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Inspired by the adaptability observed in biological materials, self-assembly processes have attracted significant interest for their potential to yield novel materials with unique properties. However, experimental methods have often fallen short in capturing the molecular details of the assembly process. In this study, we employ a multiscale molecular dynamics simulation approach, complemented by NMR quantification, to investigate the mechanism of self-assembly in a redox-fueled bioinspired system. Contrary to conventional assumptions, we have uncovered a significant role played by the monomer precursor in the assembly process, with its presence varying with concentration and the extent of conversion of the monomer to the dimer. Experimental confirmation through NMR quantification underscores the concentration-dependent incorporation of monomers into the fibrous structures. Furthermore, our simulations also shed light on the diverse intermolecular interactions, including T-shaped and parallel π stacking, as well as hydrogen bonds, in stabilizing the aggregates. Overall, the open conformation of the dimer is preferred within these aggregates. However, inside the aggregates, the distribution of conformations shifts slightly to the closed conformation compared to on the surface. These findings contribute to the growing field of bioinspired materials science by providing valuable mechanistic and structural insights to guide the design and development of self-assembling materials with biomimetic functionalities.

Adsorption and desorption of volatile organic compounds (VOCs) on indoor material surfaces can impact VOC concentrations in indoor air. In this study, we investigate the adsorption and desorption kinetics of limonene and one of its oxidation products, carvone, at 297 ± 1 K using in situ Fourier transform infrared (FTIR) spectroscopy. In particular, the adsorption and desorption kinetics of limonene and carvone on two model indoor-relevant surfaces, TiO2(a component of paint and self-cleaning surfaces) and SiO2(a model for window glass), are compared at low relative humidity as well as at higher relative humidity. Carvone readily partitions to both surfaces with slower desorption kinetics compared to limonene. Under dry conditions, the desorption kinetics of limonene is about 40 times faster than that of carvone from TiO2, and the desorption kinetics of limonene and carvone from TiO2are about two and four times slower than on SiO2, respectively. Under high relative humidity conditions, the presence of adsorbed water on both TiO2and SiO2surfaces generally increases the desorption kinetics of limonene yet has no effect on the desorption kinetics of carvone. The K2-SURF kinetics model has been previously applied to limonene adsorption/desorption on SiO2, and here, it is used to obtain a detailed mechanism for limonene interactions on TiO2as a function of relative humidity to explain the observed kinetics. Importantly, the combined experimental results with kinetic modeling and classical and ab initiomolecular dynamics simulations provide mechanistic insights into the heterogeneous interactions of volatile organic compounds on indoor-relevant surfaces and implications for indoor air quality.

Oxygenated semivolatile organic compounds are present in indoor air due to the oxidation of monoterpenes and other hydrocarbons. The partitioning of these compounds to indoor surfaces and the formation of organic thin films are of great interest as these surfaces become potential reservoirs for these compounds affecting indoor air composition. Here, we have investigated the interaction of carvone, a limonene oxidation product, with hydroxylated SiO2surfaces at 297 ± 1 K with FTIR spectroscopy. The detailed surface interactions were understood through both force field-based molecular dynamics (MD), ab initio molecular dynamics (AIMD) simulations, and electronic structure calculations. The adsorption/desorption kinetics of carvone on hydroxylated SiO2have been measured as a function of relative humidity. The desorption kinetics of carvone from the SiO2surface are slow, approximately 30 times slower when compared to limonene under dry conditions. Molecular dynamics (MD) simulations reveal that carvone forms O–H hydrogen bonding (carbonyl O to HO–Si) with the isolated hydroxyl groups and oxygen silicon associations (carbonyl O to Si–O–Si) with siloxane bridges that are also on the SiO2surface. A kinetic model was applied to further examine the carvone adsorption and desorption kinetics; the experimental measurements can be reproduced by assuming that some carvone molecules become trapped in pores between the SiO2particles. Interestingly, relative humidity does not change the desorption kinetics of carvone from the SiO2surface. Instead, water molecules adsorb onto the preadsorbed carvone, which hydrates the organic-coated surface. Overall, this study shows how carvone, an oxygenated organic compound, interacts with indoor relevant surfaces and the impact of relative humidity on these interactions. It also demonstrates how chemical transformations (e.g., oxidation) in indoor environments can play an important role in how molecules partition to surfaces and interact with condensed phase water.

Peripheral membrane proteins bind transiently to membrane surfaces as part of many signaling pathways. The bound proteins perform two-dimensional (2-D) diffusion on the membrane surface during the recruitment function. To better understand the interplay between the 2-D diffusion of these protein domains and their membrane binding modes, we performed multimicrosecond all-atom molecular dynamics simulations of two regulatory domains, a C2 domain and a pleckstrin homology (PH) domain, in their experimentally determined bound configuration to a lipid bilayer. The protein bound configurations are preserved throughout the simulation trajectories. Both protein domains exhibit anomalous diffusion with distinct features in their dynamics that reflect their different modes of binding. An analysis of their diffusive behavior reveals common features with the diffusion of lipid molecules in lipid bilayers, suggesting that the 2-D motion of protein domains bound to the membrane surface is modulated by the viscoelastic nature of the lipid bilayer.

Oxygenated organic compounds (OOCs) are widely found in indoor environments and come from either the direct emissions from indoor activities or the subsequent oxidation of nonoxygenated OCs. Adsorption and partitioning of OCs on surfaces are significant processes in indoor chemistry, yet these interactions specifically involving OOCs are still poorly understood. In this study, we investigate the interactions of three prevalent indoor OOCs (dihydromyrcenol, α-terpineol, and linalool) on an indoor surface proxy (hydroxylated SiO2) by combining vibrational spectroscopy with ab initiomolecular dynamics simulations. The adsorption of these compounds on the SiO2surface is driven by π hydrogen bonding and O–H hydrogen bonding interactions, with O–H hydrogen bonding interactions being stronger. The results of kinetic measurements suggest that indoor surfaces play a significant role in the removal of these OOCs, especially under moderate and low air exchange. Additionally, indoor surfaces can also serve as a reservoir of OOCs due to their much slower desorption kinetics when compared to other indoor relevant organic compounds such as limonene. Overall, the results gleaned by experiment and theoretical simulations provide a molecular representation of the interaction of OOCs on indoor relevant surfaces as well as implications of these interactions for indoor air chemistry.

