Rhomboid intramembrane proteases are bound to lipid membranes, where they dock and cleave other transmembrane substrates. How the lipid membrane surrounding the protease impacts the conformational dynamics of the protease is essential to understand because it informs on the reaction coordinate of substrate binding. Atomistic molecular dynamics simulations allow us to probe protein motions and characterize the coupling between protein and lipids. Simulations performed here on GlpG, the rhomboid protease from Escherichia coli, indicate that the thickness of the lipid membrane close to GlpG depends on both the composition of the lipid membrane and the conformation of GlpG. Transient binding of a lipid headgroup at the active site of the protease, as observed in some of the simulations reported here, suggests that a lipid headgroup might compete with the substrate for access to the GlpG active site. Interactions identified between lipid headgroups and the protein influence the dynamics of lipid interactions close to the substrate-binding site. These observations suggest that the lipid membrane environment shapes the energy profile of the substrate-docking region of the enzyme reaction coordinate.

Thymine DNA glycosylase (TDG) initiates the base excision repair mechanism for the deamination and oxidation products of cytosine and 5-methylcytosine. This enzyme has a key role in epigenetic regulation, and its catalytic inactivation results in, e.g., mice embryo lethality. Here, we employ molecular dynamics simulations and quantum mechanics/molecular mechanics calculations to investigate the reaction mechanism of the TDG-catalyzed N-glycosidic bond hydrolysis of the modified base 5-formylcytosine. Our results reveal a reaction pathway, which in its first step features a reorganization of the substrate that lowers the barrier height for the subsequent C1′–N1 bond dissociation. The suggested mechanism is consistent with the experimental data, as it is not acid-catalyzed and proceeds through an oxocarbenium-like transition state. It also provides insights into the catalytic roles of the Thr197 and Asn140 residues.

The diverse functionalities of membrane proteins (MPs) have garnered much interest in leveraging these biomolecules for technological applications. One challenge of studying MPs in artificial micellar surfactant environments is that many factors modulate their structures and functionalities, including the surfactants that interact with the MP or their assembly into oligomers. As oligomerization offers a means by which MPs could selectively interact among the copious environmental factors in biological environments, we hypothesized that MP function is predominantly modified by oligomerization rather than interactions with local surfactants that, by comparison, largely interact with MPs nonspecifically. To test this, we study the light-activated proton pump proteorhodopsin (PR) in micellar surfactant solutions because it is functionally active in monomeric and oligomeric forms, the light-activated functionalities of which can be assessed in detail. The surfactant composition and oligomerization are correlated with PR function, as measured by the protonation behaviors of aspartic acid residue 97, which mediates light-activated proton transport, and the associated photocycle kinetics. The results demonstrate that oligomerization dominantly mediates PR function in different surfactant environments, whereas some surfactants can subtly modulate proton-pumping kinetics. This work underscores the importance of understanding and controlling oligomerization of MPs to study and exploit their function.

Expanded polyglutamine (polyQ) tracts in proteins, which are known to induce their aggregation, are associated with numerous neurodegenerative diseases. Longer polyQ tracts correlate with faster protein aggregation kinetics and a decreased age of onset for polyQ disease symptoms. Here, we use UV resonance Raman spectroscopy, circular dichroism spectroscopy, and metadynamics simulations to investigate the solution-state structures of the D₂Q₁₅K₂ (Q15) and D₂Q₂₀K₂ (Q20) peptides. Using metadynamics, we explore the conformational energy landscapes of Q15 and Q20 and investigate the relative energies and activation barriers between these low-energy structures. We compare the solution-state structures of D₂Q₁₀K₂ (Q10), Q15, and Q20 to determine the dependence of polyQ structure on the Q tract length. We show that these peptides can adopt two distinct monomeric conformations: an aggregation-resistant PPII-like conformation and an aggregation-prone β-strand-like conformation. We find that longer polyQ peptides have an increased preference for the aggregation-prone β-strand-like conformation. This preference may play an important role in the increased aggregation rate of longer polyQ peptides that is thought to lead to decreased neurodegenerative disease age of onset for polyQ disease patients.

