The main aim of this work is to propose a rational explanation of the commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that the geometry of the water-water hydrogen bond network within solvation layer differs from the one in bulk water, and it is the result of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the structure of solvation water. Our explanation of the observed changes is based on model proposed by Tanaka (Tanaka, H. J. Chem. Phys. 2000, 112, 799). According to this model, in liquid water exist some special structures formed by water molecules thanks to their unique ability to create the branched network of hydrogen bonds. These structures have two characteristic features: a low potential energy of internal interactions and a large specific volume. We provide some evidence for the supposition that deformation of the geometry of the water-water hydrogen bond network is responsible for destabilization of these structures and therefore for increased local density of water. Our model is constructed on the basis of the analysis of solvation water of some specific protein, the motor head of kinesin. Subsequently, we used it for description of solvation of purely hydrophobic surface. It has been found that in this case an unoccupied space between the hydrophobic surface and neighboring solvation layer exists. It has been found that thickness of this region depends on local geometry of the water-protein interface, and it is a result of maintaining a balance between water-surface interactions and water-water interactions. In our opinion, existence of this space region is one of the main factors that differentiates the hydrophobic hydration from hydration of the native form of kinesin. Its existence also explains why the density is greater for solvation water around the native form of the protein than in the vicinity of the hydrophobic surface.

Despite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the system or parameters employed to describe physical properties of the mixture and interpretation of the results. Bearing this in mind, we determine two main aims of this work as follows: description of the water-water hydrogen bond network structure within the solvation layer around solute molecules (urea, trimethylamine-N-oxide, and tetramethylurea), and also comparison of rigid simple point charges (SPC) and polarizable (POL3) models of water. The following quantities have been examined: radial distribution functions of water molecules around the investigated solutes, both local and overall characteristics of the hydrogen bond network structure (using recently elaborated method), along with estimation of the mean energy of a single hydrogen bond, and also the probability distributions which describe the orientation of a single water particle plane relatively to the center of mass of the solute molecule. As an independent method for the evaluation of the degree of changes in local structural ordering, a harmonic approximation has been adopted to estimate the absolute entropy of water. It was found that within the solvation shell of the investigated solutes, the structure of hydrogen bond network changes only slightly comparing to bulk water. Therefore, we conclude that the investigated osmolyte molecules do not disturb significantly the structure of surrounding water. This conclusion was also confirmed by calculations of the absolute entropy of water using a harmonic approximation. In the immediate vicinity of the solutes, we observe that the water-water hydrogen bonds are slightly more stable; they are slightly less distorted and a little shorter than in bulk water. Nevertheless, although this local water structure is more stable and stiffer, our results do not indicate that it is more ordered compared to bulk. Finally, the comparison of both used models of water, the fixed charge and the polarizable, leads to unambiguous conclusion that rigid (SPC) water model may be successfully used in simulations instead of polarizable (POL3), as no significant differences between these two models have been observed.

Several conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer-the first solvation shell-around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within this layer, water molecules show marked orientations relative to a peptide surface. Using the two-particle contribution to entropy as a measure of structural ordering of water, we found that the first solvation shell contributes 95% or more to the total water ordering around the peptide molecule. In investigating the dynamic properties of water, diffusion coefficients and lifetime of the hydrogen bond, clear differences between solvation layer and the bulk water were observed. It was found that the translational diffusion coefficient, D(T), decreases by 30% or more compared to bulk water; also, the lifetime of the water-water hydrogen bond clearly increases. The rotational diffusion coefficient, however, decreases only slightly, no more than approximately 10%. These differences correspond to the slightly higher energy of the hydrogen bond, and to its slightly distorted geometry. Analyzing the translational dynamics of water in the vicinity of the peptide molecule, it was deduced that the structure of the first solvation shell becomes more rigid than the structure of the bulk water. Investigation of a "pure hydrophobic" form of the polypeptide shows that the structure and the properties of water within the solvation shell are predominantly determined by the hydrophobic effect. The specific interactions between water molecules and various charge groups of the peptide molecule modifies this effect only slightly.

Many hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were analyzed and compared with the properties of solvation water present at the surface of ice. The most striking observations concerned the temperature dependence of changes in water structure. In the case of solvation water of the ice-binding plane, the difference between the overall structural ordering of solvation water and bulk water diminished with increasing temperature; in the case of solvation water of the rest of the protein, the trend was opposite. In this respect, the solvation water of the ice-binding plane roughly resembled the hydration layer of ice. Simultaneously, the whole solvation shell of the protein displayed some features that are typical for solvation shells of many other proteins and are not encountered in the solvation water of ice. In the first place, this is an increase in density of water around the protein. The opposite is true for the solvation water of ice - it is less dense than bulk water. Therefore, even though the structure of solvation water of ice-binding plane and the structure of solvation water of ice seem to share some similarities, densitywise they differ.

A single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local values of diffusion coefficients (translational and rotational) of water adjacent to specific patches on the protein surface seem not to be correlated to the orientational ordering of hydration water, but instead they depend on spatial roughness and degree of exposure of the patch to the solvent. Finally, a relationship between the mobility of various surface atoms of the protein and the mean values of the diffusion coefficient of the adjacent water molecules has been observed. The latter finding suggests a close relationship between the dynamics of the inner kinesin movements and the behavior of solvation water which is in turn determined by the topography of the contact surface between the protein and the surrounding water molecules.