Hydrophobic effects on partial molar volume

The hydrophobic effects on partial molar volume (PMV) are investigated as a PMV change in the transfer of a benzenelike nonpolar solute from the nonpolar solvent to water, using an integral equation theory of liquids. The volume change is divided into two effects. One is the "packing" effect in the transfer from the nonpolar solvent to hypothetical "nonpolar water" without hydrogen bonding networks. The other is the "iceberg" effect in the transfer from nonpolar water to water. The results indicate that the packing effect is negative and a half compensated by the positive iceberg effect. The packing effect is explained by the difference in the solvent compressibility. Further investigation shows that the sign and magnitude of the volume change depend on the solute size and the solvent compressibility. The finding gives a significant implication that the exposure of a hydrophobic residue caused by protein denaturation can either increase or decrease the PMV of protein depending on the size of the residue and the fluctuation of its surroundings.     

High-density hydration layer of lysozymes: molecular dynamics decomposition of solution scattering data

A characterization of the physical properties of protein hydration water is critical for understanding protein structure and function. Recent small-angle X-ray and neutron scattering data indicate that the density of water on the surface of lysozyme is significantly higher than in bulk water. Here, we provide an interpretation of the scattering results using a molecular dynamics simulation, which allows us to make quantitative predictions about density variations in the first hydration shell. The perturbation relative to bulk water involves statistically significant changes in the average water structure in the first hydration layer. The water density in the first hydration shell is increased by 5% with respect to the bulk. In regions of higher water density, the water dipoles align more parallel to each other and the number of hydrogen bonds per water molecule is higher. Increased water density is found for water molecules interacting with hydrogen and carbon atoms in the backbone or with nonpolar or negatively charged side-chain groups.     

Potential of mean force between hydrophobic solutes in the Jagla model of water and implications for cold denaturation of proteins

Using the Jagla model potential we calculate the potential of mean force (PMF) between hard sphere solutes immersed in a liquid displaying water-like properties. Consistent estimates of the PMF are obtained by (a) umbrella sampling, (b) calculating the work done by the mean force acting on the hard spheres as a function of their separation, and (c) determining the position dependent chemical potential after calculating the void space in the liquid. We calculate the PMF for an isobar along which cold denaturation of a model protein has previously been reported. We find that the PMF at contact varies non-monotonically, which is consistent with the observed cold denaturation. The Henry constant also varies non-monotonically with temperature. We find, on the other hand, that a second (solvent separated) minimum of the PMF becomes deeper as temperature decreases. We calculate the solvent-solvent pair correlation functions for solvents near the solute and in the bulk, and show that, as temperature decreases, the two pair correlation functions become indistinguishable, suggesting that the perturbation of solvent structure by the solute diminishes as temperature decreases. The solvent-solute pair correlation function at contact grows as the temperature decreases. We calculate the cavity correlation function and show the development of a solvent-separated peak upon decrease of temperature. These observations together suggest that cold denaturation occurs when the solvent penetrates between hydrophobic solutes in configurations with favorable free energy. Our results thus suggest that cold denatured proteins are structured and that cold denaturation arises from strong solvent-solute interactions, rather than from entropic considerations as in heat denaturation.     

Pressure and temperature dependence of hydrophobic hydration: volumetric, compressibility, and thermodynamic signatures

The combined effect of pressure and temperature on hydrophobic hydration of a nonpolar methanelike solute is investigated by extensive simulations in the TIP4P model of water. Using test-particle insertion techniques, free energies of hydration under a range of pressures from 1 to 3000 atm are computed at eight temperatures ranging from 278.15 to 368.15 K. Corresponding enthalpy, entropy, and heat capacity accompanying the hydration process are estimated from the temperature dependence of the free energies. Partial molar and excess volumes calculated using pressure derivatives of the simulated free energies are consistent with those determined by direct volume simulations; but direct volume determination offers more reliable estimates for compressibility. At 298.15 K, partial molar and excess isothermal compressibilities of methane are negative at 1 atm. Partial molar and excess adiabatic (isentropic) compressibilities are estimated to be also negative under the same conditions. But partial molar and excess isothermal compressibilities are positive at high pressures, with a crossover from negative to positive compressibility at approximately 100-1000 atm. This trend is consistent with experiments on aliphatic amino acids and pressure-unfolded states of proteins. For the range of pressures simulated, hydration heat capacity exhibits little pressure dependence, also in apparent agreement with experiment. When pressure is raised at constant room temperature, hydration free energy increases while its entropic component remains essentially constant. Thus, the increasing unfavorability of hydration under raised pressure is seen as largely an enthalpic effect. Ramifications of the findings of the authors for biopolymer conformational transitions are discussed.     