The indoor environment is a dynamic one with many variables impacting indoor air quality and indoor air chemistry. These include relative humidity (RH) and the presence of different surfaces. Although it has been suggested that the indoor concentrations of gas-phase compounds increase at higher relative humidity, because of displacement of these compounds from indoor surfaces, little is known from a molecular perspective about how RH and adsorbed water impact the adsorption of indoor relevant organic compounds such as limonene with indoor relevant surfaces. Herein, we investigate the effects of RH on the adsorption of limonene, a hydrophobic molecule, on hydroxylated SiO2surfaces, a model for glass surfaces. Experimental data using infrared spectroscopy to directly measure limonene adsorption are combined with both force field-based molecular dynamics (MD) and ab initio molecular dynamics (AIMD) simulations to understand the competitive interactions between limonene, water, and the SiO2surface. The spectroscopic data provide evidence that adsorbed limonene is not completely displaced by adsorbed water, even at high RH (∼80%) when the water layer coverage is close to three monolayers (MLs). These experimental data are supported by AIMD and MD simulations, which indicate that limonene is present at the adsorbed water interface but displaced from direct interactions with SiO2. This study shows that although some limonene can desorb from the surface, even at the highest RH, more than half the limonene remains adsorbed on the surface that can undergo continued surface reactivity. A complex network of π-hydrogen bonds, water–water hydrogen bonds, and SiO2–water hydrogen bonds explains these interactions at the air/adsorbed water/SiO2interface that hold the hydrophobic limonene molecule at the interface. Importantly, these interactions are most likely present for a range of other systems involving organic compounds and solid surfaces at ambient relative humidity and may be important in a range of scientific areas, from sensor development to cultural heritage science.

We performed classical molecular dynamics simulations to quantify and understand the nonreactive, dermal uptake of volatile organic compounds formed during the ozonolysis of human skin oils. Our results include surface accommodation coefficients, partitioning constants, bulk diffusivities, and desorption lifetimes. These parameters were used to improve and to constrain the kinetic multilayer model of the surface and bulk chemistry of skin (KM-SUB-Skin). By comparing common outputs (bulk accommodation coefficients), we cross-validate the two approaches and, thus, increase the level of trust in their predictions relevant to indoor air chemistry.

The mechanisms leading to aggregation of the crystallin proteins of the eye lens remain largely unknown. We use atomistic multiscale molecular simulations to model the solution-state conformational dynamics of γD-crystallin and its cataract-related W42R variant at both infinite dilution and physiologically relevant concentrations. We find that the W42R variant assumes a distinct conformation in solution that leaves the Greek key domains of the native fold largely unaltered but lacks the hydrophobic interdomain interface that is key to the stability of wild-type γD-crystallin. At physiologically relevant concentrations, exposed hydrophobic regions in this alternative conformation become primary sites for enhanced interprotein interactions leading to large-scale aggregation.

Available experimental techniques cannot determine high-resolution three-dimensional structures of membrane proteins under a transmembrane voltage. Hence, the mechanism by which voltage-gated cation channels couple conformational changes within the four voltage sensor domains, in response to either depolarizing or polarizing transmembrane voltages, to opening or closing of the pore domain's ion channel remains unresolved. Single-membrane specimens, composed of a phospholipid bilayer containing a vectorially oriented voltage-gated K+channel protein at high in-plane density tethered to the surface of an inorganic multilayer substrate, were developed to allow the application of transmembrane voltages in an electrochemical cell. Time-resolved neutron reflectivity experiments, enhanced by interferometry enabled by the multilayer substrate, were employed to provide directly the low-resolution profile structures of the membrane containing the vectorially oriented voltage-gated K+channel for the activated, open and deactivated, closed states of the channel under depolarizing and hyperpolarizing transmembrane voltages applied cyclically. The profile structures of these single membranes were dominated by the voltage-gated K+channel protein because of the high in-plane density. Importantly, the use of neutrons allowed the determination of the voltage-dependent changes in both the profile structure of the membrane and the distribution of water within the profile structure. These two key experimental results were then compared to those predicted by three computational modeling approaches for the activated, open and deactivated, closed states of three different voltage-gated K+channels in hydrated phospholipid bilayer membrane environments. Of the three modeling approaches investigated, only one state-of-the-art molecular dynamics simulation that directly predicted the response of a voltage-gated K+channel within a phospholipid bilayer membrane to applied transmembrane voltages by utilizing very long trajectories was found to be in agreement with the two key experimental results provided by the time-resolved neutron interferometry experiments.

Photoelectron angular distributions (PADs) from aqueous solution surfaces reveal details of the spatial arrangement of solute molecules at the solution–gas-phase interface. This is demonstrated here for mixed equimolar aqueous solutions of dimethyl sulfoxide/dimethyl sulfone ((CH3)2SO)/(CH3)2SO2) and dimethyl sulfoxide/dimethyl sulfite ((CH3)2SO/(CH3)2SO3), all molecules having a propensity to reside near the solution surface. Although the surface-active molecules coexist at the surface, (CH3)2SO2yields a more intense sulfur 2p surface photoelectron signal than (CH3)2SO, and for (CH3)2SO3, the effect is even larger. To understand this behavior, we have for one of the solutions mixtures, (CH3)2SO/(CH3)2SO2, performed PAD measurements. Surprisingly, both molecules exhibit almost identical PADs, implying that the emitted photoelectrons have experienced a similar (limited) amount of scattering interactions. Hence, the molecules reside at the same distance with respect to the solution–vacuum interface rather than (CH3)2SO2being closer to the surface than (CH3)2SO, as one may have assumed based on the relative photoelectron signal intensities. Instead, the relative surface and bulk concentrations of the two compounds differ. We also report S 2p photoelectron spectra from single-component dimethyl sulfide, (CH3)2S, aqueous solutions measured at a single detection angle. The exceptionally large surface propensity of (CH3)2S is recognized by a narrow, gas-phase-like photoelectron spectrum, revealing that (CH3)2S experiences very few hydration interactions. Experimentally observed trends in surface activity for the different molecules, which are complemented here by molecular dynamics simulations, agree with findings obtained with other surface-sensitive techniques. New information on the surface structure of mixed solutions is uniquely obtained from the anisotropic angular distributions of the photoelectrons.

