Molecular dynamics simulations of pressure effects on hydrophobic interactions

Review of the Interfacial Structure and Properties of Surfactants in Petroleum Production and Geological Storage Systems from a Molecular Scale Perspective

Surfactants play a crucial role in tertiary oil recovery by reducing the interfacial tension between immiscible phases, altering surface wettability, and improving foam film stability. Oil reservoirs have high temperatures and high pressures, making it difficult and hazardous to conduct lab experiments. In this context, molecular dynamics (MD) simulation is a valuable tool for complementing experiments. It can effectively study the microscopic behaviors (such as diffusion, adsorption, and aggregation) of the surfactant molecules in the pore fluids and predict the thermodynamics and kinetics of these systems with a high degree of accuracy. MD simulation also overcomes the limitations of traditional experiments, which often lack the necessary temporal-spatial resolution. Comparing simulated results with experimental data can provide a comprehensive explanation from a microscopic standpoint. This article reviews the state-of-the-art MD simulations of surfactant adsorption and resulting interfacial properties at gas/oil-water interfaces. Initially, the article discusses interfacial properties and methods for evaluating surfactant-formed monolayers, considering variations in interfacial concentration, molecular structure of the surfactants, and synergistic effect of surfactant mixtures. Then, it covers methods for characterizing microstructure at various interfaces and the evolution process of the monolayers' packing state as a function of interfacial concentration and the surfactants' molecular structure. Next, it examines the interactions between surfactants and the aqueous phase, focusing on headgroup solvation and counterion condensation. Finally, it analyzes the influence of hydrophobic phase molecular composition on interactions between surfactants and the hydrophobic phase. This review deepened our understanding of the micro-level mechanisms of oil displacement by surfactants and is beneficial for screening and designing surfactants for oil field applications.

Thermoresponsive Polymers under Pressure with a Focus on Poly(N-isopropylacrylamide) (PNIPAM)

Pressure is a key variable in the phase behavior of responsive polymers, both for applications and from a fundamental point of view. In this feature article, we review recent developments, particularly applications of neutron techniques such as small-angle neutron scattering (SANS) and quasi-elastic neutron scattering (QENS), across the temperature-pressure phase diagram. These are complemented by kinetic SANS experiments following pressure jumps. In the prototype system poly(N-isopropylacrylamide) (PNIPAM), QENS revealed the pressure-dependent characteristics of hydration water around the lower critical solution temperature transition. The size, water content, and inner structure of the mesoglobules formed in the two-phase region depend strongly on pressure, as shown by SANS. Beside these changes at the phase transition, the mesoglobule formation at low pressure is determined by kinetic factors, namely the formation of a polymer-rich, rigid shell, which hampers further growth by coalescence. At high pressure, in contrast, the growth proceeds by diffusion-limited coalescence without any kinetic hindrance. The disintegration of the mesoglobules evolves either via chain release from their surface or via swelling, depending on the osmotic pressure of the water. Moreover, we report on the profound influence of pressure on the cononsolvency effect. In the temperature-pressure frame, the one-phase region is hugely expanded upon the addition of the cosolvent methanol. SANS experiments unveil the enthalpic and entropic contributions to the effective Flory-Huggins interaction parameter between the segments and the solvent mixture. QENS experiments demonstrate an increase in polymer associated water with pressure, whereas methanol is released. Correspondingly, the solvent phase becomes enriched in methanol, providing a mechanism for the breakdown of cononsolvency at a high pressure. Finally, we outline future opportunities for high-pressure studies of thermoresponsive polymers, with a focus on neutron methods.

Solvation free energies of alcohols in water: temperature and pressure dependences

Solvation free energies μ* of amphiphilic species, methanol and 1,2-hexanediol, are obtained as a function of temperature or pressure based on molecular dynamics simulations combined with efficient free-energy calculation methods. In general, μ* of an amphiphile can be divided into and , the nonpolar and electrostatic contributions, and the former is further divided into and which are the work of cavity formation process and the free energy change due to weak, attractive interactions between the solute molecule and surrounding solvent molecules. We demonstrate that μ* of the two amphiphilic solutes can be obtained accurately using a perturbation combining method, which relies on the exact expressions for and and requires no simulations of intermediate systems between the solute with strong, repulsive interactions and the solute with the van der Waals and electrostatic interactions. The decomposition of μ* gives us several physical insights including that μ* is an increasing function of T due to , that the contributions of hydrophilic groups to the temperature dependence of μ* are additive, and that the contribution of the van der Waals attraction to the solvation volume is greater than that of the electrostatic interactions.

