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Figure 9

Figure 9. Number of water molecules (left column), sodium ions (middle column), and chloride ions (right column) in the first hydration shell surrounding the (a-c) N-terminal, (d-f) hydrophobic, and (g-i) C-terminal domains of the protein, as well as around (j-l) the S129 residue. Inset numbers indicate the mean and standard deviation of the distributions.

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The Average Solvent Accessible Surface Area (SASA) decreases upon phosphorylation (Table 3). However, the decline is rather small (within the standard deviation) at the N-term and in the hydrophobic region.
Table 3. Calculated SASA in the Three Domains of AS and pAS
ProteinSASAN-term [Å2]SASAHydrophR [Å2]SASAC-term [Å2]
AS6112.4 ± 603.13478.1 ± 585.66952.6 ± 762.4
pAS5732.3 ± 726.33104.0 ± 472.06035.0 ± 955.3
Mean change–380.1– 374.1–917.6

Phosphate Interactions

The phosphate group is fully solvent-exposed and associated with sodium counterions without interactions with pAS residues (Figures 8 and 9). Thus, its electrostatic field is strongly reduced, and its long-range electrostatic interactions with the C-terminus and N-terminus are expected to be strongly screened (Figure 7).
The S129 side-chain in AS is less hydrated than that in pAS: while the Oγ atom is surrounded on average by two water molecules in the first hydration shell in both AS and pAS, the second and third hydration shells contain many more water molecules in pAS (Figure 8). The serine oxidril group in AS instead forms a variety of intramolecular H-bonds (with K80, K96, K97, K102, E126, E130 and E131; Figure S19). S129 backbone units are observed to interact with both the solvent and nearby protein hydrogens in both AS and pAS. Thus, S129 in AS forms many more intramolecular contacts than the corresponding phosphorylated residue in pAS.
The hydration of AS N-terminal and hydrophobic domains is comparable to that of pAS (Figure 9(a-b)). The hydration of the C-terminal domain instead increases upon phosphorylation, possibly because of the presence of the highly charged group (from 12.3(3.3) water molecules surrounding S129 to 19.5(2.7) around pSer129).

Additional Simulations

The simulations of AS and pAS with the Amber a99SB-disp force field (29) show very similar results as those presented here, except for the phosphate hydration properties, which turn out to be less accurate than those of the DES-Amber force field (See Supporting Information, Sections 4, 5).
The simulations of the protein with monoprotonated phosphate (based on the a99SB-disp force field) turn out to be rather similar to those of pAS (see Supporting Information, Section 6). Thus, we conclude that if such species exist in equilibrium with pAS, they contribute to the protein structural ensemble similarly to pAS.

Role of Phosphorylation for AS Fibril Formation

Our study in line with experimental studies shows that phosphorylation and dephosphorylation of AS are likely normal physiological processes fine-tuning binding to lipids, (107,108) and they are not a clear marker of pathology. (12,13) These findings, however, do strengthen the prevailing view that phosphorylation of the monomer is also implicated in fibril formation, due to the change in the structural ensemble and relative positioning of the domains. In addition, the content of the β-hairpin-like structure in the hydrophobic region (calculated as in ref (24)) turns out to increase upon phosphorylation (Figure S23). This content is however smaller than that observed for the nonphysiological form, see details in the Supporting Information. As discussed in ref (24), these types of structures may be associated with amyloid-forming conformations, and hence, this finding does suggest that phosphorylation increases fibril formation starting from conformations similar to those found in the fibrils. (109,110) This might be consistent with the fact that almost all the proteins in the fibrils are phosphorylated in vivo. (11)

Conclusions

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Because of the presence in vivo of phosphorylated AS, a detailed understanding of the impact of phosphorylation on this protein is important for informing therapeutic strategies aimed at targeting AS in synucleinopathies. Here, we investigated the effects of phosphorylation on the structural ensemble of AS in solution by 600 ns REST2 simulations based on apt force fields such as DES-Amber and Amber a99SB-disp. Our REST2 simulations of AS, much longer than the previously reported ones, (54) are consistent with a plethora of experimental data.The physiological form of pAS turns out to be more compact than the unmodified protein. The phosphate moiety is solvent exposed without forming specific intramolecular interactions. The phosphorylation of the protein turns out to induce β-hairpin-like, amyloid-forming conformations. The increased propensity toward fibril formation might be consistent with the fact that about 90% AS in the LBs is phosphorylated. (11)

Data Availability

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GROMACS 2022.6 patched with PLUMED 2.9.0 was used to perform all MD simulations (https://www.gromacs.org/ and https://www.plumed.org/). All analysis employing third-party software are described and referenced in the Methods section. RDFs were obtained using the authors’ open-source Python package SPEADI (https://github.com/FZJ-JSC/speadi and https://pypi.org/project/SPEADI/). Charts and plots were made using the open-source Python package ProPlot (https://github.com/proplot-dev/proplot). Molecular structures were visualized using Open-Source PyMOL (https://github.com/schrodinger/pymol-open-source). Primary data available to reproduce the study (parametrized GROMACS topologies, input files, and trajectories) are deposited in Zenodo: https://zenodo.org/records/12605636.

Supporting Information

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The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jcim.4c01172.

  • Detailed experimental setup (including all GROMACS parameters), analysis and comparison with results obtained with other force fields (PDF)

  • Structures of the 25 cluster midpoints are included for both AS and pAS (ZIP)

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Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

Author Information

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  • Corresponding Author
    • Giulia Rossetti - Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany;  Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany;  Department of Neurology, RWTH Aachen University, 52074 Aachen, Germany;  Orcidhttps://orcid.org/0000-0002-2032-4630;  Email: [email protected]
  • Authors
    • Emile de Bruyn - Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany;  Department of Physics, RWTH Aachen University, 52062 Aachen, Germany;  Orcidhttps://orcid.org/0000-0002-8748-2553
    • Anton Emil Dorn - Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany;  Faculty of Biology, University of Duisburg-Essen, 45141 Essen, Germany
    • Claudio Fernandez - Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPINAT), Partner of the Max Planck Institute for Multidisciplinary Sciences (MPINAT, MPG), Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina;  Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany;  Orcidhttps://orcid.org/0000-0003-0454-7735
    • Tiago F. Outeiro - Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37075 Göttingen, Germany;  Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany;  Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
    • Jörg B. Schulz - Department of Physics, RWTH Aachen University, 52062 Aachen, Germany;  Department of Neurology, RWTH Aachen University, 52074 Aachen, Germany;  JARA Brain Institute Molecular Neuroscience and Neuroimaging (INM-11), Research Centre Jülich and RWTH Aachen University, 52074 Aachen, Germany
    • Paolo Carloni - Department of Physics, RWTH Aachen University, 52062 Aachen, Germany;  Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
  • Author Contributions

    E.d.B. and A.E.D. equally contributed to this work.

  • Notes
    The authors declare no competing financial interest.

Acknowledgments

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TFO is supported by DFG (SFB1286-B8) and under Germany’s Excellence Strategy - EXC 2067/1- 390729940. This work was partially performed as part of the Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) and received funding from the Helmholtz Association of German Research Centers. Open Access publication funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 491111487. The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu for funding this project by providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS Supercomputer JUWELS at Jülich Supercomputing Centre (JSC). (111−114) The authors gratefully acknowledge computing time on the supercomputer JURECA (115) at Forschungszentrum Jülich under grant no. 30260. The authors gratefully acknowledge insightful discussions with Stefano Piana-Agostinetti regarding the choice of force field parameters, in particular with respect to the hydration of the phosphate group.