Efficient computational modeling of biological systems characterized by high concentrations of macromolecules often relies on rigid-body Brownian Dynamics or Monte Carlo (MC) simulations. However, the accuracy of rigid-body models is limited by the fixed conformation of the simulated biomolecules. Multi-conformation Monte Carlo (mcMC) simulations of protein solutions incorporate conformational flexibility via a conformational swap trial move within a predetermined library of discrete protein structures, thereby alleviating artifacts arising from the use of a single protein conformation. Here, we investigate the impact of the number of distinct protein structures in the conformational library and the extent of conformational sampling used in its generation on structural observables computed from simulations of hen egg white lysozyme (HEWL), human γD-Crystallin, and bovine γB-Crystallin solutions. We find that the importance of specific protocols for the construction of the protein structure library is strongly dependent on the nature of the simulated system.

Depth-dependent fluorescence quenching is an important tool for studying the penetration of proteins and peptides into lipid bilayers. Extracting quantitative information from quenching data is, however, complicated by (1) a limited number of experimentally available quenchers and (2) thermal disorder resulting in broad distributions of the transverse positions of both quenchers and fluorophores. Here we validate and refine a general approach to determining the location of a fluorescent probe along the bilayer normal from quenching data, based on a molecular dynamics (MD) simulation of a model compound, tryptophan octyl ester (TOE), in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. The TOE ring was found to lie deeply within the bilayer (most probable position of 13.3 Å and center-of-weight of the distribution of 14.8 Å from the bilayer center), and it was very broadly distributed (with 9 Å depth distribution width), which is consistent with previous experimental observations. The depth-dependent quenching profiles were simulated by treating carbon atoms of the lipid acyl chain of POPC as “pseudo-quenchers” and calculating appropriate transverse overlaps and collision rates with indole atoms of TOE. These simulated quenching profiles were well fitted by a Gaussian function of depth, as is routinely done with experimental data subjected to the distribution analysis procedure [Methods Enzymol.1997, 278, 462−473]. Comparison of the collisional pseudoquenching profiles with the actual profiles of the indole moiety of TOE allows for testing of the validity of the data analysis and identification of the possible sources of error in calculating depths of membrane penetration from quenching data.

Specific ion effects of the large halide anions have been shown to moderate anion adsorption to the air–water interface (AWI), but little quantitative attention has been paid to the behavior of alkali cations. Here we investigate the concentration and local distribution of sodium (Na+) at the AWI in dilute (<1 M) aqueous solutions of NaCl, NaBr, and NaI using a combination of molecular dynamics (MD) and SESSA simulations, and liquid jet ambient pressure photoelectron spectroscopy measurements. We use SESSA to simulate Na 2p photoelectron intensities on the basis of the atom density profiles obtained from MD simulations, and we compare the simulation results with photoelectron spectroscopy experiments to evaluate the performance of a nonpolarizable force field model versus that of an induced dipole polarizable one. Our results show that the nonpolarizable force model developed by Horinek and co-workers (Chem. Phys. Lett.2009, 479, 173–183) accurately predicts the local concentration and distribution of Na+near the AWI for all three electrolytes, whereas the polarizable model does not. To our knowledge, this is the first interface-specific spectroscopic validation of a MD force field. The molecular origins of the unique Na+distributions for the three electrolytes are analyzed on the basis of electrostatic arguments, and shown to arise from an indirect anion effect wherein the identity of the anion affects the strength of the attractive Na+–H2O electrostatic interaction. Finally, we use the photoelectron spectroscopy results to constrain the range of inelastic mean free paths (IMFPs) for the three electrolyte solutions used in the SESSA simulations that are able to reproduce the experimental intensities. Our results suggest that earlier estimates of IMFPs for aqueous solutions are likely too high.

Aquaporin 0 (AQP0) plays a key role in water circulation in the eye lens through a variety of functions. In contrast to mammalian genomes, zebrafish contains two aqp0genes leading to a separation of AQP0 multiple functions between the two gene products, Aqp0a and Aqp0b. A notable feature of the zebrafish AQP0 paralogs is the increased water permeability of Aqp0b relative to Aqp0a as well as a severa lfold increase relative to mammalian AQP0. Here, we report equilibrium molecular dynamics (MD) simulations on the microsecond timescale to identify the structural basis underlying the differences in water permeability between zebrafish AQP0 paralogs and between AQP0 mammalian and fish orthologs. Our simulations are able to reproduce the experimental trends in water permeability. Our results suggest that a substitution of a key Y23 residue in mammalian AQP0 for F23 in fish AQP0 orthologs introduces significant changes in the conformational dynamics of the CS-I structural motif, which, in conjunction with different levels of hydration of the channel vestibule, can account for the differences in permeabilities between fish and mammalian AQP0 orthologs and between zebrafish AQP0 paralogs.

In this simulation study, we investigate the influence of biomolecular confinement on dynamical processes in water. We compare water confined in a membrane protein nanopore at room temperature to pure liquid water at low temperatures with respect to structural relaxations, intermolecular vibrations, and the propagation of collective modes. We observe distinct potential energy landscapes experienced by water molecules in the two environments, which nevertheless result in comparable hydrogen bond lifetimes and sound propagation velocities. Hence, we show that a viscoelastic argument that links slow rearrangements of the water-hydrogen bond network to ice-like collective properties applies to both, the pure liquid and biologically confined water, irrespective of differences in the microscopic structure.