The effect of aqueous solutions of trimethylamine-N-oxide on pressure induced modifications of hydrophobic interactions

To understand the mechanism of protein protection by the osmolyte trimethylamine-N-oxide (TMAO) at high pressure, using molecular dynamics (MD) simulations, solvation of hydrophobic group is probed in aqueous solutions of TMAO over a wide range of pressures relevant to protein denaturation. The hydrophobic solute considered in this study is neopentane which is a considerably large molecule. The concentrations of TMAO range from 0 to 4 M and for each TMAO concentration, simulations are performed at five different pressures ranging from 1 atm to 8000 atm. Potentials of mean force are calculated and the relative stability of solvent-separated state over the associated state of hydrophobic solute are estimated. Results suggest that high pressure reduces association of hydrophobic solutes. From computations of site-site radial distribution function followed by analysis of coordination number, it is found that water molecules are tightly packed around the nonpolar particle at high pressure and the hydration number increases with increasing pressure. On the other hand, neopentane interacts preferentially with TMAO over water and although hydration of neopentane reduces in presence of this osmolyte, TMAO does not show any tendency to prevent the pressure-induced dispersion of neopentane moieties. It is also observed that TMAO molecules prefer a side-on orientation near the neopentane surface, allowing its oxygen atom to form favorable hydrogen bonds with water while maintaining some hydrophobic contacts with neopentane. Analysis of hydrogen-bond properties and solvation characteristics of TMAO reveals that TMAO can form hydrogen bonds with water and it reduces the identical nearest neighbor water molecules caused by high hydrostatic pressures. Moreover, TMAO enhances life-time of water-water hydrogen bonds and makes these hydrogen bonds more attractive. Implication of these results for counteracting effect of TMAO against protein denaturation at high pressures are discussed.     

Structural characteristics of a 0.23 mole fraction aqueous solution of tetrahydrofuran at 20 degrees C

Hydrogen/deuterium isotopic substitution neutron diffraction techniques were used to measure the structural correlation functions in a 0.23 mole fraction solution of tetrahydrofuran in water at room temperature. Empirical potential structure refinement (EPSR) was used to build a three-dimensional model of the liquid structure that is consistent with the experimental data. Detailed analysis shows a preference for nonpolar interactions between the cyclic ether molecules plus polar interactions between the ether and solvent water and hydrophobic hydration of the nonpolar regions of the solute. The increase in the number of hydrogen-bond-acceptor sites relative to the number of hydrogen-bond-donor sites in this system, compared to the balanced situation that would be found in pure water, has a marked compressive effect on the structure of the solvent. Despite the small size of the solvent water molecules, the 0.23 mole fraction aqueous solution is still found to contain small voids akin to those in pure liquid tetrahydrofuran. In contrast to the positive surface charge of the voids in the pure system, the average void in this aqueous solution is found to have a net negative charge. This is due to contributions from the water oxygen atoms that are negatively polarized by their intramolecular bonding.     

Protective effect of small amounts of sodium dodecyl sulfate on the helical structure of bovine serum albumin in thermal denaturation

In the presence of sodium dodecyl sulfate (SDS), the secondary structure of bovine serum albumin (BSA) was almost protected against thermal denaturation above 50 degrees C, where the structural change became irreversible. Beyond 30 degrees C, the helicity (66%) of the protein sharply decreased with rise of temperature. In response to this, the proportions of beta-structure and random coil increased. The helicity and the beta-structural proportion were 44% and 13% at 65 degrees C, respectively. The protective effect was observed upon the coexistence of SDS of extremely low concentrations: the molar ratio of [SDS]/[BSA] of 15 was enough to induce the maximal protective effect on the helical structure of the protein. The maximal protected helicity was 58% at 65 degrees C, increasing to 64% upon cooling down to 25 degrees C. This protective effect became greater with an increase of chain length of alkyl sulfate ion. On the other hand, a cationic surfactant did not protect the BSA structure at all against the thermal denaturation. This protective effect was characterized by the specific amphiphilic nature of anionic surfactant. Such an anionic surfactant is considered to protect the protein structure by building bridges between particular nonpolar residues and particular positively charged residues located on different loops of the protein.     