References

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    N-terminal acetylation of α-synuclein induces increased transient helical propensity and decreased aggregation rates in the intrinsically disordered monomer
    Kang, Lijuan; Moriarty, Gina M.; Woods, Lucy A.; Ashcroft, Alison E.; Radford, Sheena E.; Baum, Jean
    Protein Science (2012), 21 (7), 911-917CODEN: PRCIEI; ISSN:1469-896X. (Wiley-Blackwell)
    The conformational properties of sol. α-synuclein, the primary protein found in patients with Parkinson's disease, are thought to play a key role in the structural transition to amyloid fibrils. In this work, we report that recombinant 100% N-terminal acetylated α-synuclein purified under mild physiol. conditions presents as a primarily monomeric protein, and that the N-terminal acetyl group affects the transient secondary structure and fibril assembly rates of the protein. Residue-specific NMR chem. shift anal. indicates substantial increase in transient helical propensity in the first 9 N-terminal residues, as well as smaller long-range changes in residues 28-31, 43-46, and 50-66: regions in which the three familial mutations currently known to be causative of early onset disease are found. In addn., we show that the N-terminal acetylated protein forms fibrils that are morphol. similar to those formed from nonacetylated α-synuclein, but that their growth rates are slower. Our results highlight that N-terminal acetylation does not form significant nos. of dimers, tetramers, or higher mol. wt. species, but does alter the conformational distributions of monomeric α-synuclein species in regions known to be important in metal binding, in assocn. with membranes, and in regions known to affect fibril formation rates.
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    Trexler, A. J.; Rhoades, E. N-terminal Acetylation Is Critical for Forming α-helical Oligomer of α-synuclein. Protein Sci. 2012, 21, 601– 605,  DOI: 10.1002/pro.2056
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    N-terminal acetylation is critical for forming α-helical oligomer of α-synuclein
    Trexler, Adam J.; Rhoades, Elizabeth
    Protein Science (2012), 21 (5), 601-605CODEN: PRCIEI; ISSN:1469-896X. (Wiley-Blackwell)
    The aggregation of the protein α-synuclein (AS) is crit. to the pathogenesis of Parkinson's disease. Although generally described as an unstructured monomer, recent evidence suggests that the native form of AS may be an α-helical tetramer which resists aggregation. Here, we show that N-terminal acetylation in combination with a mild purifn. protocol results in an oligomeric form of AS with partial α-helical structure. N-terminal acetylation of AS could have important implications for both the native and pathol. structures and functions of AS. Through our demonstration of a recombinant expression system, our results represent an important step toward biochem. and biophys. characterization of this potentially important form of AS.
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    Maltsev, A. S.; Ying, J.; Bax, A. Impact of N-terminal acetylation of α-synuclein on its random coil and lipid binding properties. Biochemistry 2012, 51, 5004– 5013,  DOI: 10.1021/bi300642h
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    Impact of N-Terminal Acetylation of α-Synuclein on Its Random Coil and Lipid Binding Properties
    Maltsev, Alexander S.; Ying, Jinfa; Bax, Ad
    Biochemistry (2012), 51 (25), 5004-5013CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
    N-Terminal acetylation of α-synuclein (aS), a protein implicated in the etiol. of Parkinson's disease, is common in mammals. The impact of this modification on the protein's structure and dynamics in free soln. and on its membrane binding properties has been evaluated by high-resoln. NMR and CD spectroscopy. While no tetrameric form of acetylated aS could be isolated, N-terminal acetylation resulted in chem. shift perturbations of the first 12 residues of the protein that progressively decreased with the distance from the N-terminus. The directions of the chem. shift changes and small changes in backbone 3JHH couplings are consistent with an increase in the α-helicity of the first six residues of aS, although a high degree of dynamic conformational disorder remains and the helical structure is sampled <20% of the time. Chem. shift and 3JHH data for the intact protein are virtually indistinguishable from those recorded for the corresponding N-terminally acetylated and nonacetylated 15-residue synthetic peptides. An increase in α-helicity at the N-terminus of aS is supported by CD data on the acetylated peptide and by weak medium-range nuclear Overhauser effect contacts indicative of α-helical character. The remainder of the protein has chem. shift values that are very close to random coil values and indistinguishable between the two forms of the protein. No significant differences in the fibrillation kinetics were obsd. between acetylated and nonacetylated aS. However, the lipid binding properties of aS are strongly impacted by acetylation and exhibit distinct behavior for the first 12 residues, indicative of an initiation role for the N-terminal residues in an "initiation-elongation" process of binding to the membrane.
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    Piana, S.; Robustelli, P.; Tan, D.; Chen, S.; Shaw, D. E. Development of a force field for the simulation of single-chain proteins and protein-protein complexes. J. Chem. Theory Comput. 2020, 16, 2494– 2507,  DOI: 10.1021/acs.jctc.9b00251
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    Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes
    Piana, Stefano; Robustelli, Paul; Tan, Dazhi; Chen, Songela; Shaw, David E.
    Journal of Chemical Theory and Computation (2020), 16 (4), 2494-2507CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    The accuracy of atomistic physics-based force fields for the simulation of biol. macromols. has typically been benchmarked exptl. using biophys. data from simple, often single-chain systems. In the case of proteins, the careful refinement of force field parameters assocd. with torsion-angle potentials and the use of improved water models have enabled a great deal of progress toward the highly accurate simulation of such monomeric systems in both folded and, more recently, disordered states. In living organisms, however, proteins constantly interact with other macromols., such as proteins and nucleic acids, and these interactions are often essential for proper biol. function. Here, the authors show that state-of-the-art force fields tuned to provide an accurate description of both ordered and disordered proteins can be limited in their ability to accurately describe protein-protein complexes. This observation prompted us to perform an extensive reparameterization of one variant of the Amber protein force field. The objective involved refitting not only the parameters assocd. with torsion-angle potentials, but also the parameters used to model nonbonded interactions, the specification of which is expected to be central to the accurate description of multicomponent systems. The resulting force field, which the authors call DES-Amber, allows for more accurate simulations of protein-protein complexes, while still providing a state-of-the-art description of both ordered and disordered single-chain proteins. Despite the improvements, calcd. protein-protein assocn. free energies still appear to deviate substantially from expt., a result suggesting that more fundamental changes to the force field, such as the explicit treatment of polarization effects, may simultaneously further improve the modeling of single-chain proteins and protein-protein complexes.
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    Robustelli, P.; Piana, S.; Shaw, D. E. Developing a molecular dynamics force field for both folded and disordered protein states. Proc. Natl. Acad. Sci. U. S. A. 2018, 115, E4758– E4766,  DOI: 10.1073/pnas.1800690115
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    Developing a molecular dynamics force field for both folded and disordered protein states
    Robustelli, Paul; Piana, Stefano; Shaw, David E.
    Proceedings of the National Academy of Sciences of the United States of America (2018), 115 (21), E4758-E4766CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
    Mol. dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any phys. model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the art force fields, and compare the results to over 9000 available exptl. data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with expt. for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB-disp, should thus greatly expand the range of biol. systems amenable to MD simulation. A similar approach could be taken to improve other force fields.
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    Wang, W. Recent advances in atomic molecular dynamics simulation of intrinsically disordered proteins. Phys. Chem. Chem. Phys. 2021, 23, 777– 784,  DOI: 10.1039/D0CP05818A
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    Recent advances in atomic molecular dynamics simulation of intrinsically disordered proteins
    Wang, Wenning
    Physical Chemistry Chemical Physics (2021), 23 (2), 777-784CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
    A review. Intrinsically disordered proteins (IDPs) play important roles in cellular functions. The inherent structural heterogeneity of IDPs makes the high-resoln. exptl. characterization of IDPs extremely difficult. Mol. dynamics (MD) simulation could provide the at.-level description of the structural and dynamic properties of IDPs. This perspective reviews the recent progress in at. MD simulation studies of IDPs, including the development of force fields and sampling methods, as well as applications in IDP-involved protein-protein interactions. The employment of large-scale simulations and advanced sampling techniques allows more accurate estn. of the thermodn. and kinetics of IDP-mediated protein interactions, and the holistic landscape of the binding process of IDPs is emerging.
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    Pedersen, K. B.; Flores-Canales, J. C.; Schiøtt, B. Predicting molecular properties of α-synuclein using force fields for intrinsically disordered proteins. Proteins: Struct., Funct., Bioinf. 2023, 91, 47– 61,  DOI: 10.1002/prot.26409
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    Robustelli, P.; de Opakua, A. I.; Campbell-Bezat, C.; Giordanetto, F.; Becker, S.; Zweckstetter, M.; Pan, A. C.; Shaw, D. E. Molecular Basis of Small-Molecule Binding To α-Synuclein. J. Am. Chem. Soc. 2022, 144, 2501– 2510,  DOI: 10.1021/jacs.1c07591
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    Molecular Basis of Small-Molecule Binding to α-Synuclein
    Robustelli, Paul; Ibanez-de-Opakua, Alain; Campbell-Bezat, Cecily; Giordanetto, Fabrizio; Becker, Stefan; Zweckstetter, Markus; Pan, Albert C.; Shaw, David E.
    Journal of the American Chemical Society (2022), 144 (6), 2501-2510CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Intrinsically disordered proteins (IDPs) are implicated in many human diseases. They have generally not been amenable to conventional structure-based drug design, however, because their intrinsic conformational variability has precluded an at.-level understanding of their binding to small mols. Here we present long-time-scale, at.-level mol. dynamics (MD) simulations of monomeric α-synuclein (an IDP whose aggregation is assocd. with Parkinson's disease) binding the small-mol. drug fasudil in which the obsd. protein-ligand interactions were found to be in good agreement with previously reported NMR chem. shift data. In our simulations, fasudil, when bound, favored certain charge-charge and π-stacking interactions near the C terminus of α-synuclein but tended not to form these interactions simultaneously, rather breaking one of these interactions and forming another nearby (a mechanism we term dynamic shuttling). Further simulations with small mols. chosen to modify these interactions yielded binding affinities and key structural features of binding consistent with subsequent NMR expts., suggesting the potential for MD-based strategies to facilitate the rational design of small mols. that bind with disordered proteins.
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    Homeyer, N.; Horn, A. H.; Lanig, H.; Sticht, H. AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine. J. Mol. Model. 2006, 12, 281– 289,  DOI: 10.1007/s00894-005-0028-4
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    33
    AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine
    Homeyer, Nadine; Horn, Anselm H. C.; Lanig, Harald; Sticht, Heinrich
    Journal of Molecular Modeling (2006), 12 (3), 281-289CODEN: JMMOFK; ISSN:0948-5023. (Springer GmbH)
    We report a consistent set of AMBER force-field parameters for the most common phosphorylated amino acids, phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine in different protonation states. The calcn. of at. charges followed the original restrained electrostatic potential fitting procedure used to det. the charges for the parm94/99 parameter set, taking α-helical and β-strand conformations of the corresponding ACE-/NME-capped model peptide backbone into account. Missing force-field parameters were taken directly from the general AMBER force field (gaff) and the parm99 data set with minor modifications, or were newly generated based on ab initio calcns. for model systems. Final parameters were validated by geometry optimizations and mol.-dynamics simulations. Template libraries for the phosphorylated amino acids in Leap format and corresponding frcmod parameters files are made available.
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    Steinbrecher, T.; Latzer, J.; Case, D. Revised AMBER parameters for bioorganic phosphates. J. Chem. Theory Comput. 2012, 8, 4405– 4412,  DOI: 10.1021/ct300613v
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    Revised AMBER Parameters for Bioorganic Phosphates
    Steinbrecher, T.; Latzer, J.; Case, D. A.
    Journal of Chemical Theory and Computation (2012), 8 (11), 4405-4412CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    We report AMBER force field parameters for biol. simulations involving phosphorylation of serine, threonine, or tyrosine. The initial parameters used RESP fitting for the at. partial charges and std. values for all other parameters such as Lennard-Jones coeffs. These were refined with the aid of a thermodn. cycle consisting of exptl. detd. pKa values, solvation energies from mol. dynamics free energy simulations, and gas phase basicities from QM calcns. A polarization energy term was included to account for the charge d. change between the gas phase and soln., and solvation free energies were detd. using thermodn. integration. Parameter adjustment is required to obtain consistent thermodn. results with better balanced electrostatic interactions between water and the phosphate oxygens. To achieve this, we modified the phosphate oxygen radii. A thermodynamically consistent parameter set can be derived for monoanions and requires an increase of the van der Waals phosphate oxygen radii of approx. 0.09 Å. Larger, residue-specific radii appear to be needed for dianions. The revised parameters developed here should be of particular interest for environments where simulations of multiple protonation states may be of interest.
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    Khoury, G. A.; Thompson, J. P.; Smadbeck, J.; Kieslich, C. A.; Floudas, C. A. Forcefield_PTM: Ab initio charge and AMBER forcefield parameters for frequently occurring post-translational modifications. J. Chem. Theory Comput. 2013, 9, 5653– 5674,  DOI: 10.1021/ct400556v
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    Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications
    Khoury, George A.; Thompson, Jeff P.; Smadbeck, James; Kieslich, Chris A.; Floudas, Christodoulos A.
    Journal of Chemical Theory and Computation (2013), 9 (12), 5653-5674CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    The authors introduce Forcefield_PTM, a set of AMBER forcefield parameters consistent with ff03 for 32 common post-translational modifications. Partial charges were calcd. through ab initio calcns. and a two-stage RESP-fitting procedure in an ether-like implicit solvent environment. The charges are generally consistent with others previously reported for phosphorylated amino acids, and trimethyllysine, using different parametrization methods. Pairs of modified structures and their corresponding unmodified structures were curated from the PDB for both single and multiple modifications. Background structural similarity was assessed in the context of secondary and tertiary structures from the global data set. Next, the charges derived for Forcefield_PTM were tested on a macroscopic scale using unrestrained all-atom Langevin mol. dynamics simulations in AMBER for 34 (17 pairs of modified/unmodified) systems in implicit solvent. Assessment was performed in the context of secondary structure preservation, stability in energies, and correlations between the modified and unmodified structure trajectories on the aggregate. As an illustration of their utility, the parameters were used to compare the structural stability of the phosphorylated and dephosphorylated forms of OdhI. Microscopic comparisons between quantum and AMBER single point energies along key χ torsions on several PTMs were performed, and corrections to improve their agreement in terms of mean-squared errors and squared correlation coeffs. were parametrized. This forcefield for post-translational modifications in condensed-phase simulations can be applied to a no. of biol. relevant and timely applications including protein structure prediction, protein and peptide design, and docking and to study the effect of PTMs on folding and dynamics. The authors make the derived parameters and an assocd. interactive webtool capable of performing post-translational modifications on proteins using Forcefield_PTM available at http://selene.princeton.edu/FFPTM.
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    Petrov, D.; Margreitter, C.; Grandits, M.; Oostenbrink, C.; Zagrovic, B. A systematic framework for molecular dynamics simulations of protein post-translational modifications. PLoS computational biology 2013, 9, e1003154,  DOI: 10.1371/journal.pcbi.1003154
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    A systematic framework for molecular dynamics simulations of protein post-translational modifications
    Petrov, Drazen; Margreitter, Christian; Grandits, Melanie; Oostenbrink, Chris; Zagrovic, Bojan
    PLoS Computational Biology (2013), 9 (7), e1003154CODEN: PCBLBG; ISSN:1553-7358. (Public Library of Science)
    By directly affecting structure, dynamics and interaction networks of their targets, post-translational modifications (PTMs) of proteins play a key role in different cellular processes ranging from enzymic activation to regulation of signal transduction to cell-cycle control. Despite the great importance of understanding how PTMs affect proteins at the atomistic level, a systematic framework for treating post-translationally modified amino acids by mol. dynamics (MD) simulations, a premier high-resoln. computational biol. tool, has never been developed. Here, we report and validate force field parameters (GROMOS 45a3 and 54a7) required to run and analyze MD simulations of more than 250 different types of enzymic and non-enzymic PTMs. The newly developed GROMOS 54a7 parameters in particular exhibit near chem. accuracy in matching exptl. measured hydration free energies (RMSE = 4.2 kJ/mol over the validation set). Using this tool, we quant. show that the majority of PTMs greatly alter the hydrophobicity and other physico-chem. properties of target amino acids, with the extent of change in many cases being comparable to the complete range spanned by native amino acids.
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    Zhong, B.; Song, G.; Chen, H.-F. Balanced Force Field ff03CMAP Improving the Dynamics Conformation Sampling of Phosphorylation Site. International Journal of Molecular Sciences 2022, 23, 11285,  DOI: 10.3390/ijms231911285
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    Vymětal, J.; Jurásková, V.; Vondrášek, J. AMBER and CHARMM force fields inconsistently portray the microscopic details of phosphorylation. J. Chem. Theory Comput. 2019, 15, 665– 679,  DOI: 10.1021/acs.jctc.8b00715
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    AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation
    Vymetal, Jiri; Juraskova, Veronika; Vondrasek, Jiri
    Journal of Chemical Theory and Computation (2019), 15 (1), 665-679CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    Phosphorylation of serine, threonine, and tyrosine is one of the most frequently occurring and crucial post-translational modifications of proteins often assocd. with important structural and functional changes. The authors studied the direct effect of phosphorylation on the intrinsic conformational preferences of amino acids as a potential trigger of larger structural events. The authors conducted a comparative study of force fields on terminally capped amino acids (dipeptides) as the simplest model for phosphorylation. The authors' bias-exchange metadynamics simulations revealed that all model dipeptides sampled a great heterogeneity of ensembles affected by introduction of mono- and dianionic phosphate groups. However, the detected changes in populations of backbone conformers and side-chain rotamers did not reveal a strong discriminatory shift in preferences, as could be anticipated for the bulky, charged phosphate group. Furthermore, the AMBER and CHARMM force fields provided inconsistent populations of individual conformers as well as net structural trends upon phosphorylation. Detailed anal. of ensembles revealed competition between hydration and formation of internal hydrogen bonds involving amide hydrogens and the phosphate group. The obsd. difference in hydration free energy and potential for hydrogen bonding in individual force fields could be attributed to the different partial at. charges used in each force field and, hence, the different parametrization strategies. Nevertheless, conformational propensities and net structural changes upon phosphorylation are difficult to ext. from exptl. measurements, and existing exptl. data provide limited guidance for force field assessment and further development.
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    Rieloff, E.; Skepö, M. Phosphorylation of a disordered peptide─Structural effects and force field inconsistencies. J. Chem. Theory Comput. 2020, 16, 1924– 1935,  DOI: 10.1021/acs.jctc.9b01190
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    Phosphorylation of a Disordered Peptide-Structural Effects and Force Field Inconsistencies
    Rieloff, Ellen; Skepoe, Marie
    Journal of Chemical Theory and Computation (2020), 16 (3), 1924-1935CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    Phosphorylation is one of the most abundant types of post-translational modifications of intrinsically disordered proteins (IDPs). This study examines the conformational changes in the 15-residue-long N-terminal fragment of the IDP statherin upon phosphorylation, using computer simulations with two different force fields: AMBER ff99SB-ILDN and CHARMM36m. The results from the simulations are compared with exptl. small-angle X-ray scattering (SAXS) and CD data. In the unphosphorylated state, the two force fields are in excellent agreement regarding global structural properties such as size and shape. However, they exhibit some differences in the extent and type of the secondary structure. In the phosphorylated state, neither of the force fields performs well compared to the exptl. data. Both force fields show a compaction of the peptide upon phosphorylation, greater than what is seen in SAXS expts., although they differ in the local structure. While the CHARMM force field increases the fraction of bends in the peptide as a response to strong interactions between the phosphorylated residues and arginines, the AMBER force field shows an increase of the helical content in the N-terminal part of the peptide, where the phosphorylated residues reside, in better agreement with CD results.
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    Rieloff, E.; Skepö, M. Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: a Force Field Comparison. International Journal of Molecular Sciences 2021, 22, 10174,  DOI: 10.3390/ijms221810174
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    Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: A Force Field Comparison
    Rieloff, Ellen; Skepoe, Marie
    International Journal of Molecular Sciences (2021), 22 (18), 10174CODEN: IJMCFK; ISSN:1422-0067. (MDPI AG)
    Phosphorylation is a common post-translational modification among intrinsically disordered proteins and regions, which helps regulate function by changing the protein conformations, dynamics, and interactions with binding partners. To fully comprehend the effects of phosphorylation, computer simulations are a helpful tool, although they are dependent on the accuracy of the force field used. Here, we compared the conformational ensembles produced by Amber ff99SB-ILDN+TIP4P-D and CHARMM36m, for four phosphorylated disordered peptides ranging in length from 14-43 residues. CHARMM36m consistently produced more compact conformations with a higher content of bends, mainly due to more stable salt bridges. Based on comparisons with exptl. size ests. for the shortest and longest peptide, CHARMM36m appeared to overestimate the compactness. The difference between the force fields was largest for the peptide showing the greatest sepn. between pos. charged and phosphorylated residues, in line with the importance of charge distribution. For this peptide, the conformational ensemble did not change significantly upon increasing the ionic strength from 0 mM to 150 mM, despite a redn. of the salt-bridging probability in the CHARMM36m simulations, implying that salt concn. has negligible effects in this study.
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    Man, V. H.; He, X.; Gao, J.; Wang, J. Phosphorylation of Tau R2 Repeat Destabilizes Its Binding to Microtubules: A Molecular Dynamics Simulation Study. ACS Chem. Neurosci. 2023, 14, 458,  DOI: 10.1021/acschemneuro.2c00611
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    Phosphorylation of Tau R2 Repeat Destabilizes Its Binding to Microtubules: A Molecular Dynamics Simulation Study
    Man, Viet Hoang; He, Xibing; Gao, Jie; Wang, Junmei
    ACS Chemical Neuroscience (2023), 14 (3), 458-467CODEN: ACNCDM; ISSN:1948-7193. (American Chemical Society)
    Phosphorylation, the most popular post-translational modification of tau protein, plays an important role in regulating tau physiol. functions. However, aberrant phosphorylation attenuates the binding affinity of tau to a microtubule (MT), resulting in MT destabilization followed by accumulation of neurofibrillary tangles in the brain. There are in total 85 potential phosphorylation sites in a full-length tau protein, and about half of them are abnormal as they occur in tau of Alzheimer's disease (AD) brain only. The authors studied the impact of abnormal Ser289, Ser293, and Ser289/Ser293 phosphorylation on tau R2-MT binding and the conformation of tau R2 using mol. dynamics simulation. The phosphorylation significantly affected R2-MT interaction and reduced the binding affinity of tau R2 peptides to MTs. Free energy decompn. anal. suggested that the post-translational modified residues themselves made a significant contribution to destabilize tau repeat R2-MT binding. Therefore, the phosphorylation may attenuate the binding affinity of tau to MTs. Addnl., the phosphorylation also enhanced helix-coil transition of monomeric R2 peptides, which may result in the acceleration of tau aggregation. Since these phosphorylated sites were not examd. in previous exptl. studies, the authors' finding through all-atom mol. dynamics simulations and free energy anal. can inspire exptl. scientists to study the impact of the phosphorylation on MT binding and aggregation of full-length tau and the pathol. roles of the phosphorylation at those sites in AD development through in vitro/in vivo assays.
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    Tucker, M. R.; Piana, S.; Tan, D.; LeVine, M. V.; Shaw, D. E. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded Dna Molecules and Dna-Protein Complexes. J. Phys. Chem. B 2022, 126, 4442– 4457,  DOI: 10.1021/acs.jpcb.1c10971
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    Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes
    Tucker, Maxwell R.; Piana, Stefano; Tan, Dazhi; LeVine, Michael V.; Shaw, David E.
    Journal of Physical Chemistry B (2022), 126 (24), 4442-4457CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
    Although mol. dynamics (MD) simulations have been used extensively to study the structural dynamics of proteins, the role of MD simulation in studies of nucleic acid based systems has been more limited. One contributing factor to this disparity is the historically lower level of accuracy of the phys. models used in such simulations to describe interactions involving nucleic acids. By modifying nonbonded and torsion parameters of a force field from the Amber family of models, we recently developed force field parameters for RNA that achieve a level of accuracy comparable to that of state-of-the-art protein force fields. Here we report force field parameters for DNA, which we developed by transferring nonbonded parameters from our recently reported RNA force field and making subsequent adjustments to torsion parameters. We have also modified the backbone charges in both the RNA and DNA parameter sets to make the treatment of electrostatics compatible with our recently developed variant of the Amber protein and ion force field. We name the force field resulting from the union of these three parameter sets (the new DNA parameters, the revised RNA parameters, and the existing protein and ion parameters) DES-Amber. Extensive testing of DES-Amber indicates that it can describe the thermal stability and conformational flexibility of single- and double-stranded DNA systems with a level of accuracy comparable to or, esp. for disordered systems, exceeding that of state-of-the-art nucleic acid force fields. Finally, we show that, in certain favorable cases, DES-Amber can be used for long-timescale simulations of protein-nucleic acid complexes.
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    Irbäck, A.; Mohanty, S. Profasi: a Monte Carlo Simulation Package for Protein Folding and Aggregation. J. Comput. Chem. 2006, 27, 1548– 1555,  DOI: 10.1002/jcc.20452
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    PROFASI: A Monte Carlo simulation package for protein folding and aggregation
    Irback Anders; Mohanty Sandipan
    Journal of computational chemistry (2006), 27 (13), 1548-55 ISSN:0192-8651.
    We present a flexible and efficient program package written in C++, PROFASI, for simulating protein folding and aggregation. The systems are modeled using an all-atom description of the protein chains with only torsional degrees of freedom, and implicit water. The program package has a modular structure that makes the interaction potential easy to modify. The currently implemented potential is able to fold several peptides with about 20 residues, and has also been used to study aggregation and force-induced unfolding. The simulation methods implemented in PROFASI are Monte Carlo-based and include a semilocal move and simulated tempering. Adding new updates is easy. The code runs fast in both single- and multi-chain applications, as is illustrated by several examples.
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    D’Urzo, A.; Konijnenberg, A.; Rossetti, G.; Habchi, J.; Li, J.; Carloni, P.; Sobott, F.; Longhi, S.; Grandori, R. Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound To a Partner By Combined Esi-Im-Ms and Modeling. Journal of The American Society for Mass Spectrometry 2015, 26, 472– 481,  DOI: 10.1007/s13361-014-1048-z
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    Cragnell, C.; Rieloff, E.; Skepö, M. Utilizing Coarse-Grained Modeling and Monte Carlo Simulations To Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions. J. Mol. Biol. 2018, 430, 2478– 2492,  DOI: 10.1016/j.jmb.2018.03.006
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    Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions
    Cragnell, Carolina; Rieloff, Ellen; Skepoe, Marie
    Journal of Molecular Biology (2018), 430 (16), 2478-2492CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)
    In this study, we have used the coarse-grained model developed for the intrinsically disordered saliva protein (IDP) Histatin 5, on an exptl. selection of monomeric IDPs, and we show that the model is generally applicable when electrostatic interactions dominate the intra-mol. interactions. Exptl. and theor. calcd. small-angle X-ray scattering data are presented in the form of Kratky plots, and discussions are made with respect to polymer theory and the self-avoiding walk model. Furthermore, the impact of electrostatic interactions is shown and related to estns. of the conformational ensembles obtained from computer simulations and "Flexible-meccano.". Special attention is given to the form factor and how it is affected by the salt concn., as well as the approxn. of using the form factor obtained under physiol. conditions to obtain the structure factor.
  46. 46
    Rieloff, E.; Tully, M. D.; Skepö, M. Assessing the Intricate Balance of Intermolecular Interactions Upon Self-Association of Intrinsically Disordered Proteins. J. Mol. Biol. 2019, 431, 511– 523,  DOI: 10.1016/j.jmb.2018.11.027
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    46
    Assessing the intricate balance of intermolecular interactions upon self-association of intrinsically disordered proteins
    Rieloff, Ellen; Tully, Mark D.; Skepoe, Marie
    Journal of Molecular Biology (2019), 431 (3), 511-523CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)
    Attractive interactions between intrinsically disordered proteins (IDPs) can be crucial for the functionality or, on the contrary, lead to the formation of harmful aggregates. For obtaining a mol. understanding of IDPs and their interactions, computer simulations have proven to be a valuable complement to expts. Here, we present a coarse-grained model and its applications to a system dominated by attractive interactions, namely, the self-assocn. of the saliva protein, statherin. SAXS expts. showed that statherin self-assocs. with increased protein concn., and that both an increased temp. and a lower ionic strength decreased the size of the formed complexes. The model captured the obsd. trends and provided insight into the size distribution. Hydrophobic interaction is considered to be the major driving force of self-assocn., while electrostatic repulsion represses growth. In addn., the model suggests that the decrease of assocn. no. with increased temp. is of entropic origin.
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    Shrestha, U. R.; Smith, J. C.; Petridis, L. Full Structural Ensembles of Intrinsically Disordered Proteins From Unbiased Molecular Dynamics Simulations. Communications Biology 2021, 4, 243,  DOI: 10.1038/s42003-021-01759-1
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    Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations
    Shrestha, Utsab R.; Smith, Jeremy C.; Petridis, Loukas
    Communications Biology (2021), 4 (1), 243CODEN: CBOIDQ; ISSN:2399-3642. (Nature Research)
    Mol. dynamics (MD) simulation is widely used to complement ensemble-averaged expts. of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chem. shift expts., for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, std. MD can reproduce exptl. NMR chem. shifts, but not small-angle scattering data, suggesting chem. shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.
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    Gupta, A.; Dey, S.; Hicks, A.; Zhou, H.-X. Artificial Intelligence Guided Conformational Mining of Intrinsically Disordered Proteins. Communications Biology 2022, 5, 610,  DOI: 10.1038/s42003-022-03562-y
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    Artificial intelligence guided conformational mining of intrinsically disordered proteins
    Gupta, Aayush; Dey, Souvik; Hicks, Alan; Zhou, Huan-Xiang
    Communications Biology (2022), 5 (1), 610CODEN: CBOIDQ; ISSN:2399-3642. (Nature Portfolio)
    Artificial intelligence recently achieved the breakthrough of predicting the three-dimensional structures of proteins. The next frontier is presented by intrinsically disordered proteins (IDPs), which, representing 30% to 50% of proteomes, readily access vast conformational space. Mol. dynamics (MD) simulations are promising in sampling IDP conformations, but only at extremely high computational cost. Here, we developed generative autoencoders that learn from short MD simulations and generate full conformational ensembles. An encoder represents IDP conformations as vectors in a reduced-dimensional latent space. The mean vector and covariance matrix of the training dataset are calcd. to define a multivariate Gaussian distribution, from which vectors are sampled and fed to a decoder to generate new conformations. The ensembles of generated conformations cover those sampled by long MD simulations and are validated by small-angle X-ray scattering profile and NMR chem. shifts. This work illustrates the vast potential of artificial intelligence in conformational mining of IDPs.
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    Yu, H.; Han, W.; Ma, W.; Schulten, K. Transient β-hairpin Formation in α-synuclein Monomer Revealed By Coarse-Grained Molecular Dynamics Simulation. J. Chem. Phys. 2015, 143, 243142,  DOI: 10.1063/1.4936910
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    Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation
    Yu, Hang; Han, Wei; Ma, Wen; Schulten, Klaus
    Journal of Chemical Physics (2015), 143 (24), 243142/1-243142/15CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
    Parkinson's disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform mol. dynamics simulations (over 180 μs in aggregated time) using a hybrid-resoln. model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in at. detail structural ensembles of wild type and mutant monomeric α-synuclein in aq. soln. The simulations reproduce structural properties of α-synuclein characterized in expts., such as secondary structure content, long-range contacts, chem. shifts, and 3J(HNHCα)-coupling consts. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation. (c) 2015 American Institute of Physics.
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    Cragnell, C.; Durand, D.; Cabane, B.; Skepö, M. Coarse-Grained Modeling of the Intrinsically Disordered Protein Histatin 5 in Solution: Monte Carlo Simulations in Combination With Saxs. Proteins: Struct., Funct., Bioinf. 2016, 84, 777– 791,  DOI: 10.1002/prot.25025
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    Coarse-grained modeling of the intrinsically disordered protein Histatin 5 in solution: Monte Carlo simulations in combination with SAXS
    Cragnell, Carolina; Durand, Dominique; Cabane, Bernard; Skepoe, Marie
    Proteins: Structure, Function, and Bioinformatics (2016), 84 (6), 777-791CODEN: PSFBAF; ISSN:1097-0134. (Wiley-Blackwell)
    Monte Carlo simulations and coarse-grained modeling have been used to analyze histatin 5 (His5), an unstructured short cationic salivary peptide known to have anticandidical properties. The calcd. scattering functions have been compared with intensity curves and the distance distribution function P(r) obtained from small angle X-ray scattering (SAXS), at both high and low salt concns. The aim was to achieve a mol. understanding and a physico-chem. insight of the obtained SAXS results and to gain information of the conformational changes of Histatin 5 due to altering salt content, charge distribution, and net charge. From a modeling perspective, the accuracy of the electrostatic interactions are of special interest. The used coarse-grained model was based on the primitive model in which charged hard spheres differing in charge and in size represent the ionic particles, and the solvent only enters the model through its relative permittivity. The Hamiltonian of the model comprises three different contributions: (i) excluded vols., (ii) electrostatic, and (iii) van der Waals interactions. Even though the model can be considered as gross omitting all atomistic details, a great correspondence is obtained with the exptl. results. Proteins 2016. © 2016 Wiley Periodicals, Inc.
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    Hyltegren, K.; Polimeni, M.; Skepö, M.; Lund, M. Integrating All-Atom and Coarse-Grained Simulations-Toward Understanding of Idps At Surfaces. J. Chem. Theory Comput. 2020, 16, 1843– 1853,  DOI: 10.1021/acs.jctc.9b01041
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    Garaizar, A.; Espinosa, J. R. Salt Dependent Phase Behavior of Intrinsically Disordered Proteins From a Coarse-Grained Model With Explicit Water and Ions. J. Chem. Phys. 2021, 155, 125103,  DOI: 10.1063/5.0062687
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    Salt dependent phase behavior of intrinsically disordered proteins from a coarse-grained model with explicit water and ions
    Garaizar, Adiran; Espinosa, Jorge R.
    Journal of Chemical Physics (2021), 155 (12), 125103CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
    Multivalent proteins and nucleic acids can self-assemble into biomol. condensates that contribute to compartmentalize the cell interior. Computer simulations offer a unique view to elucidate the mechanisms and key intermol. interactions behind the dynamic formation and dissoln. of these condensates. In this work, we present a novel approach to include explicit water and salt in sequence-dependent coarse-grained (CG) models for proteins and RNA, enabling the study of biomol. condensate formation in a salt-dependent manner. Our framework combines a reparameterized version of the HPS protein force field with the monoat. mW water model and the mW-ion potential for NaCl. We show how our CG model qual. captures the exptl. radius of the gyration trend of a subset of intrinsically disordered proteins and reproduces the exptl. protein concn. and water percentage of the human fused in sarcoma (FUS) low-complexity-domain droplets at physiol. salt concn. Moreover, we perform seeding simulations as a function of salt concn. for two antagonist systems: the engineered peptide PR25 and poly-uridine/poly-arginine mixts., finding good agreement with their reported in vitro phase behavior with salt concn. in both cases. Taken together, our work represents a step forward towards extending sequence-dependent CG models to include water and salt, and to consider their key role in biomol. condensate self-assembly. (c) 2021 American Institute of Physics.
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    Wang, L.; Friesner, R. A.; Berne, B. Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). J. Phys. Chem. B 2011, 115, 9431– 9438,  DOI: 10.1021/jp204407d
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    Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)
    Wang, Lingle; Friesner, Richard A.; Berne, B. J.
    Journal of Physical Chemistry B (2011), 115 (30), 9431-9438CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