We report molecular dynamics simulations of acetonitrile–water binary solutions at concentrations of 0.032–0.59 mole fraction. We find that at low bulk concentration acetonitrile has an enhanced population near the liquid/vapor interface. The surface-bound acetonitrile molecules exhibit anisotropic orientations and lie nearly flat along the solution surface with their terminal methyl groups directed toward the vapor. Upon increasing the bulk concentration, the formation of acetonitrile domains is promoted by interactions between hydrophobic methyl moieties. Dipole–dipole interactions facilitate a pseudonematic, antiparallel pairing of near-neighbor molecules both in the bulk solution and near the liquid/vapor interface. Near the interface the preferred orientation of acetonitrile flattens further to accommodate antiparallel pairing of neighboring molecules such that the methyl group remains above the solution. This study paints a surprisingly complex picture of a binary organic–water solution that manifests behavior similar to liquid crystals through preferred orientations and pseudonematic antiparallel pairing.

Network Hamiltonian models (NHMs) are a framework for topological coarse-graining of protein–protein interactions, in which each node corresponds to a protein, and edges are drawn between nodes representing proteins that are noncovalently bound. Here, this framework is applied to aggregates of γD-crystallin, a structural protein of the eye lens implicated in cataract disease. The NHMs in this study are generated from atomistic simulations of equilibrium distributions of wild-type and the cataract-causing variant W42R in solution, performed by Wong, E. K.; Prytkova, V.; Freites, J. A.; Butts, C. T.; Tobias, D. J. Molecular Mechanism of Aggregation of the Cataract-Related γD-Crystallin W42R Variant from Multiscale Atomistic Simulations. Biochemistry2019, 58(35), 3691–3699. Network models are shown to successfully reproduce the aggregate size and structure observed in the atomistic simulation, and provide information about the transient protein–protein interactions therein. The system size is scaled from the original 375 monomers to a system of 10000 monomers, revealing a lowering of the upper tail of the aggregate size distribution of the W42R variant. Extrapolation to higher and lower concentrations is also performed. These results provide an example of the utility of NHMs for coarse-grained simulation of protein systems, as well as their ability to scale to large system sizes and high concentrations, reducing computational costs while retaining topological information about the system.

In this study, we calculate free-energy profiles for the dissociation of the strong acids XH (HBr, HCl, and HNO3), specifically, for the deprotonation and subsequent formation of ion pairs, X–···H3O+, in the vicinity of the air–water interface. We show that the free-energy profiles for the dissociation of HCl and HNO3are significantly different at the air–water interface compared to in the bulk, and we predict that the undissociated, molecular form of these two acids is stable at the interface. For the strongest acid we consider, HBr the traditional picture of completely dissociated strong acids is preserved in the vicinity of the air–water interface. Our results have implications for our understanding of the interfacial chemistry of acids, as well as the effects of acids on the surface tensions of aqueous solutions.

We use a number of computational and experimental approaches to investigate the membrane topology of the membrane-interacting C-terminal domain of the HIV-1 gp41 fusion protein. Several putative transmembrane regions are identified using hydrophobicity analysis based on the Wimley-White scales, including the membrane-proximal external region (MPER). The MPER region is an important target for neutralizing anti-HIV monoclonal antibodies and is believed to have an interfacial topology in the membrane. To assess the possibility of a transmembrane topology of MPER, we examined the membrane interactions of a peptide corresponding to a 22-residue stretch of the MPER sequence (residues 662–683) using fluorescence spectroscopy and oriented circular dichroism. In addition to the previously reported interfacial location, we identify a stable transmembrane conformation of the peptide in synthetic lipid bilayers. All-atom molecular dynamics simulations of the MPER-derived peptide in a lipid bilayer demonstrate a stable helical structure with an average tilt of 24 degrees, with the five tryptophan residues sampling different environments inside the hydrocarbon core of the lipid bilayer, consistent with the observed spectral properties of intrinsic fluorescence. The degree of lipid bilayer penetration obtained by computer simulation was verified using depth-dependent fluorescence quenching of a selectively attached fluorescence probe. Overall, our data indicate that the MPER sequence can have at least two stable conformations in the lipid bilayer, interfacial and transmembrane, and suggest a possibility that external perturbations can switch the topology during physiological functioning.

Ambient pressure X-ray photoelectron spectroscopy (AP-XPS) was used to explore ion behavior at liquid/vapor interfaces of aqueous NaCl, RbCl, and RbBr solutions. Interfacial depth profiles of ions were obtained from XPS spectra at a series of photoelectron kinetic energies. Depth profiles of the ratio of anion to cation show little difference among the solutions. Previously, these depth profiles were determined from the ratio of anion to cation signal-peak areas. However, using molecular dynamics simulations (MD), the individual anion and cation depth profiles are both observed to differ as a function of solution, but the differences are masked when only the anion-to-cation ratios are considered. Using the Cl–/Owaterratio determined from the XPS measurements, surface-enhanced concentrations of Cl–are observed in the NaCl solution, but not in the RbCl solution, in agreement with predictions from MD simulations. We also report studies of aqueous solutions of RbBr. In contrast to an aqueous RbCl solution, our combination of AP-XPS experiments and MD simulations suggests that anion/cation ratios are enhanced at the surface for this system due to the separation of bromide and rubidium in the double layer near the surface, while the interfacial concentration of bromide does not differ considerably from the bulk.

