Temperature dependence of hydrophobic interactions: A mean force perspective, effects of water density, and nonadditivity of thermodynamic signatures

Acidic Conditions Impact Hydrophobe Transfer across the Oil-Water Interface in Unusual Ways

Molecular dynamics simulation and enhanced free energy sampling are used to study hydrophobic solute transfer across the water-oil interface with explicit consideration of the effect of different electrolytes: hydronium cation (hydrated excess proton) and sodium cation, both with chloride counterions (i.e., dissociated acid and salt, HCl and NaCl). With the Multistate Empirical Valence Bond (MS-EVB) methodology, we find that, surprisingly, hydronium can to a certain degree stabilize the hydrophobic solute, neopentane, in the aqueous phase and including at the oil-water interface. At the same time, the sodium cation tends to "salt out" the hydrophobic solute in the expected fashion. When it comes to the solvation structure of the hydrophobic solute in the acidic conditions, hydronium shows an affinity to the hydrophobic solute, as suggested by the radial distribution functions (RDFs). Upon consideration of this interfacial effect, we find that the solvation structure of the hydrophobic solute varies at different distances from the oil-liquid interface due to a competition between the bulk oil phase and the hydrophobic solute phase. Together with an observed orientational preference of the hydroniums and the lifetime of water molecules in the first solvation shell of neopentane, we conclude that hydronium stabilizes to a certain degree the dispersal of neopentane in the aqueous phase and eliminates any salting out effect in the acid solution; i.e., the hydronium acts like a surfactant. The present molecular dynamics study provides new insight into the hydrophobic solute transfer across the water-oil interface process, including for acid and salt solutions.

Temperature Dependence of Hydrophobic and Hydrophilic Forces and Interactions

Molecular dynamics simulations are used to compare the forces and Gibbs free energies associated with bringing small hydrophobic and hydrophilic solutes together in an aqueous solution at different temperatures between 280 and 360 °K. For the hydrophilic solutes, different relative orientations are used to distinguish between direct, intersolute hydrogen bonds (Hbond) and solutes simultaneously hydrogen bonding to a solvent water bridge. Interestingly, the temperature dependence of the hydrophobic and directly hydrogen bonding solutes turns out to be opposite to that of the bridged hydrophilic solutes, with the ΔG becoming more negative for the former and less negative for the latter with increasing temperature. Dissection of the free energy curves into enthalpy and entropy contributions, and further separation of the enthalpy term into solute-solute, solute-solvent, and solvent-solvent components provides insight into the physical molecular causes for the distinctive thermodynamic results. Finally, it is reasoned how the opposite temperature dependencies of the two types of hydrophilic interactions provide a rationale for the cold denaturation of proteins.

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.

Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models

The study provides a deep computational analysis of the thermodynamic and structural features associated with the hydration of xenon, Xe, and its pairwise hydrophobic interaction (i.e., the potential of mean force, PMF), over a large temperature range. Xe is described both as a Lennard-Jones particle, LJ-Xe, and as a Mie particle, Mie-Xe (pseudo hard sphere). Three different water models are used: TIP3P-Ew, SPCE and TIP4P-2005. Mie-Xe is more hydrophobic than LJ-Xe due to the lack of the attractive energetic interactions with water molecules; its hydration, around room temperature, is opposed by a large and negative entropy change and a positive enthalpy change. The PMF of Mie-Xe is characterized by a deep minimum at contact distance whose depth increases with temperature, and whose magnitude is significantly larger than that obtained for LJ-Xe. The contact minimum configuration of Mie-Xe is favoured by a large positive entropy change and contrasted by a positive enthalpy change. These results are qualitatively the same regardless of the water model used. There is no clear connection between the values determined for the thermodynamic functions and the structural features of the hydration shells surrounding the single Mie-Xe and the couple of Mie-Xe particles in the contact minimum configuration. This confirms that the structural reorganization of water associated with such processes is characterized by an almost complete enthalpy-entropy compensation.