    A small change in the Hamiltonian scaling in Replica Exchange with Solute Tempering (REST) is found to improve its sampling efficiency greatly, esp. for the sampling of aq. protein solns. in which there are large-scale solute conformation changes. Like the original REST (REST1), the new version (which the authors call REST2) also bypasses the poor scaling with system size of the std. Temp. Replica Exchange Method (TREM), reducing the no. of replicas (parallel processes) from what must be used in TREM. This redn. is accomplished by deforming the Hamiltonian function for each replica in such a way that the acceptance probability for the exchange of replica configurations does not depend on the no. of explicit water mols. in the system. For proof of concept, REST2 is compared with TREM and with REST1 for the folding of the trpcage and β-hairpin in water. The comparisons confirm that REST2 greatly reduces the no. of CPUs required by regular replica exchange and greatly increases the sampling efficiency over REST1. This method reduces the CPU time required for calcg. thermodn. avs. and for the ab initio folding of proteins in explicit water.
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    Rossetti, G.; Musiani, F.; Abad, E.; Dibenedetto, D.; Mouhib, H.; Fernandez, C. O.; Carloni, P. Conformational ensemble of human α-synuclein physiological form predicted by molecular simulations. Phys. Chem. Chem. Phys. 2016, 18, 5702– 5706,  DOI: 10.1039/C5CP04549E
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    Conformational ensemble of human α-synuclein physiological form predicted by molecular simulations
    Rossetti, G.; Musiani, F.; Abad, E.; Dibenedetto, D.; Mouhib, H.; Fernandez, C. O.; Carloni, P.
    Physical Chemistry Chemical Physics (2016), 18 (8), 5702-5706CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
    The authors performed enhanced sampling mol. dynamics simulations of N-terminally acetylated human α-synuclein, an intrinsically disordered protein involved in Parkinson's disease. The calcns., consistent with expts., suggested that the post-translational modification leads to the formation of a transient amphipathic α-helix. The latter, absent in the non-physiol. form, alters protein dynamics at the N-terminal and intramol. interactions.
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    Palomino-Hernandez, O.; Buratti, F. A.; Sacco, P. S.; Rossetti, G.; Carloni, P.; Fernandez, C. O. Role of Tyr-39 for the Structural Features of α-Synuclein and for the Interaction with a Strong Modulator of Its Amyloid Assembly. International journal of molecular sciences 2020, 21, 5061,  DOI: 10.3390/ijms21145061
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    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
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    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.
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    Uluca, B.; Viennet, T.; Petrović, D.; Shaykhalishahi, H.; Weirich, F.; Gönülalan, A.; Strodel, B.; Etzkorn, M.; Hoyer, W.; Heise, H. DNP-enhanced MAS NMR: a tool to snapshot conformational ensembles of α-synuclein in different states. Biophysical journal 2018, 114, 1614– 1623,  DOI: 10.1016/j.bpj.2018.02.011
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    Jain, K.; Ghribi, O.; Delhommelle, J. Folding free-energy landscape of α-synuclein (35–97) via replica exchange molecular dynamics. J. Chem. Inf. Model. 2021, 61, 432– 443,  DOI: 10.1021/acs.jcim.0c01278
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    Folding Free-Energy Landscape of α-Synuclein (35-97) Via Replica Exchange Molecular Dynamics
    Jain, Karnesh; Ghribi, Othman; Delhommelle, Jerome
    Journal of Chemical Information and Modeling (2021), 61 (1), 432-443CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
    The misfolding and aggregation of α-synuclein (α-syn) in Lewy bodies are implicated in the pathogenesis of various neurodegenerative disorders, such as Parkinson's disease and dementia. The formation of α-syn fibrils is a complex process, involving various intermediates and oligomeric forms. These intermediates establish at an early stage of aggregation and subsequently lead to fibrillation. Detg. which conformations are accessible to monomeric α-syn and esp., as shown in a recent work, to the central amino acids from residue 35 to residue 97 (63 residues) is thus crucial to understand the formation of these oligomers. Here, the authors carry out extensive replica exchange mol. dynamics (total time-18 μs) with an all-atom model and explicit solvent to characterize the free-energy landscape of human α-syn (residue 35 to residue 97). The simulation results lead the authors to identify two free-energy basins. Clustering anal. for the deepest free-energy min. reveals a compact structure, with a secondary structure predominantly α-helix, while the shallower min. corresponds to an elongated conformation, also predominantly α-helix. Furthermore, at physiol. temp., conformational rearrangements happen via helix breaks due to the presence of glycine. Also the most likely conformations were characterized by the α-helix structure rather than the β-hairpin structure (for residue 38 to residue 53), in contrast with prior simulation studies using coarse-grained models or an implicit solvent. For higher temps., a shift in secondary structure with a decrease in the population of α-helix in favor of random coils, β-bend, and β-turns. were obsd.
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    Ilie, I. M.; Nayar, D.; Den Otter, W. K.; Van Der Vegt, N. F.; Briels, W. J. Intrinsic conformational preferences and interactions in α-synuclein fibrils: insights from molecular dynamics simulations. J. Chem. Theory Comput. 2018, 14, 3298– 3310,  DOI: 10.1021/acs.jctc.8b00183
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    Intrinsic Conformational Preferences and Interactions in α-Synuclein Fibrils: Insights from Molecular Dynamics Simulations
    Ilie, Ioana M.; Nayar, Divya; den Otter, Wouter K.; van der Vegt, Nico F. A.; Briels, Wim J.
    Journal of Chemical Theory and Computation (2018), 14 (6), 3298-3310CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    Amyloid formation by the intrinsically disordered α-synuclein protein is the hallmark of Parkinson's disease. We present atomistic Mol. Dynamics simulations of the core of α-synuclein using enhanced sampling techniques to describe the conformational and binding free energy landscapes of fragments implicated in fibril stabilization. The theor. framework is derived to combine the free energy profiles of the fragments into the reaction free energy of a protein binding to a fibril. Our study shows that individual fragments in soln. have a propensity towards attaining non-β conformations in soln., indicating that in a fibril β-strands are stabilized by interactions with other strands. We show that most dimers of hydrogen-bonded fragments are unstable in soln., while hydrogen bonding stabilizes the collective binding of five fragments to the end of a fibril. Hydrophobic effects make further contributions to the stability of fibrils. This study is the first of its kind where structural and binding preferences of the five major fragments of the hydrophobic core of α-synuclein have been investigated. This approach improves sampling of intrinsically disordered proteins, provides information on the binding mechanism between the core sequences of α-synuclein and enables the parametrization of coarse grained models.
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    Chwastyk, M.; Cieplak, M. Conformational biases of α-synuclein and formation of transient knots. J. Phys. Chem. B 2020, 124, 11– 19,  DOI: 10.1021/acs.jpcb.9b08481
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    Conformational Biases of α-Synuclein and Formation of Transient Knots
    Chwastyk, Mateusz; Cieplak, Marek
    Journal of Physical Chemistry B (2020), 124 (1), 11-19CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
    We study local conformational biases in the dynamics of α-synuclein by using all-atom simulations with explicit and implicit solvents. The biases are related to the frequency of the specific contact formation. In both approaches, the protein is intrinsically disordered and its strongest bias is to make bend, and then turn, local structures. The explicit-solvent conformations can be substantially more extended which allows for formation of transient trefoil knots, both deep and shallow, that may last for up to 5 μs. The two-chain self-assocn. events, both short- and long-lived, are dominated by formation of contacts in the central part of the sequence. This part tends to form helixes when bound to a micelle.
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    Perlmutter, J. D.; Braun, A. R.; Sachs, J. N. Curvature dynamics of α-synuclein familial parkinson disease mutants. J. Biol. Chem. 2009, 284, 7177– 7189,  DOI: 10.1074/jbc.M808895200
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    Allison, J. R.; Varnai, P.; Dobson, C. M.; Vendruscolo, M. Determination of the free energy landscape of α-synuclein using spin label nuclear magnetic resonance measurements. J. Am. Chem. Soc. 2009, 131, 18314– 18326,  DOI: 10.1021/ja904716h
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    Determination of the Free Energy Landscape of α-Synuclein Using Spin Label Nuclear Magnetic Resonance Measurements
    Allison, Jane R.; Varnai, Peter; Dobson, Christopher M.; Vendruscolo, Michele
    Journal of the American Chemical Society (2009), 131 (51), 18314-18326CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Natively unfolded proteins present a challenge for structure detn. because they populate highly heterogeneous ensembles of conformations. A useful source of structural information about these states is provided by paramagnetic relaxation enhancement measurements by NMR spectroscopy, from which long-range interat. distances can be estd. Here we describe a method for using such distances as restraints in mol. dynamics simulations to obtain a mapping of the free energy landscapes of natively unfolded proteins. We demonstrate the method in the case of α-synuclein and validate the results by a comparison with electron transfer measurements. Our findings indicate that our procedure provides an accurate est. of the relative statistical wts. of the different conformations populated by α-synuclein in its natively unfolded state.
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    Amos, S.-B. T.; Schwarz, T. C.; Shi, J.; Cossins, B. P.; Baker, T. S.; Taylor, R. J.; Konrat, R.; Sansom, M. S. Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR. J. Phys. Chem. B 2021, 125, 2929– 2941,  DOI: 10.1021/acs.jpcb.1c01281
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    Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR
    Amos, Sarah-Beth T. A.; Schwarz, Thomas C.; Shi, Jiye; Cossins, Benjamin P.; Baker, Terry S.; Taylor, Richard J.; Konrat, Robert; Sansom, Mark S. P.
    Journal of Physical Chemistry B (2021), 125 (11), 2929-2941CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
    α-Synuclein (αS) is a presynaptic protein that binds to cell membranes and is linked to Parkinson's disease (PD). Binding of αS to membranes is a likely first step in the mol. pathophysiol. of PD. The αS mol. can adopt multiple conformations, being largely disordered in water, adopting a β-sheet conformation when present in amyloid fibrils, and forming a dynamic multiplicity of α-helical conformations when bound to lipid bilayers and related membrane-mimetic surfaces. Multiscale mol. dynamics simulations in conjunction with NMR and crosslinking mass spectrometry (XLMS) measurements were used to explore the interactions of αS with an anionic lipid bilayer. The simulations and NMR measurements together reveal a break in the helical structure of the central non-amyloid-β component (NAC) region of αS in the vicinity of residues 65-70, which may facilitate subsequent oligomer formation. Coarse-grained simulations of αS starting from the structure of αS when bound to a detergent micelle reveal the overall pattern of protein contacts to anionic lipid bilayers, while subsequent all-atom simulations provide details of conformational changes upon membrane binding. In particular, simulations and NMR data for liposome-bound αS indicate incipient β-strand formation in the NAC region, which is supported by intramol. contacts seen via XLMS and simulations. Markov state models based on the all-atom simulations suggest a mechanism of conformational change of membrane-bound αS via a dynamic helix break in the region of residue 65 in the NAC region. The emergent dynamic model of membrane-interacting αS advances the authors' understanding of the mechanism of PD, potentially aiding the design of novel therapeutic approaches.
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    Herrera, F. E.; Chesi, A.; Paleologou, K. E.; Schmid, A.; Munoz, A.; Vendruscolo, M.; Gustincich, S.; Lashuel, H. A.; Carloni, P. Inhibition of α-synuclein fibrillization by dopamine is mediated by interactions with five C-terminal residues and with E83 in the NAC region. PloS one 2008, 3, e3394,  DOI: 10.1371/journal.pone.0003394
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    Robustelli, P.; Ibanez-de Opakua, A.; Campbell-Bezat, C.; Giordanetto, F.; Becker, S.; Zweckstetter, M.; Pan, A. C.; Shaw, D. E. Molecular basis of small-molecule binding to α-synuclein. J. Am. Chem. Soc. 2022, 144, 2501– 2510,  DOI: 10.1021/jacs.1c07591
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    Molecular Basis of Small-Molecule Binding to α-Synuclein
    Robustelli, Paul; Ibanez-de-Opakua, Alain; Campbell-Bezat, Cecily; Giordanetto, Fabrizio; Becker, Stefan; Zweckstetter, Markus; Pan, Albert C.; Shaw, David E.
    Journal of the American Chemical Society (2022), 144 (6), 2501-2510CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Intrinsically disordered proteins (IDPs) are implicated in many human diseases. They have generally not been amenable to conventional structure-based drug design, however, because their intrinsic conformational variability has precluded an at.-level understanding of their binding to small mols. Here we present long-time-scale, at.-level mol. dynamics (MD) simulations of monomeric α-synuclein (an IDP whose aggregation is assocd. with Parkinson's disease) binding the small-mol. drug fasudil in which the obsd. protein-ligand interactions were found to be in good agreement with previously reported NMR chem. shift data. In our simulations, fasudil, when bound, favored certain charge-charge and π-stacking interactions near the C terminus of α-synuclein but tended not to form these interactions simultaneously, rather breaking one of these interactions and forming another nearby (a mechanism we term dynamic shuttling). Further simulations with small mols. chosen to modify these interactions yielded binding affinities and key structural features of binding consistent with subsequent NMR expts., suggesting the potential for MD-based strategies to facilitate the rational design of small mols. that bind with disordered proteins.
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    Balesh, D.; Ramjan, Z. Unfolded annealing molecular dynamics conformers for wild-type and disease-associated variants of alpha-synuclein show no propensity for beta-sheetformation. Journal of Biophysical Chemistry 2011, 2, 124,  DOI: 10.4236/jbpc.2011.22015
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    Allison, J. R.; Rivers, R. C.; Christodoulou, J. C.; Vendruscolo, M.; Dobson, C. M. A relationship between the transient structure in the monomeric state and the aggregation propensities of α-synuclein and β-synuclein. Biochemistry 2014, 53, 7170– 7183,  DOI: 10.1021/bi5009326
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    A relationship between the transient structure in the monomeric state and the aggregation propensities of α-synuclein and β-synuclein
    Allison, Jane R.; Rivers, Robert C.; Christodoulou, John C.; Vendruscolo, Michele; Dobson, Christopher M.
    Biochemistry (2014), 53 (46), 7170-7183CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
    α-Synuclein (αS) is an intrinsically disordered protein whose aggregation is implicated in Parkinson's disease. A 2nd member of the synuclein family, β-synuclein (βS), shares significant sequence similarity with αS, but is much more resistant to aggregation. βS is missing an 11-residue stretch in the central non-β-amyloid component region that forms the core of αS amyloid fibrils, yet insertion of these residues into βS to produce the βSHC construct did not markedly increase the aggregation propensity. To investigate the structural basis of these different behaviors, quant. NMR data, in the form of paramagnetic relaxation enhancement-derived interat. distances, were combined with mol. dynamics simulations to generate ensembles of structures representative of the soln. states of αS, βS, and βSHC. Comparison of these ensembles revealed that the differing aggregation propensities of αS and βS was assocd. with differences in the degree of residual structure in the C-terminus coupled to the shorter sepn. between the N- and C-termini in βS and βSHC, making protective intramol. contacts more likely.
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    Dedmon, M. M.; Lindorff-Larsen, K.; Christodoulou, J.; Vendruscolo, M.; Dobson, C. M. Mapping long-range interactions in α-synuclein using spin-label NMR and ensemble molecular dynamics simulations. J. Am. Chem. Soc. 2005, 127, 476– 477,  DOI: 10.1021/ja044834j
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    Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations
    Dedmon, Matthew M.; Lindorff-Larsen, Kresten; Christodoulou, John; Vendruscolo, Michele; Dobson, Christopher M.
    Journal of the American Chemical Society (2005), 127 (2), 476-477CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    The intrinsically disordered protein α-synuclein plays a key role in the pathogenesis of Parkinson's disease (PD). We show here that the native state of α-synuclein consists of a broad distribution of conformers with an ensemble-averaged hydrodynamic radius significantly smaller than that expected for a random coil structure. This partial condensation is driven by interactions between the highly charged C-terminus and a large hydrophobic central region of the protein sequence. We suggest that this structure could inhibit the formation of α-synuclein aggregates, which are thought to be the cytotoxic species responsible for neurodegeneration in PD.
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    Park, S.; Yoon, J.; Jang, S.; Lee, K.; Shin, S. The role of the acidic domain of α-synuclein in amyloid fibril formation: a molecular dynamics study. J. Biomol. Struct. Dyn. 2016, 34, 376– 383,  DOI: 10.1080/07391102.2015.1033016
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    The role of the acidic domain of α-synuclein in amyloid fibril formation: a molecular dynamics study
    Park, SeongByeong; Yoon, Jeseong; Jang, Soonmin; Lee, Kyunghee; Shin, Seokmin
    Journal of Biomolecular Structure and Dynamics (2016), 34 (2), 376-383CODEN: JBSDD6; ISSN:0739-1102. (Taylor & Francis Ltd.)
    The detailed mechanism of the pathol. of α-synuclein in the Parkinson's disease has not been clearly elucidated. Recent studies suggested a possible chaperone-like role of the acidic C-terminal region of α-synuclein in the formation of amyloid fibrils. It was also previously demonstrated that the α-synuclein amyloid fibril formation is accelerated by mutations of proline residues to alanine in the acidic region. We performed replica exchange mol. dynamics simulations of the acidic and nonamyloid component (NAC) domains of the wild type and proline-to-alanine mutants of α-synuclein under various conditions. Our results showed that structural changes induced by a change in pH or an introduction of mutations lead to a redn. in mutual contacts between the NAC and acidic regions. Our data suggest that the highly charged acidic region of α-synuclein may act as an intramol. chaperone by protecting the hydrophobic domain from aggregation. Understanding the function of such chaperone-like parts of fibril-forming proteins may provide novel insights into the mechanism of amyloid formation.
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    Brodie, N. I.; Popov, K. I.; Petrotchenko, E. V.; Dokholyan, N. V.; Borchers, C. H. Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. PLoS computational biology 2019, 15, e1006859,  DOI: 10.1371/journal.pcbi.1006859
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    Tsigelny, I. F.; Bar-On, P.; Sharikov, Y.; Crews, L.; Hashimoto, M.; Miller, M. A.; Keller, S. H.; Platoshyn, O.; Yuan, J. X.-J.; Masliah, E. Dynamics of α-synuclein aggregation and inhibition of pore-like oligomer development by β-synuclein. FEBS journal 2007, 274, 1862– 1877,  DOI: 10.1111/j.1742-4658.2007.05733.x
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    71
    Dynamics of α-synuclein aggregation and inhibition of pore-like oligomer development by β-synuclein
    Tsigelny, Igor F.; Bar-On, Pazit; Sharikov, Yuriy; Crews, Leslie; Hashimoto, Makoto; Miller, Mark A.; Keller, Steve H.; Platoshyn, Oleksandr; Yuan, Jason X.-J.; Masliah, Eliezer
    FEBS Journal (2007), 274 (7), 1862-1877CODEN: FJEOAC; ISSN:1742-464X. (Blackwell Publishing Ltd.)
    Accumulation of α-synuclein resulting in the formation of oligomers and protofibrils has been linked to Parkinson's disease and Lewy body dementia. In contrast, β-synuclein (β-syn), a close homolog, does not aggregate and reduces α-synuclein (α-syn)-related pathol. Although considerable information is available about the conformation of α-syn at the initial and end stages of fibrillation, less is known about the dynamic process of α-syn conversion to oligomers and how interactions with antiaggregation chaperones such as β-synuclein might occur. Mol. modeling and mol. dynamics simulations based on the micelle-derived structure of α-syn showed that α-syn homodimers can adopt nonpropagating (head-to-tail) and propagating (head-to-head) conformations. Propagating α-syn dimers on the membrane incorporate addnl. α-syn mols., leading to the formation of pentamers and hexamers forming a ring-like structure. In contrast, β-syn dimers do not propagate and block the aggregation of α-syn into ring-like oligomers. Under in vitro cell-free conditions, α-syn aggregates formed ring-like structures that were disrupted by β-syn. Similarly, cells expressing α-syn displayed increased ion current activity consistent with the formation of Zn2+-sensitive nonselective cation channels. These results support the contention that in Parkinson's disease and Lewy body dementia, α-syn oligomers on the membrane might form pore-like structures, and that the beneficial effects of β-synuclein might be related to its ability to block the formation of pore-like structures.
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    Ramis, R.; Ortega-Castro, J.; Casasnovas, R.; Mariño, L.; Vilanova, B.; Adrover, M.; Frau, J. A coarse-grained molecular dynamics approach to the study of the intrinsically disordered protein α-synuclein. J. Chem. Inf. Model. 2019, 59, 1458– 1471,  DOI: 10.1021/acs.jcim.8b00921
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    A Coarse-Grained Molecular Dynamics Approach to the Study of the Intrinsically Disordered Protein α-Synuclein
    Ramis, Rafael; Ortega-Castro, Joaquin; Casasnovas, Rodrigo; Marino, Laura; Vilanova, Bartolome; Adrover, Miquel; Frau, Juan
    Journal of Chemical Information and Modeling (2019), 59 (4), 1458-1471CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
    Intrinsically disordered proteins (IDPs) are not well described by a single 3D conformation but by an ensemble of them, which makes their structural characterization esp. challenging, both exptl. and computationally. Most all-atom force fields are designed for folded proteins and give too compact IDP conformations. α-Synuclein is a well-known IDP because of its relation to Parkinson's disease (PD). To understand its role in this disease at the mol. level, an efficient methodol. is needed for the generation of conformational ensembles that are consistent with its known properties (in particular, with its dimensions) and that is readily extensible to posttranslationally modified forms of the protein, commonly found in PD patients. Herein, the authors have contributed to this goal by performing explicit-solvent, microsecond-long Replica Exchange with Solute Scaling (REST2) simulations of α-synuclein with the coarse-grained force field SIRAH, finding that a 30% increase in the default strength of protein-water interactions yields a much better reprodn. of its radius of gyration. Other known properties of α-synuclein, such as chem. shifts, secondary structure content, and long-range contacts, are also reproduced. Furthermore, the authors have simulated a glycated form of α-synuclein to suggest the extensibility of the method to its posttranslationally modified forms. The computationally efficient REST2 methodol. in combination with coarse-grained representations will facilitate the simulations of this relevant IDP and its modified forms, enabling a better understanding of their roles in disease and potentially leading to efficient therapies.
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    Yu, H.; Han, W.; Ma, W.; Schulten, K. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation. J. Chem. Phys. 2015, 143, 243142,  DOI: 10.1063/1.4936910
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    Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation
    Yu, Hang; Han, Wei; Ma, Wen; Schulten, Klaus
    Journal of Chemical Physics (2015), 143 (24), 243142/1-243142/15CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
    Parkinson's disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform mol. dynamics simulations (over 180 μs in aggregated time) using a hybrid-resoln. model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in at. detail structural ensembles of wild type and mutant monomeric α-synuclein in aq. soln. The simulations reproduce structural properties of α-synuclein characterized in expts., such as secondary structure content, long-range contacts, chem. shifts, and 3J(HNHCα)-coupling consts. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation. (c) 2015 American Institute of Physics.
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    Narayanan, C.; Weinstock, D. S.; Wu, K.-P.; Baum, J.; Levy, R. M. Investigation of the polymeric properties of α-synuclein and comparison with NMR experiments: a replica exchange molecular dynamics study. J. Chem. Theory Comput. 2012, 8, 3929– 3942,  DOI: 10.1021/ct300241t
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    Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study
    Narayanan, Chitra; Weinstock, Daniel S.; Wu, Kuen-Phon; Baum, Jean; Levy, Ronald M.
    Journal of Chemical Theory and Computation (2012), 8 (10), 3929-3942CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    Intrinsically disordered proteins (IDPs) have been shown to be involved in a no. of cellular functions, in addn. to their predominance in diseased states. α-Synuclein may be described as one such IDP, implicated in the pathol. of Parkinson's disease. Understanding the conformational characteristics of the monomeric state of α-synuclein is necessary for understanding the role of the monomer conformation in aggregation. Polymer theories have been applied to investigate the statistical properties of homopolymeric IDPs. Here, we use Replica Exchange Mol. Dynamics (REMD) simulations using temp. as a proxy for solvent quality to examine how well these theories developed for homopolymeric chains describe heteropolymeric α-synuclein. Our results indicate that α-synuclein behaves like a homopolymer at the extremes of solvent quality, while in the intermediate solvent regime, the uneven distribution of charged residues along the sequence strongly influences the conformations adopted by the chain. We refine the ensemble extd. from the REMD simulations of α-synuclein, which shows the best qual. agreement with exptl. results, by fitting to the exptl. NMR Residual Dipolar Couplings (RDCs) and Paramagnetic Relaxation Enhancements (PREs). Our results demonstrate that the detailed shapes of the RDC patterns are sensitive to the angular correlations that are local in sequence while longer range anticorrelations which arise from packing constraints affect the RDC magnitudes.
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    Dibenedetto, D.; Rossetti, G.; Caliandro, R.; Carloni, P. A molecular dynamics simulation-based interpretation of nuclear magnetic resonance multidimensional heteronuclear spectra of α-synuclein·dopamine adducts. Biochemistry 2013, 52, 6672– 6683,  DOI: 10.1021/bi400367r
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    A Molecular Dynamics Simulation-Based Interpretation of Nuclear Magnetic Resonance Multidimensional Heteronuclear Spectra of α-Synuclein·Dopamine Adducts
    Dibenedetto, Domenica; Rossetti, Giulia; Caliandro, Rocco; Carloni, Paolo
    Biochemistry (2013), 52 (38), 6672-6683CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
    Multidimensional heteronuclear NMR (NMR) spectroscopy provides valuable structural information about adducts between naturally unfolded proteins and their ligands. These are often highly pharmacol. relevant. Unfortunately, the detn. of the contributions to obsd. chem. shifts changes upon ligand binding is complicated. Here we present a tool that uses mol. dynamics (MD) trajectories to help interpret two-dimensional (2D) NMR data. We apply this tool to the naturally unfolded protein human α-synuclein interacting with dopamine, an inhibitor of fibril formation, and with its oxidn. products in water solns. By coupling 2D NMR expts. with MD simulations of the adducts in explicit water, the tool confirms with exptl. data that the ligands bind preferentially to 125YEMPS129 residues in the C-terminal region and to a few residues of the so-called NAC region consistently. It also suggests that the ligands might cause conformational rearrangements of distal residues located at the N-terminus. Hence, the performed anal. provides a rationale for the obsd. changes in chem. shifts in terms of direct contacts with the ligand and conformational changes in the protein.
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    Tsigelny, I. F.; Sharikov, Y.; Miller, M. A.; Masliah, E. Mechanism of alpha-synuclein oligomerization and membrane interaction: theoretical approach to unstructured proteins studies. Nanomedicine: Nanotechnology, Biology and Medicine 2008, 4, 350– 357,  DOI: 10.1016/j.nano.2008.05.005
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    Zhang, T.; Tian, Y.; Li, Z.; Liu, S.; Hu, X.; Yang, Z.; Ling, X.; Liu, S.; Zhang, J. Molecular dynamics study to investigate the dimeric structure of the full-length α-synuclein in aqueous solution. J. Chem. Inf. Model. 2017, 57, 2281– 2293,  DOI: 10.1021/acs.jcim.7b00210
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    Molecular Dynamics Study to Investigate the Dimeric Structure of the Full-Length α-Synuclein in Aqueous Solution
    Zhang, Tingting; Tian, Yuanxin; Li, Zhonghuang; Liu, Siming; Hu, Xiang; Yang, Zichao; Ling, Xiaotong; Liu, Shuwen; Zhang, Jiajie
    Journal of Chemical Information and Modeling (2017), 57 (9), 2281-2293CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
    The mechanisms of dimerization of α-synuclein from full-length monomers and their structural features have been studied through mol. dynamics simulations. The dimerization of α-syn plays a crit. role in the fibrillogenesis mechanism and could initiate and trigger α-syn to aggregate by conformational transforming. According to the alignment between three regions of α-syn monomer, eight diverse starting structures have been constructed. However, only five configurations show the dimeric structures, and the detailed properties of three dimers of them are discussed. During the simulations, both identical α-syn peptides (P1 and P2) of these three dimers reduce the high contents of α-helix from their native folded structures, while the contents of β-sheet increase. Antiparallel β-hairpin motifs within the α-syn peptide are formed by intramol. interactions. The β-hairpin regions are adjacent to the nonamyloid β component (NAC) of α-syn, and these structural features are consistent with the exptl. observation. Moreover, intermol. β-sheets also were generated between P1 and P2 through hydrogen bonding interactions. The dimers produce both intramol. β-hairpin and intermol. β-sheet characters; the former is presented in the monomer and oligomer of α-syn, and the latter occurs in the fibril structure. The simulations also show several other interactions such as hydrophobic interactions and salt-bridges, which would contribute to making the α-syn dimers more stable with the aforementioned effects. The results may pave the way to design small mols. to inhibit the dimerization to block the aggregation of α-syn in the future.
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    Savva, L.; Platts, J. A. How Cu (II) binding affects structure and dynamics of α-synuclein revealed by molecular dynamics simulations. Journal of Inorganic Biochemistry 2023, 239, 112068,  DOI: 10.1016/j.jinorgbio.2022.112068
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    Razzokov, J.; Fazliev, S.; Makhkamov, M.; Marimuthu, P.; Baev, A.; Kurganov, E. Effect of Electric Field on α-Synuclein Fibrils: Revealed by Molecular Dynamics Simulations. International Journal of Molecular Sciences 2023, 24, 6312,  DOI: 10.3390/ijms24076312
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    Savva, L.; Platts, J. A. Exploring the Impact of Mutation and Post-Translational Modification on α-Synuclein: Insights From Molecular Dynamics Simulations With and Without Copper. Journal of Inorganic Biochemistry 2023, 249, 112395,  DOI: 10.1016/j.jinorgbio.2023.112395
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    Jin, F.; Gräter, F. How Multisite Phosphorylation Impacts the Conformations of Intrinsically Disordered Proteins. PLOS Computational Biology 2021, 17, e1008939,  DOI: 10.1371/journal.pcbi.1008939
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    Rieloff, E.; Skepö, M. The Effect of Multisite Phosphorylation on the Conformational Properties of Intrinsically Disordered Proteins. International Journal of Molecular Sciences 2021, 22, 11058,  DOI: 10.3390/ijms222011058
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    Martin, I. M.; Aponte-Santamaría, C.; Schmidt, L.; Hedtfeld, M.; Iusupov, A.; Musacchio, A.; Gräter, F. Phosphorylation Tunes Elongation Propensity and Cohesiveness of Incenp’s Intrinsically Disordered Region. J. Mol. Biol. 2022, 434, 167387,  DOI: 10.1016/j.jmb.2021.167387
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    Adhikari, S.; Mondal, J. Machine Learning Subtle Conformational Change Due To Phosphorylation in Intrinsically Disordered Proteins. J. Phys. Chem. B 2023, 127, 9433– 9449,  DOI: 10.1021/acs.jpcb.3c05136
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    Amith, W. D.; Dutagaci, B. Complex Conformational Space of the Rna Polymerase Ii C-Terminal Domain Upon Phosphorylation. J. Phys. Chem. B 2023, 127, 9223– 9235,  DOI: 10.1021/acs.jpcb.3c02655
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    Roche, J.; Ying, J.; Maltsev, A. S.; Bax, A. Impact of Hydrostatic Pressure on an Intrinsically Disordered Protein: A High-Pressure NMR Study of α-Synuclein. ChemBioChem. 2013, 14, 1754– 1761,  DOI: 10.1002/cbic.201300244
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    Impact of Hydrostatic Pressure on an Intrinsically Disordered Protein: A High-Pressure NMR Study of α-Synuclein
    Roche, Julien; Ying, Jinfa; Maltsev, Alexander S.; Bax, Ad
    ChemBioChem (2013), 14 (14), 1754-1761CODEN: CBCHFX; ISSN:1439-4227. (Wiley-VCH Verlag GmbH & Co. KGaA)
    The impact of pressure on the backbone 15N, 1H and 13C chem. shifts in N-terminally acetylated α-synuclein has been evaluated over a pressure range 1-2500 bar. Even while the chem. shifts fall very close to random coil values, as expected for an intrinsically disordered protein, substantial deviations in the pressure dependence of the chem. shifts are seen relative to those in short model peptides. In particular, the nonlinear pressure response of the 1HN chem. shifts, which commonly is assocd. with the presence of low-lying "excited states", is much larger in α-synuclein than in model peptides. The linear pressure response of 1HN chem. shift, commonly linked to H-bond length change, correlates well with those in short model peptides, and is found to be anticorrelated with its temp. dependence. The pressure dependence of 13C chem. shifts shows remarkably large variations, even when accounting for residue type, and do not point to a clear shift in population between different regions of the Ramachandran map. However, a nearly universal decrease in 3JHN-Ha by 0.22±0.05 Hz suggests a slight increase in population of the polyproline II region at 2500 bar. The first six residues of N-terminally acetylated synuclein show a transient of approx. 15% population of α-helix, which slightly diminishes at 2500 bar. The backbone dynamics of the protein is not visibly affected beyond the effect of slight increase in water viscosity at 2500 bar.
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    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
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    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.
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    Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N log (N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089– 10092,  DOI: 10.1063/1.464397
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    Darden, Tom; York, Darrin; Pedersen, Lee
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    An N·log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolution using fast Fourier transforms. Timings and accuracies are presented for three large cryst. ionic systems.
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    Journal of Chemical Physics (1985), 83 (8), 4069-74CODEN: JCPSA6; ISSN:0021-9606.
    In a theory of the linear response, to an external field, of a thermostatted many-body system, equil. time correlation functions (relating to fluctuations in the internal energy, vol.-pressure tensor, etc.) were calcd. by using the algorithm of S. Nose (1984) and W. G. Hoover (1985) based on statistical-mech. equation for expressing thermostatting (E. and W. G. H., 1985). In the thermodn. limit, the response was the same as that of the corresponding Gaussian isothermal system. Nonequil. mol.-dynamics simulations of planar Couette flow showed that the calcd. shear-viscosity coeff. was remarkably independent of the type of thermostatting algorithm used in the calcn.
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    Journal of Chemical Physics (1980), 72 (4), 2384-93CODEN: JCPSA6; ISSN:0021-9606.
    In the mol. dynamics simulation method for fluids, the equations of motion for a collection of particles in a fixed vol. are solved numerically. The energy, vol., and no. of particles are const. for a particular simulation, and it is assumed that time avs. of properties of the simulated fluid are equal to microcanonical ensemble avs. of the same properties. In some situations, it is desirable to perform simulations of a fluid for particular values of temp. and/or pressure or under conditions in which the energy and vol. of the fluid can fluctuate. Three methods for performing mol. dynamics simulations under conditions of const. temp. and/or pressure are discussed. Time avs. of properties of the simulated fluid are equal to avs. over the isenthalpic-isobaric, canonical, and isothermal-isobaric ensembles. Each method is a way of describing the dynamics of a certain no. of particles in a vol. element of a fluid while taking into account the influence of surrounding particles in changing the energy and/or d. of the simulated vol. element. The influence of the surroundings is taken into account without unwanted surface effects. Examples of situations where these methods may be useful are discussed.
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    We present a new LINear Constraint Solver (LINCS) for mol. simulations with bond constraints using the enzyme lysozyme and a 32-residue peptide as test systems. The algorithm is inherently stable, as the constraints themselves are reset instead of derivs. of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrixes, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large mols. At the same accuracy, the LINCS algorithm is 3-4 times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward.
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    Appadurai, R.; Koneru, J. K.; Bonomi, M.; Robustelli, P.; Srivastava, A. Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins With T-Distributed Stochastic Neighbor Embedding. J. Chem. Theory Comput. 2023, 19, 4711– 4727,  DOI: 10.1021/acs.jctc.3c00224
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    Biophysical Journal (2015), 109 (8), 1528-1532CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
    As mol. dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomol. systems, the necessity of flexible and easy-to-use software tools for the anal. of these simulations is growing. We have developed MDTraj, a modern, lightwt., and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large no. of trajectory anal. capabilities including minimal root-mean-square-deviation calcns., secondary structure assignment, and the extn. of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-std. statistical anal. and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the anal. of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.
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    Shen, Y.; Bax, A. Sparta+: a Modest Improvement in Empirical Nmr Chemical Shift Prediction By Means of an Artificial Neural Network. Journal of Biomolecular NMR 2010, 48, 13– 22,  DOI: 10.1007/s10858-010-9433-9
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    Abstr.: CD (CD) spectroscopy is highly sensitive to the secondary structure (SS) compn. of proteins. Several methods exist to either est. the SS compn. of a protein or to validate existing structural models using its CD spectrum. The accuracy and precision of these methods depend on the quality of both the measured CD spectrum and the used ref. structure. Using a large ref. protein set with high-quality CD spectra and synthetic data derived from this set, we quantified deviations from both ideal spectra and ref. structures due to exptl. limitations. We also detd. the impact of these deviations on SS estn., CD prediction, and SS validation methods of the SESCA anal. package. With regard to the CD spectra, our results suggest intensity scaling errors and non-SS contributions as the main causes of inaccuracies. These factors also can lead to overestimated model errors during validation. The errors of the used ref. structures combine non-additively with errors caused by the CD spectrum, which increases the uncertainty of model validation. We have further shown that the effects of scaling errors in the CD spectrum can be nearly eliminated by appropriate re-scaling, and that the accuracy of model validation methods can be improved by accounting for typical non-SS contributions.
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  • Abstract

