Collective solvent flows around a protein investigated by molecular dynamics simulation.
Translational motions of water molecules in various systems equilibrated at room temperature are thought to be diffusive and nondirectional. We performed molecular dynamics simulations of a protein system and showed that the water molecules collectively move around the protein. The motions of two water molecules, which were about 12 A away from each other, are correlated to each other. Such collective motions of water can be regarded as flows around the protein, and the flows exhibited various coherent patterns: fair currents, vortices, and divergent flows. The patterns were highly fluctuating: a set of patterns changed to a different set of patterns within a time scale of 10 ps. Thus, the water motions observed in a scale of length smaller than 12 A and a time scale shorter than 10 ps were nondiffusive, and the motions above these scales were diffusive, where the flows disappeared. The flows near the protein surface had an orientational propensity to be highly parallel to the protein surface, and this propensity gradually vanished with an increment of distance from the protein surface. The divergent patterns of flows, which frequently emerge during the fluctuations of flows, may temporarily cause solvent drying in the vicinity of solutes. The current simulation is supportive of a molecular interaction mechanism that the fluctuations of hydration structure induce attractive interactions between solutes.
School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
Koji
K
Umezawa
Junichi
J
Higo
Sakurako
S
Shimotakahara
Heisaburo
H
Shindo
D003102:Colloids / Q000737:chemistry*; D003198:Computer Simulation; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D044085:Microfluidics / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D003102:Colloids; D029968:Escherichia coli Proteins; C111946:SirA protein, E coli; D012997:Solvents; D014867:Water