Desiccation tolerance of prokaryotes.

The use of molecular dynamics simulation to investigate the properties of hydration water around proteins is outlined. A variety of structural and dynamical properties of the protein hydration water are reviewed and compared with those of bulk and with the corresponding experimental results. In particular, the accessibility to the protein medium, the hydrogen bond networking capability, the residence times, the diffusive mobility, the relaxation behavior, and the inelastic vibrational features of hydration water are analyzed in framework of the peculiar interactions of water at the protein surface. All these features, which can be traced back to the complexity of the overall protein−solvent energy landscape, are discussed in connection with the role played by hydration water in the biological functionality.

Molecular Dynamics of Water at the Protein-Solvent Interface

We describe the model dynamical behavior of the solvent between two nanoscopic hydrophobic solutes. The dynamics of the vicinal water in various sized traps is found to be significantly different from bulk behavior. We consider the dynamics at normal temperature and pressure at three intersolute distances corresponding to the three solvent separated minima in the free energy profile between the solutes with attractions. These three states correspond to one, two, and three intervening layers of water molecules. Results are obtained from a molecular dynamics simulation at constant temperature and pressure (NPT) ensemble. Translational diffusion of water molecules trapped between the two solutes has been analyzed from the velocity correlation function as well as from the mean square displacement of the water molecules. The rotational behavior has been analyzed through the reorientational dynamics of the dipole moment vector of the water molecule by calculating both first and second rank dipole-dipole correlation functions. Both the translational and reorientational mobilities of water are found to be much slower at the smaller separation and increases as the separation between solutes becomes larger. The occupation time distribution functions calculated from the trajectories also show that the relaxation is much slower for the smallest intersolute separation as compared to other wider separations. The sublinear trend in mean square displacement and the stretched exponential decay of the relaxation of dipolar correlation and occupation distribution function indicate that the dynamical behavior of water in the confined region between two large hydrophobic solutes departs from usual Brownian behavior. This behavior is reminiscent of the behavior of water in the vicinity of protein surface clefts or trapped between two domains of a protein.

Dynamics of water trapped between hydrophobic solutes.

http://www.ks.uiuc.edu/Publications/Papers/PDF/WRIG98B/WRIG98B.pdf

Structure and Dynamics of Calmodulin in Solution

Molecular dynamics simulations have been used to model the aqueous solvation of the nonreducing sugar α,α-trehalose. The anisotropic structuring of water around the trehalose molecule was calculated in a Cartesian coordinate frame fixed with respect to the sugar molecule by averaging water positions over the trajectories and was plotted in two and three dimensions relative to the sugar. The hydrogen bonding of this sugar to solvent was calculated and compared to other sugar solutes. Hydration was required to produce the experimental conformation, through the exchange of an internal hydrogen bond for similar bonds to solvent. This equilibrium conformation was found to impose extensive structuring on the adjacent solvent, with structuring extending out to at least the third “solvation shell”, while pure liquid water exhibits such structure only in its nearest neighbors. The details of the structuring are determined by both the specific stereochemical topology of the molecule and its conformation, with consi...

Molecular Dynamics Studies of the Hydration of α,α-Trehalose

A global model of the protein-solvent interface

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A global model of the protein-solvent interface