Visualization of Self-Assembly and Hydration of a β-Hairpin through Integrated Small and Wide-Angle Neutron Scattering

Fundamental understanding of the structure and assembly of nanoscale building blocks is crucial for the development of novel biomaterials with defined architectures and function. However, accessing self-consistent structural information across multiple length scales is challenging. This limits opportunities to exploit atomic scale interactions to achieve emergent macroscale properties. In this work we present an integrative small- and wide-angle neutron scattering approach coupled with computational modeling to reveal the multiscale structure of hierarchically self-assembled β hairpins in aqueous solution across 4 orders of magnitude in length scale from 0.1 Å to 300 nm. Our results demonstrate the power of this self-consistent cross-length scale approach and allows us to model both the large-scale self-assembly and small-scale hairpin hydration of the model β hairpin CLN025. Using this combination of techniques, we map the hydrophobic/hydrophilic character of this model self-assembled biomolecular surface with atomic resolution. These results have important implications for the multiscale investigation of aqueous peptides and proteins, for the prediction of ligand binding and molecular associations for drug design, and for understanding the self-assembly of peptides and proteins for functional biomaterials.

Does freezing induce self-assembly of polymers? A molecular dynamics study

This work investigates the freezing-induced self-assembly (FISA) of polyvinyl alcohol (PVA) and PVA-like polymers using molecular dynamics simulations. In particular, the effect of the degree of supercooling, degree of polymerization, polymer type, and initial local concentration on the FISA was studied. It was found that the preeminent factor responsible for FISA is not the diffusion of the polymers away from the nucleating ice front, but the increase in the polymer's local concentration upon freezing of the solvent (water). At a higher degree of supercooling, the polymers are engulfed by the growing ice front, impeding their diffusion into the supercooled solution and finally inhibiting their self-assembly. Conversely, at a relatively lower degree of supercooling, the rate of diffusion of the polymers into the supercooled solution is higher, which increases their local concentration and results in FISA. FISA was also observed to depend on the polymer-solvent interactions. Strongly favorable solute-solvent interactions hinder the self-assembly, whereas unfavorable solute-solvent interactions promote the self-assembly. The polymer and aggregate morphology were investigated using the radius of gyration, end-to-end distance, and asphericity analysis. This study brings molecular insights into the quintessential factors governing self-assembly via freezing of the solvent, which is a novel self-assembly technique especially suitable for biomedical applications.

Molecular Dynamics Simulation of the Effects of Complex Surfactants on Oil-Water Interaction and Aggregation Characteristics at the Interface

In response to the problem of complex interaction between oil and water in the oil-water interface, especially heavy oil and water, this study investigated the effects of complex surfactants on the interaction of two phases and their aggregation characteristics by molecular dynamics simulation. The results showed that increasing the content of sodium lauryl polyether carboxylate (AEC-9Na) was beneficial to the coordination between it and alkyl glycoside (APG-10), improved the interfacial activity, and enhanced the interfacial stability of the composite system, and the best effect was achieved when AEC-9Na:APG-10 = 8:2. The thickness of the oil and water film on the oil-water interface was irregular. When the concentration of AEC-9Na was lower than that of APG-10, the total thickness of the interfacial film (ttotal) first increased. When the content of AEC-9Na is higher, a large number of sodium ions were adsorbed near the -COO- group of AEC-9Na, which will polarize out of the hydration layer structure and attract water molecules from the second hydration layer on the heavy oil surface to the first hydration layer through electrostatic interaction. Then, the thickness of the interface film was compressed, and the interface film was reduced. When the ratio increased to 10:0, the oil and water phase competed to adsorb surfactant molecules, and the headgroup tended to lay on the interface. Moreover, the hydrophilicity of the surfactant layer was weakened, and the thickness of the water film decreased. The distribution of surfactant was looser than 8:2, the light components of heavy oil molecules (saturated and aromatic hydrocarbons) entered the gap between surfactants in large quantities, and the hydrophobic tail chain tended to be laid on the oil-water interface. The oleophilicity of the surfactant layer increased, and the thickness of the oil film remarkably increased, so the total thickness of the interface film increased again.

