Structure, dynamics, and energetics of water at the surface of a small globular protein: A molecular dynamics simulation

The dynamics of water around a biomolecular surface has attracted a lot of attention recently. We report here protein-solvent simulation studies of the small globular protein ubiquitin (human). The simulations are run unconstrained, without freezing the bonds. The mean square displacements of the water oxygen atoms show a sublinear trend with time. The diffusion coefficient data indicate that the water in the first hydration layer behaves like water at a temperature that is roughly $12°\mathrm{C}$ lower than the average temperature of the system $\left(27\mathrm{}°\mathrm{C}\right).\mathrm{}$ Both the dipolar second-rank relaxation and the survival time correlation function of the water layers show two decay constants, indicating contributions from fast and slow dynamics. A calculation of the interaction energy between the water layers and protein indicates that the interaction energy sharply decreases beyond 4 Å from the protein surface.