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    Figure 1

    Figure 1. Sequence of amino acid residues in AS; positively charged residues are highlighted in blue, and negatively charged ones are highlighted in red. Three domains can be identified: the positively charged N-terminus (residues 1–60), the overall neutral hydrophobic region (residues 61–95), and the negatively charged C-terminal domain (residues 96–104). In physiological conditions, the protein is acetylated on the first residue, although this post-translational modification does not significantly affect the fibrillization propensity in vitro. (18) In LBs, a significant fraction of AS is phosphorylated on S129. (11) A novel phosphorylation site at T64 has also been recently described. (10)

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    Figure 2

    Figure 2. Calculated chemical shifts of (a) N, (b) Cα, (c) Cβ, (d) C, and (e) H atoms and in AS and pAS against the experimental data from Roche et al. (86) Correlation coefficients are given for AS (blue) and pAS (orange), respectively.

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    Figure 3

    Figure 3. Circular Dichroism spectra of the AS and pAS cluster midpoint structures obtained during the converged part of the simulations. Shading indicates the standard error.

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    Figure 4

    Figure 4. Structures of cluster midpoints representing the structural ensembles of AS (a-c) and pAS (d-f), from (a) 6.80% to (b) 48.85%, (c) 100%, (d) 5.80%, (e) 49.63%, and (f) 100%. See Table S7 for details.

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    Figure 5

    Figure 5. AS (blue) and pAS (orange) Rg distributions (a) and corresponding approximate free energy landscapes over the distance between the protein termini and radii of gyration (b-c).

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    Figure 6

    Figure 6. (a) Contact maps of AS (triangle above) and pAS (triangle below) and (b) their differences. Brighter values correspond to closer distances in the corresponding triangle compared to the opposite triangle.

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    Figure 7

    Figure 7. Distribution of the total number of salt bridges (a) and hydrogen bonds (b) in AS (blue) and pAS (orange). Frequency with which intradomain (black labels) and interdomain (red labels) salt bridges (c) and hydrogen bonds (d) are found in AS and pAS. Salt bridges and hydrogen bonds are displayed that occur during at least 2 and 25% of the converged trajectory, respectively, in either the AS or pAS simulation.

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    Figure 8

    Figure 8. RDFs (g(r)) of (a-e) water oxygen atoms surrounding (a-b) backbone carbon atoms, (c) side-chain carbon, and (d-e) side-chain oxygen atoms. (f-g) RDFs of sodium ions surrounding side-chain oxygen atoms. (h) Integral of the TRRDF (n(r,t)) of sodium ions over 1 ns time windows. Insets show the integral of g(r) up to 5 Å.

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    Figure 9

    Figure 9. Number of water molecules (left column), sodium ions (middle column), and chloride ions (right column) in the first hydration shell surrounding the (a-c) N-terminal, (d-f) hydrophobic, and (g-i) C-terminal domains of the protein, as well as around (j-l) the S129 residue. Inset numbers indicate the mean and standard deviation of the distributions.