Individual degrees of freedom and the solvation properties of water

Using molecular dynamics simulations in conjunction with home-developed Split Integration Symplectic Method we effectively decouple individual degrees of freedom of water molecules and connect them to corresponding thermostats. In this way, we facilitate elucidation of structural, dynamical, spectral, and hydration properties of bulk water at any given combination of rotational, translational, and vibrational temperatures. Elevated rotational temperature of the water medium is found to severely hinder hydration of polar molecules, to affect hydration of ionic species in a nonmonotonous way and to somewhat improve hydration of nonpolar species. As proteins consist of charged, polar, and nonpolar amino-acid residues, the developed methodology is also applied to critically evaluate the hypothesis that the overall decrease in protein hydration and the change in the subtle balance between hydration of various types of amino-acid residues provide a plausible physical mechanism through which microwaves enhance aberrant protein folding and aggregation.     

Cold denaturation of yeast frataxin offers the clue to understand the effect of alcohols on protein stability

Although alcohols are well-known to be protein denaturants when present at high concentrations, their effect on proteins at low concentrations is much less well characterized. In this paper, we present a study of the effects of alcohols on protein stability using Yfh1, the yeast ortholog of the human protein frataxin. Exploiting the unusual property of this protein of undergoing cold denaturation around 0 degrees C without any ad hoc destabilization, we determined the stability curve on the basis of both high and low temperature unfolding in the presence of three commonly used alcohols: trifluoroethanol, ethanol, and methanol. In all cases, we observed an extended temperature range of protein stability as determined by a modest increase of the high temperature of unfolding but an appreciable decrease in the low temperature of unfolding. On the basis of simple thermodynamic considerations, we are able to interpret the literature on the effects of alcohols on proteins and to generalize our findings. We suggest that alcohols, at low concentration and physiological pH, stabilize proteins by greatly widening the range of temperatures over which the protein is stable. Our results also clarify the molecular mechanism of the interaction and validate the current theoretical interpretation of the mechanism of cold denaturation.     

尿素/氧化三甲胺混合溶剂影响单壁碳纳米管内部水合性质的分子动力学模拟

尿素是早已被人们认识的蛋白质变性剂,而氧化三甲胺则是最常用的蛋白质结构保护剂。虽然多年来被广泛应用在生物实验中,但是它们是如何在蛋白质结构形成中起作用,特别是氧化三甲胺是如何在高浓度尿素环境中起到抑制尿素蛋白变性作用的分子机制,至今仍然没有得到圆满解答。本文以单壁碳纳米管为模型疏水体系,采用分子动力学模拟研究尿素/氧化三甲胺混合溶液中纳米管内部水合性质,结果表明氧化三甲胺更易与水分子和尿素分子形成较强相互作用从而稳定了水溶液结构,这一结果亦表明了氧化三甲胺可以通过间接机制抵消尿素分子对于碳纳米管内部水合性质的影响。     

Hydration free energies and entropies for water in protein interiors

Free energy calculations for the transfer of a water molecule from the pure liquid to an interior cavity site in a protein are presented. Two different protein cavities, in bovine pancreatic trypsin inhibitor (BPTI) and in the I76A mutant of barnase, represent very different environments for the water molecule: one which is polar, forming four water-protein hydrogen bonds, and one which is more hydrophobic, forming only one water-protein hydrogen bond. The calculations give very different free energies for the different cavities, with only the polar BPTI cavity predicted to be hydrated. The corresponding entropies for the transfer to the interior cavities are calculated as well and show that the transfer to the polar cavity is significantly entropically unfavorable while the transfer to the nonpolar cavity is entropically favorable. For both proteins an analysis of the fluctuations in the positions of the protein atoms shows that the addition of a water molecule makes the protein more flexible. This increased flexibility appears to be due to an increased length and weakened strength of protein-protein hydrogen bonds near the cavity.     