Hydrophobic residues of melittin mediate its binding to αA-crystallin

The molecular chaperone αA-crystallin, mainly localized in the human ocular lens, is believed to protect the lens from opacification and cataract, by suppressing the aggregation of the other lens proteins. The present study provides structural and thermodynamic insights into the ability of human αA-crystallin (HAA) to bind to its partially unfolded clients in the lens, using a small peptide, melittin from bee venom, as a model client. We characterized the thermodynamic parameters of the binding process between melittin and HAA through isothermal titration calorimetry (ITC), and found the binding to be endothermic and entropy-driven. We identified the amino acids in melittin important for binding to HAA by saturation-transfer difference (STD) nuclear magnetic resonance (NMR) experiments, and analysis of NMR line broadening upon titration of melittin with HAA. Our results suggest that hydrophobic residues Ile17 and Ile20 on the C-terminal region of melittin are in close contact with HAA in the melittin-HAA complex. Information obtained from NMR experiments was used to generate structural models of the melittin-HAA complex by molecular docking with high-ambiguity driven docking (HADDOCK). Structural models of the melittin-HAA complex reveal important principles underlying the interaction of HAA with its clients.

Temperature, Hydrostatic Pressure, and Osmolyte Effects on Liquid-Liquid Phase Separation in Protein Condensates: Physical Chemistry and Biological Implications

Liquid-liquid phase separation (LLPS) of proteins and other biomolecules play a critical role in the organization of extracellular materials and membrane-less compartmentalization of intra-organismal spaces through the formation of condensates. Structural properties of such mesoscopic droplet-like states were studied by spectroscopy, microscopy, and other biophysical techniques. The temperature dependence of biomolecular LLPS has been studied extensively, indicating that phase-separated condensed states of proteins can be stabilized or destabilized by increasing temperature. In contrast, the physical and biological significance of hydrostatic pressure on LLPS is less appreciated. Summarized here are recent investigations of protein LLPS under pressures up to the kbar-regime. Strikingly, for the cases studied thus far, LLPSs of both globular proteins and intrinsically disordered proteins/regions are typically more sensitive to pressure than the folding of proteins, suggesting that organisms inhabiting the deep sea and sub-seafloor sediments, under pressures up to 1 kbar and beyond, have to mitigate this pressure-sensitivity to avoid unwanted destabilization of their functional biomolecular condensates. Interestingly, we found that trimethylamine-N-oxide (TMAO), an osmolyte upregulated in deep-sea fish, can significantly stabilize protein droplets under pressure, pointing to another adaptive advantage for increased TMAO concentrations in deep-sea organisms besides the osmolyte's stabilizing effect against protein unfolding. As life on Earth might have originated in the deep sea, pressure-dependent LLPS is pertinent to questions regarding prebiotic proto-cells. Herein, we offer a conceptual framework for rationalizing the recent experimental findings and present an outline of the basic thermodynamics of temperature-, pressure-, and osmolyte-dependent LLPS as well as a molecular-level statistical mechanics picture in terms of solvent-mediated interactions and void volumes.

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.

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.

Charge and hydration structure of dendritic polyelectrolytes: molecular simulations of polyglycerol sulphate

Macromolecules based on dendritic or hyperbranched polyelectrolytes have been emerging as high potential candidates for biomedical applications. Here we study the charge and solvation structure of dendritic polyglycerol sulphate (dPGS) of generations 0 to 3 in aqueous sodium chloride solution by explicit-solvent molecular dynamics computer simulations. We characterize dPGS by calculating several important properties such as relevant dPGS radii, molecular distributions, the solvent accessible surface area, and the partial molecular volume. In particular, as the dPGS exhibits high charge renormalization effects, we address the challenges of how to obtain a well-defined effective charge and surface potential of dPGS for practical applications. We compare implicit- and explicit-solvent approaches in our all-atom simulations with the coarse-grained simulations from our previous work. We find consistent values for the effective electrostatic size (i.e., the location of the effective charge of a Debye-Hückel sphere) within all the approaches, deviating at most by the size of a water molecule. Finally, the excess chemical potential of water insertion into dPGS and its thermodynamic signature are presented and rationalized.

Surface Nanobubbles Are Stabilized by Hydrophobic Attraction

The remarkably long lifetime of surface nanobubbles has perplexed researchers for two decades. The current understanding is that both contact line pinning and supersaturation of the ambient liquid are strictly required for the stability of nanobubbles, yet experiments show nanobubbles surviving in open systems and undersaturated environments. We find that this discrepancy can be addressed if the effects of an attractive hydrophobic potential at the solid substrate on the spatial distribution of the gas concentration is taken into account. We also show that, in our model, only substrate pinning is strictly required for stabilization; while hydrophobicity and supersaturation both aid stability, neither is mandatory-the absence of one can be compensated by an excess of the other.

Can Simple Interaction Models Explain Sequence-Dependent Effects in Peptide Homodimerization?