Long MD simulations are carried out using a detailed all-atom force field to investigate the effect of pH or, equivalently, degree of ionization α^– (= 0, 50, 100%) and degree of polymerization N (= 20, 23, 46, 70, and 110) on the structure and dynamics of poly(acrylic acid) (PAA) at infinite dilution. To ensure the validity and add to the reliability of our research conclusions, a systematic validation of several molecular mechanics force fields is performed. It is observed that the generalized AMBER force field in combination with the RESP charge fitting method best describes both the structural and dynamical behavior of PAA in comparison to experimentally obtained data. It is found that ⟨R_g²⟩^0.5changes with N as ⟨R_g²⟩^0.5 ∼ N^ν, with ν = 0.27 at α^– = 0% degree of ionization (acidic conditions), ν = 0.94 at α^– = 50% degree of ionization (neutral conditions), and ν = 0.87 at α^– = 100% degree of ionization (basic conditions), which is in perfect agreement with theory. The global shape of the PAA chain in the solution is quantified in terms of the three eigenvalues of the average radius-of-gyration tensor, the relative shape anisotropy κ², and the asphericity parameter b. It is revealed that at α^– = 0%, the chain adopts a spherelike conformation, while at α^– = 50 and 100%, its conformation is flattened and flexible. In addition, it is revealed that as the degree of ionization increases, the persistence length L_p increases, which suggests that PAA chains become stiffer with increasing pH. The global and local conformational changes of the PAA chain with the degree of ionization are found to be highly related to the solvation of the polymer. Finally, it is revealed that the diffusion coefficient D of the center of mass of PAA also exhibits a power law scaling with N, D ∼ N^ν, with ν = 0.25 at α^– = 0% degree of ionization, ν = 0.46 at α^– = 50% degree of ionization (neutral conditions), and ν = 0.44 at α^– = 100% degree of ionization (basic conditions), in excellent agreement with recent experimental data and theoretical predictions.

Hydration sites are locations of interest to water and they can be used to classify the behavior of water around chemical motifs commonly found on the surface of proteins. Inhomogeneous fluid solvation theory (IFST) is a method for calculating hydration free-energy changes from molecular dynamics (MD) trajectories. In this paper, hydration sites are identified from MD simulations of 380 diverse protein structures. The hydration free energies of the hydration sites are calculated using IFST and distributions of these free-energy changes are analyzed. The results show that for some hydration sites near features conventionally regarded as attractive to water, such as hydrogen bond donors, the water molecules are actually relatively weakly bound and are easily displaced. We also construct plots of the spatial density of hydration sites with high, medium, and low hydration free-energy changes which represent weakly and strongly bound hydration sites. It is found that these plots show consistent features around common polar amino acids for all of the proteins studied.

Triosephosphate isomerase (TIM) catalyzes the interconversion between dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde 3-phosphate (GAP) via an enediol(ate) intermediate. The active-site residue Glu165 serves as the catalytic base during catalysis. It abstracts a proton from C1 carbon of DHAP to form the reaction intermediate and donates a proton to C2 carbon of the intermediate to form product GAP. Our difference Fourier transform infrared spectroscopy studies on the yeast TIM (YeTIM)/phosphate complex revealed a C═O stretch band at 1706 cm^–1 from the protonated Glu165 carboxyl group at pH 7.5, indicating that the pK_a of the catalytic base is increased by >3.0 pH units upon phosphate binding, and that the Glu165 carboxyl environment in the complex is still hydrophilic in spite of the increased pK_a. Hence, the results show that the binding of the phosphodianion group is part of the activation mechanism which involves the pK_a elevation of the catalytic base Glu165. The deprotonation kinetics of Glu165 in the μs to ms time range were determined via infrared (IR) T-jump studies on the YeTIM/phosphate and (“heavy enzyme”) [U-¹³C,-¹⁵N]YeTIM/phosphate complexes. The slower deprotonation kinetics in the ms time scale is due to phosphate dissociation modulated by the loop motion, which slows down by enzyme mass increase to show a normal heavy enzyme kinetic isotope effect (KIE) ∼1.2 (i.e., slower rate in the heavy enzyme). The faster deprotonation kinetics in the tens of μs time scale is assigned to temperature-induced pK_a decrease, while phosphate is still bound, and it shows an inverse heavy enzyme KIE ∼0.89 (faster rate in the heavy enzyme). The IR static and T-jump spectroscopy provides atomic-level resolution of the catalytic mechanism because of its ability to directly observe the bond breaking/forming process.