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      Lewy bodies (LBs) are hallmark lesions of degenerating neurons in the brains of patients with Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Recently, a point mutation in the gene encoding the presynaptic α-synuclein protein was identified in some autosomal-dominantly inherited familial PD pedigrees, and light microscopic studies demonstrated α-synuclein immunoreactivity in LBs of sporadic PD and DLB. To characterize α-synuclein in LBs, the authors raised monoclonal antibodies (MAbs) to LBs purified from DLB brains and obtained a MAb specific for α-synuclein that intensely labeled LBs. Light and electron microscopic immunocytochem. studies performed with this MAb as well as other antibodies to α-and β-synuclein showed that α-synuclein, but not β-synuclein, is a component of LBs in sporadic PD and DLB. Western blot analyses of highly purified LBs from DLB brains showed that full-length as well as partially truncated and insol. aggregates of α-synuclein are deposited in LBs. Thus, these data strongly implicate α-synuclein in the formation of LBs and the selective degeneration of neurons in sporadic PD and DLB.
    5. 5
      Gibb, W.; Lees, A. The relevance of the Lewy body to the pathogenesis of idiopathic Parkinson’s disease. Journal of Neurology, Neurosurgery & Psychiatry 1988, 51, 745– 752,  DOI: 10.1136/jnnp.51.6.745
      5
      The relevance of the Lewy body to the pathogenesis of idiopathic Parkinson's disease
      Gibb W R; Lees A J
      Journal of neurology, neurosurgery, and psychiatry (1988), 51 (6), 745-52 ISSN:0022-3050.
      The Lewy body is a distinctive neuronal inclusion that is always found in the substantia nigra and other specific brain regions in Parkinson's disease. It is mainly composed of structurally altered neurofilament, and occurs wherever there is excessive loss of neurons. It occurs in some elderly individuals and rarely in other degenerative diseases of the central nervous system. In 273 brains of patients dying from disorders other than Parkinson's disease, the age-specific prevalence of Lewy bodies increased from 3.8% to 12.8% between the sixth and ninth decades. Associated pathological findings suggest that these cases of incidental Lewy body disease are presymptomatic cases of Parkinson's disease, and confirm the importance of age (time) in the evolution of the disease. In view of the common and widespread occurrence of this disorder we propose that endogenous mechanisms operating in early life may be more important than environmental agents in the pathogenesis of Lewy bodies and Parkinson's disease.
    6. 6
      Nguyen, P. H.; Ramamoorthy, A.; Sahoo, B. R.; Zheng, J.; Faller, P.; Straub, J. E.; Dominguez, L.; Shea, J.-E.; Dokholyan, N. V.; De Simone, A. Amyloid oligomers: A joint experimental/computational perspective on Alzheimer’s disease, Parkinson’s disease, type II diabetes, and amyotrophic lateral sclerosis. Chem. Rev. 2021, 121, 2545– 2647,  DOI: 10.1021/acs.chemrev.0c01122
      6
      Amyloid Oligomers: A joint experimental/computational perspective on Alzheimer's disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis
      Nguyen, Phuong H.; Ramamoorthy, Ayyalusamy; Sahoo, Bikash R.; Zheng, Jie; Faller, Peter; Straub, John E.; Dominguez, Laura; Shea, Joan-Emma; Dokholyan, Nikolay V.; De Simone, Alfonso; Ma, Buyong; Nussinov, Ruth; Najafi, Saeed; Ngo, Son Tung; Loquet, Antoine; Chiricotto, Mara; Ganguly, Pritam; McCarty, James; Li, Mai Suan; Hall, Carol; Wang, Yiming; Miller, Yifat; Melchionna, Simone; Habenstein, Birgit; Timr, Stepan; Chen, Jiaxing; Hnath, Brianna; Strodel, Birgit; Kayed, Rakez; Lesne, Sylvain; Wei, Guanghong; Sterpone, Fabio; Doig, Andrew J.; Derreumaux, Philippe
      Chemical Reviews (Washington, DC, United States) (2021), 121 (4), 2545-2647CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
      A review. Protein misfolding and aggregation is obsd. in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by exptl. and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacol. expts. tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, resp., for many years.
    7. 7
      Snead, D.; Eliezer, D. Alpha-synuclein function and dysfunction on cellular membranes. Experimental neurobiology 2014, 23, 292,  DOI: 10.5607/en.2014.23.4.292
      There is no corresponding record for this reference.
    8. 8
      Waudby, C. A.; Camilloni, C.; Fitzpatrick, A. W.; Cabrita, L. D.; Dobson, C. M.; Vendruscolo, M.; Christodoulou, J. In-cell NMR characterization of the secondary structure populations of a disordered conformation of α-synuclein within E. coli cells. PloS one 2013, 8, e72286,  DOI: 10.1371/journal.pone.0072286
      8
      In-cell NMR characterization of the secondary structure populations of a disordered conformation of α-synuclein within E. coli cells
      Waudby, Christopher A.; Camilloni, Carlo; Fitzpatrick, Anthony W. P.; Cabrita, Lisa D.; Dobson, Christopher M.; Vendruscolo, Michele; Christodoulou, John
      PLoS One (2013), 8 (8), e72286CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)
      α-Synuclein is a small protein strongly implicated in the pathogenesis of Parkinson's disease and related neurodegenerative disorders. We report here the use of in-cell NMR spectroscopy to observe directly the structure and dynamics of this protein within E. coli cells. To improve the accuracy in the measurement of backbone chem. shifts within crowded in-cell NMR spectra, we have developed a deconvolution method to reduce inhomogeneous line broadening within cellular samples. The resulting chem. shift values were then used to evaluate the distribution of secondary structure populations which, in the absence of stable tertiary contacts, are a most effective way to describe the conformational fluctuations of disordered proteins. The results indicate that, at least within the bacterial cytosol, α-synuclein populates a highly dynamic state that, despite the highly crowded environment, has the same characteristics as the disordered monomeric form obsd. in aq. soln.
    9. 9
      Goedert, M.; Griesinger, C.; Outeiro, T. F.; Riek, R.; Schröder, G. F.; Spillantini, M. G. Abandon the Nac in α-synuclein. Lancet Neurology 2024, 23, 669,  DOI: 10.1016/S1474-4422(24)00176-5
      There is no corresponding record for this reference.
    10. 10
      Matsui, H.; Ito, S.; Matsui, H.; Ito, J.; Gabdulkhaev, R.; Hirose, M.; Yamanaka, T.; Koyama, A.; Kato, T.; Tanaka, M. Phosphorylation of α-synuclein at T64 results in distinct oligomers and exerts toxicity in models of Parkinson’s disease. Proc. Natl. Acad. Sci. U. S. A. 2023, 120, e2214652120  DOI: 10.1073/pnas.2214652120
      There is no corresponding record for this reference.
    11. 11
      Fujiwara, H.; Hasegawa, M.; Dohmae, N.; Kawashima, A.; Masliah, E.; Goldberg, M. S.; Shen, J.; Takio, K.; Iwatsubo, T. α-Synuclein Is Phosphorylated in Synucleinopathy Lesions. Nat. Cell Biol. 2002, 4, 160– 164,  DOI: 10.1038/ncb748
      11
      α-Synuclein is phosphorylated in synucleinopathy lesions
      Fujiwara, Hideo; Hasegawa, Masato; Dohmae, Naoshi; Kawashima, Akiko; Masliah, Eliezer; Goldberg, Matthew S.; Shen, Jie; Takio, Koji; Iwatsubo, Takeshi
      Nature Cell Biology (2002), 4 (2), 160-164CODEN: NCBIFN; ISSN:1465-7392. (Nature Publishing Group)
      The deposition of the abundant presynaptic brain protein α-synuclein as fibrillary aggregates in neurons or glial cells is a hallmark lesion in a subset of neurodegenerative disorders. These disorders include Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy, collectively referred to as synucleinopathies1,2. Importantly, the identification of missense mutations in the α-synuclein gene in some pedigrees of familial PD has strongly implicated α-synuclein in the pathogenesis of PD and other synucleinopathies. However, specific post-translational modifications that underlie the aggregation of α-synuclein in affected brains have not, as yet, been identified. Here, we show by mass spectrometry anal. and studies with an antibody that specifically recognizes phospho-Ser 129 of α-synuclein, that this residue is selectively and extensively phosphorylated in synucleinopathy lesions. Furthermore, phosphorylation of α-synuclein at Ser 129 promoted fibril formation in vitro. These results highlight the importance of phosphorylation of filamentous proteins in the pathogenesis of neurodegenerative disorders.
    12. 12
      Ramalingam, N.; Jin, S.-X.; Moors, T. E.; Fonseca-Ornelas, L.; Shimanaka, K.; Lei, S.; Cam, H. P.; Watson, A. H.; Brontesi, L.; Ding, L. Dynamic Physiological α-synuclein S129 Phosphorylation Is Driven By Neuronal Activity. npj Parkinson’s Disease 2023, 9, 4,  DOI: 10.1038/s41531-023-00444-w
      There is no corresponding record for this reference.
    13. 13
      Ramalingam, N.; Haass, C.; Dettmer, U. Physiological Roles of α-synuclein Serine-129 Phosphorylation - Not an Oxymoron. Trends in Neurosciences 2024, 47, 480,  DOI: 10.1016/j.tins.2024.05.005
      There is no corresponding record for this reference.
    14. 14
      Ghanem, S. S.; Majbour, N. K.; Vaikath, N. N.; Ardah, M. T.; Erskine, D.; Jensen, N. M.; Fayyad, M.; Sudhakaran, I. P.; Vasili, E.; Melachroinou, K. α-Synuclein phosphorylation at serine 129 occurs after initial protein deposition and inhibits seeded fibril formation and toxicity. Proc. Natl. Acad. Sci. U. S. A. 2022, 119, e2109617119,  DOI: 10.1073/pnas.2109617119
      14
      Alpha Synuclein phosphorylation at serine 129 occurs after initial protein deposition and inhibits seeded fibril formation and toxicity
      Ghanem, Simona S.; Majbour, Nour K.; Vaikath, Nishant N.; Ardah, Mustafa T.; Erskine, Daniel; Jensen, Nanna Moeller; Fayyad, Muneera; Sudhakaran, Indulekha P.; Vasili, Eftychia; Melachroinou, Katerina; Abdi, Ilham Y.; Poggiolini, Ilaria; Santos, Patricia; Dorn, Anton; Carloni, Paolo; Vekrellis, Kostas; Attems, Johannes; McKeith, Ian; Outeiro, Tiago F.; Jensen, Poul Henning; El-Agnaf, Omar M. A.
      Proceedings of the National Academy of Sciences of the United States of America (2022), 119 (15), e2109617119CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      α-Synuclein (α-syn) phosphorylation at serine 129 (pS129-α-syn) is substantially increased in Lewy body disease, such as Parkinson's disease (PD) and dementia with Lewy bodies (DLB). However, the pathogenic relevance of pS129-α-syn remains controversial, so we sought to identify when pS129 modification occurs during α-syn aggregation and its role in initiation, progression and cellular toxicity of disease. Using diverse aggregation assays, including real-time quaking-induced conversion (RT-QuIC) on brain homogenates from PD and DLB cases, we demonstrated that pS129-α-syn inhibits α-syn fibril formation and seeded aggregation. We also identified lower seeding propensity of pS129-α-syn in cultured cells and correspondingly attenuated cellular toxicity. To build upon these findings, we developed a monoclonal antibody (4B1) specifically recognizing nonphosphorylated S129-α-syn (WT-α-syn) and noted that S129 residue is more efficiently phosphorylated when the protein is aggregated. Using this antibody, we characterized the time-course of α-syn phosphorylation in organotypic mouse hippocampal cultures and mice injected with α-syn preformed fibrils, and we obsd. aggregation of nonphosphorylated a-syn followed by later pS129-α-syn. Furthermore, in postmortem brain tissue from PD and DLB patients, we obsd. an inverse relationship between relative abundance of nonphosphorylated α-syn and disease duration. These findings suggest that pS129-α-syn occurs subsequent to initial protein aggregation and apparently inhibits further aggregation. This could possibly imply a potential protective role for pS129-α-syn, which has major implications for understanding the pathobiol. of Lewy body disease and the continued use of reduced pS129-α-syn as a measure of efficacy in clin. trials.
    15. 15
      Wang, Y.; Shi, M.; Chung, K. A.; Zabetian, C. P.; Leverenz, J. B.; Berg, D.; Srulijes, K.; Trojanowski, J. Q.; Lee, V. M.-Y.; Siderowf, A. D. Phosphorylated α-synuclein in Parkinson’s disease. Science translational medicine 2012, 4, 121ra20,  DOI: 10.1126/scitranslmed.3002566
      There is no corresponding record for this reference.
    16. 16
      Kawahata, I.; Finkelstein, D. I.; Fukunaga, K. Pathogenic Impact of α-Synuclein Phosphorylation and Its Kinases in α-Synucleinopathies. International Journal of Molecular Sciences 2022, 23, 6216,  DOI: 10.3390/ijms23116216
      There is no corresponding record for this reference.
    17. 17
      Oueslati, A.; Fournier, M.; Lashuel, H. A. Role of post-translational modifications in modulating the structure, function and toxicity of α-synuclein: implications for Parkinson’s disease pathogenesis and therapies. Progress in brain research 2010, 183, 115– 145,  DOI: 10.1016/S0079-6123(10)83007-9
      17
      Role of post-translational modifications in modulating the structure, function and toxicity of α-synuclein: implications for Parkinson's disease pathogenesis and therapies
      Oueslati, Abid; Fournier, Margot; Lashuel, Hilal A.
      Progress in Brain Research (2010), 183 (Recent Advances in Parkinson's Disease), 115-145CODEN: PBRRA4; ISSN:0079-6123. (Elsevier B.V.)
      A review. A better understanding of the mol. and cellular determinants that influence the pathol. of Parkinson's disease (PD) is essential for developing effective diagnostic, preventative and therapeutic strategies to treat this devastating disease. A no. of post-translational modifications to α-syn are present within the Lewy bodies in the brains of affected patients and transgenic models of PD and related disorders. However, whether disease-assocd. α-syn post-translational modifications promote or inhibit α-syn aggregation and neurotoxicity in vivo remains unknown. Herein, we summarize and discuss the major disease-assocd. post-translational modifications (phosphorylation, truncation and ubiquitination) and present our current understanding of the effect of these modifications on α-syn aggregation and toxicity. Elucidating the mol. mechanisms underlying post-translation modifications of α-syn and the consequences of such modifications on the biochem., structural, aggregation and toxic properties of the protein is essential for unravelling the mol. basis of its function(s) in health and disease. Furthermore, the identification of the natural enzymes involved in regulating the post-translational modifications of α-synuclein will yield novel and more tractable therapeutic targets to treat PD and related synucleinopathies.
    18. 18
      Fauvet, B.; Fares, M.-B.; Samuel, F.; Dikiy, I.; Tandon, A.; Eliezer, D.; Lashuel, H. A. Characterization of Semisynthetic and Naturally Nα-Acetylated α-Synuclein in Vitro and in Intact Cells. J. Biol. Chem. 2012, 287, 28243– 28262,  DOI: 10.1074/jbc.M112.383711
      18
      Characterization of Semisynthetic and Naturally Nα-Acetylated α-Synuclein in Vitro and in Intact Cells
      Fauvet, Bruno; Fares, Mohamed-Bilal; Samuel, Filsy; Dikiy, Igor; Tandon, Anurag; Eliezer, David; Lashuel, Hilal A.
      Journal of Biological Chemistry (2012), 287 (34), 28243-28262CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
      N-terminal acetylation is a very common post-translational modification, although its role in regulating protein phys. properties and function remains poorly understood. α-Synuclein (α-syn), a protein that has been linked to the pathogenesis of Parkinson disease, is constitutively Nα-acetylated in vivo. Nevertheless, most of the biochem. and biophys. studies on the structure, aggregation, and function of α-syn in vitro utilize recombinant α-syn from Escherichia coli, which is not N-terminally acetylated. To elucidate the effect of Nα-acetylation on the biophys. and biol. properties of α-syn, we produced Nα-acetylated α-syn first using a semisynthetic methodol. based on expressed protein ligation and then a recombinant expression strategy, to compare its properties to unacetylated α-syn. We demonstrate that both WT and Nα-acetylated α-syn share a similar secondary structure and oligomeric state using both purified protein prepns. and in-cell NMR on E. coli overexpressing Nα-acetylated α-syn. The two proteins have very close aggregation propensities as shown by thioflavin T binding and sedimentation assays. Furthermore, both Nα-acetylated and WT α-syn exhibited similar ability to bind synaptosomal membranes in vitro and in HeLa cells, where both internalized proteins exhibited prominent cytosolic subcellular distribution. We then detd. the effect of attenuating Nα-acetylation in living cells, first by using a nonacetylable mutant and then by silencing the enzyme responsible for α-syn Nα-acetylation. Both approaches revealed similar subcellular distribution and membrane binding for both the nonacetylable mutant and WT α-syn, suggesting that N-terminal acetylation does not significantly affect its structure in vitro and in intact cells.
    19. 19
      Xie, Y.; Jiang, Y.; Ben-Amotz, D. Detection of amino acid and peptide phosphate protonation using Raman spectroscopy. Analytical biochemistry 2005, 343, 223– 230,  DOI: 10.1016/j.ab.2005.05.038
      19
      Detection of amino acid and peptide phosphate protonation using Raman spectroscopy
      Xie, Yong; Jiang, Yanan; Ben-Amotz, Dor
      Analytical Biochemistry (2005), 343 (2), 223-230CODEN: ANBCA2; ISSN:0003-2697. (Elsevier)
      Raman spectra of phosphorylated amino acids and peptides undergo pH-dependent changes attributed to protonation of -OPO32- (dibasic) to -OPO3H- (monobasic). Bands at approx. 980 and 1080 cm-1 in soln. Raman spectra of phosphoserine and phosphothreonine are assigned to the monobasic and dibasic phosphate groups, resp. Calibrated Raman peak area ratio measurements, performed as a function of pH, are used to det. the corresponding pKa values of 5.6 (phosphoserine) and 5.9 (phosphothreonine). In peptides, the phosphate Raman bands are difficult to distinguish due to interference from other neighboring bands (particularly those derived from arom. amino acid residues) as well as the relatively low soly. of peptides. Nevertheless, drop coating deposition Raman (DCDR) spectra obtained from 100-μM peptide solns. reveal pH-dependent second deriv. features at approx. 980 and 1080 cm-1, which are indicative of phosphate protonation.
    20. 20
      Schreurs, S.; Gerard, M.; Derua, R.; Waelkens, E.; Taymans, J.-M.; Baekelandt, V.; Engelborghs, Y. In vitro phosphorylation does not influence the aggregation kinetics of WT α-synuclein in contrast to its phosphorylation mutants. International journal of molecular sciences 2014, 15, 1040– 1067,  DOI: 10.3390/ijms15011040
      There is no corresponding record for this reference.
    21. 21
      Samuel, F.; Flavin, W. P.; Iqbal, S.; Pacelli, C.; Renganathan, S. D. S.; Trudeau, L.-E.; Campbell, E. M.; Fraser, P. E.; Tandon, A. Effects of serine 129 phosphorylation on α-synuclein aggregation, membrane association, and internalization. J. Biol. Chem. 2016, 291, 4374– 4385,  DOI: 10.1074/jbc.M115.705095
      There is no corresponding record for this reference.
    22. 22
      Paleologou, K. E.; Schmid, A. W.; Rospigliosi, C. C.; Kim, H.-Y.; Lamberto, G. R.; Fredenburg, R. A.; Lansbury, P. T.; Fernandez, C. O.; Eliezer, D.; Zweckstetter, M. Phosphorylation at Ser-129 but not the phosphomimics S129E/D inhibits the fibrillation of α-synuclein. J. Biol. Chem. 2008, 283, 16895– 16905,  DOI: 10.1074/jbc.M800747200
      22
      Phosphorylation at Ser-129 but Not the Phosphomimics S129E/D Inhibits the Fibrillation of α-Synuclein
      Paleologou, Katerina E.; Schmid, Adrian W.; Rospigliosi, Carla C.; Kim, Hai-Young; Lamberto, Gonzalo R.; Fredenburg, Ross A.; Lansbury, Peter T., Jr.; Fernandez, Claudio O.; Eliezer, David; Zweckstetter, Markus; Lashuel, Hilal A.
      Journal of Biological Chemistry (2008), 283 (24), 16895-16905CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
      α-Synuclein (α-syn) phosphorylation at serine 129 is characteristic of Parkinson disease (PD) and related α-synucleinopathies. However, whether phosphorylation promotes or inhibits α-syn aggregation and neurotoxicity in vivo remains unknown. This understanding is crit. for elucidating the role of α-syn in the pathogenesis of PD and for development of therapeutic strategies for PD. To better understand the structural and mol. consequences of Ser-129 phosphorylation, we compared the biochem., structural, and membrane binding properties of wild type α-syn to those of the phosphorylation mimics (S129E, S129D) as well as of in vitro phosphorylated α-syn using a battery of biophys. techniques. Our results demonstrate that phosphorylation at Ser-129 increases the conformational flexibility of α-syn and inhibits its fibrillogenesis in vitro but does not perturb its membrane-bound conformation. In addn., we show that the phosphorylation mimics (S129E/D) do not reproduce the effect of phosphorylation on the structural and aggregation properties of α-syn in vitro. Our findings have significant implications for current strategies to elucidate the role of phosphorylation in modulating protein structure and function in health and disease and provide novel insight into the underlying mechanisms that govern α-syn aggregation and toxicity in PD and related α-synulceinopathies.
    23. 23
      Huang, J.; Rauscher, S.; Nawrocki, G.; Ran, T.; Feig, M.; de Groot, B. L.; Grubmüller, H.; MacKerell, A. D. Charmm36m: an Improved Force Field for Folded and Intrinsically Disordered Proteins. Nat. Methods 2017, 14, 71– 73,  DOI: 10.1038/nmeth.4067
      23
      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.
    24. 24
      Semenyuk, P. I. Alpha-Synuclein Phosphorylation Induces Amyloid Conversion Via Enhanced Electrostatic Bridging: Insights From Molecular Modeling of the Full-Length Protein. Biophys. Chem. 2024, 307, 107196,  DOI: 10.1016/j.bpc.2024.107196
      There is no corresponding record for this reference.
    25. 25
      Kang, L.; Moriarty, G. M.; Woods, L. A.; Ashcroft, A. E.; Radford, S. E.; Baum, J. N-Terminal Acetylation of α-synuclein Induces Increased Transient Helical Propensity and Decreased Aggregation Rates in the Intrinsically Disordered Monomer. Protein Sci. 2012, 21, 911– 917,  DOI: 10.1002/pro.2088
      25
      N-terminal acetylation of α-synuclein induces increased transient helical propensity and decreased aggregation rates in the intrinsically disordered monomer
      Kang, Lijuan; Moriarty, Gina M.; Woods, Lucy A.; Ashcroft, Alison E.; Radford, Sheena E.; Baum, Jean
      Protein Science (2012), 21 (7), 911-917CODEN: PRCIEI; ISSN:1469-896X. (Wiley-Blackwell)
      The conformational properties of sol. α-synuclein, the primary protein found in patients with Parkinson's disease, are thought to play a key role in the structural transition to amyloid fibrils. In this work, we report that recombinant 100% N-terminal acetylated α-synuclein purified under mild physiol. conditions presents as a primarily monomeric protein, and that the N-terminal acetyl group affects the transient secondary structure and fibril assembly rates of the protein. Residue-specific NMR chem. shift anal. indicates substantial increase in transient helical propensity in the first 9 N-terminal residues, as well as smaller long-range changes in residues 28-31, 43-46, and 50-66: regions in which the three familial mutations currently known to be causative of early onset disease are found. In addn., we show that the N-terminal acetylated protein forms fibrils that are morphol. similar to those formed from nonacetylated α-synuclein, but that their growth rates are slower. Our results highlight that N-terminal acetylation does not form significant nos. of dimers, tetramers, or higher mol. wt. species, but does alter the conformational distributions of monomeric α-synuclein species in regions known to be important in metal binding, in assocn. with membranes, and in regions known to affect fibril formation rates.
    26. 26
      Trexler, A. J.; Rhoades, E. N-terminal Acetylation Is Critical for Forming α-helical Oligomer of α-synuclein. Protein Sci. 2012, 21, 601– 605,  DOI: 10.1002/pro.2056
      26
      N-terminal acetylation is critical for forming α-helical oligomer of α-synuclein
      Trexler, Adam J.; Rhoades, Elizabeth
      Protein Science (2012), 21 (5), 601-605CODEN: PRCIEI; ISSN:1469-896X. (Wiley-Blackwell)
      The aggregation of the protein α-synuclein (AS) is crit. to the pathogenesis of Parkinson's disease. Although generally described as an unstructured monomer, recent evidence suggests that the native form of AS may be an α-helical tetramer which resists aggregation. Here, we show that N-terminal acetylation in combination with a mild purifn. protocol results in an oligomeric form of AS with partial α-helical structure. N-terminal acetylation of AS could have important implications for both the native and pathol. structures and functions of AS. Through our demonstration of a recombinant expression system, our results represent an important step toward biochem. and biophys. characterization of this potentially important form of AS.
    27. 27
      Maltsev, A. S.; Ying, J.; Bax, A. Impact of N-terminal acetylation of α-synuclein on its random coil and lipid binding properties. Biochemistry 2012, 51, 5004– 5013,  DOI: 10.1021/bi300642h
      27
      Impact of N-Terminal Acetylation of α-Synuclein on Its Random Coil and Lipid Binding Properties
      Maltsev, Alexander S.; Ying, Jinfa; Bax, Ad
      Biochemistry (2012), 51 (25), 5004-5013CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
      N-Terminal acetylation of α-synuclein (aS), a protein implicated in the etiol. of Parkinson's disease, is common in mammals. The impact of this modification on the protein's structure and dynamics in free soln. and on its membrane binding properties has been evaluated by high-resoln. NMR and CD spectroscopy. While no tetrameric form of acetylated aS could be isolated, N-terminal acetylation resulted in chem. shift perturbations of the first 12 residues of the protein that progressively decreased with the distance from the N-terminus. The directions of the chem. shift changes and small changes in backbone 3JHH couplings are consistent with an increase in the α-helicity of the first six residues of aS, although a high degree of dynamic conformational disorder remains and the helical structure is sampled <20% of the time. Chem. shift and 3JHH data for the intact protein are virtually indistinguishable from those recorded for the corresponding N-terminally acetylated and nonacetylated 15-residue synthetic peptides. An increase in α-helicity at the N-terminus of aS is supported by CD data on the acetylated peptide and by weak medium-range nuclear Overhauser effect contacts indicative of α-helical character. The remainder of the protein has chem. shift values that are very close to random coil values and indistinguishable between the two forms of the protein. No significant differences in the fibrillation kinetics were obsd. between acetylated and nonacetylated aS. However, the lipid binding properties of aS are strongly impacted by acetylation and exhibit distinct behavior for the first 12 residues, indicative of an initiation role for the N-terminal residues in an "initiation-elongation" process of binding to the membrane.
    28. 28
      Piana, S.; Robustelli, P.; Tan, D.; Chen, S.; Shaw, D. E. Development of a force field for the simulation of single-chain proteins and protein-protein complexes. J. Chem. Theory Comput. 2020, 16, 2494– 2507,  DOI: 10.1021/acs.jctc.9b00251
      28
      Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes
      Piana, Stefano; Robustelli, Paul; Tan, Dazhi; Chen, Songela; Shaw, David E.
      Journal of Chemical Theory and Computation (2020), 16 (4), 2494-2507CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      The accuracy of atomistic physics-based force fields for the simulation of biol. macromols. has typically been benchmarked exptl. using biophys. data from simple, often single-chain systems. In the case of proteins, the careful refinement of force field parameters assocd. with torsion-angle potentials and the use of improved water models have enabled a great deal of progress toward the highly accurate simulation of such monomeric systems in both folded and, more recently, disordered states. In living organisms, however, proteins constantly interact with other macromols., such as proteins and nucleic acids, and these interactions are often essential for proper biol. function. Here, the authors show that state-of-the-art force fields tuned to provide an accurate description of both ordered and disordered proteins can be limited in their ability to accurately describe protein-protein complexes. This observation prompted us to perform an extensive reparameterization of one variant of the Amber protein force field. The objective involved refitting not only the parameters assocd. with torsion-angle potentials, but also the parameters used to model nonbonded interactions, the specification of which is expected to be central to the accurate description of multicomponent systems. The resulting force field, which the authors call DES-Amber, allows for more accurate simulations of protein-protein complexes, while still providing a state-of-the-art description of both ordered and disordered single-chain proteins. Despite the improvements, calcd. protein-protein assocn. free energies still appear to deviate substantially from expt., a result suggesting that more fundamental changes to the force field, such as the explicit treatment of polarization effects, may simultaneously further improve the modeling of single-chain proteins and protein-protein complexes.
    29. 29
      Robustelli, P.; Piana, S.; Shaw, D. E. Developing a molecular dynamics force field for both folded and disordered protein states. Proc. Natl. Acad. Sci. U. S. A. 2018, 115, E4758– E4766,  DOI: 10.1073/pnas.1800690115
      29
      Developing a molecular dynamics force field for both folded and disordered protein states
      Robustelli, Paul; Piana, Stefano; Shaw, David E.
      Proceedings of the National Academy of Sciences of the United States of America (2018), 115 (21), E4758-E4766CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      Mol. dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any phys. model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the art force fields, and compare the results to over 9000 available exptl. data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with expt. for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB-disp, should thus greatly expand the range of biol. systems amenable to MD simulation. A similar approach could be taken to improve other force fields.
    30. 30
      Wang, W. Recent advances in atomic molecular dynamics simulation of intrinsically disordered proteins. Phys. Chem. Chem. Phys. 2021, 23, 777– 784,  DOI: 10.1039/D0CP05818A
      30
      Recent advances in atomic molecular dynamics simulation of intrinsically disordered proteins
      Wang, Wenning
      Physical Chemistry Chemical Physics (2021), 23 (2), 777-784CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
      A review. Intrinsically disordered proteins (IDPs) play important roles in cellular functions. The inherent structural heterogeneity of IDPs makes the high-resoln. exptl. characterization of IDPs extremely difficult. Mol. dynamics (MD) simulation could provide the at.-level description of the structural and dynamic properties of IDPs. This perspective reviews the recent progress in at. MD simulation studies of IDPs, including the development of force fields and sampling methods, as well as applications in IDP-involved protein-protein interactions. The employment of large-scale simulations and advanced sampling techniques allows more accurate estn. of the thermodn. and kinetics of IDP-mediated protein interactions, and the holistic landscape of the binding process of IDPs is emerging.
    31. 31
      Pedersen, K. B.; Flores-Canales, J. C.; Schiøtt, B. Predicting molecular properties of α-synuclein using force fields for intrinsically disordered proteins. Proteins: Struct., Funct., Bioinf. 2023, 91, 47– 61,  DOI: 10.1002/prot.26409