The development of rapid methods to explain and predict peptide interactions, aggregation, and self-assembly has become important to understanding amyloid disease pathology, the shelf stability of peptide therapeutics, and the design of novel peptide materials. Although experimental aggregation databases have been used to develop correlative and statistical models, molecular simulations offer atomic-level details that potentially provide greater physical insight and allow one to single out the most explanatory simple models. Here, we outline one such approach using a case study that develops homodimerization models for serine-glycine peptides with various hydrophobic leucine mutations. Using detailed all-atom simulations, we calculate reference dimerization free energy profiles and binding constants for a small peptide library. We then use statistical methods to systematically assess whether simple interaction models, which do not require expensive simulations and free energy calculation, can capture them. Surprisingly, some combinations of a few simple scaling laws well recapitulate the detailed, all-atom results with high accuracy. Specifically, we find that a recently proposed phenomenological hydrophobic force law and coarse measures of entropic effects in binding offer particularly high explanatory power, underscoring the physical relevance to association that these driving forces can play.

Unified elucidation of the entropy-driven and -opposed hydrophobic effects

The association of nonpolar solutes is generally believed to be entropy driven, which has been shown to be true for the contact of small molecules, ellipsoids, and plates.

Shedding light on the hydrophobicity puzzle

A general theory of hydrophobic hydration and pairwise hydrophobic interaction has been developed in the last years. The main ingredient is the recognition that: (a) cavity creation (necessary to insert a solute molecule into water) causes a solvent-excluded volume effect that leads to a loss in the translational entropy of water molecules; (b) the merging of two cavities (necessary to form the contact minimum configuration of two nonpolar molecules) causes a decrease in the solvent-excluded volume effect and so an increase in the translational entropy of water molecules. The performance of the theoretical approach is tested by reproducing both the hydration thermodynamics of xenon and the thermodynamics associated with the formation of the contact minimum configuration of two xenon atoms, over a large temperature range.

Thermodynamics of Aβ16-21 dissociation from a fibril: Enthalpy, entropy, and volumetric properties

Here, we provide insights into the thermodynamic properties of A β16-21 dissociation from an amyloid fibril using all-atom molecular dynamics simulations in explicit water. An umbrella sampling protocol is used to compute potentials of mean force (PMF) as a function of the distance ξ between centers-of-mass of the A β16-21 peptide and the preformed fibril at nine temperatures. Changes in the enthalpy and the entropic energy are determined from the temperature dependence of these PMF(s) and the average volume of the simulation box is computed as a function of ξ. We find that the PMF at 310 K is dominated by enthalpy while the entropic energy does not change significantly during dissociation. The volume of the system decreases during dissociation. Moreover, the magnitude of this volume change also decreases with increasing temperature. By defining dock and lock states using the solvent accessible surface area (SASA), we find that the behavior of the electrostatic energy is different in these two states. It increases (unfavorable) and decreases (favorable) during dissociation in lock and dock states, respectively, while the energy due to Lennard-Jones interactions increases continuously in these states. Our simulations also highlight the importance of hydrophobic interactions in accounting for the stability of A β16-21.

Theoretical Studies of Interactions between O-Phosphorylated and Standard Amino-Acid Side-Chain Models in Water

Phosphorylation is a common post-translational modification of the amino-acid side chains (serine, tyrosine, and threonine) that contain hydroxyl groups. The transfer of the negatively charged phosphate group from an ATP molecule to such amino-acid side chains leads to changes in the local conformations of proteins and the pattern of interactions with other amino-acid side-chains. A convenient characteristic of the side chain-side chain interactions in the context of an aqueous environment is the potential of mean force (PMF) in water. A series of umbrella-sampling molecular dynamic (MD) simulations with the AMBER force field were carried out for pairs of O-phosphorylated serine (pSer), threonine (pThr), and tyrosine, (pTyr) with natural amino acids in a TIP3P water model as a solvent at 298 K. The weighted-histogram analysis method was used to calculate the four-dimensional potentials of mean force. The results demonstrate that the positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the relative orientation depend on the character of the interacting pairs. More distinct minima are observed for oppositely charged pairs such as, e.g., O-phosphorylated side-chains and positively charged ones, such as the side-chains of lysine and arginine.