Nitric acid is a prevalent component of atmospheric aerosols, and the extent of nitric acid dissociation at aqueous interfaces is relevant to its role in heterogeneous atmospheric chemistry. Several experimental and theoretical studies have suggested that the extent of dissociation of nitric acid near aqueous interfaces is less than that in bulk solution. Here dissociation of HNO3at the surface of aqueous solution is quantified using X-ray photoelectron spectroscopy of the nitrogen local electronic structure. The relative amounts of undissociated HNO3(aq) and dissociated NO3–(aq) are identified by the distinguishable N1s core-level photoelectron spectra of the two species, and we determine the degree of dissociation, αint, in the interface (approximately the first three layers of solution) as a function of HNO3concentration. Our measurements show that dissociation is decreased by ∼20% near the solution interface compared with bulk solution and furthermore that dissociation occurs in the topmost solution layer. The experimental results are supported by first-principles MD simulations, which show that hydrogen bonds between HNO3and water molecules at the solution surface stabilize the molecular form even at low concentration by analogy to the stabilization of molecular HNO3that occurs in bulk solution at high concentration.

A central feature of the lipid raft concept is the formation of cholesterol-rich lipid domains. The introduction of relatively rigid cholesterol molecules into fluid liquid-disordered (Ld) phospholipid bilayers can produce liquid-ordered (Lo) mixtures in which the rigidity of cholesterol causes partial ordering of the flexible hydrocarbon acyl chains of the phospholipids. Several lines of evidence support this concept, but direct structural information about Lomembranes is lacking. Here we present the structure of Lomembranes formed from cholesterol and dioleoylphosphatidylcholine (DOPC). Specific deuteration of the DOPC acyl-chain methyl groups and neutron diffraction measurements reveal an extraordinary disorder of the acyl chains of neat LdDOPC bilayers. The disorder is so great that 20% of the methyl groups are in intimate contact with water in the bilayer interface. The ordering of the DOPC acyl chains by cholesterol leads to retraction of the methyl groups away from the interface. Molecular dynamics simulations based on experimental systems reveal asymmetric transbilayer distributions of the methyl groups associated with each bilayer leaflet.

Molecular dynamics (MD) simulations, circular dichroism (CD), and dynamic light scattering (DLS) measurements were used to investigate the aggregation propensity of the eye-lens protein γS-crystallin. The wild-type protein was investigated along with the cataract-related G18V variant and the symmetry-related G106V variant. The MD simulations suggest that local sequence differences result in dramatic differences in dynamics and hydration between these two apparently similar point mutations. This finding is supported by the experimental measurements, which show that although both variants appear to be mostly folded at room temperature, both display increased aggregation propensity. Although the disease-related G18V variant is not the most strongly destabilized, it aggregates more readily than either the wild-type or the G106V variant. These results indicate that γS-crystallin provides an excellent model system for investigating the role of dynamics and hydration in aggregation by locally unfolded proteins.

The light-induced isomerization of the retinal from 11-cisto all-transtriggers changes in the conformation of visual rhodopsins that lead to the formation of the activated state, which is ready to interact with the G protein. To begin to understand how changes in the structure and dynamics of the retinal are transmitted to the protein, we performed molecular dynamics simulations of squid rhodopsin with 11-cisand all-transretinal, and with two different force fields for describing the retinal molecule. The results indicate that structural rearrangements in the binding pocket, albeit small, propagate toward the cytoplasmic side of the protein, and affect the dynamics of internal water molecules. The sensitivity of the active-site interactions on the retinal force-field parameters highlights the coupling between the retinal molecule and its immediate protein environment.

Voltage-sensing domains (VSDs) of voltage-gated potassium (Kv) channels undergo a series of conformational changes upon membrane depolarization, from a down state when the channel is at rest to an up state, all of which lead to the opening of the channel pore. The crystal structures reported to date reveal the pore in an open state and the VSDs in an up state. To gain insights into the structure of the down state, we used a set of experiment-based restraints to generate a model of the down state of the KvAP VSD using molecular-dynamics simulations of the VSD in a lipid bilayer in excess water. The equilibrated VSD configuration is consistent with the biotin-avidin accessibility and internal salt-bridge data used to generate it, and with additional biotin-avidin accessibility data. In the model, both the S3b and S4 segments are displaced ∼10 Å toward the intracellular side with respect to the up-state configuration, but they do not move as a rigid body. Arginine side chains that carry the majority of the gating charge also make large excursions between the up and down states. In both states, arginines interact with water and participate in salt bridges with acidic residues and lipid phosphate groups. An important feature that emerges from the down-state model is that the N-terminal half of the S4 segment adopts a 310-helical conformation, which appears to be necessary to satisfy a complex salt-bridge network.

We have used a combination of temperature-programmed desorption (TPD) experiments and molecular dynamics (MD) simulations to characterize interactions between water and carboxylic acid-terminated surfaces. In the TPD experiments, D2O water interacts with alkylthiol self-assembled monolayers (SAMs) comprised of 3-mercaptopropionic acid (C3acid), 15-mercaptopentadecaonic acid (C15acid), 16-mercaptohexadenoic acid (C16acid), or two-component monolayers of these constituents. Water TPD spectra exhibit broad, first-order desorption profiles with maximum desorption temperatures ranging from 168 K during desorption from the C16acid to a maximum desorption temperature of 200 K when water desorbs from the C3acid surface. For water desorption from the C15acid and for the two-component surfaces, desorption traces adopt intermediate profiles between these two extremes. Desorption activation energies range from 42 and 50 kJ mol−1. In the MD studies, submonolayer concentrations of adsorbed water interact with slabs that simulate the one- and two-component SAMs employed in the TPD experiments as well as 4-mercaptobutanoic acid (C4acid). The MD simulations are characterized by distributions of the water−carboxylic acid interaction energies and the orientation of the carbonyl groups. The water−carboxylic acid interaction energy distributions show excellent qualitative agreement with the desorption activation energy values determined from the TPD experiments. Analysis of the carbonyl group orientation from the MD simulations shows strong effects of SAM chain length and whether the SAM contains an odd or even number of carbon atoms. These “odd−even” and chain length effects support many of the results from the TPD experiments and the MD simulations. We discuss the effectiveness of employing MD simulations in concert with TPD studies as well as the atmospheric implications for the interaction of water with highly oxidized, multicomponent surfaces.