Microbial rhodopsins constitute a key protein family in optobiotechnological applications such as optogenetics and voltage imaging. Spectral tuning of rhodopsins into the deep-red and near-infrared spectral regions is of great demand in such applications because more bathochromic light into the near-infrared range penetrates deeper in living tissue. Recently, retinal analogues have been successfully used in ion transporting and fluorescent rhodopsins to achieve red-shifted absorption, activity, and emission properties. Understanding their photochemical mechanism is essential for further design of appropriate retinal analogues but is yet only poorly understood for most retinal analogue pigments. Here, we report the photoreaction dynamics of red-shifted analogue pigments of the proton pump proteorhodopsin (PR) containing A2 (all-trans-3,4-dehydroretinal), MOA2 (all-trans-3-methoxy-3,4-dehydroretinal), or DMAR (all-trans-3-dimethylamino-16-nor-1,2,3,4-didehydroretinal), utilizing femto- to submillisecond transient absorption spectroscopy. We found that the A2 analogue photoisomerizes in 1.4, 3.0, and/or 13 ps upon 510 nm light illumination, which is comparable to the native retinal (A1) in PR. On the other hand, the deprotonation of the A2 pigment Schiff base was observed with a dominant time constant of 67 μs, which is significantly slower than the A1 pigment. In the MOA2 pigment, no isomerization or photoproduct formation was detected upon 520 nm excitation, implying that all the excited molecules returned to the initial ground state in 2.0 and 4.2 ps. The DMAR pigment showed very slow excited state dynamics similar to the previously studied MMAR pigment, but only very little photoproduct was formed. The low efficiency of the photoproduct formation likely is the reason why DMAR analogue pigments of PR showed very weak proton pumping activity.

Water is vital to many biochemical processes and is necessary for driving fundamental interactions of cell membranes with their external environments, yet it is difficult to probe the membrane/water interface directly and without the use of external labels. Here, we employ vibrational sum frequency generation spectroscopy to understand the role of interfacial water molecules above bilayers formed from zwitterionic (phosphatidylcholine) and anionic (phosphatidylglycerol, PG, and phosphatidylserine, PS) lipids as they are exposed to the common polycation poly(allylamine hydrochloride) (PAH) in 100 mM NaCl. We show that as the concentration of PAH is increased, the interfacial water molecules are irreversibly displaced and find that it requires 10 times more PAH to displace interfacial water molecules from membranes formed from purely zwitterionic lipids when compared to membranes that contain the anionic PG and PS lipids. This outcome is likely due to the difference in (1) the energy with which water molecules are bound to the lipid headgroups, (2) the number of water molecules bound to the headgroups, which is related to the headgroup area, and (3) the electrostatic interactions between the PAH molecules and the negatively charged lipids that are favored when compared to the zwitterionic lipid headgroups. The findings presented here contribute to establishing causal relationships in nanotoxicology and to understanding, controlling, and predicting the initial steps that lead to the lysis of cells exposed to membrane-disrupting polycations or to transfection.

The surface charge densities, apparent equilibrium binding constants, and free energies of binding of nickel ions to supported and suspended lipid membranes prepared from POPC and two types of lipopolysaccharide (LPS) are reported. Second- and third-order nonlinear optical mixing shows that rough LPS (rLPS)-incorporated bilayers carry the highest charge density and provide the most binding sites for nickel ions while LPS-free bilayers exhibit the lowest charge density and fewest binding sites. Ni²⁺ binding is almost fully reversible at low concentrations but less so at higher Ni²⁺ concentrations. Ni²⁺ adsorption isotherms exhibit hysteresis loops. The role of interfacial depth on the observed second harmonic generation (SHG) responses is discussed in the context of complementary dynamic light scattering, X-ray spectroscopy, and cryogenic transmission electron microscopy experiments. The latter reveal considerable Ni²⁺-induced structural deformations to the bacterial membrane models containing the short, O-antigen-free rLPS, consistent with complex formation on the vesicle surfaces that involve Ni²⁺ ions and carboxylate groups in the inner core of rLPS. In contrast, Ni²⁺ ion complexation to the charged groups (phosphates and carboxylate) of the considerably longer O-antigen units in sLPS appears to protect the phospholipid backbone against metal binding and thus preserve the vesicle structure.

The development of photodynamic therapy (PDT) at depth requires photosensitizers which have both sufficient quantum yield for singlet oxygen generation and strong two-photon absorption. Here, we show that this can be achieved by conjugated linkage of zinc porphyrins to make dimers. We determined the quantum yield of generation of ¹O₂ , ϕ_Δ, by measuring emission at 1270 nm using a near-infrared streak camera and found it to increase from 15% for a single porphyrin unit to 27–47% for the dimers with a conjugated linker. Then, we recorded the spectra of two-photon absorption cross section, σ₂, by a focus-tunable Z-scan method, which allows for nondestructive investigation of light-sensitive materials. We observed a strong enhancement of the two-photon absorption coefficient in the dimers, especially those with an alkyne linker. These results lead to an excellent figure of merit for two-photon production of singlet oxygen (expressed by the product σ₂ × ϕ_Δ) in the porphyrin dimers, of around 3700 GM, which is very promising for applications involving treatment of deep tumors by PDT.