Hydrophobic Ambivalence: Teetering on the Edge of Randomness

Processes ranging from oil-water phase separation to the formation of solid clathrate hydrates send mixed messages regarding whether oil molecules hate or love to be surrounded by water. Recent experimental and theoretical results help decipher these mixed messages by illuminating the conditions under which the stability of a hydrophobic contact is expected to exceed thermal energy fluctuations - thus facilitating hydrophobic self-assembly and the emergence of structure from randomness. Important open questions remain regarding the dependence of hydrophobic interactions on molecular size and temperature, as well as the balance of direct and water-mediated interactions.

Role of side-chain interactions on the formation of α-helices in model peptides

The role played by side-chain interactions on the formation of α-helices is studied using extensive all-atom molecular dynamics simulations of polyalanine-like peptides in explicit TIP4P water. The peptide is described by the OPLS-AA force field except for the Lennard-Jones interaction between Cβ-Cβ atoms, which is modified systematically. We identify values of the Lennard-Jones parameter that promote α-helix formation. To rationalize these results, potentials of mean force (PMF) between methane-like molecules that mimic side chains in our polyalanine-like peptides are computed. These PMF exhibit a complex distance dependence where global and local minima are separated by an energy barrier. We show that α-helix propensity correlates with values of these PMF at distances corresponding to Cβ-Cβ of i-i+3 and other nearest neighbors in the α-helix. In particular, the set of Lennard-Jones parameters that promote α-helices is characterized by PMF that exhibit a global minimum at distances corresponding to i-i+3 neighbors in α-helices. Implications of these results are discussed.

Solvent effects on kinetic mechanisms of self-assembly by peptide amphiphiles via molecular dynamics simulations

Peptide amphiphiles are known to form a variety of distinctive self-assembled nanostructures (including cylindrical nanofibers in hydrogels) dependent upon the solvent conditions. Using a novel coarse-grained model, large-scale molecular dynamics simulations are performed on a system of 800 peptide amphiphiles (sequence, palmitoyl-Val3Ala3Glu3) to elucidate kinetic mechanisms of molecular assembly as a function of the solvent conditions. The assembly process is found to occur via a multistep process with transient intermediates that ultimately leads to the stabilized nanostructures including open networks of β-sheets, cylindrical nanofibers, and elongated micelles. Different kinetic mechanisms are compared in terms of peptide secondary structures, solvent-accessible surface area, radius of gyration, relative shape anisotropy, intra/intermolecular interactions, and aggregate size dynamics to provide insightful information for the design of functional biomaterials.

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

The energy landscape used by nature over evolutionary timescales to select protein sequences is essentially the same as the one that folds these sequences into functioning proteins, sometimes in microseconds. We show that genomic data, physical coarse-grained free energy functions, and family-specific information theoretic models can be combined to give consistent estimates of energy landscape characteristics of natural proteins. One such characteristic is the effective temperature T(sel) at which these foldable sequences have been selected in sequence space by evolution. T(sel) quantifies the importance of folded-state energetics and structural specificity for molecular evolution. Across all protein families studied, our estimates for T(sel) are well below the experimental folding temperatures, indicating that the energy landscapes of natural foldable proteins are strongly funneled toward the native state.

Role of hydrophobicity on self-assembly by peptide amphiphiles via molecular dynamics simulations

Using a novel coarse-grained model, large-scale molecular dynamics simulations were performed to examine self-assembly of 800 peptide amphiphiles (sequence palmitoyl-V3A3E3). Under suitable physiological conditions, these molecules readily assemble into nanofibers leading to hydrogel construction as observed in experiments. Our simulations capture this spontaneous self-assembly process, including formation of secondary structure, to identify morphological transitions of distinctive nanostructures. As the hydrophobic interaction is increased, progression from open networks of secondary structures toward closed cylindrical nanostructures containing either β-sheets or random coils are observed. Moreover, temperature effects are also determined to play an important role in regulating formation of secondary structures within those nanostructures. These understandings of the molecular interactions involved and the role of environmental factors on hydrogel formation provide useful insight for development of innovative smart biomaterials for biomedical applications.

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.