      There is no corresponding record for this reference.
    32. 32
      Robustelli, P.; de Opakua, A. I.; Campbell-Bezat, C.; Giordanetto, F.; Becker, S.; Zweckstetter, M.; Pan, A. C.; Shaw, D. E. Molecular Basis of Small-Molecule Binding To α-Synuclein. J. Am. Chem. Soc. 2022, 144, 2501– 2510,  DOI: 10.1021/jacs.1c07591
      32
      Molecular Basis of Small-Molecule Binding to α-Synuclein
      Robustelli, Paul; Ibanez-de-Opakua, Alain; Campbell-Bezat, Cecily; Giordanetto, Fabrizio; Becker, Stefan; Zweckstetter, Markus; Pan, Albert C.; Shaw, David E.
      Journal of the American Chemical Society (2022), 144 (6), 2501-2510CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Intrinsically disordered proteins (IDPs) are implicated in many human diseases. They have generally not been amenable to conventional structure-based drug design, however, because their intrinsic conformational variability has precluded an at.-level understanding of their binding to small mols. Here we present long-time-scale, at.-level mol. dynamics (MD) simulations of monomeric α-synuclein (an IDP whose aggregation is assocd. with Parkinson's disease) binding the small-mol. drug fasudil in which the obsd. protein-ligand interactions were found to be in good agreement with previously reported NMR chem. shift data. In our simulations, fasudil, when bound, favored certain charge-charge and π-stacking interactions near the C terminus of α-synuclein but tended not to form these interactions simultaneously, rather breaking one of these interactions and forming another nearby (a mechanism we term dynamic shuttling). Further simulations with small mols. chosen to modify these interactions yielded binding affinities and key structural features of binding consistent with subsequent NMR expts., suggesting the potential for MD-based strategies to facilitate the rational design of small mols. that bind with disordered proteins.
    33. 33
      Homeyer, N.; Horn, A. H.; Lanig, H.; Sticht, H. AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine. J. Mol. Model. 2006, 12, 281– 289,  DOI: 10.1007/s00894-005-0028-4
      33
      AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine
      Homeyer, Nadine; Horn, Anselm H. C.; Lanig, Harald; Sticht, Heinrich
      Journal of Molecular Modeling (2006), 12 (3), 281-289CODEN: JMMOFK; ISSN:0948-5023. (Springer GmbH)
      We report a consistent set of AMBER force-field parameters for the most common phosphorylated amino acids, phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine in different protonation states. The calcn. of at. charges followed the original restrained electrostatic potential fitting procedure used to det. the charges for the parm94/99 parameter set, taking α-helical and β-strand conformations of the corresponding ACE-/NME-capped model peptide backbone into account. Missing force-field parameters were taken directly from the general AMBER force field (gaff) and the parm99 data set with minor modifications, or were newly generated based on ab initio calcns. for model systems. Final parameters were validated by geometry optimizations and mol.-dynamics simulations. Template libraries for the phosphorylated amino acids in Leap format and corresponding frcmod parameters files are made available.
    34. 34
      Steinbrecher, T.; Latzer, J.; Case, D. Revised AMBER parameters for bioorganic phosphates. J. Chem. Theory Comput. 2012, 8, 4405– 4412,  DOI: 10.1021/ct300613v
      34
      Revised AMBER Parameters for Bioorganic Phosphates
      Steinbrecher, T.; Latzer, J.; Case, D. A.
      Journal of Chemical Theory and Computation (2012), 8 (11), 4405-4412CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      We report AMBER force field parameters for biol. simulations involving phosphorylation of serine, threonine, or tyrosine. The initial parameters used RESP fitting for the at. partial charges and std. values for all other parameters such as Lennard-Jones coeffs. These were refined with the aid of a thermodn. cycle consisting of exptl. detd. pKa values, solvation energies from mol. dynamics free energy simulations, and gas phase basicities from QM calcns. A polarization energy term was included to account for the charge d. change between the gas phase and soln., and solvation free energies were detd. using thermodn. integration. Parameter adjustment is required to obtain consistent thermodn. results with better balanced electrostatic interactions between water and the phosphate oxygens. To achieve this, we modified the phosphate oxygen radii. A thermodynamically consistent parameter set can be derived for monoanions and requires an increase of the van der Waals phosphate oxygen radii of approx. 0.09 Å. Larger, residue-specific radii appear to be needed for dianions. The revised parameters developed here should be of particular interest for environments where simulations of multiple protonation states may be of interest.
    35. 35
      Khoury, G. A.; Thompson, J. P.; Smadbeck, J.; Kieslich, C. A.; Floudas, C. A. Forcefield_PTM: Ab initio charge and AMBER forcefield parameters for frequently occurring post-translational modifications. J. Chem. Theory Comput. 2013, 9, 5653– 5674,  DOI: 10.1021/ct400556v
      35
      Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications
      Khoury, George A.; Thompson, Jeff P.; Smadbeck, James; Kieslich, Chris A.; Floudas, Christodoulos A.
      Journal of Chemical Theory and Computation (2013), 9 (12), 5653-5674CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      The authors introduce Forcefield_PTM, a set of AMBER forcefield parameters consistent with ff03 for 32 common post-translational modifications. Partial charges were calcd. through ab initio calcns. and a two-stage RESP-fitting procedure in an ether-like implicit solvent environment. The charges are generally consistent with others previously reported for phosphorylated amino acids, and trimethyllysine, using different parametrization methods. Pairs of modified structures and their corresponding unmodified structures were curated from the PDB for both single and multiple modifications. Background structural similarity was assessed in the context of secondary and tertiary structures from the global data set. Next, the charges derived for Forcefield_PTM were tested on a macroscopic scale using unrestrained all-atom Langevin mol. dynamics simulations in AMBER for 34 (17 pairs of modified/unmodified) systems in implicit solvent. Assessment was performed in the context of secondary structure preservation, stability in energies, and correlations between the modified and unmodified structure trajectories on the aggregate. As an illustration of their utility, the parameters were used to compare the structural stability of the phosphorylated and dephosphorylated forms of OdhI. Microscopic comparisons between quantum and AMBER single point energies along key χ torsions on several PTMs were performed, and corrections to improve their agreement in terms of mean-squared errors and squared correlation coeffs. were parametrized. This forcefield for post-translational modifications in condensed-phase simulations can be applied to a no. of biol. relevant and timely applications including protein structure prediction, protein and peptide design, and docking and to study the effect of PTMs on folding and dynamics. The authors make the derived parameters and an assocd. interactive webtool capable of performing post-translational modifications on proteins using Forcefield_PTM available at http://selene.princeton.edu/FFPTM.
    36. 36
      Petrov, D.; Margreitter, C.; Grandits, M.; Oostenbrink, C.; Zagrovic, B. A systematic framework for molecular dynamics simulations of protein post-translational modifications. PLoS computational biology 2013, 9, e1003154,  DOI: 10.1371/journal.pcbi.1003154
      36
      A systematic framework for molecular dynamics simulations of protein post-translational modifications
      Petrov, Drazen; Margreitter, Christian; Grandits, Melanie; Oostenbrink, Chris; Zagrovic, Bojan
      PLoS Computational Biology (2013), 9 (7), e1003154CODEN: PCBLBG; ISSN:1553-7358. (Public Library of Science)
      By directly affecting structure, dynamics and interaction networks of their targets, post-translational modifications (PTMs) of proteins play a key role in different cellular processes ranging from enzymic activation to regulation of signal transduction to cell-cycle control. Despite the great importance of understanding how PTMs affect proteins at the atomistic level, a systematic framework for treating post-translationally modified amino acids by mol. dynamics (MD) simulations, a premier high-resoln. computational biol. tool, has never been developed. Here, we report and validate force field parameters (GROMOS 45a3 and 54a7) required to run and analyze MD simulations of more than 250 different types of enzymic and non-enzymic PTMs. The newly developed GROMOS 54a7 parameters in particular exhibit near chem. accuracy in matching exptl. measured hydration free energies (RMSE = 4.2 kJ/mol over the validation set). Using this tool, we quant. show that the majority of PTMs greatly alter the hydrophobicity and other physico-chem. properties of target amino acids, with the extent of change in many cases being comparable to the complete range spanned by native amino acids.
    37. 37
      Zhong, B.; Song, G.; Chen, H.-F. Balanced Force Field ff03CMAP Improving the Dynamics Conformation Sampling of Phosphorylation Site. International Journal of Molecular Sciences 2022, 23, 11285,  DOI: 10.3390/ijms231911285
      There is no corresponding record for this reference.
    38. 38
      Vymětal, J.; Jurásková, V.; Vondrášek, J. AMBER and CHARMM force fields inconsistently portray the microscopic details of phosphorylation. J. Chem. Theory Comput. 2019, 15, 665– 679,  DOI: 10.1021/acs.jctc.8b00715
      38
      AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation
      Vymetal, Jiri; Juraskova, Veronika; Vondrasek, Jiri
      Journal of Chemical Theory and Computation (2019), 15 (1), 665-679CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      Phosphorylation of serine, threonine, and tyrosine is one of the most frequently occurring and crucial post-translational modifications of proteins often assocd. with important structural and functional changes. The authors studied the direct effect of phosphorylation on the intrinsic conformational preferences of amino acids as a potential trigger of larger structural events. The authors conducted a comparative study of force fields on terminally capped amino acids (dipeptides) as the simplest model for phosphorylation. The authors' bias-exchange metadynamics simulations revealed that all model dipeptides sampled a great heterogeneity of ensembles affected by introduction of mono- and dianionic phosphate groups. However, the detected changes in populations of backbone conformers and side-chain rotamers did not reveal a strong discriminatory shift in preferences, as could be anticipated for the bulky, charged phosphate group. Furthermore, the AMBER and CHARMM force fields provided inconsistent populations of individual conformers as well as net structural trends upon phosphorylation. Detailed anal. of ensembles revealed competition between hydration and formation of internal hydrogen bonds involving amide hydrogens and the phosphate group. The obsd. difference in hydration free energy and potential for hydrogen bonding in individual force fields could be attributed to the different partial at. charges used in each force field and, hence, the different parametrization strategies. Nevertheless, conformational propensities and net structural changes upon phosphorylation are difficult to ext. from exptl. measurements, and existing exptl. data provide limited guidance for force field assessment and further development.
    39. 39
      Rieloff, E.; Skepö, M. Phosphorylation of a disordered peptide─Structural effects and force field inconsistencies. J. Chem. Theory Comput. 2020, 16, 1924– 1935,  DOI: 10.1021/acs.jctc.9b01190
      39
      Phosphorylation of a Disordered Peptide-Structural Effects and Force Field Inconsistencies
      Rieloff, Ellen; Skepoe, Marie
      Journal of Chemical Theory and Computation (2020), 16 (3), 1924-1935CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      Phosphorylation is one of the most abundant types of post-translational modifications of intrinsically disordered proteins (IDPs). This study examines the conformational changes in the 15-residue-long N-terminal fragment of the IDP statherin upon phosphorylation, using computer simulations with two different force fields: AMBER ff99SB-ILDN and CHARMM36m. The results from the simulations are compared with exptl. small-angle X-ray scattering (SAXS) and CD data. In the unphosphorylated state, the two force fields are in excellent agreement regarding global structural properties such as size and shape. However, they exhibit some differences in the extent and type of the secondary structure. In the phosphorylated state, neither of the force fields performs well compared to the exptl. data. Both force fields show a compaction of the peptide upon phosphorylation, greater than what is seen in SAXS expts., although they differ in the local structure. While the CHARMM force field increases the fraction of bends in the peptide as a response to strong interactions between the phosphorylated residues and arginines, the AMBER force field shows an increase of the helical content in the N-terminal part of the peptide, where the phosphorylated residues reside, in better agreement with CD results.
    40. 40
      Rieloff, E.; Skepö, M. Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: a Force Field Comparison. International Journal of Molecular Sciences 2021, 22, 10174,  DOI: 10.3390/ijms221810174
      40
      Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: A Force Field Comparison
      Rieloff, Ellen; Skepoe, Marie
      International Journal of Molecular Sciences (2021), 22 (18), 10174CODEN: IJMCFK; ISSN:1422-0067. (MDPI AG)
      Phosphorylation is a common post-translational modification among intrinsically disordered proteins and regions, which helps regulate function by changing the protein conformations, dynamics, and interactions with binding partners. To fully comprehend the effects of phosphorylation, computer simulations are a helpful tool, although they are dependent on the accuracy of the force field used. Here, we compared the conformational ensembles produced by Amber ff99SB-ILDN+TIP4P-D and CHARMM36m, for four phosphorylated disordered peptides ranging in length from 14-43 residues. CHARMM36m consistently produced more compact conformations with a higher content of bends, mainly due to more stable salt bridges. Based on comparisons with exptl. size ests. for the shortest and longest peptide, CHARMM36m appeared to overestimate the compactness. The difference between the force fields was largest for the peptide showing the greatest sepn. between pos. charged and phosphorylated residues, in line with the importance of charge distribution. For this peptide, the conformational ensemble did not change significantly upon increasing the ionic strength from 0 mM to 150 mM, despite a redn. of the salt-bridging probability in the CHARMM36m simulations, implying that salt concn. has negligible effects in this study.
    41. 41
      Man, V. H.; He, X.; Gao, J.; Wang, J. Phosphorylation of Tau R2 Repeat Destabilizes Its Binding to Microtubules: A Molecular Dynamics Simulation Study. ACS Chem. Neurosci. 2023, 14, 458,  DOI: 10.1021/acschemneuro.2c00611
      41
      Phosphorylation of Tau R2 Repeat Destabilizes Its Binding to Microtubules: A Molecular Dynamics Simulation Study
      Man, Viet Hoang; He, Xibing; Gao, Jie; Wang, Junmei
      ACS Chemical Neuroscience (2023), 14 (3), 458-467CODEN: ACNCDM; ISSN:1948-7193. (American Chemical Society)
      Phosphorylation, the most popular post-translational modification of tau protein, plays an important role in regulating tau physiol. functions. However, aberrant phosphorylation attenuates the binding affinity of tau to a microtubule (MT), resulting in MT destabilization followed by accumulation of neurofibrillary tangles in the brain. There are in total 85 potential phosphorylation sites in a full-length tau protein, and about half of them are abnormal as they occur in tau of Alzheimer's disease (AD) brain only. The authors studied the impact of abnormal Ser289, Ser293, and Ser289/Ser293 phosphorylation on tau R2-MT binding and the conformation of tau R2 using mol. dynamics simulation. The phosphorylation significantly affected R2-MT interaction and reduced the binding affinity of tau R2 peptides to MTs. Free energy decompn. anal. suggested that the post-translational modified residues themselves made a significant contribution to destabilize tau repeat R2-MT binding. Therefore, the phosphorylation may attenuate the binding affinity of tau to MTs. Addnl., the phosphorylation also enhanced helix-coil transition of monomeric R2 peptides, which may result in the acceleration of tau aggregation. Since these phosphorylated sites were not examd. in previous exptl. studies, the authors' finding through all-atom mol. dynamics simulations and free energy anal. can inspire exptl. scientists to study the impact of the phosphorylation on MT binding and aggregation of full-length tau and the pathol. roles of the phosphorylation at those sites in AD development through in vitro/in vivo assays.
    42. 42
      Tucker, M. R.; Piana, S.; Tan, D.; LeVine, M. V.; Shaw, D. E. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded Dna Molecules and Dna-Protein Complexes. J. Phys. Chem. B 2022, 126, 4442– 4457,  DOI: 10.1021/acs.jpcb.1c10971
      42
      Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes
      Tucker, Maxwell R.; Piana, Stefano; Tan, Dazhi; LeVine, Michael V.; Shaw, David E.
      Journal of Physical Chemistry B (2022), 126 (24), 4442-4457CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
      Although mol. dynamics (MD) simulations have been used extensively to study the structural dynamics of proteins, the role of MD simulation in studies of nucleic acid based systems has been more limited. One contributing factor to this disparity is the historically lower level of accuracy of the phys. models used in such simulations to describe interactions involving nucleic acids. By modifying nonbonded and torsion parameters of a force field from the Amber family of models, we recently developed force field parameters for RNA that achieve a level of accuracy comparable to that of state-of-the-art protein force fields. Here we report force field parameters for DNA, which we developed by transferring nonbonded parameters from our recently reported RNA force field and making subsequent adjustments to torsion parameters. We have also modified the backbone charges in both the RNA and DNA parameter sets to make the treatment of electrostatics compatible with our recently developed variant of the Amber protein and ion force field. We name the force field resulting from the union of these three parameter sets (the new DNA parameters, the revised RNA parameters, and the existing protein and ion parameters) DES-Amber. Extensive testing of DES-Amber indicates that it can describe the thermal stability and conformational flexibility of single- and double-stranded DNA systems with a level of accuracy comparable to or, esp. for disordered systems, exceeding that of state-of-the-art nucleic acid force fields. Finally, we show that, in certain favorable cases, DES-Amber can be used for long-timescale simulations of protein-nucleic acid complexes.
    43. 43
      Irbäck, A.; Mohanty, S. Profasi: a Monte Carlo Simulation Package for Protein Folding and Aggregation. J. Comput. Chem. 2006, 27, 1548– 1555,  DOI: 10.1002/jcc.20452
      43
      PROFASI: A Monte Carlo simulation package for protein folding and aggregation
      Irback Anders; Mohanty Sandipan
      Journal of computational chemistry (2006), 27 (13), 1548-55 ISSN:0192-8651.
      We present a flexible and efficient program package written in C++, PROFASI, for simulating protein folding and aggregation. The systems are modeled using an all-atom description of the protein chains with only torsional degrees of freedom, and implicit water. The program package has a modular structure that makes the interaction potential easy to modify. The currently implemented potential is able to fold several peptides with about 20 residues, and has also been used to study aggregation and force-induced unfolding. The simulation methods implemented in PROFASI are Monte Carlo-based and include a semilocal move and simulated tempering. Adding new updates is easy. The code runs fast in both single- and multi-chain applications, as is illustrated by several examples.
    44. 44
      D’Urzo, A.; Konijnenberg, A.; Rossetti, G.; Habchi, J.; Li, J.; Carloni, P.; Sobott, F.; Longhi, S.; Grandori, R. Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound To a Partner By Combined Esi-Im-Ms and Modeling. Journal of The American Society for Mass Spectrometry 2015, 26, 472– 481,  DOI: 10.1007/s13361-014-1048-z
      There is no corresponding record for this reference.
    45. 45
      Cragnell, C.; Rieloff, E.; Skepö, M. Utilizing Coarse-Grained Modeling and Monte Carlo Simulations To Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions. J. Mol. Biol. 2018, 430, 2478– 2492,  DOI: 10.1016/j.jmb.2018.03.006
      45
      Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions
      Cragnell, Carolina; Rieloff, Ellen; Skepoe, Marie
      Journal of Molecular Biology (2018), 430 (16), 2478-2492CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)
      In this study, we have used the coarse-grained model developed for the intrinsically disordered saliva protein (IDP) Histatin 5, on an exptl. selection of monomeric IDPs, and we show that the model is generally applicable when electrostatic interactions dominate the intra-mol. interactions. Exptl. and theor. calcd. small-angle X-ray scattering data are presented in the form of Kratky plots, and discussions are made with respect to polymer theory and the self-avoiding walk model. Furthermore, the impact of electrostatic interactions is shown and related to estns. of the conformational ensembles obtained from computer simulations and "Flexible-meccano.". Special attention is given to the form factor and how it is affected by the salt concn., as well as the approxn. of using the form factor obtained under physiol. conditions to obtain the structure factor.
    46. 46
      Rieloff, E.; Tully, M. D.; Skepö, M. Assessing the Intricate Balance of Intermolecular Interactions Upon Self-Association of Intrinsically Disordered Proteins. J. Mol. Biol. 2019, 431, 511– 523,  DOI: 10.1016/j.jmb.2018.11.027
      46
      Assessing the intricate balance of intermolecular interactions upon self-association of intrinsically disordered proteins
      Rieloff, Ellen; Tully, Mark D.; Skepoe, Marie
      Journal of Molecular Biology (2019), 431 (3), 511-523CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)
      Attractive interactions between intrinsically disordered proteins (IDPs) can be crucial for the functionality or, on the contrary, lead to the formation of harmful aggregates. For obtaining a mol. understanding of IDPs and their interactions, computer simulations have proven to be a valuable complement to expts. Here, we present a coarse-grained model and its applications to a system dominated by attractive interactions, namely, the self-assocn. of the saliva protein, statherin. SAXS expts. showed that statherin self-assocs. with increased protein concn., and that both an increased temp. and a lower ionic strength decreased the size of the formed complexes. The model captured the obsd. trends and provided insight into the size distribution. Hydrophobic interaction is considered to be the major driving force of self-assocn., while electrostatic repulsion represses growth. In addn., the model suggests that the decrease of assocn. no. with increased temp. is of entropic origin.
    47. 47
      Shrestha, U. R.; Smith, J. C.; Petridis, L. Full Structural Ensembles of Intrinsically Disordered Proteins From Unbiased Molecular Dynamics Simulations. Communications Biology 2021, 4, 243,  DOI: 10.1038/s42003-021-01759-1
      47
      Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations
      Shrestha, Utsab R.; Smith, Jeremy C.; Petridis, Loukas
      Communications Biology (2021), 4 (1), 243CODEN: CBOIDQ; ISSN:2399-3642. (Nature Research)
      Mol. dynamics (MD) simulation is widely used to complement ensemble-averaged expts. of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chem. shift expts., for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, std. MD can reproduce exptl. NMR chem. shifts, but not small-angle scattering data, suggesting chem. shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.
    48. 48
      Gupta, A.; Dey, S.; Hicks, A.; Zhou, H.-X. Artificial Intelligence Guided Conformational Mining of Intrinsically Disordered Proteins. Communications Biology 2022, 5, 610,  DOI: 10.1038/s42003-022-03562-y
      48
      Artificial intelligence guided conformational mining of intrinsically disordered proteins
      Gupta, Aayush; Dey, Souvik; Hicks, Alan; Zhou, Huan-Xiang
      Communications Biology (2022), 5 (1), 610CODEN: CBOIDQ; ISSN:2399-3642. (Nature Portfolio)
      Artificial intelligence recently achieved the breakthrough of predicting the three-dimensional structures of proteins. The next frontier is presented by intrinsically disordered proteins (IDPs), which, representing 30% to 50% of proteomes, readily access vast conformational space. Mol. dynamics (MD) simulations are promising in sampling IDP conformations, but only at extremely high computational cost. Here, we developed generative autoencoders that learn from short MD simulations and generate full conformational ensembles. An encoder represents IDP conformations as vectors in a reduced-dimensional latent space. The mean vector and covariance matrix of the training dataset are calcd. to define a multivariate Gaussian distribution, from which vectors are sampled and fed to a decoder to generate new conformations. The ensembles of generated conformations cover those sampled by long MD simulations and are validated by small-angle X-ray scattering profile and NMR chem. shifts. This work illustrates the vast potential of artificial intelligence in conformational mining of IDPs.
    49. 49
      Yu, H.; Han, W.; Ma, W.; Schulten, K. Transient β-hairpin Formation in α-synuclein Monomer Revealed By Coarse-Grained Molecular Dynamics Simulation. J. Chem. Phys. 2015, 143, 243142,  DOI: 10.1063/1.4936910
      49
      Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation
      Yu, Hang; Han, Wei; Ma, Wen; Schulten, Klaus
      Journal of Chemical Physics (2015), 143 (24), 243142/1-243142/15CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      Parkinson's disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform mol. dynamics simulations (over 180 μs in aggregated time) using a hybrid-resoln. model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in at. detail structural ensembles of wild type and mutant monomeric α-synuclein in aq. soln. The simulations reproduce structural properties of α-synuclein characterized in expts., such as secondary structure content, long-range contacts, chem. shifts, and 3J(HNHCα)-coupling consts. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation. (c) 2015 American Institute of Physics.
    50. 50
      Cragnell, C.; Durand, D.; Cabane, B.; Skepö, M. Coarse-Grained Modeling of the Intrinsically Disordered Protein Histatin 5 in Solution: Monte Carlo Simulations in Combination With Saxs. Proteins: Struct., Funct., Bioinf. 2016, 84, 777– 791,  DOI: 10.1002/prot.25025
      50
      Coarse-grained modeling of the intrinsically disordered protein Histatin 5 in solution: Monte Carlo simulations in combination with SAXS
      Cragnell, Carolina; Durand, Dominique; Cabane, Bernard; Skepoe, Marie
      Proteins: Structure, Function, and Bioinformatics (2016), 84 (6), 777-791CODEN: PSFBAF; ISSN:1097-0134. (Wiley-Blackwell)
      Monte Carlo simulations and coarse-grained modeling have been used to analyze histatin 5 (His5), an unstructured short cationic salivary peptide known to have anticandidical properties. The calcd. scattering functions have been compared with intensity curves and the distance distribution function P(r) obtained from small angle X-ray scattering (SAXS), at both high and low salt concns. The aim was to achieve a mol. understanding and a physico-chem. insight of the obtained SAXS results and to gain information of the conformational changes of Histatin 5 due to altering salt content, charge distribution, and net charge. From a modeling perspective, the accuracy of the electrostatic interactions are of special interest. The used coarse-grained model was based on the primitive model in which charged hard spheres differing in charge and in size represent the ionic particles, and the solvent only enters the model through its relative permittivity. The Hamiltonian of the model comprises three different contributions: (i) excluded vols., (ii) electrostatic, and (iii) van der Waals interactions. Even though the model can be considered as gross omitting all atomistic details, a great correspondence is obtained with the exptl. results. Proteins 2016. © 2016 Wiley Periodicals, Inc.
    51. 51
      Hyltegren, K.; Polimeni, M.; Skepö, M.; Lund, M. Integrating All-Atom and Coarse-Grained Simulations-Toward Understanding of Idps At Surfaces. J. Chem. Theory Comput. 2020, 16, 1843– 1853,  DOI: 10.1021/acs.jctc.9b01041
      There is no corresponding record for this reference.
    52. 52
      Garaizar, A.; Espinosa, J. R. Salt Dependent Phase Behavior of Intrinsically Disordered Proteins From a Coarse-Grained Model With Explicit Water and Ions. J. Chem. Phys. 2021, 155, 125103,  DOI: 10.1063/5.0062687
      52
      Salt dependent phase behavior of intrinsically disordered proteins from a coarse-grained model with explicit water and ions
      Garaizar, Adiran; Espinosa, Jorge R.
      Journal of Chemical Physics (2021), 155 (12), 125103CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      Multivalent proteins and nucleic acids can self-assemble into biomol. condensates that contribute to compartmentalize the cell interior. Computer simulations offer a unique view to elucidate the mechanisms and key intermol. interactions behind the dynamic formation and dissoln. of these condensates. In this work, we present a novel approach to include explicit water and salt in sequence-dependent coarse-grained (CG) models for proteins and RNA, enabling the study of biomol. condensate formation in a salt-dependent manner. Our framework combines a reparameterized version of the HPS protein force field with the monoat. mW water model and the mW-ion potential for NaCl. We show how our CG model qual. captures the exptl. radius of the gyration trend of a subset of intrinsically disordered proteins and reproduces the exptl. protein concn. and water percentage of the human fused in sarcoma (FUS) low-complexity-domain droplets at physiol. salt concn. Moreover, we perform seeding simulations as a function of salt concn. for two antagonist systems: the engineered peptide PR25 and poly-uridine/poly-arginine mixts., finding good agreement with their reported in vitro phase behavior with salt concn. in both cases. Taken together, our work represents a step forward towards extending sequence-dependent CG models to include water and salt, and to consider their key role in biomol. condensate self-assembly. (c) 2021 American Institute of Physics.
    53. 53
      Wang, L.; Friesner, R. A.; Berne, B. Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). J. Phys. Chem. B 2011, 115, 9431– 9438,  DOI: 10.1021/jp204407d
      53
      Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)
      Wang, Lingle; Friesner, Richard A.; Berne, B. J.
      Journal of Physical Chemistry B (2011), 115 (30), 9431-9438CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