We performed first-principles molecular dynamics simulations of relatively dilute aqueous solutions of sulfate and thiosulfate dianions to analyze the structure, dynamics, and vibrational spectral properties of water molecules around the solute, especially the spatially patterned solvent molecules in the first solvation layer and the extended layers. This study also involves the investigation of dynamics of dangling OH groups in these layers and their role in patterning the water molecules around the dianions. Structural evaluation of the systems is carried out by radial distribution functions, number integrals, and spatial distribution functions. The lifetime of dangling OH groups inside the solvation shell is compared more to that of the bulk. By constructing the O–H groups in three ensembles (S1, S2, and S3) around the anion, we show that the frequency distribution of OH modes in the S1 ensemble show red-shifting for both sulfate and thiosulfate. The O–H groups in the S2 ensemble of the sulfate–water system show red-shifting by 10 cm^–1, while in the case of thiosulfate–water, these O–H groups show blue-shifting by 8 cm^–1. The water molecules in S1 and S2 subensembles have slower dynamics compared to those in the bulk (S3). The dynamics of various kinds of hydrogen bonds were characterized by hydrogen bond population correlation functions. The spectral diffusion of solvation shell O–H modes was performed through a frequency–time correlation function. We find a significant amount of orientational retardation of water molecules in the S1 layer and moderate retardation in the S2 layer as compared to that in the bulk, S3 layer. All these findings, the red shift of the OH stretching frequency in S1 and S2 layers, slowing down of the orientational dynamics of OH vectors in S1 and S2 layers, and less diffusivity of water in S1 and S2 layers, show the long-range kosmotropic effect of multivalent sulfate and thiosulfate oxyanions. Due to the long-range effect, heterogeneous occupancy of water molecules is observed, and the water molecules are found to arrange in a patterned manner in the vicinity of anions with varied local density.

Broadband transient absorption spectroscopy is used to study the photoisomerization of stiffened stilbenes in solution, specifically E/Z mixtures of bis(benzocyclobutylidene) (t4, c4) and (E)-1-(2,2-dimethyltetralinylidene)-2-2-dimethyltetraline (t6). Upon excitation to S₁, all evolve to perpendicular molecular conformation P, followed by decay to S₀, while the spectra and the kinetic behavior crucially depend on the size of the stiffening ring. In 4, contrary to all previously studied stilbenes, the trans and cis absorption and excited-state spectra are nearly indistinguishable, while the corresponding isomerization times are comparable: τ_i = 166 ps for t4 and τ_i = 64 ps for c4 in n-hexane, as opposed to 114 and 45 ps in acetonitrile, respectively. Faster isomerization in polar solvents agrees with the zwitterionic character of the P state. In t6, torsion to P is effectively barrier-less and completes within 0.3 ps, the S₁ → P evolution being directly traceable through the transient spectra of stimulated emission and that of excited-state absorption. In n-hexane, the P state is remarkably long-lived, τ_P = 1840 ps, but the lifetime drops down to 35 ps in acetonitrile. The trans-to-cis photoisomerization yield for t6 is measured to be 20%, while for t4, it remains uncertain. We discuss the effects of stiffening and substitution on the formation and lifetime of the intermediate states through which the stilbene molecules evolve on the S₁ energy surface.

The rational design of photoacids requires accessible predictive models of the electronic effect of functional groups on chemical templates of interest. Here, the effect of substituents on the photoacidity and excited-state proton transfer (PT) pathways of prototype 2-naphthol (2OH) at the symmetric C7 position was investigated through photochemical and computational studies of 7-amino-2-naphthol (7N2OH) and 7-methoxy-2-naphthol (7OMe2OH). Time-resolved emission experiments of 7N2OH revealed that the presence of an electron-withdrawing versus electron-donating group (EWG vs EDG, NH₃⁺ vs NH₂) led to a drastic decline in photoacidity: pK_a* = 1.1 ± 0.2 vs 9.6 ± 0.2. Time-dependent density functional theory calculations with explicit water molecules confirmed that the excited neutral state (x = NH₂) is greatly stabilized by water, with equation-of-motion coupled cluster singles and doubles calculations supporting potential mixing between the L_a and L_b states. Similar suppression of photoacidity, however, was not observed for 7OMe2OH with EDG OCH₃, pK_a* = 2.7 ± 0.1. Hammett plots of the ground- and excited-state PT reactions of substituted 7-x-2OH compounds (x = CN, NH₃⁺, H, CH₃, OCH₃, OH, and NH₂) vs Hammett parameters σ_p showed breaks in the linearity between the EDG and EWG regions: ρ ∼ 0 vs 1.14 and ρ* ∼ 0 vs 3.86. The divergent acidic behavior most likely arises from different mixing mechanisms of the lowest L_b state with the L_a and possible B_b states upon substitution of naphthalene in water.