Classification of PTEN missense VUS through exascale simulations

Phosphatase and tensin homolog (PTEN), a tumor suppressor with dual phosphatase properties, is a key factor in PI3K/AKT signaling pathway. Pathogenic germline variation in PTEN can abrogate its ability to dephosphorylate, causing high cancer risk. Lack of functional evidence lets numerous PTEN variants be classified as variants of uncertain significance (VUS). Utilizing Molecular Dynamics (MD) simulations, we performed a thorough evaluation for 147 PTEN missense VUS, sorting them into 66 deleterious and 81 tolerated variants. Utilizing replica exchange molecular dynamic (REMD) simulations, we further assessed the variants situated in the catalytic core of PTEN's phosphatase domain and uncovered conformational alterations influencing the structural stability of the phosphatase domain. There was a high degree of agreement between our results and the variants classified by Variant Abundance by Massively Parallel Sequencing, saturation mutagenesis, multiplexed functional data and experimental assays. Our extensive analysis of PTEN missense VUS should benefit their clinical applications in PTEN-related cancer.

SIGNIFICANCE STATEMENT

Classification of PTEN variants affecting its lipid phosphatase activity is important for understanding the roles of PTEN variation in the pathogenesis of hereditary and sporadic malignancies. Of the 3000 variants identified in PTEN, 1296 (43%) were assigned as VUS. Here, we applied MD and REMD simulations to investigate the effects of PTEN missense VUS on the structural integrity of the PTEN phosphatase domain consisting the WPD, P and TI active sites. We classified a total of 147 missense VUS into 66 deleterious and 81 tolerated variants by referring to the control group comprising 54 pathogenic and 12 benign variants. The classification was largely in concordance with these classified by experimental approaches.

Correlation between protein conformations and water structure and thermodynamics at high pressure: A molecular dynamics study of the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein

Pressure-induced perturbation of a protein structure leading to its folding-unfolding mechanism is an important yet not fully understood phenomenon. The key point here is the role of water and its coupling with protein conformations as a function of pressure. In the current work, using extensive molecular dynamics simulation at 298 K, we systematically examine the coupling between protein conformations and water structures of pressures of 0.001, 5, 10, 15, 20 kbar, starting from (partially) unfolded structures of the protein Bovine Pancreatic Trypsin Inhibitor (BPTI). We also calculate localized thermodynamics at those pressures as a function of protein-water distance. Our findings show that both protein-specific and generic effects of pressure are operating. In particular, we found that (1) the amount of increase in water density near the protein depends on the protein structural heterogeneity; (2) the intra-protein hydrogen bond decreases with pressure, while the water-water hydrogen bond per water in the first solvation shell (FSS) increases; protein-water hydrogen bonds also found to increase with pressure, (3) with pressure hydrogen bonds of waters in the FSS getting twisted; and (4) water's tetrahedrality in the FSS decreases with pressure, but it is dependent on the local environment. Thermodynamically, at higher pressure, the structural perturbation of BPTI is due to the pressure-volume work, while the entropy decreases with the increase of pressure due to the higher translational and rotational rigidity of waters in the FSS. The local and subtle effects of pressure, found in this work, are likely to be typical of pressure-induced protein structure perturbation.

Predicting efficacy of drug-carrier nanoparticle designs for cancer treatment: a machine learning-based solution

Molecular Dynamic (MD) simulations are very effective in the discovery of nanomedicines for treating cancer, but these are computationally expensive and time-consuming. Existing studies integrating machine learning (ML) into MD simulation to enhance the process and enable efficient analysis cannot provide direct insights without the complete simulation. In this study, we present an ML-based approach for predicting the solvent accessible surface area (SASA) of a nanoparticle (NP), denoting its efficacy, from a fraction of the MD simulations data. The proposed framework uses a time series model for simulating the MD, resulting in an intermediate state, and a second model to calculate the SASA in that state. Empirically, the solution can predict the SASA value 260 timesteps ahead 7.5 times faster with a very low average error of 1956.93. We also introduce the use of an explainability technique to validate the predictions. This work can reduce the computational expense of both processing and data size greatly while providing reliable solutions for the nanomedicine design process.

