Probability distributions of hydration water molecules around polar protein atoms obtained by a database analysis

Hydration structures on protein surfaces are visualized by high-resolution cryogenic X-ray crystallography. We calculated the probability distributions of 4 831 570 hydration water molecules found around the 4 214 227 polar atoms in main chains and hydrophilic side chains from the 17 984 crystal structures in the Protein Data Bank. The structures are refined using the diffraction data collected below 150 K and at resolutions of better than 2.2 Å. The calculated distributions were nonrandom but condensed into a few clusters. The clusters were decomposed into the distance and angular distributions by viewing from the polar coordinate system. The major peaks in the clusters were almost located along the directions of the N-H and O-H bonds or the lone pairs of oxygen atoms. The Gaussian fitting method was applied for the distribution profiles to evaluate quantitatively the peak positions and the widths. The parameters characterizing the distributions apparently depended on the hydrogen-bond partners of water molecules and on the modes whether the water molecules acted as donors or acceptors of protons. This led to propose the different roles of NH_n (n = 1, 3), OH, and CO groups in protein hydration and possible in protein-ligand and protein-protein interaction: While CdO groups appear to control the H-bond distances, NH_n groups likely limit the angular range of H-bonds. The OH groups have both characteristics. In addition, it was also demonstrated that polar protein atoms were arranged to satisfy the tetrahedral hydrogen-bond geometry of water molecules, suggesting essential roles of water molecules in the folding process and in the stabilization of protein structures. These probability distributions are probably one of fundamental data to better understand the roles of hydration water molecules in the folding process and the stability of proteins in solution.