Understanding the mechanism of G-protein coupled receptors action is of major interest for drug design. The visual rhodopsin is the prototype structure for the family A of G-protein coupled receptors. Upon photoisomerization of the covalently bound retinal chromophore, visual rhodopsins undergo a large-scale conformational change that prepares the receptor for a productive interaction with the G-protein. The mechanism by which the local perturbation of the retinal cis-trans isomerization is transmitted throughout the protein is not well understood. The crystal structure of the visual rhodopsin from squid solved recently suggests that a chain of water molecules extending from the retinal toward the cytoplasmic side of the protein may play a role in the signal transduction from the all-trans retinal geometry to the activated receptor. As a first step toward understanding the role of water in rhodopsin function, we performed a molecular dynamics simulation of squid rhodopsin embedded in a hydrated bilayer of polyunsaturated lipid molecules. The simulation indicates that the water molecules present in the crystal structure participate in favorable interactions with side chains in the interhelical region and form a persistent hydrogen-bond network in connecting Y315 to W274 via D80.

Atomistic molecular dynamics simulations are used to probe changes in the nature and subnanosecond dynamical behavior of solvation waters that accompany partial denaturation of the globular protein, human α-lactalbumin. A simulated ensemble of subcompact conformers, similar to the molten globule state of human α-lactalbumin, demonstrates a marginal increase in the amount of surface solvation relative to the native state. This increase is accompanied by subtle but distinct enhancement in surface water dynamics, less favorable protein-water interactions, and a marginal decrease in the anomalous behavior of solvation water dynamics. The extent of solvent influx is not proportional to the increased surface area, and the partially denatured conformers are less uniformly solvated compared to their native counterpart. The observed solvation in partially denatured conformers is lesser in extent compared to earlier experimental estimates in molten globule states, and is consistent with more recent descriptions based on nuclear magnetic relaxation dispersion studies.

As a first step toward understanding the principles of the targeting of C2 domains to membranes, we have carried out a molecular dynamics simulation of the C2 domain of cytosolic phospholipase A2 (cPLA2-C2) in a 1-palmitoyl-2-oleoyl-phosphatidylcholine bilayer at constant pressure and temperature (NPT, 300K and 1atm). Using the high-resolution crystal structure of cPLA2-C2 as a starting point, we embedded two copies of the C2 domain into a preequilibrated membrane at the depth and orientation previously defined by electron paramagnetic resonance (EPR). Noting that in the membrane-bound state the three calcium binding loops are complexed to two calcium ions, we initially restrained the calcium ions at the membrane depth determined by EPR. But the depth and orientation of the domains remained within EPR experimental errors when the restraints were later removed. We find that the thermally disordered, chemically heterogeneous interfacial zones of phosphatidylcholine bilayers allow local lipid remodeling to produce a nearly perfect match to the shape and polarity of the C2 domain, thereby enabling the C2 domain to assemble and optimize its own lipid docking site. The result is a cuplike docking site with a hydrophobic bottom and hydrophilic rim. Contrary to expectations, we did not find direct interactions between the protein-bound calcium ions and lipid headgroups, which were sterically excluded from the calcium binding cleft. Rather, the lipid phosphate groups provided outer-sphere calcium coordination through intervening water molecules. These results show that the combined use of high-resolution protein structures, EPR measurements, and molecular dynamics simulations provides a general approach for analyzing the molecular interactions between membrane-docked proteins and lipid bilayers.

We have recently shown that current molecular dynamics (MD) atomic force fields are not yet able to produce lipid bilayer structures that agree with experimentally-determined structures within experimental errors. Because of the many advantages offered by experimentally validated simulations, we have developed a novel restraint method for membrane MD simulations that uses experimental diffraction data. The restraints, introduced into the MD force field, act upon specified groups of atoms to restrain their mean positions and widths to values determined experimentally. The method was first tested using a simple liquid argon system, and then applied to a neat dioleoylphosphatidylcholine (DOPC) bilayer at 66% relative humidity and to the same bilayer containing the peptide melittin. Application of experiment-based restraints to the transbilayer double-bond and water distributions of neat DOPC bilayers led to distributions that agreed with the experimental values. Based upon the experimental structure, the restraints improved the simulated structure in some regions while introducing larger differences in others, as might be expected from imperfect force fields. For the DOPC-melittin system, the experimental transbilayer distribution of melittin was used as a restraint. The addition of the peptide caused perturbations of the simulated bilayer structure, but which were larger than observed experimentally. The melittin distribution of the simulation could be fit accurately to a Gaussian with parameters close to the observed ones, indicating that the restraints can be used to produce an ensemble of membrane-bound peptide conformations that are consistent with experiments. Such ensembles pave the way for understanding peptide-bilayer interactions at the atomic level.

A novel protocol has been developed for comparing the structural properties of lipid bilayers determined by simulation with those determined by diffraction experiments, which makes it possible to test critically the ability of molecular dynamics simulations to reproduce experimental data. This model-independent method consists of analyzing data from molecular dynamics bilayer simulations in the same way as experimental data by determining the structure factors of the system and, via Fourier reconstruction, the overall transbilayer scattering-density profiles. Multi-nanosecond molecular dynamics simulations of a dioleoylphosphatidylcholine bilayer at 66% RH (5.4 waters/lipid) were performed in the constant pressure and temperature ensemble using the united-atom GROMACS and the all-atom CHARMM22/27 force fields with the GROMACS and NAMD software packages, respectively. The quality of the simulated bilayer structures was evaluated by comparing simulation with experimental results for bilayer thickness, area/lipid, individual molecular-component distributions, continuous and discrete structure factors, and overall scattering-density profiles. Neither the GROMACS nor the CHARMM22/27 simulations reproduced experimental data within experimental error. The widths of the simulated terminal methyl distributions showed a particularly strong disagreement with the experimentally observed distributions. A comparison of the older CHARMM22 with the newer CHARMM27 force fields shows that significant progress is being made in the development of atomic force fields for describing lipid bilayer systems empirically.