Pressure Unfolding of Proteins: New Insights into the Role of Bound Water

High pressures can be detrimental for protein stability, resulting in unfolding and loss of function. This phenomenon occurs because the unfolding transition is accompanied by a decrease in volume, which is typically attributed to the elimination of cavities that are present within the native state as a result of packing defects. We present a novel computational approach that enables the study of pressure unfolding in atomistically detailed protein models in implicit solvent. We include the effect of pressure using a transfer free energy term that allows us to decouple the effect of protein residues and bound water molecules on the volume change upon unfolding. We discuss molecular dynamics simulations results using this protocol for two model proteins, Trp-cage and staphylococcal nuclease (SNase). We find that the volume reduction of bound water is the key energetic term that drives protein denaturation under the effect of pressure, for both Trp-cage and SNase. However, we note differences in unfolding mechanisms between the smaller Trp-cage and the larger SNase protein. Indeed, the unfolding of SNase, but not Trp-cage, is seen to be further accompanied by a reduction in the volume of internal cavities. Our results indicate that, for small peptides, like Trp-cage, pressure denaturation is driven by the increase in solvent accessibility upon unfolding, and the subsequent increase in the number of bound water molecules. For larger proteins, like SNase, the cavities within the native fold act as weak spots, determining the overall resistance to pressure denaturation. Our simulations display a striking agreement with the pressure-unfolding profile experimentally obtained for SNase and represent a promising approach for a computationally efficient and accurate exploration of pressure-induced denaturation of proteins.

Behavior of Proteins under Pressure from Experimental Pressure-Dependent Structures

Structure-based models are coarse-grained representations of the interactions responsible for the protein folding process. In their simplest form, they use only the native contact map of a given protein to predict the main features of its folding process by computer simulation. Given their limitations, these models are frequently complemented with sequence-dependent contributions or additional information. Specifically, to analyze the effect of pressure on the folding/unfolding transition, special forms of these interaction potentials are employed, which may a priori determine the outcome of the simulations. In this work, we have tried to keep the original simplicity of structure-based models. Therefore, we have used folded structures that have been experimentally determined at different pressures to define native contact maps and thus interactions dependent on pressure. Despite the apparently tiny structural differences induced by pressure, our simulation results provide different thermodynamic and kinetic behaviors, which roughly correspond to experimental observations (when there is a possible comparison) of two proteins used as benchmarks, hen egg-white lysozyme and dihydrofolate reductase. Therefore, this work shows the feasibility of using experimental native structures at different pressures to analyze the global effects of this physical property on the protein folding process.

Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR

We have investigated the pressure- and temperature-induced conformational changes associated with the low complexity domain of hnRNP A1, an RNA-binding protein able to phase separate in response to cellular stress. Solution NMR spectra of the hnRNP A1 low-complexity domain fused with protein-G B1 domain were collected from 1 to 2500 bar and from 268 to 290 K. While the GB1 domain shows the typical pressure-induced and cold temperature-induced unfolding expected for small globular domains, the low-complexity domain of hnRNP A1 exhibits unusual pressure and temperature dependences. We observed that the low-complexity domain is pressure sensitive, undergoing a major conformational transition within the prescribed pressure range. Remarkably, this transition has the inverse temperature dependence of a typical folding-unfolding transition. Our results suggest the presence of a low-lying extended and fully solvated state(s) of the low-complexity domain that may play a role in phase separation. This study highlights the exquisite sensitivity of solution NMR spectroscopy to observe subtle conformational changes and illustrates how pressure perturbation can be used to determine the properties of metastable conformational ensembles.

Influence of Ionic Strength on Hydrophobic Interactions in Water: Dependence on Solute Size and Shape

Hydrophobicity is a phenomenon of great importance in biology, chemistry, and biochemistry. It is defined as the interaction between nonpolar molecules or groups in water and their low solubility. Hydrophobic interactions affect many processes in water, for example, complexation, surfactant aggregation, and coagulation. These interactions play a pivotal role in the formation and stability of proteins or biological membranes. In the present study, we assessed the effect of ionic strength, solute size, and shape on hydrophobic interactions between pairs of nonpolar particles. Pairs of methane, neopentane, adamantane, fullerene, ethane, propane, butane, hexane, octane, and decane were simulated by molecular dynamics in AMBER 16.0 force field. As a solvent, TIP3P and TIP4PEW water models were used. Potential of mean force (PMF) plots of these dimers were determined at four values of ionic strength, 0, 0.04, 0.08, and 0.40 mol/dm³, to observe its impact on hydrophobic interactions. The characteristic shape of PMFs with three extrema (contact minimum, solvent-separated minimum, and desolvation maximum) was observed for most of the compounds for hydrophobic interactions. Ionic strength affected hydrophobic interactions. We observed a tendency to deepen contact minima with an increase in ionic strength value in the case of spherical and spheroidal molecules. Additionally, two-dimensional distribution functions describing water density and average number of hydrogen bonds between water molecules were calculated in both water models for adamantane and hexane. It was observed that the density of water did not significantly change with the increase in ionic strength, but the average number of hydrogen bonds changed. The latter tendency strongly depends on the water model used for simulations.

