Abstract
Hydrogen-bond (H-bond) patterns of water molecules around a small protein molecule were studied with a molecular dynamics simulation. By using a coordinate system fixed on the protein, time-averaged H-bond patterns were calculated from the trajectory. Coherent H-bond patterns appeared only near the protein surface, in spite that the H-bond ability near the protein surface was the same as that in bulk-water regions. Thus, the patterns were consequence of highly preferential H-bond formation between specific sites on the protein surface and water molecules. Furthermore, the sites characterized by the coherent H-bond patterns displayed large solvent densities and strong solvent site-dipoles.
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