Pulmonary surfactant is a complex mixture of lipids and proteins that lines the air/liquid interface of the alveolar hypophase and confers mechanical stability to the alveoli during the breathing process. The desire to formulate synthetic mixtures for low-cost prophylactic and therapeutic applications has motivated the study of the specific roles and interactions of the different components. All-atom molecular dynamics simulations were carried out on a model system composed of a monolayer of palmitic acid (PA) and a surfactant protein B peptide, SP-B1–25. A detailed structural characterization as a function of the lipid monolayer specific area revealed that the peptide remains inserted in the monolayer up to values of specific area corresponding to an untilted condensed phase of the the pure palmitic acid monolayer. The system remains stable by altering the conformational order of both the anionic lipid monolayer and the peptide secondary structure. Two elements appear to be key for the constitution of this phase: an electrostatic interaction between the cationic peptide residues with the anionic headgroups, and an exclusion of the aromatic residues on the hydrophobic end of the peptide from the hydrophilic and aqueous regions.

The anisotropic molecular polarizability of the nitrate anion and its decomposition into atomic contributions is studied using ab initio quantum chemistry and the Atoms in Molecules theory. Aqueous solvation of NO₃− in interfacial environments is investigated by a Car–Parrinello molecular dynamics simulation of a cluster, and classical molecular dynamics of an extended slab system with bulk interfaces using a polarizable force field based on the Atoms in Molecules analysis. Both in aqueous clusters and in systems with extended interfaces the nitrate anion clearly prefers interfacial over bulk solvation. This is primarily due to its large value of molecular polarizability, the gas phase value of which is reduced by only 5–10% in the aqueous environment. For polarizable force field simulations of ionic solvation, we recommend to cast the NO₃− polarizability into three equal contributions of roughly 1.3 Å3 placed on the oxygen atoms of the anion.

We present results from an extensive molecular dynamics simulation study of water hydrating the protein Ribonuclease A, at a series of temperatures in cluster, crystal, and powder environments. The dynamics of protein hydration water appear to be very similar in crystal and powder environments at moderate to high hydration levels. Thus, we contend that experiments performed on powder samples are appropriate for discussing hydration water dynamics in native protein environments. Our analysis reveals that simulations performed on cluster models consisting of proteins surrounded by a finite water shell with free boundaries are not appropriate for the study of the solvent dynamics. Detailed comparison to available x-ray diffraction and inelastic neutron-scattering data shows that current generation force fields are capable of accurately reproducing the structural and dynamical observables. On the time scale of tens of picoseconds, at room temperature and high hydration, significant water translational diffusion and rotational motion occur. At low hydration, the water molecules are translationally confined but display appreciable rotational motion. Below the protein dynamical transition temperature, both translational and rotational motions of the water molecules are essentially arrested. Taken together, these results suggest that water translational motion is necessary for the structural relaxation that permits anharmonic and diffusive motions in proteins. Furthermore, it appears that the exchange of protein–water hydrogen bonds by water rotational/librational motion is not sufficient to permit protein structural relaxation. Rather, the complete exchange of protein-bound water molecules by translational displacement seems to be required.

Commonly found in atmospheric aerosols, cooking oils, and human sebum, unsaturated lipids rapidly decay upon exposure to ozone, following the Criegee mechanism. Here, the gas-surface ozonolysis of three oleic acid-based compounds was studied in a reactor and indoors. Under dry conditions, quantitative product analyses by 1H NMR indicate up to 79% molar yield of stable secondary ozonides (SOZs) in oxidized triolein and methyl oleate coatings. Elevated relative humidity (RH) significantly suppresses the SOZ yields, enhancing the formation of condensed-phase aldehydes and volatile C9 products. Along with kinetic parameters informed by molecular dynamics simulations, these results were used as constraints in a kinetic multilayer model (KM-GAP) simulating triolein ozonolysis. Covering a wide range of coating thicknesses and ozone levels, the model predicts a much faster decay near the gas–lipid interface compared to the bulk. Although the dependence of RH on SOZ yields is well predicted, the model overestimates the production of H2O2and aldehydes. With negligible dependence on RH, the product composition for oxidized oleic acid is substantially affected by a competitive reaction between Criegee intermediates (CIs) and carboxylic acids. The resulting α-acyloxyalkyl hydroperoxides (α-AAHPs) have much higher molar yields (29–38%) than SOZs (12–16%). Overall, the ozone–lipid chemistry could affect the indoor environment through “crust” accumulation on surfaces and volatile organic compound (VOC) emission. In the atmosphere, the peroxide formation and changes in particle hygroscopicity may have effects on climate. The related health impacts are also discussed.

Molecular dynamics simulations have been used to investigate the structure of hybrid bilayers (HB) formed by dipalmitoylphosphatidylcholine (DPPC) lipid monolayers adsorbed on a hydrophobic alkanethiol self-assembled monolayer (SAM). The HB system was studied at 20°C and 60°C, and the results were compared with recent neutron reflectivity measurements (Meuse, C. W., S. Krueger, C. F. Majkrzak, J. A. Dura, J. Fu, J. T. Connor, and A. L. Plant. 1998. Biophys. J. 74:1388) and previous simulations of hydrated multilamellar bilayers (MLB) of DPPC (Tu, K., D. J. Tobias, and M. L. Klein. 1995. Biophys. J. 69:2558; and 1996. 70:595). The overall structures of the HBs are in very good agreement with experiment. The structure of the SAM monolayer is hardly perturbed by the presence of the DPPC overlayer. The DPPC layer presents characteristics very similar to the MLB gel phase at low temperature and to the liquid crystal phase at high temperature. Subtle changes have been found for the lipid/water interface of the HBs compared to the MLBs. The average phosphatidylcholine headgroup orientation is less disordered, and this produces changes in the electric properties of the HB lipid/water interface. These changes are attributed to the fact that the aqueous environment of the lipids in these unilamellar films is different from that of MLB stacks. Finally, examination of the intramolecular and whole-molecule dynamics of the DPPC molecules in the fluid phase HB and MLB membranes revealed that the reorientations of the upper part of the acyl chains (near the acyl ester linkage) are slower, the single molecule protrusions are slightly damped, and the lateral rattling motions are significantly reduced in the HB compared with the MLB.