In this study, a coumarin disk was examined as a simple self-propelled object under a chemical reaction. A coumarin disk placed on an aqueous phase containing Na₃PO₄ as a base exhibited continuous and oscillatory motion at lower and higher initial concentrations of Na₃PO₄, [Na₃PO₄]₀, respectively. In addition, the period of the oscillation between rest and motion increased with increasing [Na₃PO₄]₀. The mechanism of mode bifurcation between continuous and oscillatory motion and a change in the period of oscillation were discussed in terms of hydrolysis of coumarin and the surface tension of the aqueous solution as a driving force. A reduced mathematical model based on the reaction kinetics of coumarin around the air/aqueous interface, which adequately reproduced the experimental observation, was constructed. These results suggest that the characteristics of the self-propelled motion were determined by the kinetics of hydrolysis.

We study the translocation of a polymer with oppositely charged segments at both ends of the chain passing through a pore under the effect of an external electric field in the presence of a pH gradient using Langevin dynamics simulations. As observed in experiments, the electrostatic interactions between the pore and the polymer are tuned by altering the pH gradient. Our simulation studies show that with the change in charge distribution on the polymer and the pore that can mimic different pH conditions, the external driving force and the polymer–pore electrostatic interactions play a significant role in the translocation process. The external electric forces are dominant during the entry stage, and the entry time decreases with increase in the charge asymmetry of the pore-trapped polymer. During the exit stage, the electrostatic interactions as well as the external electric field act in concert in determining the exit time through the pore. Our simulation results can capture many features observed in experiments. Our results are explained qualitatively by calculating the free-energy change of the polymer chain during the translocation process.

By introducing an oleyl group at the end of the straight rodlike molecule, the effect of the tail shape on the liquid crystallinity, biaxiality, and lateral switching behavior of the smectic A phase was investigated. Three types of molecules possessing a fluorinated phenyl (pentafluorophenyl, 2,3,4-trifluorophenyl, or 2,3-difluorophenyl) group and a cis-octadec-9-enyl group were synthesized, and their liquid crystallinities were compared with the corresponding molecules with a straight alkyl (trans-octadec-9-enyl or n-octadecanyl) group. In switching experiments, the molecules with a bent terminal chain showed higher spontaneous polarization (P_s) values than those with a straight terminal chain. Further, the directional changes of the long molecular axes were suppressed for the molecules possessing a bent terminal chain. These results show that the introduction of a bent terminal chain is highly effective for stabilizing ferroelectric switching behaviors.

The future bioeconomy depends on the increased utilization of renewable lignocellulosic resources from trees and other bioenergy crops. However, considering that the diffusion of ions, chemicals, and enzymes into secondary cell walls is critical to effectively utilize lignocellulosic biomass, the unidentified mechanisms underpinning this diffusion have hindered progress. Here, nanomechanical spectroscopy was used to measure changes in moisture-dependent relaxations of amorphous polysaccharides inside loblolly pine (Pinus taeda) cell wall layers. The comparison with recent ion mobility measurements made in similar cell wall layers revealed that the mineral ion diffusion occurs via interconnecting nanoscale pathways of rubbery amorphous polysaccharides. This result contradicts previous assertions of cell wall transport being an aqueous process occurring through simple interconnecting water pathways. Because polymer diffusion and aqueous transport via water channels are such different phenomena, the identification of the diffusion mechanism in this manuscript opens up a new paradigm in lignocellulosic research. The utilization of lignocellulosic resources is expected to be accelerated because the extensive polymer science literature can now be used to design the molecular architecture of lignocellulosic biomass to optimize diffusion properties for specific uses, including biorefinery feedstocks, advanced materials, and wood-based construction materials.

We investigated the formation kinetics of a single monolayer nanotube from bolaamphiphiles (consisting of a sugar residue, an alkyl chain, and an amino group) in solution. In this bolaamphiphile, a transition from a monomerically dispersed state to the nanotube takes place by changing the solvent condition. This transition was induced by fast mixing with a stopped-flow apparatus. From just after the mixing, this transition process was monitored in situ by time-resolved small-angle X-ray scattering. In this manner, we were able to derive the direct structural information as a function of time during the nanotube formation. The results revealed that disklike aggregates initially formed, which then grew and closed to produce a tubular structure.