A general algorithm for computing Voronoi volumes: Application to the hydrated crystal of myoglobin

In this study is presented a general algorithm for computing Voronoi volumes of atoms of group of atoms in condensed phases. The method is essentially an extension of the Medvedev procedure to allow vertice determination for any Voronoi polyhedron, primitive or with degenerate vertices. The algorithm has been employed for computing time-averaged volumes in the hydrated crystal of met-myoglobin, using the data of a molecular dynamics simulation. The results, compared to previous volume determination in myoglobin, emphasize the fundamental role of solvent structure close to the protein surface in relation to the packing density properties of the residues. Relative volumes fluctuations of myoglobin residues have been found to be correlated to the corresponding mean square displacements from X-ray diffraction studies and to the theoretical hydration energies.     

On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy

Implicit solvent hydration free energy models are an important component of most modern computational methods aimed at protein structure prediction, binding affinity prediction, and modeling of conformational equilibria. The nonpolar component of the hydration free energy, consisting of a repulsive cavity term and an attractive van der Waals solute-solvent interaction term, is often modeled using estimators based on the solvent exposed solute surface area. In this paper, we analyze the accuracy of linear surface area models for predicting the van der Waals solute-solvent interaction energies of native and non-native protein conformations, peptides and small molecules, and the desolvation penalty of protein-protein and protein-ligand binding complexes. The target values are obtained from explicit solvent simulations and from a continuum solvent van der Waals interaction energy model. The results indicate that the standard surface area model, while useful on a coarse-grained scale, may not be accurate or transferable enough for high resolution modeling studies of protein folding and binding. The continuum model constructed in the course of this study provides one path for the development of a computationally efficient implicit solvent nonpolar hydration free energy estimator suitable for high-resolution structural and thermodynamic modeling of biological macromolecules.     

Calorimetric study of myoglobin embedded in trehalose-water matrixes

It has been suggested that in ‘dry’ protein-trehalose-water systems, water-mediated hydrogen bond network, whose strength increases by drying, anchors the protein to its surroundings. To further characterize this effect, we performed a DSC study on low-water myoglobin-trehalose systems. The denaturation temperature resulted to increase by decreasing hydration, and linearly correlated to the glass transition temperature of both the ternary protein-water-trehalose and the binary water-trehalose systems. Further measurements are being performed to investigate eventual differences among different saccharides.     

Studies on gelation of soybean globulin solutions

Thermal denaturation of soybean globulin fraction (SBGF) in diluted solution (protein concentration 0.15–0.63%) has been studied by the method of differential adiabatic scanning calorimetry. SBGF thermograms have two maxima. The low temperature maximum is consistent with denaturation of 7S component, while the high temperature maximum with denaturation of 11S components of this fraction. In the investigated range of protein concentrations the thermodynamic parameters (temperature and enthalpy) of denaturation of SBGF and its main components are constant. This fact suggests that differential adiabatic scanning calorimetry gives information purporting a change in the protein state at molecular level. The temperatures and enthalpies of denaturation of the main SBGF components linearly rise with increase of NaCl concentration. The slope of dependences of denaturation temperature on salt concentration,K _s, is extremely large (nearly 20 K · l/mole). The elementary thermodynamic theory of lyotropic effects in thermal denaturation of proteins has been developed based on the two-state model and linear approximation of protein-salt interactions by means of the corresponding second virial coefficient. It shows that the dependences of thermodynamic parameters of thermal denaturation on salt concentration should be linear in the initial section. This conclusion is consistent with the experiment. The differences of enthalpies and entropies of transferring denatured and native forms of the main SBGF components from water into NaCl solution have been determined. They are positive and their quantity increases linearly with salt concentration. This fact is consistent with the concept to the effect that the main factor of salt influence on thermal denaturation of SBGF is confined to a decrease of protein hydration. The effect of protein nature on the quantity of lyotropic effect in thermal denaturation has been considered. Using simple considerations as a basis, the dependence of the ratio betweenK _s and the denaturation temperature in water has been obtained, which characterizes the lyotropic effect, on the molar fraction of hydrophobic residues in the protein molecule. This dependence is linear and the lyotropic effect rises with increase in the content of hydrophobic residues. It is satisfactorily consistent with the experimental data on NaCl effect on thermal denaturation temperature for ichthyocol gelatin, ribonuclease, lysozyme, 7S and 11S SBGF components. An extraordinary strong influence of NaCl on thermal denaturation temperatures for the main SBGF components can be accounted for by a relatively high content of hydrophobic residues.     