High pressure inhibits signaling protein binding to the flagellar motor and bacterial chemotaxis through enhanced hydration

High pressure below 100 MPa interferes inter-molecular interactions without causing pressure denaturation of proteins. In Escherichia coli, the binding of the chemotaxis signaling protein CheY to the flagellar motor protein FliM induces reversal of the motor rotation. Using molecular dynamics (MD) simulations and parallel cascade selection MD (PaCS-MD), we show that high pressure increases the water density in the first hydration shell of CheY and considerably induces water penetration into the CheY-FliM interface. PaCS-MD enabled us to observe pressure-induced dissociation of the CheY-FliM complex at atomic resolution. Pressure dependence of binding free energy indicates that the increase of pressure from 0.1 to 100 MPa significantly weakens the binding. Using high-pressure microscopy, we observed that high hydrostatic pressure fixes the motor rotation to the counter-clockwise direction. In conclusion, the application of pressure enhances hydration of the proteins and weakens the binding of CheY to FliM, preventing reversal of the flagellar motor.

Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when

The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical-chemical properties to predict whether replacement of one amino acid residue with another will be tolerated or cause disease. Those approaches achieve up to 80-85% accuracy as binary classifiers (neutral/pathogenic). As such accuracy is insufficient for medical decision to be based on, and it does not appear to be increasing, more precise methods, such as full-atom molecular dynamics (MD) simulations in explicit solvent, are also discussed. Then, to describe the goal of interpreting human genetic variations at large scale through MD simulations, we restrictively refer to all possible protein variants carrying single-amino-acid substitutions arising from single-nucleotide variations as the human variome. We calculate its size and develop a simple model that allows calculating the simulation time needed to have a 0.99 probability of observing unfolding events of any unstable variant. The knowledge of that time enables performing a binary classification of the variants (stable-potentially neutral/unstable-pathogenic). Our model indicates that the human variome cannot be simulated with present computing capabilities. However, if they continue to increase as per Moore's law, it could be simulated (at 65°C) spending only 3 years in the task if we started in 2031. The simulation of individual protein variomes is achievable in short times starting at present. International coordination seems appropriate to embark upon massive MD simulations of protein variants.

Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics

BACKGROUND

Molecular dynamics (MD) simulation is well-recognized as a powerful tool to investigate protein structure, function, and thermodynamics. MD simulation is also used to investigate high pressure effects on proteins. For conducting better MD simulation under high pressure, the main issues to be addressed are: (i) protein force fields and water models were originally developed to reproduce experimental properties obtained at ambient pressure; and (ii) the timescale to observe the pressure effect is often much longer than that of conventional MD simulations.

SCOPE OF REVIEW

First, we describe recent developments in MD simulation methodologies for studying the high-pressure structure and dynamics of protein molecules. These developments include force fields for proteins and water molecules, and enhanced simulation techniques. Then, we summarize recent studies of MD simulations of proteins in water under high pressure.

MAJOR CONCLUSIONS

Recent MD simulations of proteins in solution under pressure have reproduced various phenomena identified by experiments using high pressure, such as hydration, water penetration, conformational change, helix stabilization, and molecular stiffening.

GENERAL SIGNIFICANCE

MD simulations demonstrate differences in the properties of proteins and water molecules between ambient and high-pressure conditions. Comparing the results obtained by MD calculations with those obtained experimentally could reveal the mechanism by which biological molecular machines work well in collaboration with water molecules.