We report a 1.4-ns constant-pressure molecular dynamics simulation of cholesterol at 12.5 mol% in a dipalmitoylphosphatidylcholine (DPPC) bilayer at 50°C and compare the results to our previous simulation of a pure DPPC bilayer. The interlamellar spacing was increased by 2.5Å in the cholesterol-containing bilayer, consistent with x-ray diffraction results, whereas the bilayer thickness was increased by only 1Å. The bilayer/water interface was more abrupt because the lipid headgroups lie flatter to fill spaces left by the cholesterol molecules. This leads to less compensation by the lipid headgroups of the oriented water contribution to the membrane dipole potential and could explain the experimentally observed increase in the magnitude of the dipole potential by cholesterol. Our calculations suggested that 12.5 mol% cholesterol does not significantly affect the conformations and packing of the hydrocarbon chains and produces only a slight reduction in the empty free volume. However, cholesterol has a significant influence on the subnanosecond time scale lipid dynamics: the diffusion constant for the center-of-mass “rattling” motion was reduced by a factor of 3, and the reorientational motion of the methylene groups was slowed along the entire length of the hydrocarbon chains.

In the past few years there have been dozens of reports of atomic-scale molecular dynamics simulations of lipid membranes. Regarding recent methodological developments, it is now generally accepted that there are advantages to doing membrane simulations at constant pressure, but there is also a debate on whether the external pressure should be isotropic or whether tension should be applied in the plane of the bilayer. Also, it has become clear that serious artifacts can be introduced into computer simulations if all electrostatic interactions are not taken into account. Simulations can now faithfully reproduce many known aspects of the structures of gel and liquid crystal phase bilayers, and simulators have begun to include cholesterol and proteins in membrane simulations. There is some disagreement between simulations on the details of the bilayer/water interface, and there has not been enough effort to analyze the dynamics afforded by simulations.

A simple molecular dynamics (MD) simulations is shown to predict protocol whether a residue is in a structured α-helical segment or in a mobile loop or terminal segment of a membrane protein. The results are verified by comparisons with experimental NMR data. The protocol consists of performing several independent MD simulations on a polypeptide sequence of interest in a dielectric continuum with a relative permittivity ε = 2. The time histories of the individual angles between NH bond vectors at time 0 and timetlater are calculated, and then Gaussian smoothing of typically 50 ps is applied.The smoothed data are subtracted from the original data to yield the short time fluctuations of the NH bond vectors, and then the rms deviations of the angles are calculated and compared to experimental NMR results. Pf1 coat protein and the c subunit of theE. coliF₁F₀ATP synthase are used as examples of membrane proteins. The calculated NH bond rms fluctuations are in qualitative agreement with experimental NMR data in showing that each of these proteins has a mobile segment connecting two helices, as well as mobile N and C-terminal regions. This MD simulations protocol can demonstrate the presence of both the amphipathic and hydrophobic helices while hydropathy plots are able to detect only the hydrophobic helices present in membrane proteins.

Work from our laboratory using molecular dynamics applied to the study of peptide/protein folding dynam ics and thermodynamics in aqueous solution, and the exploration and development of molecular solvent in teraction models including electronic polarizability is described. The basic computational techniques we have used in developing algorithms for vector/parallel, shared memory, multiple instruction, multiple data (MIMD) and massively parallel single instruction, multi ple data (SIMD) architectures are discussed in the con text of these application areas. The technique we have used to parallelize the molecular dynamics/molecular mechanics code CHARMM is detailed, with special fo cus given to the performance issues faced in develop ing algorithms for the CRAY Y-MP. New developments of a molecular dynamics kernel for simulation of elec tronically polarizable solvent systems using a parallel- extended Fortran language (Fortran-9X) on the mas sively parallel Connection Machine (CM-2) are out lined. We provide examples of applications using both of these platforms and discuss the development of software for such simulations in a heterogeneous com putational environment.

Voltage-dependent ion channels open and close in response to changes in membrane electrical potential due to the motion of their voltage-sensing domains (VSDs). VSD charge displacements within the membrane electric field are observed in electrophysiology experiments as gating currents preceding ionic conduction. The elementary charge motions that give rise to the gating current cannot be observed directly, but appear as discrete current pulses that generate fluctuations in gating current measurements. Here we report direct observation of gating-charge displacements in an atomistic molecular dynamics simulation of the isolated VSD from the KvAP channel in a hydrated lipid bilayer on the timescale (10-μs) expected for elementary gating charge transitions. The results reveal that gating-charge displacements are associated with the water-catalyzed rearrangement of salt bridges between the S4 arginines and a set of conserved acidic side chains on the S1–S3 transmembrane segments in the hydrated interior of the VSD.

Human skin oils are significant scavengers of atmospheric oxidants in occupied indoor environments, and squalene is a major ozone-active constituent. Here, we present a combined spectroscopic and atomistic modeling approach to elucidate the conformational and orientational preferences of squalene at the air/oil interface and their implications for reactions with ozone. We find that squalene chains have a tendency to align with the surface normal, resulting in different concentrations of the various types of its double bonds and thus different reactivities. We also observe the presence of water at the surface of this hydrophobic compound. Both findings have possible implications for the design and outcomes of kinetic models describing this important aspect of indoor air chemistry.

Voltage-sensor (VS) domains cause the pore of voltage-gated ion channels to open and close in response to changes in transmembrane potential. Recent experimental studies suggest that VS domains are independent structural units. This independence is revealed dramatically by a voltage-dependent proton-selective channel (Hv), which has a sequence homologous to the VS domains of voltage-gated potassium channels (Kv). Here we show by means of molecular dynamics simulations that the isolated open-state VS domain of the KvAP channel in a lipid membrane has a configuration consistent with a water channel, which we propose as a common feature underlying the conductance of protons, and perhaps other cations, through VS domains.