Low-temperature and high-pressure induced swelling of a hydrophobic polymer-chain in aqueous solution

We report molecular dynamics simulations of a hydrophobic polymer-chain in aqueous solution between 260 K and 420 K at pressures of 1 bar, 3000 bar, and 4500 bar. The simulations reveal a hydrophobically collapsed structure at low pressures and high temperatures. At 3000 bar and about 260 K and at 4500 bar and about 260 K, however, an abrupt transition to a swelled state is observed. The transition is driven by a smaller volume and a remarkably strong lower enthalpy of the swelled state, indicating a steep positive slope of the corresponding transition line. The swelling is strongly stabilized by the energetically favorable state of water in the polymer's hydrophobic first hydration shell at low temperatures. This finding is consistent with the observation of a positive heat capacity of hydrophobic solvation. Moreover, the slope and location of the estimated swelling transition line for the collapsed hydrophobic chain coincides remarkably well with the cold denaturation transition of proteins.     

Low-temperature studies of encapsulated proteins

Water-soluble proteins encapsulated within reverse micelles may be studied under a variety of conditions, including low temperature and a wide range of buffer conditions. Direct high-resolution detection of information relating to protein folding intermediates and pathways can be monitored by low-temperature solution NMR. Ubiquitin encapsulated within AOT reverse micelles was studied using multidimensional multinuclear solution NMR to determine the relationship between protein structure, temperature, and ionic strength. Ubiquitin resonances were monitored by 15N HSQC NMR experiments at varying temperatures and salt concentrations. Our results indicate that the structure of the encapsulated protein at low temperature experiences perturbation arising from two major influences, which are reverse micelle-protein interactions and low-temperature effects (e.g., cold denaturation). These two effects are impossible to distinguish under conditions of low ionic strength. Elevated concentrations of nondenaturing salt solutions defeat the effects of reverse micelle-protein interactions and reveal low-temperature protein unfolding. High ionic strength shielding stabilizes the reverse micelle at low temperatures, which reduces the electrostatic interaction between the protein and reverse micelle surfaces, allowing the phenomenon of cold denaturation to be explored.     

Hydration-dependent protein dynamics revealed by molecular dynamics simulation of crystalline staphylococcal nuclease

Molecular dynamics simulations of crystalline Staphylococcal nuclease in full and minimal hydration states were performed to study hydration effects on protein dynamics at temperatures ranging from 100 to 300 K. In a full hydration state (hydration ratio in weight, h=0.49), gaps are fully filled with water molecules, whereas only crystal waters are included in a minimal hydration state (h=0.09). The inflection of the atomic mean-square fluctuation of protein as a function of temperature, known as the glass-like transition, is observed at approximately 220 K in both cases, which is more significant in the full hydration state. By examining the temperature dependence of residual fluctuation, we found that the increase of fluctuations in the loop and terminal regions, which are exposed to water, is much greater than that in other regions in the full hydration state, but the mobilities of the corresponding regions are relatively restricted in the minimal hydration state by intermolecular contact. The atomic mean-square fluctuation of water molecules in the full hydration state at 300 K is 1 order of magnitude greater than that in the minimal hydration state. Above the transition temperature, most water molecules in the full hydration state behave like bulk water and act as a lubricant for protein dynamics. In contrast, water molecules in the minimal hydration state tend to form more hydrogen bonds with the protein, restricting the fluctuation of these water molecules to the level of the protein. Thus, intermolecular interaction and solvent mobility are important to understand the glass-like transition in proteins.     

Transition State of Heat Denaturation of Methionine Aminopeptidase from a Hyperthermophile

Heat denaturation of methionine aminopeptidase from a hyperthermophile Pyrococcus furiosus (PfMAP) was studied by differential scanning calorimetry at acid pH. Analysis of the calorimetric data has shown that denaturation of PfMAP is non-equilibrium at heating rates from 0.125 to 2 K min^–1. This means that the protein structure at these conditions is metastable and its stability (the apparent temperature of denaturation T _m) is under kinetic control. It was shown that heat denaturation of this protein is a one-step kinetic process. The enthalpy of the process and its activation energy were measured as functions of temperature. The obtained data allowed us to estimate the heat capacity increment and the change in the number of bound protons during activation of the molecule. The data also suggest that the conformation of PfMAP at the transition state only slightly differs from its native conformation with respect to compactness, hydration extent and hydroxyl protonation. This revised version was published online in July 2006 with corrections to the Cover Date.