      A small change in the Hamiltonian scaling in Replica Exchange with Solute Tempering (REST) is found to improve its sampling efficiency greatly, esp. for the sampling of aq. protein solns. in which there are large-scale solute conformation changes. Like the original REST (REST1), the new version (which the authors call REST2) also bypasses the poor scaling with system size of the std. Temp. Replica Exchange Method (TREM), reducing the no. of replicas (parallel processes) from what must be used in TREM. This redn. is accomplished by deforming the Hamiltonian function for each replica in such a way that the acceptance probability for the exchange of replica configurations does not depend on the no. of explicit water mols. in the system. For proof of concept, REST2 is compared with TREM and with REST1 for the folding of the trpcage and β-hairpin in water. The comparisons confirm that REST2 greatly reduces the no. of CPUs required by regular replica exchange and greatly increases the sampling efficiency over REST1. This method reduces the CPU time required for calcg. thermodn. avs. and for the ab initio folding of proteins in explicit water.
    54. 54
      Rossetti, G.; Musiani, F.; Abad, E.; Dibenedetto, D.; Mouhib, H.; Fernandez, C. O.; Carloni, P. Conformational ensemble of human α-synuclein physiological form predicted by molecular simulations. Phys. Chem. Chem. Phys. 2016, 18, 5702– 5706,  DOI: 10.1039/C5CP04549E
      54
      Conformational ensemble of human α-synuclein physiological form predicted by molecular simulations
      Rossetti, G.; Musiani, F.; Abad, E.; Dibenedetto, D.; Mouhib, H.; Fernandez, C. O.; Carloni, P.
      Physical Chemistry Chemical Physics (2016), 18 (8), 5702-5706CODEN: PPCPFQ; ISSN:1463-9076. (Royal Society of Chemistry)
      The authors performed enhanced sampling mol. dynamics simulations of N-terminally acetylated human α-synuclein, an intrinsically disordered protein involved in Parkinson's disease. The calcns., consistent with expts., suggested that the post-translational modification leads to the formation of a transient amphipathic α-helix. The latter, absent in the non-physiol. form, alters protein dynamics at the N-terminal and intramol. interactions.
    55. 55
      Palomino-Hernandez, O.; Buratti, F. A.; Sacco, P. S.; Rossetti, G.; Carloni, P.; Fernandez, C. O. Role of Tyr-39 for the Structural Features of α-Synuclein and for the Interaction with a Strong Modulator of Its Amyloid Assembly. International journal of molecular sciences 2020, 21, 5061,  DOI: 10.3390/ijms21145061
      There is no corresponding record for this reference.
    56. 56
      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
      56
      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.
    57. 57
      Uluca, B.; Viennet, T.; Petrović, D.; Shaykhalishahi, H.; Weirich, F.; Gönülalan, A.; Strodel, B.; Etzkorn, M.; Hoyer, W.; Heise, H. DNP-enhanced MAS NMR: a tool to snapshot conformational ensembles of α-synuclein in different states. Biophysical journal 2018, 114, 1614– 1623,  DOI: 10.1016/j.bpj.2018.02.011
      There is no corresponding record for this reference.
    58. 58
      Jain, K.; Ghribi, O.; Delhommelle, J. Folding free-energy landscape of α-synuclein (35–97) via replica exchange molecular dynamics. J. Chem. Inf. Model. 2021, 61, 432– 443,  DOI: 10.1021/acs.jcim.0c01278
      58
      Folding Free-Energy Landscape of α-Synuclein (35-97) Via Replica Exchange Molecular Dynamics
      Jain, Karnesh; Ghribi, Othman; Delhommelle, Jerome
      Journal of Chemical Information and Modeling (2021), 61 (1), 432-443CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
      The misfolding and aggregation of α-synuclein (α-syn) in Lewy bodies are implicated in the pathogenesis of various neurodegenerative disorders, such as Parkinson's disease and dementia. The formation of α-syn fibrils is a complex process, involving various intermediates and oligomeric forms. These intermediates establish at an early stage of aggregation and subsequently lead to fibrillation. Detg. which conformations are accessible to monomeric α-syn and esp., as shown in a recent work, to the central amino acids from residue 35 to residue 97 (63 residues) is thus crucial to understand the formation of these oligomers. Here, the authors carry out extensive replica exchange mol. dynamics (total time-18 μs) with an all-atom model and explicit solvent to characterize the free-energy landscape of human α-syn (residue 35 to residue 97). The simulation results lead the authors to identify two free-energy basins. Clustering anal. for the deepest free-energy min. reveals a compact structure, with a secondary structure predominantly α-helix, while the shallower min. corresponds to an elongated conformation, also predominantly α-helix. Furthermore, at physiol. temp., conformational rearrangements happen via helix breaks due to the presence of glycine. Also the most likely conformations were characterized by the α-helix structure rather than the β-hairpin structure (for residue 38 to residue 53), in contrast with prior simulation studies using coarse-grained models or an implicit solvent. For higher temps., a shift in secondary structure with a decrease in the population of α-helix in favor of random coils, β-bend, and β-turns. were obsd.
    59. 59
      Ilie, I. M.; Nayar, D.; Den Otter, W. K.; Van Der Vegt, N. F.; Briels, W. J. Intrinsic conformational preferences and interactions in α-synuclein fibrils: insights from molecular dynamics simulations. J. Chem. Theory Comput. 2018, 14, 3298– 3310,  DOI: 10.1021/acs.jctc.8b00183
      59
      Intrinsic Conformational Preferences and Interactions in α-Synuclein Fibrils: Insights from Molecular Dynamics Simulations
      Ilie, Ioana M.; Nayar, Divya; den Otter, Wouter K.; van der Vegt, Nico F. A.; Briels, Wim J.
      Journal of Chemical Theory and Computation (2018), 14 (6), 3298-3310CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      Amyloid formation by the intrinsically disordered α-synuclein protein is the hallmark of Parkinson's disease. We present atomistic Mol. Dynamics simulations of the core of α-synuclein using enhanced sampling techniques to describe the conformational and binding free energy landscapes of fragments implicated in fibril stabilization. The theor. framework is derived to combine the free energy profiles of the fragments into the reaction free energy of a protein binding to a fibril. Our study shows that individual fragments in soln. have a propensity towards attaining non-β conformations in soln., indicating that in a fibril β-strands are stabilized by interactions with other strands. We show that most dimers of hydrogen-bonded fragments are unstable in soln., while hydrogen bonding stabilizes the collective binding of five fragments to the end of a fibril. Hydrophobic effects make further contributions to the stability of fibrils. This study is the first of its kind where structural and binding preferences of the five major fragments of the hydrophobic core of α-synuclein have been investigated. This approach improves sampling of intrinsically disordered proteins, provides information on the binding mechanism between the core sequences of α-synuclein and enables the parametrization of coarse grained models.
    60. 60
      Chwastyk, M.; Cieplak, M. Conformational biases of α-synuclein and formation of transient knots. J. Phys. Chem. B 2020, 124, 11– 19,  DOI: 10.1021/acs.jpcb.9b08481
      60
      Conformational Biases of α-Synuclein and Formation of Transient Knots
      Chwastyk, Mateusz; Cieplak, Marek
      Journal of Physical Chemistry B (2020), 124 (1), 11-19CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
      We study local conformational biases in the dynamics of α-synuclein by using all-atom simulations with explicit and implicit solvents. The biases are related to the frequency of the specific contact formation. In both approaches, the protein is intrinsically disordered and its strongest bias is to make bend, and then turn, local structures. The explicit-solvent conformations can be substantially more extended which allows for formation of transient trefoil knots, both deep and shallow, that may last for up to 5 μs. The two-chain self-assocn. events, both short- and long-lived, are dominated by formation of contacts in the central part of the sequence. This part tends to form helixes when bound to a micelle.
    61. 61
      Perlmutter, J. D.; Braun, A. R.; Sachs, J. N. Curvature dynamics of α-synuclein familial parkinson disease mutants. J. Biol. Chem. 2009, 284, 7177– 7189,  DOI: 10.1074/jbc.M808895200
      There is no corresponding record for this reference.
    62. 62
      Allison, J. R.; Varnai, P.; Dobson, C. M.; Vendruscolo, M. Determination of the free energy landscape of α-synuclein using spin label nuclear magnetic resonance measurements. J. Am. Chem. Soc. 2009, 131, 18314– 18326,  DOI: 10.1021/ja904716h
      62
      Determination of the Free Energy Landscape of α-Synuclein Using Spin Label Nuclear Magnetic Resonance Measurements
      Allison, Jane R.; Varnai, Peter; Dobson, Christopher M.; Vendruscolo, Michele
      Journal of the American Chemical Society (2009), 131 (51), 18314-18326CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Natively unfolded proteins present a challenge for structure detn. because they populate highly heterogeneous ensembles of conformations. A useful source of structural information about these states is provided by paramagnetic relaxation enhancement measurements by NMR spectroscopy, from which long-range interat. distances can be estd. Here we describe a method for using such distances as restraints in mol. dynamics simulations to obtain a mapping of the free energy landscapes of natively unfolded proteins. We demonstrate the method in the case of α-synuclein and validate the results by a comparison with electron transfer measurements. Our findings indicate that our procedure provides an accurate est. of the relative statistical wts. of the different conformations populated by α-synuclein in its natively unfolded state.
    63. 63
      Amos, S.-B. T.; Schwarz, T. C.; Shi, J.; Cossins, B. P.; Baker, T. S.; Taylor, R. J.; Konrat, R.; Sansom, M. S. Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR. J. Phys. Chem. B 2021, 125, 2929– 2941,  DOI: 10.1021/acs.jpcb.1c01281
      63
      Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR
      Amos, Sarah-Beth T. A.; Schwarz, Thomas C.; Shi, Jiye; Cossins, Benjamin P.; Baker, Terry S.; Taylor, Richard J.; Konrat, Robert; Sansom, Mark S. P.
      Journal of Physical Chemistry B (2021), 125 (11), 2929-2941CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
      α-Synuclein (αS) is a presynaptic protein that binds to cell membranes and is linked to Parkinson's disease (PD). Binding of αS to membranes is a likely first step in the mol. pathophysiol. of PD. The αS mol. can adopt multiple conformations, being largely disordered in water, adopting a β-sheet conformation when present in amyloid fibrils, and forming a dynamic multiplicity of α-helical conformations when bound to lipid bilayers and related membrane-mimetic surfaces. Multiscale mol. dynamics simulations in conjunction with NMR and crosslinking mass spectrometry (XLMS) measurements were used to explore the interactions of αS with an anionic lipid bilayer. The simulations and NMR measurements together reveal a break in the helical structure of the central non-amyloid-β component (NAC) region of αS in the vicinity of residues 65-70, which may facilitate subsequent oligomer formation. Coarse-grained simulations of αS starting from the structure of αS when bound to a detergent micelle reveal the overall pattern of protein contacts to anionic lipid bilayers, while subsequent all-atom simulations provide details of conformational changes upon membrane binding. In particular, simulations and NMR data for liposome-bound αS indicate incipient β-strand formation in the NAC region, which is supported by intramol. contacts seen via XLMS and simulations. Markov state models based on the all-atom simulations suggest a mechanism of conformational change of membrane-bound αS via a dynamic helix break in the region of residue 65 in the NAC region. The emergent dynamic model of membrane-interacting αS advances the authors' understanding of the mechanism of PD, potentially aiding the design of novel therapeutic approaches.
    64. 64
      Herrera, F. E.; Chesi, A.; Paleologou, K. E.; Schmid, A.; Munoz, A.; Vendruscolo, M.; Gustincich, S.; Lashuel, H. A.; Carloni, P. Inhibition of α-synuclein fibrillization by dopamine is mediated by interactions with five C-terminal residues and with E83 in the NAC region. PloS one 2008, 3, e3394,  DOI: 10.1371/journal.pone.0003394
      There is no corresponding record for this reference.
    65. 65
      Robustelli, P.; Ibanez-de Opakua, A.; Campbell-Bezat, C.; Giordanetto, F.; Becker, S.; Zweckstetter, M.; Pan, A. C.; Shaw, D. E. Molecular basis of small-molecule binding to α-synuclein. J. Am. Chem. Soc. 2022, 144, 2501– 2510,  DOI: 10.1021/jacs.1c07591
      65
      Molecular Basis of Small-Molecule Binding to α-Synuclein
      Robustelli, Paul; Ibanez-de-Opakua, Alain; Campbell-Bezat, Cecily; Giordanetto, Fabrizio; Becker, Stefan; Zweckstetter, Markus; Pan, Albert C.; Shaw, David E.
      Journal of the American Chemical Society (2022), 144 (6), 2501-2510CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Intrinsically disordered proteins (IDPs) are implicated in many human diseases. They have generally not been amenable to conventional structure-based drug design, however, because their intrinsic conformational variability has precluded an at.-level understanding of their binding to small mols. Here we present long-time-scale, at.-level mol. dynamics (MD) simulations of monomeric α-synuclein (an IDP whose aggregation is assocd. with Parkinson's disease) binding the small-mol. drug fasudil in which the obsd. protein-ligand interactions were found to be in good agreement with previously reported NMR chem. shift data. In our simulations, fasudil, when bound, favored certain charge-charge and π-stacking interactions near the C terminus of α-synuclein but tended not to form these interactions simultaneously, rather breaking one of these interactions and forming another nearby (a mechanism we term dynamic shuttling). Further simulations with small mols. chosen to modify these interactions yielded binding affinities and key structural features of binding consistent with subsequent NMR expts., suggesting the potential for MD-based strategies to facilitate the rational design of small mols. that bind with disordered proteins.
    66. 66
      Balesh, D.; Ramjan, Z. Unfolded annealing molecular dynamics conformers for wild-type and disease-associated variants of alpha-synuclein show no propensity for beta-sheetformation. Journal of Biophysical Chemistry 2011, 2, 124,  DOI: 10.4236/jbpc.2011.22015
      There is no corresponding record for this reference.
    67. 67
      Allison, J. R.; Rivers, R. C.; Christodoulou, J. C.; Vendruscolo, M.; Dobson, C. M. A relationship between the transient structure in the monomeric state and the aggregation propensities of α-synuclein and β-synuclein. Biochemistry 2014, 53, 7170– 7183,  DOI: 10.1021/bi5009326
      67
      A relationship between the transient structure in the monomeric state and the aggregation propensities of α-synuclein and β-synuclein
      Allison, Jane R.; Rivers, Robert C.; Christodoulou, John C.; Vendruscolo, Michele; Dobson, Christopher M.
      Biochemistry (2014), 53 (46), 7170-7183CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
      α-Synuclein (αS) is an intrinsically disordered protein whose aggregation is implicated in Parkinson's disease. A 2nd member of the synuclein family, β-synuclein (βS), shares significant sequence similarity with αS, but is much more resistant to aggregation. βS is missing an 11-residue stretch in the central non-β-amyloid component region that forms the core of αS amyloid fibrils, yet insertion of these residues into βS to produce the βSHC construct did not markedly increase the aggregation propensity. To investigate the structural basis of these different behaviors, quant. NMR data, in the form of paramagnetic relaxation enhancement-derived interat. distances, were combined with mol. dynamics simulations to generate ensembles of structures representative of the soln. states of αS, βS, and βSHC. Comparison of these ensembles revealed that the differing aggregation propensities of αS and βS was assocd. with differences in the degree of residual structure in the C-terminus coupled to the shorter sepn. between the N- and C-termini in βS and βSHC, making protective intramol. contacts more likely.
    68. 68
      Dedmon, M. M.; Lindorff-Larsen, K.; Christodoulou, J.; Vendruscolo, M.; Dobson, C. M. Mapping long-range interactions in α-synuclein using spin-label NMR and ensemble molecular dynamics simulations. J. Am. Chem. Soc. 2005, 127, 476– 477,  DOI: 10.1021/ja044834j
      68
      Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations
      Dedmon, Matthew M.; Lindorff-Larsen, Kresten; Christodoulou, John; Vendruscolo, Michele; Dobson, Christopher M.
      Journal of the American Chemical Society (2005), 127 (2), 476-477CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      The intrinsically disordered protein α-synuclein plays a key role in the pathogenesis of Parkinson's disease (PD). We show here that the native state of α-synuclein consists of a broad distribution of conformers with an ensemble-averaged hydrodynamic radius significantly smaller than that expected for a random coil structure. This partial condensation is driven by interactions between the highly charged C-terminus and a large hydrophobic central region of the protein sequence. We suggest that this structure could inhibit the formation of α-synuclein aggregates, which are thought to be the cytotoxic species responsible for neurodegeneration in PD.
    69. 69
      Park, S.; Yoon, J.; Jang, S.; Lee, K.; Shin, S. The role of the acidic domain of α-synuclein in amyloid fibril formation: a molecular dynamics study. J. Biomol. Struct. Dyn. 2016, 34, 376– 383,  DOI: 10.1080/07391102.2015.1033016
      69
      The role of the acidic domain of α-synuclein in amyloid fibril formation: a molecular dynamics study
      Park, SeongByeong; Yoon, Jeseong; Jang, Soonmin; Lee, Kyunghee; Shin, Seokmin
      Journal of Biomolecular Structure and Dynamics (2016), 34 (2), 376-383CODEN: JBSDD6; ISSN:0739-1102. (Taylor & Francis Ltd.)
      The detailed mechanism of the pathol. of α-synuclein in the Parkinson's disease has not been clearly elucidated. Recent studies suggested a possible chaperone-like role of the acidic C-terminal region of α-synuclein in the formation of amyloid fibrils. It was also previously demonstrated that the α-synuclein amyloid fibril formation is accelerated by mutations of proline residues to alanine in the acidic region. We performed replica exchange mol. dynamics simulations of the acidic and nonamyloid component (NAC) domains of the wild type and proline-to-alanine mutants of α-synuclein under various conditions. Our results showed that structural changes induced by a change in pH or an introduction of mutations lead to a redn. in mutual contacts between the NAC and acidic regions. Our data suggest that the highly charged acidic region of α-synuclein may act as an intramol. chaperone by protecting the hydrophobic domain from aggregation. Understanding the function of such chaperone-like parts of fibril-forming proteins may provide novel insights into the mechanism of amyloid formation.
    70. 70
      Brodie, N. I.; Popov, K. I.; Petrotchenko, E. V.; Dokholyan, N. V.; Borchers, C. H. Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. PLoS computational biology 2019, 15, e1006859,  DOI: 10.1371/journal.pcbi.1006859
      There is no corresponding record for this reference.
    71. 71
      Tsigelny, I. F.; Bar-On, P.; Sharikov, Y.; Crews, L.; Hashimoto, M.; Miller, M. A.; Keller, S. H.; Platoshyn, O.; Yuan, J. X.-J.; Masliah, E. Dynamics of α-synuclein aggregation and inhibition of pore-like oligomer development by β-synuclein. FEBS journal 2007, 274, 1862– 1877,  DOI: 10.1111/j.1742-4658.2007.05733.x
      71
      Dynamics of α-synuclein aggregation and inhibition of pore-like oligomer development by β-synuclein
      Tsigelny, Igor F.; Bar-On, Pazit; Sharikov, Yuriy; Crews, Leslie; Hashimoto, Makoto; Miller, Mark A.; Keller, Steve H.; Platoshyn, Oleksandr; Yuan, Jason X.-J.; Masliah, Eliezer
      FEBS Journal (2007), 274 (7), 1862-1877CODEN: FJEOAC; ISSN:1742-464X. (Blackwell Publishing Ltd.)
      Accumulation of α-synuclein resulting in the formation of oligomers and protofibrils has been linked to Parkinson's disease and Lewy body dementia. In contrast, β-synuclein (β-syn), a close homolog, does not aggregate and reduces α-synuclein (α-syn)-related pathol. Although considerable information is available about the conformation of α-syn at the initial and end stages of fibrillation, less is known about the dynamic process of α-syn conversion to oligomers and how interactions with antiaggregation chaperones such as β-synuclein might occur. Mol. modeling and mol. dynamics simulations based on the micelle-derived structure of α-syn showed that α-syn homodimers can adopt nonpropagating (head-to-tail) and propagating (head-to-head) conformations. Propagating α-syn dimers on the membrane incorporate addnl. α-syn mols., leading to the formation of pentamers and hexamers forming a ring-like structure. In contrast, β-syn dimers do not propagate and block the aggregation of α-syn into ring-like oligomers. Under in vitro cell-free conditions, α-syn aggregates formed ring-like structures that were disrupted by β-syn. Similarly, cells expressing α-syn displayed increased ion current activity consistent with the formation of Zn2+-sensitive nonselective cation channels. These results support the contention that in Parkinson's disease and Lewy body dementia, α-syn oligomers on the membrane might form pore-like structures, and that the beneficial effects of β-synuclein might be related to its ability to block the formation of pore-like structures.
    72. 72
      Ramis, R.; Ortega-Castro, J.; Casasnovas, R.; Mariño, L.; Vilanova, B.; Adrover, M.; Frau, J. A coarse-grained molecular dynamics approach to the study of the intrinsically disordered protein α-synuclein. J. Chem. Inf. Model. 2019, 59, 1458– 1471,  DOI: 10.1021/acs.jcim.8b00921
      72
      A Coarse-Grained Molecular Dynamics Approach to the Study of the Intrinsically Disordered Protein α-Synuclein
      Ramis, Rafael; Ortega-Castro, Joaquin; Casasnovas, Rodrigo; Marino, Laura; Vilanova, Bartolome; Adrover, Miquel; Frau, Juan
      Journal of Chemical Information and Modeling (2019), 59 (4), 1458-1471CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
      Intrinsically disordered proteins (IDPs) are not well described by a single 3D conformation but by an ensemble of them, which makes their structural characterization esp. challenging, both exptl. and computationally. Most all-atom force fields are designed for folded proteins and give too compact IDP conformations. α-Synuclein is a well-known IDP because of its relation to Parkinson's disease (PD). To understand its role in this disease at the mol. level, an efficient methodol. is needed for the generation of conformational ensembles that are consistent with its known properties (in particular, with its dimensions) and that is readily extensible to posttranslationally modified forms of the protein, commonly found in PD patients. Herein, the authors have contributed to this goal by performing explicit-solvent, microsecond-long Replica Exchange with Solute Scaling (REST2) simulations of α-synuclein with the coarse-grained force field SIRAH, finding that a 30% increase in the default strength of protein-water interactions yields a much better reprodn. of its radius of gyration. Other known properties of α-synuclein, such as chem. shifts, secondary structure content, and long-range contacts, are also reproduced. Furthermore, the authors have simulated a glycated form of α-synuclein to suggest the extensibility of the method to its posttranslationally modified forms. The computationally efficient REST2 methodol. in combination with coarse-grained representations will facilitate the simulations of this relevant IDP and its modified forms, enabling a better understanding of their roles in disease and potentially leading to efficient therapies.
    73. 73
      Yu, H.; Han, W.; Ma, W.; Schulten, K. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation. J. Chem. Phys. 2015, 143, 243142,  DOI: 10.1063/1.4936910
      73
      Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation
      Yu, Hang; Han, Wei; Ma, Wen; Schulten, Klaus
      Journal of Chemical Physics (2015), 143 (24), 243142/1-243142/15CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      Parkinson's disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform mol. dynamics simulations (over 180 μs in aggregated time) using a hybrid-resoln. model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in at. detail structural ensembles of wild type and mutant monomeric α-synuclein in aq. soln. The simulations reproduce structural properties of α-synuclein characterized in expts., such as secondary structure content, long-range contacts, chem. shifts, and 3J(HNHCα)-coupling consts. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation. (c) 2015 American Institute of Physics.
    74. 74
      Narayanan, C.; Weinstock, D. S.; Wu, K.-P.; Baum, J.; Levy, R. M. Investigation of the polymeric properties of α-synuclein and comparison with NMR experiments: a replica exchange molecular dynamics study. J. Chem. Theory Comput. 2012, 8, 3929– 3942,  DOI: 10.1021/ct300241t
      74
      Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study
      Narayanan, Chitra; Weinstock, Daniel S.; Wu, Kuen-Phon; Baum, Jean; Levy, Ronald M.
      Journal of Chemical Theory and Computation (2012), 8 (10), 3929-3942CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      Intrinsically disordered proteins (IDPs) have been shown to be involved in a no. of cellular functions, in addn. to their predominance in diseased states. α-Synuclein may be described as one such IDP, implicated in the pathol. of Parkinson's disease. Understanding the conformational characteristics of the monomeric state of α-synuclein is necessary for understanding the role of the monomer conformation in aggregation. Polymer theories have been applied to investigate the statistical properties of homopolymeric IDPs. Here, we use Replica Exchange Mol. Dynamics (REMD) simulations using temp. as a proxy for solvent quality to examine how well these theories developed for homopolymeric chains describe heteropolymeric α-synuclein. Our results indicate that α-synuclein behaves like a homopolymer at the extremes of solvent quality, while in the intermediate solvent regime, the uneven distribution of charged residues along the sequence strongly influences the conformations adopted by the chain. We refine the ensemble extd. from the REMD simulations of α-synuclein, which shows the best qual. agreement with exptl. results, by fitting to the exptl. NMR Residual Dipolar Couplings (RDCs) and Paramagnetic Relaxation Enhancements (PREs). Our results demonstrate that the detailed shapes of the RDC patterns are sensitive to the angular correlations that are local in sequence while longer range anticorrelations which arise from packing constraints affect the RDC magnitudes.
    75. 75
      Dibenedetto, D.; Rossetti, G.; Caliandro, R.; Carloni, P. A molecular dynamics simulation-based interpretation of nuclear magnetic resonance multidimensional heteronuclear spectra of α-synuclein·dopamine adducts. Biochemistry 2013, 52, 6672– 6683,  DOI: 10.1021/bi400367r
      75
      A Molecular Dynamics Simulation-Based Interpretation of Nuclear Magnetic Resonance Multidimensional Heteronuclear Spectra of α-Synuclein·Dopamine Adducts
      Dibenedetto, Domenica; Rossetti, Giulia; Caliandro, Rocco; Carloni, Paolo
      Biochemistry (2013), 52 (38), 6672-6683CODEN: BICHAW; ISSN:0006-2960. (American Chemical Society)
      Multidimensional heteronuclear NMR (NMR) spectroscopy provides valuable structural information about adducts between naturally unfolded proteins and their ligands. These are often highly pharmacol. relevant. Unfortunately, the detn. of the contributions to obsd. chem. shifts changes upon ligand binding is complicated. Here we present a tool that uses mol. dynamics (MD) trajectories to help interpret two-dimensional (2D) NMR data. We apply this tool to the naturally unfolded protein human α-synuclein interacting with dopamine, an inhibitor of fibril formation, and with its oxidn. products in water solns. By coupling 2D NMR expts. with MD simulations of the adducts in explicit water, the tool confirms with exptl. data that the ligands bind preferentially to 125YEMPS129 residues in the C-terminal region and to a few residues of the so-called NAC region consistently. It also suggests that the ligands might cause conformational rearrangements of distal residues located at the N-terminus. Hence, the performed anal. provides a rationale for the obsd. changes in chem. shifts in terms of direct contacts with the ligand and conformational changes in the protein.
    76. 76
      Tsigelny, I. F.; Sharikov, Y.; Miller, M. A.; Masliah, E. Mechanism of alpha-synuclein oligomerization and membrane interaction: theoretical approach to unstructured proteins studies. Nanomedicine: Nanotechnology, Biology and Medicine 2008, 4, 350– 357,  DOI: 10.1016/j.nano.2008.05.005
      There is no corresponding record for this reference.
    77. 77
      Zhang, T.; Tian, Y.; Li, Z.; Liu, S.; Hu, X.; Yang, Z.; Ling, X.; Liu, S.; Zhang, J. Molecular dynamics study to investigate the dimeric structure of the full-length α-synuclein in aqueous solution. J. Chem. Inf. Model. 2017, 57, 2281– 2293,  DOI: 10.1021/acs.jcim.7b00210
      77
      Molecular Dynamics Study to Investigate the Dimeric Structure of the Full-Length α-Synuclein in Aqueous Solution
      Zhang, Tingting; Tian, Yuanxin; Li, Zhonghuang; Liu, Siming; Hu, Xiang; Yang, Zichao; Ling, Xiaotong; Liu, Shuwen; Zhang, Jiajie
      Journal of Chemical Information and Modeling (2017), 57 (9), 2281-2293CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
      The mechanisms of dimerization of α-synuclein from full-length monomers and their structural features have been studied through mol. dynamics simulations. The dimerization of α-syn plays a crit. role in the fibrillogenesis mechanism and could initiate and trigger α-syn to aggregate by conformational transforming. According to the alignment between three regions of α-syn monomer, eight diverse starting structures have been constructed. However, only five configurations show the dimeric structures, and the detailed properties of three dimers of them are discussed. During the simulations, both identical α-syn peptides (P1 and P2) of these three dimers reduce the high contents of α-helix from their native folded structures, while the contents of β-sheet increase. Antiparallel β-hairpin motifs within the α-syn peptide are formed by intramol. interactions. The β-hairpin regions are adjacent to the nonamyloid β component (NAC) of α-syn, and these structural features are consistent with the exptl. observation. Moreover, intermol. β-sheets also were generated between P1 and P2 through hydrogen bonding interactions. The dimers produce both intramol. β-hairpin and intermol. β-sheet characters; the former is presented in the monomer and oligomer of α-syn, and the latter occurs in the fibril structure. The simulations also show several other interactions such as hydrophobic interactions and salt-bridges, which would contribute to making the α-syn dimers more stable with the aforementioned effects. The results may pave the way to design small mols. to inhibit the dimerization to block the aggregation of α-syn in the future.
    78. 78
      Savva, L.; Platts, J. A. How Cu (II) binding affects structure and dynamics of α-synuclein revealed by molecular dynamics simulations. Journal of Inorganic Biochemistry 2023, 239, 112068,  DOI: 10.1016/j.jinorgbio.2022.112068
      There is no corresponding record for this reference.