Heterogeneous Hydration of p53/MDM2 Complex

Water-mediated interactions play critical roles in biomolecular recognition processes. Explicit solvent molecular dynamics (MD) simulations and the variational implicit-solvent model (VISM) are used to study those hydration properties during binding for the biologically important p53/MDM2 complex. Unlike simple model solutes, in such a realistic and heterogeneous solute–solvent system with both geometrical and chemical complexity, the local water distribution sensitively depends on nearby amino acid properties and the geometric shape of the protein. We show that the VISM can accurately describe the locations of high and low density solvation shells identified by the MD simulations and can explain them by a local coupling balance of solvent–solute interaction potentials and curvature. In particular, capillary transitions between local dry and wet hydration states in the binding pocket are captured for interdomain distance between 4 to 6 Å, right at the onset of binding. The underlying physical connection between geometry and polarity is illustrated and quantified. Our study offers a microscopic and physical insight into the heterogeneous hydration behavior of the biologically highly relevant p53/MDM2 system and demonstrates the fundamental importance of hydrophobic effects for biological binding processes. We hope our study can help to establish new design rules for drugs and medical substances.

The application of the integral equation theory to study the hydrophobic interaction

The Wertheim's integral equation theory was tested against newly obtained Monte Carlo computer simulations to describe the potential of mean force between two hydrophobic particles. An excellent agreement was obtained between the theoretical and simulation results. Further, the Wertheim's integral equation theory with polymer Percus-Yevick closure qualitatively correctly (with respect to the experimental data) describes the solvation structure under conditions where the simulation results are difficult to obtain with good enough accuracy.

The hydrophobic force: measurements and methods

The hydrophobic force describes the attraction between water-hating molecules (and surfaces) that draws them together, causing aggregation, phase separation, protein folding and many other inherent physical phenomena.

Length-scale crossover of the hydrophobic interaction in a coarse-grained water model

It has been difficult to establish a clear connection between the hydrophobic interaction among small molecules typically studied in molecular simulations (a weak, oscillatory force) and that found between large, macroscopic surfaces in experiments (a strong, monotonic force). Here, we show that both types of interaction can emerge with a simple, core-softened water model that captures water's unique pairwise structure. As in hydrophobic hydration, we find that the hydrophobic interaction manifests a length-scale dependence, exhibiting distinct driving forces in the molecular and macroscopic regimes. Moreover, the ability of this simple model to capture both regimes suggests that several features of the hydrophobic force can be understood merely through water's pair correlations.

The role of electrostatics and temperature on morphological transitions of hydrogel nanostructures self-assembled by peptide amphiphiles via molecular dynamics simulations

Smart biomaterials that are self-assembled from peptide amphiphiles (PA) are known to undergo morphological transitions in response to specific physiological stimuli. The design of such customizable hydrogels is of significant interest due to their potential applications in tissue engineering, biomedical imaging, and drug delivery. Using a novel coarse-grained peptide/polymer model, which has been validated by comparison of equilibrium conformations from atomistic simulations, large-scale molecular dynamics simulations are performed to examine the spontaneous self-assembly process. Starting from initial random configurations, these simulations result in the formation of nanostructures of various sizes and shapes as a function of the electrostatics and temperature. At optimal conditions, the self-assembly mechanism for the formation of cylindrical nanofibers is deciphered involving a series of steps: (1) PA molecules quickly undergo micellization whose driving force is the hydrophobic interactions between alkyl tails; (2) neighboring peptide residues within a micelle engage in a slow ordering process that leads to the formation of β-sheets exposing the hydrophobic core; (3) spherical micelles merge together through an end-to-end mechanism to form cylindrical nanofibers that exhibit high structural fidelity to the proposed structure based on experimental data. As the temperature and electrostatics vary, PA molecules undergo alternative kinetic mechanisms, resulting in the formation of a wide spectrum of nanostructures. A phase diagram in the electrostatics-temperature plane is constructed delineating regions of morphological transitions in response to external stimuli.

Soft collective fluctuations governing hydrophobic association

The interaction between two associating hydrophobic particles has traditionally been explained in terms of the release of entropically frustrated hydration shell water molecules. However, this picture cannot account for the kinetics of hydrophobic association and is therefore not capable of providing a microscopic description of the hydrophobic interaction (HI). Here, Monte Carlo simulations of a pair of molecular-scale apolar solutes in aqueous solution reveal the critical role of collective fluctuations in the hydrogen bond (HB) network for the microscopic picture of the HI. The main contribution to the HI is the relaxation of solute-water translational correlations. The existence of a heat capacity maximum at the desolvation barrier is shown to arise from softening of non-HB water fluctuations and the relaxation of many-body correlations in the labile HB network. The microscopic event governing the kinetics of hydrophobic association has turned out to be a relatively large critical collective fluctuation in hydration water displacing a substantial fraction of HB clusters from the inner to the outer region of the first hydration shell.