Effects of Sodium and Magnesium Cations on the Aggregation of Chromonic Solutions Using Molecular Dynamics

Lyotropic chromonic liquid crystals (LCLCs) constitute a unique variety of water-soluble mesogens that spontaneously assemble into elongated aggregates, thereby resulting in the formation of liquid crystal phases depending on the temperature and concentration. The influence of ionic additives on the aggregation of LCLC has been extensively studied, but the molecular mechanisms governing these effects remain unclear. In this investigation, we perform atomistic molecular dynamics simulations of dilute sunset yellow (SSY) LCLC solutions doped with NaCl and MgCl₂ salts. Structural and dynamical properties of SSY hydration shells are considerably modified by the partial substitution of their H bonds with sodium/magnesium-sulfonate ion pairs. Although the intermolecular distance of ∼3.4 Å between SSY mesogens is preserved regardless of the ionic content, the growing number of ion pairs favors the reduction of the electrostatic repulsion between mesogens, increasing the length of SSY stacks. Moreover, magnesium cations exert the strongest electrostatic effects due to their higher hydration capabilities and acute electrostatic binding to SSY. For these reasons, experimental observations of dilute SSY solutions doped with Mg²⁺ exhibit higher nematic-to-isotropic transition temperatures than Na⁺. This work provides a fundamental understanding of the influence of ionic additives on the self-assembly of diluted LCLC solutions derived from the synergistic molecular mechanisms between mesogens, the solvent, and cations.

Comparative Study of the Effects of Temperature and Pressure on the Water-Mediated Interactions between Apolar Nanoscale Solutes

We perform molecular dynamics simulations to study the effects of temperature and pressure on the water-mediated interaction (WMI) between two nanoscale (apolar) graphene plates at 240 ≤ T ≤ 400 K and -100 ≤ P ≤ 1200 MPa. These are thermodynamic conditions relevant to, for example, cooling-, heating-, compression-, and decompression-induced protein denaturation. We find that at all ( T, P) studied, the potential of mean force between the graphene plates, as a function of plate separation r, exhibits local minima at specific plate separations r = r _n that can accommodate n water layers ( n = 0,1,2,3). In particular, our results show that isobaric cooling and isothermal compression have a similar effect on WMI between the plates; both processes tend to suppress the attraction and ultimate collapse of the graphene plates by kinetically trapping the plates at the metastable states with r = r _n ( n > 0). In addition, isobaric heating and isothermal decompression also have a similar effect; both processes tend to reduce the range and strength of the interactions between the graphene plates. Interestingly, at low temperatures, the WMI between the plates is affected by crystallization. However, crystallization depends deeply on the water model considered, SPC/E and TIP4P/2005 water models, with the crystallization occurring at different ( T, P) conditions, into different forms of ice.

Factors Promoting the Formation of Clathrate-Like Ordering of Water in Biomolecular Structure at Ambient Temperature and Pressure

Clathrate hydrate forms when a hydrophobic molecule is entrapped inside a water cage or cavity. Although biomolecular structures also have hydrophobic patches, clathrate-like water is found in only a limited number of biomolecules. Also, while clathrate hydrates form at low temperature and moderately higher pressure, clathrate-like water is observed in biomolecular structure at ambient temperature and pressure. These indicate presence of other factors along with hydrophobic environment behind the formation of clathrate-like water in biomolecules. In the current study, we presented a systematic approach to explore the factors behind the formation of clathrate-like water in biomolecules by means of molecular dynamics simulation of a model protein, maxi, which is a naturally occurring nanopore and has clathrate-like water inside the pore. Removal of either confinement or hydrophobic environment results in the disappearance of clathrate-like water ordering, indicating a coupled role of these two factors. Apart from these two factors, clathrate-like water ordering also requires anchoring groups that can stabilize the clathrate-like water through hydrogen bonding. Our results uncover crucial factors for the stabilization of clathrate-like ordering in biomolecular structure which can be used for the development of new biomolecular structure promoting clathrate formation.

Influence of glycerol on the cooling effect of pair hydrophobicity in water: relevance to proteins’ stabilization at low temperature

Glycerol reduces the cooling effect of pair hydrophobicity (reduction of hydrophobicity with decreasing temperature) in water.

Molecular Insights into the Unusual Structure of an Antifreeze Protein with a Hydrated Core

The primary driving force for protein folding is the formation of a well-packed, anhydrous core. However, recently, the crystal structure of an antifreeze protein, maxi, has been resolved where the core of the protein is filled with water, which apparently contradicts the existing notion of protein folding. Here, we have performed standard molecular dynamics (MD) simulation, replica exchange MD (REMD) simulation, and umbrella sampling using TIP4P water at various temperatures (300, 260, and 240 K) to explore the origin of this unusual structural feature. It is evident from standard MD and REMD simulations that the protein is found to be stable at 240 K in its unusual state. The core of protein has two layers of semi-clathrate water separating the methyl groups of alanine residues from different helical strands. However, with increasing temperature (260 and 300 K), the stability decreases as the core becomes dehydrated, and methyl groups of alanine are tightly packed driven by hydrophobic interactions. Calculation of the potential of mean force by an umbrella sampling technique between a pair of model hydrophobes resembling maxi protein at 240 K shows the stabilization of second solvent-separated minima (SSM), which provides a thermodynamic rationale of the unusual structural feature in terms of weakening of the hydrophobic interaction. Because the stabilization of SSMs is implicated for cold denaturation, it suggests that the maxi protein is so designed by nature where the cold denatured-like state becomes the biologically active form as it works near or below the freezing point of water.