    79. 79
      Razzokov, J.; Fazliev, S.; Makhkamov, M.; Marimuthu, P.; Baev, A.; Kurganov, E. Effect of Electric Field on α-Synuclein Fibrils: Revealed by Molecular Dynamics Simulations. International Journal of Molecular Sciences 2023, 24, 6312,  DOI: 10.3390/ijms24076312
      There is no corresponding record for this reference.
    80. 80
      Savva, L.; Platts, J. A. Exploring the Impact of Mutation and Post-Translational Modification on α-Synuclein: Insights From Molecular Dynamics Simulations With and Without Copper. Journal of Inorganic Biochemistry 2023, 249, 112395,  DOI: 10.1016/j.jinorgbio.2023.112395
      There is no corresponding record for this reference.
    81. 81
      Jin, F.; Gräter, F. How Multisite Phosphorylation Impacts the Conformations of Intrinsically Disordered Proteins. PLOS Computational Biology 2021, 17, e1008939,  DOI: 10.1371/journal.pcbi.1008939
      There is no corresponding record for this reference.
    82. 82
      Rieloff, E.; Skepö, M. The Effect of Multisite Phosphorylation on the Conformational Properties of Intrinsically Disordered Proteins. International Journal of Molecular Sciences 2021, 22, 11058,  DOI: 10.3390/ijms222011058
      There is no corresponding record for this reference.
    83. 83
      Martin, I. M.; Aponte-Santamaría, C.; Schmidt, L.; Hedtfeld, M.; Iusupov, A.; Musacchio, A.; Gräter, F. Phosphorylation Tunes Elongation Propensity and Cohesiveness of Incenp’s Intrinsically Disordered Region. J. Mol. Biol. 2022, 434, 167387,  DOI: 10.1016/j.jmb.2021.167387
      There is no corresponding record for this reference.
    84. 84
      Adhikari, S.; Mondal, J. Machine Learning Subtle Conformational Change Due To Phosphorylation in Intrinsically Disordered Proteins. J. Phys. Chem. B 2023, 127, 9433– 9449,  DOI: 10.1021/acs.jpcb.3c05136
      There is no corresponding record for this reference.
    85. 85
      Amith, W. D.; Dutagaci, B. Complex Conformational Space of the Rna Polymerase Ii C-Terminal Domain Upon Phosphorylation. J. Phys. Chem. B 2023, 127, 9223– 9235,  DOI: 10.1021/acs.jpcb.3c02655
      There is no corresponding record for this reference.
    86. 86
      Roche, J.; Ying, J.; Maltsev, A. S.; Bax, A. Impact of Hydrostatic Pressure on an Intrinsically Disordered Protein: A High-Pressure NMR Study of α-Synuclein. ChemBioChem. 2013, 14, 1754– 1761,  DOI: 10.1002/cbic.201300244
      86
      Impact of Hydrostatic Pressure on an Intrinsically Disordered Protein: A High-Pressure NMR Study of α-Synuclein
      Roche, Julien; Ying, Jinfa; Maltsev, Alexander S.; Bax, Ad
      ChemBioChem (2013), 14 (14), 1754-1761CODEN: CBCHFX; ISSN:1439-4227. (Wiley-VCH Verlag GmbH & Co. KGaA)
      The impact of pressure on the backbone 15N, 1H and 13C chem. shifts in N-terminally acetylated α-synuclein has been evaluated over a pressure range 1-2500 bar. Even while the chem. shifts fall very close to random coil values, as expected for an intrinsically disordered protein, substantial deviations in the pressure dependence of the chem. shifts are seen relative to those in short model peptides. In particular, the nonlinear pressure response of the 1HN chem. shifts, which commonly is assocd. with the presence of low-lying "excited states", is much larger in α-synuclein than in model peptides. The linear pressure response of 1HN chem. shift, commonly linked to H-bond length change, correlates well with those in short model peptides, and is found to be anticorrelated with its temp. dependence. The pressure dependence of 13C chem. shifts shows remarkably large variations, even when accounting for residue type, and do not point to a clear shift in population between different regions of the Ramachandran map. However, a nearly universal decrease in 3JHN-Ha by 0.22±0.05 Hz suggests a slight increase in population of the polyproline II region at 2500 bar. The first six residues of N-terminally acetylated synuclein show a transient of approx. 15% population of α-helix, which slightly diminishes at 2500 bar. The backbone dynamics of the protein is not visibly affected beyond the effect of slight increase in water viscosity at 2500 bar.
    87. 87
      DeLano, W. L. Pymol: An open-source molecular graphics tool. CCP4 Newsletter on protein crystallography 2002, 40, 82– 92
      There is no corresponding record for this reference.
    88. 88
      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
      88
      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.
    89. 89
      Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N log (N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089– 10092,  DOI: 10.1063/1.464397
      89
      Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems
      Darden, Tom; York, Darrin; Pedersen, Lee
      Journal of Chemical Physics (1993), 98 (12), 10089-92CODEN: JCPSA6; ISSN:0021-9606.
      An N·log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolution using fast Fourier transforms. Timings and accuracies are presented for three large cryst. ionic systems.
    90. 90
      Evans, D. J.; Holian, B. L. The nose-hoover thermostat. J. Chem. Phys. 1985, 83, 4069– 4074,  DOI: 10.1063/1.449071
      90
      The Nose-Hoover thermostat
      Evans, Denis J.; Holian, Brad Lee
      Journal of Chemical Physics (1985), 83 (8), 4069-74CODEN: JCPSA6; ISSN:0021-9606.
      In a theory of the linear response, to an external field, of a thermostatted many-body system, equil. time correlation functions (relating to fluctuations in the internal energy, vol.-pressure tensor, etc.) were calcd. by using the algorithm of S. Nose (1984) and W. G. Hoover (1985) based on statistical-mech. equation for expressing thermostatting (E. and W. G. H., 1985). In the thermodn. limit, the response was the same as that of the corresponding Gaussian isothermal system. Nonequil. mol.-dynamics simulations of planar Couette flow showed that the calcd. shear-viscosity coeff. was remarkably independent of the type of thermostatting algorithm used in the calcn.
    91. 91
      Andersen, H. C. Molecular dynamics simulations at constant pressure and/or temperature. J. Chem. Phys. 1980, 72, 2384– 2393,  DOI: 10.1063/1.439486
      91
      Molecular dynamics simulations at constant pressure and/or temperature
      Andersen, Hans C.
      Journal of Chemical Physics (1980), 72 (4), 2384-93CODEN: JCPSA6; ISSN:0021-9606.
      In the mol. dynamics simulation method for fluids, the equations of motion for a collection of particles in a fixed vol. are solved numerically. The energy, vol., and no. of particles are const. for a particular simulation, and it is assumed that time avs. of properties of the simulated fluid are equal to microcanonical ensemble avs. of the same properties. In some situations, it is desirable to perform simulations of a fluid for particular values of temp. and/or pressure or under conditions in which the energy and vol. of the fluid can fluctuate. Three methods for performing mol. dynamics simulations under conditions of const. temp. and/or pressure are discussed. Time avs. of properties of the simulated fluid are equal to avs. over the isenthalpic-isobaric, canonical, and isothermal-isobaric ensembles. Each method is a way of describing the dynamics of a certain no. of particles in a vol. element of a fluid while taking into account the influence of surrounding particles in changing the energy and/or d. of the simulated vol. element. The influence of the surroundings is taken into account without unwanted surface effects. Examples of situations where these methods may be useful are discussed.
    92. 92
      Hess, B.; Bekker, H.; Berendsen, H. J.; Fraaije, J. G. LINCS: a linear constraint solver for molecular simulations. Journal of computational chemistry 1997, 18, 1463– 1472,  DOI: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
      92
      LINCS: a linear constraint solver for molecular simulations
      Hess, Berk; Bekker, Henk; Berendsen, Herman J. C.; Fraaije, Johannes G. E. M.
      Journal of Computational Chemistry (1997), 18 (12), 1463-1472CODEN: JCCHDD; ISSN:0192-8651. (Wiley)
      We present a new LINear Constraint Solver (LINCS) for mol. simulations with bond constraints using the enzyme lysozyme and a 32-residue peptide as test systems. The algorithm is inherently stable, as the constraints themselves are reset instead of derivs. of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrixes, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large mols. At the same accuracy, the LINCS algorithm is 3-4 times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward.
    93. 93
      Appadurai, R.; Koneru, J. K.; Bonomi, M.; Robustelli, P.; Srivastava, A. Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins With T-Distributed Stochastic Neighbor Embedding. J. Chem. Theory Comput. 2023, 19, 4711– 4727,  DOI: 10.1021/acs.jctc.3c00224
      There is no corresponding record for this reference.
    94. 94
      McGibbon, R. T.; Beauchamp, K. A.; Harrigan, M. P.; Klein, C.; Swails, J. M.; Hernández, C. X.; Schwantes, C. R.; Wang, L.-P.; Lane, T. J.; Pande, V. S. MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophys. J. 2015, 109, 1528– 1532,  DOI: 10.1016/j.bpj.2015.08.015
      94
      MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
      McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernandez, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.
      Biophysical Journal (2015), 109 (8), 1528-1532CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
      As mol. dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomol. systems, the necessity of flexible and easy-to-use software tools for the anal. of these simulations is growing. We have developed MDTraj, a modern, lightwt., and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large no. of trajectory anal. capabilities including minimal root-mean-square-deviation calcns., secondary structure assignment, and the extn. of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-std. statistical anal. and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the anal. of MD data and connects these datasets with the modern interactive data science software ecosystem in Python.
    95. 95
      Shen, Y.; Bax, A. Sparta+: a Modest Improvement in Empirical Nmr Chemical Shift Prediction By Means of an Artificial Neural Network. Journal of Biomolecular NMR 2010, 48, 13– 22,  DOI: 10.1007/s10858-010-9433-9
      95
      SPARTA+: a modest improvement in empirical NMR chemical shift prediction by an artificial neural network
      Shen, Yang; Bax, Ad
      Journal of Biomolecular NMR (2010), 48 (1), 13-22CODEN: JBNME9; ISSN:0925-2738. (Springer)
      NMR chem. shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. The authors describe a new chem. shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, contg. 580 proteins for which high-resoln. X-ray structures and nearly complete backbone and 13Cβ chem. shifts are available. The neural network is trained to establish quant. relations between chem. shifts and protein structures, including backbone and side-chain conformation, H-bonding, elec. fields and ring-current effects. The trained neural network yields rapid chem. shift prediction for backbone and 13Cβ atoms, with std. deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for δ15N, δ13C', δ13Cα, δ13Cβ, δ1Hα and δ1HN, resp., between the SPARTA+ predicted and exptl. shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chem. shifts.
    96. 96
      Nagy, G.; Igaev, M.; Jones, N. C.; Hoffmann, S. V.; Grubmüller, H. Sesca: Predicting Circular Dichroism Spectra From Protein Molecular Structures. J. Chem. Theory Comput. 2019, 15, 5087– 5102,  DOI: 10.1021/acs.jctc.9b00203
      96
      SESCA: Predicting Circular Dichroism Spectra from Protein Molecular Structures
      Nagy, Gabor; Igaev, Maxim; Jones, Nykola C.; Hoffmann, Soeren V.; Grubmueller, Helmut
      Journal of Chemical Theory and Computation (2019), 15 (9), 5087-5102CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      CD spectroscopy is a highly sensitive, but low-resoln. technique to study the structure of proteins. Combined with mol. modeling or other complementary techniques, CD spectroscopy can provide essential information at higher resoln. To this end, the authors introduce a new computational method to calc. the electronic CD spectra of proteins from a structural model or ensemble using the av. secondary structure compn. and a precalcd. set of basis spectra. The method is designed for model validation to est. the error of a given protein structural model based on the measured CD spectrum. The authors compared the predictive power of the method to existing algorithms -- namely DichroCalc and PDB2CD -- and found that it predicts CD spectra more accurately. The results indicate that the derived basis sets are robust to both exptl. errors in the ref. spectra and the choice of the secondary structure classification algorithm. For over 80% of the globular ref. proteins, the basis sets accurately predict the exptl. spectrum solely from their secondary structure compn. For the remaining 20%, correcting for intensity normalization considerably improves the prediction power. Addnl., the authors show that the predictions for short peptides and an example complex of intrinsically disordered proteins strongly benefit from accounting for side-chain contributions and structural flexibility.
    97. 97
      Nagy, G.; Grubmüller, H. How Accurate Is Circular Dichroism-Based Model Validation?. Eur. Biophys. J. 2020, 49, 497– 510,  DOI: 10.1007/s00249-020-01457-6
      97
      How accurate is circular dichroism-based model validation
      Nagy, Gabor; Grubmueller, Helmut
      European Biophysics Journal (2020), 49 (6), 497-510CODEN: EBJOE8; ISSN:0175-7571. (Springer)
      Abstr.: CD (CD) spectroscopy is highly sensitive to the secondary structure (SS) compn. of proteins. Several methods exist to either est. the SS compn. of a protein or to validate existing structural models using its CD spectrum. The accuracy and precision of these methods depend on the quality of both the measured CD spectrum and the used ref. structure. Using a large ref. protein set with high-quality CD spectra and synthetic data derived from this set, we quantified deviations from both ideal spectra and ref. structures due to exptl. limitations. We also detd. the impact of these deviations on SS estn., CD prediction, and SS validation methods of the SESCA anal. package. With regard to the CD spectra, our results suggest intensity scaling errors and non-SS contributions as the main causes of inaccuracies. These factors also can lead to overestimated model errors during validation. The errors of the used ref. structures combine non-additively with errors caused by the CD spectrum, which increases the uncertainty of model validation. We have further shown that the effects of scaling errors in the CD spectrum can be nearly eliminated by appropriate re-scaling, and that the accuracy of model validation methods can be improved by accounting for typical non-SS contributions.
    98. 98
      Nagy, G.; Grubmuller, H. Implementation of a Bayesian Secondary Structure Estimation Method for the Sesca Circular Dichroism Analysis Package. Comput. Phys. Commun. 2021, 266, 108022,  DOI: 10.1016/j.cpc.2021.108022
      98
      Implementation of a Bayesian secondary structure estimation method for the SESCA circular dichroism analysis package
      Nagy, Gabor; Grubmuller, Helmut
      Computer Physics Communications (2021), 266 (), 108022CODEN: CPHCBZ; ISSN:0010-4655. (Elsevier B.V.)
      CD spectroscopy is a structural biol. technique frequently applied to det. the secondary structure compn. of sol. proteins. Our recently introduced computational anal. package SESCA aids the interpretation of protein CD spectra and enables the validation of proposed corresponding structural models. To further these aims, we present the implementation and characterization of a new Bayesian secondary structure estn. method in SESCA, termed SESCA_bayes. SESCA_bayes samples possible secondary structures using a Monte Carlo scheme, driven by the likelihood of estd. scaling errors and non-secondary-structure contributions of the measured spectrum. SESCA_bayes provides an estd. secondary structure compn. and sep. uncertainties on the fraction of residues in each secondary structure class. It also assists efficient model validation by providing a posterior secondary structure probability distribution based on the measured spectrum. Our presented study indicates that SESCA_bayes ests. the secondary structure compn. with a significantly smaller uncertainty than its predecessor, SESCA_deconv, which is based on spectrum deconvolution. Further, the mean accuracy of the two methods in our anal. is comparable, but SESCA_bayes provides more accurate ests. for CD spectra that contain considerable non-SS contributions.Program Title: SESCA_bayesCPC Library link to program files:https://doi.org/10.17632/5nnsbn6ync.1Developer's repository link:https://www.mpibpc.mpg.de/sescaLicensing provisions: GPLv3Programming language: PythonNature of problem: The CD spectrum of a protein is strongly correlated with its secondary structure compn. However, detg. the secondary structure from a spectrum is hindered by non-secondary structure contributions and by scaling errors due the uncertainty of the protein concn. If not taken properly into account, these exptl. factors can cause considerable errors when conventional secondary-structure estn. methods are used. Because these errors combine with errors of the proposed structural model in a non-additive fashion, it is difficult to assess how much uncertainty the exptl. factors introduce to model validation approaches based on CD spectra.Soln. method: For a given measured CD spectrum, the SESCA_bayes algorithm applies Bayesian statistics to account for scaling errors and non-secondary structure contributions and to det. the conditional secondary structure probability distribution. This approach relies on fast spectrum predictions based on empirical basis spectrum sets and joint probability distribution maps for scaling factors and non-secondary structure distributions. Because SESCA_bayes ests. the most probable secondary structure compn. based on a probability-weighted sample distribution, it avoids the typical fitting errors that occur during conventional spectrum deconvolution methods. It also ests. the uncertainty of CD based model validation more accurately than previous methods of the SESCA anal. package.
    99. 99
      de Bruyn, E. SPEADI: Scalable Protein Environment Analysis for Dynamics and Ions (v1.0.0) . 2022;https://zenodo.org/records/7436713.
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    100. 100
      de Bruyn, E.; Dorn, A. E.; Zimmermann, O.; Rossetti, G. Speadi: Accelerated Analysis of Idp-Ion Interactions From MD-Trajectories. Biology 2023, 12, 581,  DOI: 10.3390/biology12040581
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    101. 101
      Wernet, P.; Nordlund, D.; Bergmann, U.; Cavalleri, M.; Odelius, M.; Ogasawara, H.; Näslund, L. A.; Hirsch, T. K.; Ojamäe, L.; Glatzel, P. The Structure of the First Coordination Shell in Liquid Water. Science 2004, 304, 995– 999,  DOI: 10.1126/science.1096205
      101
      The Structure of the First Coordination Shell in Liquid Water
      Wernet, Ph.; Nordlund, D.; Bergmann, U.; Cavalleri, M.; Odelius, M.; Ogasawara, H.; Naeslund, L. A.; Hirsch, T. K.; Ojamaee, L.; Glatzel, P.; Pettersson, L. G. M.; Nilsson, A.
      Science (Washington, DC, United States) (2004), 304 (5673), 995-999CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
      X-ray absorption spectroscopy and x-ray Raman scattering were used to probe the mol. arrangement in the 1st coordination shell of liq. H2O. The local structure is characterized by comparison with bulk and surface of ordinary hexagonal ice Ih and with calcd. spectra. Most mols. in liq. H2O are in 2 H-bonded configurations with 1 strong donor and 1 strong acceptor H bond in contrast to the 4 H-bonded tetrahedral structure in ice. Upon heating from 25° to 90°, 5 to 10% of the mols. change from tetrahedral environments to 2 H-bonded configurations. Findings are consistent with neutron and x-ray diffraction data, and combining the results sets a strong limit for possible local structure distributions in liq. H2O. Serious discrepancies with structures based on current mol. dynamics simulations are obsd.
    102. 102
      Donald, J. E.; Kulp, D. W.; DeGrado, W. F. Salt Bridges: Geometrically Specific, Designable Interactions. Proteins: Struct., Funct., Bioinf. 2011, 79, 898– 915,  DOI: 10.1002/prot.22927
      102
      Salt bridges: geometrically specific, designable interactions
      Donald, Jason E.; Kulp, Daniel W.; DeGrado, William F.
      Proteins: Structure, Function, and Bioinformatics (2011), 79 (3), 898-915CODEN: PSFBAF ISSN:. (Wiley-Liss, Inc.)
      Salt bridges occur frequently in proteins, providing conformational specificity and contributing to mol. recognition and catalysis. We present a comprehensive anal. of these interactions in protein structures by surveying a large database of protein structures. Salt bridges between Asp or Glu and His, Arg, or Lys display extremely well-defined geometric preferences. Several previously obsd. preferences are confirmed, and others that were previously unrecognized are discovered. Salt bridges are explored for their preferences for different sepns. in sequence and in space, geometric preferences within proteins and at protein-protein interfaces, co-operativity in networked salt bridges, inclusion within metal-binding sites, preference for acidic electrons, apparent conformational side chain entropy redn. on formation, and degree of burial. Salt bridges occur far more frequently between residues at close than distant sequence sepns., but, at close distances, there remain strong preferences for salt bridges at specific sepns. Specific types of complex salt bridges, involving three or more members, are also discovered. As the authors observe a strong relationship between the propensity to form a salt bridge and the placement of salt-bridging residues in protein sequences, the authors discuss the role that salt bridges might play in kinetically influencing protein folding and thermodynamically stabilizing the native conformation. We also develop a quant. method to select appropriate crystal structure resoln. and B-factor cutoffs. Detailed knowledge of these geometric and sequence dependences should aid de novo design and prediction algorithms.
    103. 103
      Kabsch, W.; Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers: Original Research on Biomolecules 1983, 22, 2577– 2637,  DOI: 10.1002/bip.360221211
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      Tavernelli, I.; Cotesta, S.; Iorio, E. E. D. Protein Dynamics, Thermal Stability, and Free-Energy Landscapes: a Molecular Dynamics Investigation. Biophys. J. 2003, 85, 2641– 2649,  DOI: 10.1016/S0006-3495(03)74687-6
      104
      Protein dynamics, thermal stability, and free-energy landscapes: A molecular dynamics investigation
      Tavernelli, Ivano; Cotesta, Simona; Di Iorio, Ernesto E.
      Biophysical Journal (2003), 85 (4), 2641-2649CODEN: BIOJAU; ISSN:0006-3495. (Biophysical Society)
      Proteins have a complex free-energy landscape because of their rich topol. and the nature of their nonbonded interaction potential. This has important consequences because the roughness of the landscape affects the ease with which a chain folds and also dets. the dynamic behavior of the folded structure, thus influencing its functional and stability properties. A detailed description of the free-energy landscape is therefore of paramount importance for a quant. understanding of the relationships between structure, dynamics, stability, and functional behavior of proteins. The free-energy landscape of a protein is a high-dimensional hypersurface, difficult to rationalize. Therefore, achieving its detailed graphical representation in a way that goes beyond the familiar funnel-like free-energy model is still a big challenge. We describe here an approach based on global structural parameters that allows a two-dimensional representation of the free-energy landscape from simulated at. trajectories. As shown in this and in the accompanying article, our representation of the landscape, combined with other conformational analyses, provides valuable information on its roughness and on how at. trajectories evolve with time.
    105. 105
      Lazar, T.; Guharoy, M.; Vranken, W.; Rauscher, S.; Wodak, S. J.; Tompa, P. Distance-Based metrics for comparing conformational ensembles of intrinsically disordered proteins. Biophys. J. 2020, 118, 2952– 2965,  DOI: 10.1016/j.bpj.2020.05.015
      105
      Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins
      Lazar, Tamas; Guharoy, Mainak; Vranken, Wim; Rauscher, Sarah; Wodak, Shoshana J.; Tompa, Peter
      Biophysical Journal (2020), 118 (12), 2952-2965CODEN: BIOJAU; ISSN:0006-3495. (Cell Press)
      Intrinsically disordered proteins are proteins whose native functional states represent ensembles of highly diverse conformations. Such ensembles are a challenge for quant. structure comparisons because their conformational diversity precludes optimal superimposition of the at. coordinates necessary for deriving common similarity measures such as the root mean-square deviation of these coordinates. Here, we introduce superimposition-free metrics that are based on computing matrixes of the Cα-Cα distance distributions within ensembles and comparing these matrixes between ensembles. Differences between two matrixes yield information on the similarity between specific regions of the polypeptide, whereas the global structural similarity is captured by the root mean-square difference between the medians of the Cα-Cα distance distributions of two ensembles. Together, our metrics enable rigorous investigations of structure-function relationships in conformational ensembles of intrinsically disordered proteins derived using exptl. restraints or by mol. simulations and for proteins contg. both structured and disordered regions.
    106. 106
      Li, J.; Bennett, K. C.; Liu, Y.; Martin, M. V.; Head-Gordon, T. Accurate Prediction of Chemical Shifts for Aqueous Protein Structure on ”Real World” Data. Chemical Science 2020, 11, 3180– 3191,  DOI: 10.1039/C9SC06561J
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      Bell, R.; Vendruscolo, M. Modulation of the Interactions Between α-Synuclein and Lipid Membranes By Post-Translational Modifications. Frontiers in Neurology 2021, 12, 661117,  DOI: 10.3389/fneur.2021.661117
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    108. 108
      Killinger, B. A.; Mercado, G.; Choi, S.; Tittle, T.; Chu, Y.; Brundin, P.; Kordower, J. H. Distribution of Phosphorylated Alpha-Synuclein in Non-Diseased Brain Implicates Olfactory Bulb Mitral Cells in Synucleinopathy Pathogenesis. npj Parkinson’s Disease 2023, 9, 43,  DOI: 10.1038/s41531-023-00491-3
      There is no corresponding record for this reference.
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      Guerrero-Ferreira, R.; Taylor, N. M.; Mona, D.; Ringler, P.; Lauer, M. E.; Riek, R.; Britschgi, M.; Stahlberg, H. Cryo-Em Structure of Alpha-Synuclein Fibrils. eLife 2018, 7, e36402,  DOI: 10.7554/eLife.36402
      109
      Cryo-EM structure of alpha-synuclein fibrils
      Guerrero-Ferreira, Ricardo; Taylor, Nicholas M. I.; Mona, Daniel; Ringler, Philippe; Lauer, Matthias E.; Riek, Roland; Britschgi, Markus; Stahlberg, Henning
      eLife (2018), 7 (), e36402/1-e36402/18CODEN: ELIFA8; ISSN:2050-084X. (eLife Sciences Publications Ltd.)
      Parkinson's disease is a progressive neuropathol. disorder that belongs to the class of synucleinopathies, in which the protein alpha-synuclein is found at abnormally high concns. in affected neurons. Its hallmark are intracellular inclusions called Lewy bodies and Lewy neurites. We here report the structure of cytotoxic alpha-synuclein fibrils (residues 1-121), detd. by cryo-electron microscopy at a resoln. of 3.4 Å . Two protofilaments form a polar fibril composed of staggered b-strands. The backbone of residues 38 to 95, including the fibril core and the non-amyloid component region, are well resolved in the EM map. Residues 50-57, contg. three of the mutation sites assocd. with familial synucleinopathies, form the interface between the two protofilaments and contribute to fibril stability. A hydrophobic cleft at one end of the fibril may have implications for fibril elongation, and invites for the design of mols. for diagnosis and treatment of synucleinopathies.
    110. 110
      Guerrero-Ferreira, R.; Taylor, N. M.; Arteni, A.-A.; Kumari, P.; Mona, D.; Ringler, P.; Britschgi, M.; Lauer, M. E.; Makky, A.; Verasdonck, J. Two New Polymorphic Structures of Human Full-Length Alpha-Synuclein Fibrils Solved By Cryo-Electron Microscopy. eLife 2019, 8, e48907,  DOI: 10.7554/eLife.48907
      110
      Two new polymorphic structures of human full-length alpha-synuclein fibrils solved by cryo-electron microscopy
      Guerrero-Ferreira†, Ricardo; Taylor, Nicholas Mi; Arteni, Ana-Andreea; Kumari, Pratibha; Mona, Daniel; Ringler, Philippe; Britschgi, Markus; Lauer, Matthias E.; Makky, Ali; Verasdonck, Joeri; Riek, Roland; Melki, Ronald; Meier, Beat H.; Ckmann, Anja Bo; Bousset, Luc; Stahlberg, Henning
      eLife (2019), 8 (), e48907CODEN: ELIFA8; ISSN:2050-084X. (eLife Sciences Publications Ltd.)
      Intracellular inclusions rich in alpha-synuclein are a hallmark of several neuropathol. diseases including Parkinson's disease (PD). Previously, we reported the structure of alpha-synuclein fibrils (residues 1-121), composed of two protofibrils that are connected via a densely-packed interface formed by residues 50-57 (Guerrero-Ferreira, eLife 218;7: e36402). We here report two new polymorphic at. structures of alpha-synuclein fibrils termed polymorphs 2a and 2b, at 3.0 Å and 3.4 Å resoln., resp. These polymorphs show a radically different structure compared to previously reported polymorphs. The new structures have a 10 nm fibril diam. and are composed of two protofilaments which interact via intermol. salt-bridges between amino acids K45, E57 (polymorph 2a) or E46 (polymorph 2b). The nonamyloid component (NAC) region of alpha-synuclein is fully buried by previously non-described interactions with the N-terminus. A hydrophobic cleft, the location of familial PD mutation sites, and the nature of the protofilament interface now invite to formulate hypotheses about fibril formation, growth and stability.
    111. 111
      Krause, D. Juwels: Modular Tier-0/1 Supercomputer At Jülich Supercomputing Centre. Journal of large-scale research facilities JLSRF 2019, 5, A135,  DOI: 10.17815/jlsrf-5-171
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      Alvarez, D. Juwels Cluster and Booster: Exascale Pathfinder With Modular Supercomputing Architecture At Juelich Supercomputing Centre. Journal of large-scale research facilities JLSRF 2021, 7, A183,  DOI: 10.17815/jlsrf-7-183
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      Herten, A. JUWELS Booster - Early User Experiences. Proceedings of the 2021 on Performance EngineeRing, Modelling, Analysis, and VisualizatiOn STrategy 2021, 1
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      Kesselheim, S.; Herten, A.; Krajsek, K.; Ebert, J.; Jitsev, J.; Cherti, M.; Langguth, M.; Gong, B.; Stadtler, S.; Mozaffari, A. Lecture Notes in Computer Science; Lecture Notes in Computer Science; Springer International Publishing; 2021; pp 453– 468.
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      Thörnig, P. Jureca: Data Centric and Booster Modules Implementing the Modular Supercomputing Architecture At Jülich Supercomputing Centre. Journal of large-scale research facilities JLSRF 2021, 7, A182,  DOI: 10.17815/jlsrf-7-182
      There is no corresponding record for this reference.

  • Supporting Information

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    • Detailed experimental setup (including all GROMACS parameters), analysis and comparison with results obtained with other force fields (PDF)

    • Structures of the 25 cluster midpoints are included for both AS and pAS (ZIP)


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