Hydrostatic pressure effect on hydrophobic hydration and pairwise hydrophobic interaction of methane

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.

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.

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.

Shedding light on the extra thermal stability of thermophilic proteins

An entropic stabilization mechanism has recently gained attention and credibility as the physical ground for the extra thermal stability of globular proteins from thermophilic microorganisms. An empirical result, obtained from the analysis of thermodynamic data for a large set of proteins, strengthens the general reliability of the theoretical approach originally devised to rationalize the occurrence of cold denaturation [Graziano, PCCP 2014, 16, 21755-21767]. It is shown that this theoretical approach can readily account for the entropic stabilization mechanism. On decreasing the conformational entropy gain associated with denaturation, the thermal stability of a model globular protein increases markedly.

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.

On the mechanism of cold denaturation

A theoretical rationalization of the occurrence of cold denaturation for globular proteins was devised, assuming that the effective size of water molecules depends upon temperature [G. Graziano, Phys. Chem. Chem. Phys., 2010, 12, 14245-14252]. In the present work, it is shown that the latter assumption is not necessary. By performing the same type of calculations in water, 40% (by weight) methanol, methanol, and carbon tetrachloride, it emerges that cold denaturation occurs only in water due to the special temperature dependence of its density and the small size of its molecules. These two coupled factors determine the magnitude and the temperature dependence of the stabilizing term that measures the gain in configurational/translational entropy of water molecules upon folding of the protein. This term has to be contrasted with the destabilizing contribution measuring the loss in conformational entropy of the polypeptide chain upon folding.

The solvent-induced interaction of spherical solutes in associated and non-associated liquids

We propose an efficient method for studying the solvent-induced interaction of two solvophobic particles immersed in a liquid solvent. The method is based on the combination of the probabilistic hydrogen bond model with the density functional theory. An analytic expression for the number of hydrogen bonds per water molecule near two spherical hydrophobes is derived as a function of the molecule distance to both hydrophobes, distance between hydrophobes, and their radii. Using this expression, one can construct an approximation for the distribution of fluid (liquid water) molecules in the system which provides a reasonably good (much faster and accurate enough) alternative to a standard iteration procedure. Such an approximate density distribution constitutes an efficient foundation for studying the length-scale and temperature dependence of hydrophobic interactions. The model is applied to the interaction of solvophobic solutes in both associated and non-associated liquids. Of these two cases, the model predictions for the solvent-induced potential of mean force between two solutes in associated liquids are closer to the results of molecular dynamics simulation of hydrophobic interactions in the SPC/E model water. Our results suggest that the hydrogen bonding ability of water molecules may play a major role in hydrophobic phenomena.