Lessons from pressure denaturation of proteins

Although it is now relatively well understood how sequence defines and impacts global protein stability in specific structural contexts, the question of how sequence modulates the configurational landscape of proteins remains to be defined. Protein configurational equilibria are generally characterized by using various chemical denaturants or by changing temperature or pH. Another thermodynamic parameter which is less often used in such studies is high hydrostatic pressure. This review discusses the basis for pressure effects on protein structure and stability, and describes how the unique mechanisms of pressure-induced unfolding can provide unique insights into protein conformational landscapes.

Temperature Effects on Water-Mediated Interactions at the Nanoscale

We perform molecular dynamics simulations to study the effects of temperature on the water-mediated interactions between nanoscale apolar solutes. Specifically, we calculate the potential of mean force (PMF) between two graphene plates immersed in water at 240 ≤ T ≤ 400 K and P = 0.1 MPa. These are thermodynamic conditions relevant to cooling- and heating-induced protein denaturation. It is found that both cooling and heating tend to suppress the attraction, and ultimate collapse, of the graphene plates. However, the underlying role played by water upon heating and cooling is different. Isobaric heating reduces the strength and range of the interactions between the plates. Instead, isobaric cooling stabilizes the plates separations that can accommodate an integer number of water layers between the graphene plates. In particular, the energy barriers separating these plate separations increase linearly with 1/ T. We also explore the sensitivity of the plates PMF to the water model employed. In the case of the TIP4P/2005 model, water confined between the plates crystallizes into a defective bilayer ice at low temperatures, whereas in the case of the SPC/E model, water remains in the liquid state at same thermodynamic conditions. The effects of varying water-graphene interactions on the plates PMF are also studied.

Hydrophobicity Varying with Temperature, Pressure, and Salt Concentration

Temperature-, pressure-, and salt-concentration-induced variations in the solubility of small nonpolar solutes in aqueous solution and the corresponding variations in the solvent-induced pair attraction between such solute molecules are investigated. The variations in the solvation free energy of a solute and those in the solvent-induced pair attraction are well reproduced by a mean-field approximation in which the repulsive cores of solute molecules are treated as hard spheres and the mean-field energy of a solute molecule is taken to be the average potential energy that the solute molecule feels in solution. The mechanisms of variation in the solvation free energy and those of variation in the solvent-induced pair potential, with increasing temperature, pressure, and salt concentration, are clarified. Correlations between the solvation free energy and the solvent-induced pair potential at a contact distance in temperature, pressure, and salt concentration variations are near linear in any mode of variation, but the slope of the linear relation is dependent on the mode of variation and is determined by a ratio of the solvation thermodynamic quantities characteristic of each mode of variation.

Effects of High Pressure on Phospholipid Bilayers

The response of lipid membranes to changes in external pressure is important for many biological processes, and it can also be exploited for technological applications. In this work, we employ all-atom molecular dynamics simulations to characterize the changes in the physical properties of phospholipid bilayers brought about by high pressure (1000 bar). In particular, we study how the response differs, in relation to different chain unsaturation levels, by comparing monounsaturated 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and biunsaturated dioleoyl-phosphatidylcholine (DOPC) bilayers. Various structural, mechanical, and dynamical features are found to be altered by the pressure increase in both bilayers. Notably, for most properties, including bilayer area and thickness, lipid order parameters, lateral pressure profile, and curvature frustration energy, we observe significantly more pronounced effects for monounsaturated POPC than biunsaturated DOPC. Possible biological implications of the results obtained are discussed, especially in relation to how different lipids can control the structure and function of membrane proteins.

On the Role of Nonspherical Cavities in Short Length-Scale Density Fluctuations in Water

Density fluctuations in liquid water are at the heart of numerous phenomena associated with hydrophobic effects such as protein folding and the interaction between biomolecules. One of the most fundamental processes in this regard is the solvation of hydrophobic solutes in water. The vast majority of theoretical and numerical studies examine density fluctuations at the short length scale focusing exclusively on spherical cavities. In this work, we use both first-principles and classical molecular dynamics simulations to demonstrate that density fluctuations in liquid water can deviate significantly from the canonical spherical shapes. We show that regions of empty space are frequently characterized by exotic, highly asymmetric shapes that can be quite delocalized over the hydrogen bond network. Interestingly, density fluctuations of these shapes are characterized by Gaussian statistics with larger fluctuations. An important consequence of this is that the work required to create non spherical cavities can be substantially smaller than that of spheres. This feature is also qualitatively captured by the Lum-Chandler-Weeks theory. The scaling behavior of the free energy as a function of the volume at short length scales is qualitatively different for the nonspherical entities. We also demonstrate that nonspherical density fluctuations are important for accommodating the hydrophobic amino acid alanine and are thus likely to have significant implications when it comes to solvating highly asymmetrical species such as alkanes, polymers, or biomolecules.

Contribution of Water to Pressure and Cold Denaturation of Proteins

The mechanisms of cold and pressure denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here, we study several cases of proteins, with or without a unique native state, with or without hydrophilic residues, by means of a coarse-grain protein model in explicit solvent. We show, using Monte Carlo simulations, that taking into account how water at the protein interface changes its hydrogen bond properties and its density fluctuations is enough to predict protein stability regions with elliptic shapes in the temperature-pressure plane, consistent with previous theories. Our results clearly identify the different mechanisms with which water participates to denaturation and open the perspective to develop advanced computational design tools for protein engineering.

Driving Forces in Pressure-Induced Protein Transitions

The molecular mechanisms underlying pressure-induced protein denaturation can be analyzed based on the pressure-dependent differences in the apparent volume occupied by amino acids inside the protein and when exposed to water in an unfolded conformation. This chapter presents a volumetric analysis of the peptide group and the 20 naturally occurring amino acid side chains in the interior of the native state, the micelle-like interior of the pressure-induced denatured state, and in the unfolded conformation modeled by low-molecular analogs of proteins. The transfer of a peptide group from the protein interior to water becomes increasingly favorable as pressure increases. This observation classifies solvation of peptide groups as a major driving force in pressure-induced protein denaturation. Polar side chains do not appear to exhibit significant pressure-dependent changes in their preference for the protein interior or solvent. The transfer of nonpolar side chains from the protein interior to water becomes more unfavorable as pressure increases. An inference can be drawn that a sizeable population of nonpolar side chains remains buried inside a solvent-inaccessible core of the pressure-induced denatured state. At elevated pressures this core, owing to the absence of structural constraints, may become packed almost as tightly as the interior of the native state. The presence and partial disappearance of large intraglobular voids is another driving force facilitating pressure-induced protein denaturation. Volumetric data presented here have implications for the kinetics of protein folding and shed light on the nature of the folding transition state ensembles.

A nucleation-based method to study hydrophobic interactions under confinement: enhanced hydrophobic association driven by energetic contributions

A novel simulation approach was developed and applied to the study of hydrophobic interactions for a small hydrophobic solute pair under confinement. In this method, the aggregation-volume-bias Monte Carlo algorithm, developed originally for nucleation studies, is used to evaluate the association free energy with water molecules for a methane pair through the gradual addition of water molecules into a nanometer-sized sphere. Through a thermodynamic cycle, this method allows for a convenient examination of the free energy difference between two different solvated configurations without sampling any of the configurations in between. The potential of mean force (PMF) for a methane pair under confinement obtained from this method reveals that the stability of the contact pair configuration can be enhanced compared to that in bulk water, which is in agreement with previous studies. Also, constraining the center of this methane pair at the center of this confined volume yields a PMF with a metastable solvent separated configuration, resembling more closely the PMF from the bulk-phase system compared to previous studies in which this solvent-separated minimum was found to be completely absent. A combination with histogram reweighting enables the study of this association behavior at different thermodynamic conditions without additional simulations. From a comprehensive thermodynamic analysis, it is evident that such hydrophobic association, known to be entropically driven in the bulk-phase system at ambient conditions, is entropically favorable only when a suitable range of solvent molecules is added to the confined system. More importantly, the energetic contributions are a favorable factor that explains the enhanced hydrophobic association toward the high number of solvent molecules.