Solvent flow patterns fluctuating largely around a protein and correlation with solvent density fluctuations: A molecular dynamics study.
The authors demonstrated recently that translational motions of water molecules around a protein are collective in a short (approximately 10 ps) time scale. The patterns can be regarded as "flows" of three specific patterns-fair current, drying/wetting, and vortex-although the patterns disappear eventually over a longer time scale. Our earlier study suggested a hypothesis that the solvent flows are related to the intersolute interaction. However, the connection between the flows and the interaction was left unexamined. The current simulation study analyzed flow patterns around a protein, human lysozyme, revealing that the drying flows correlate with decreased solvent density. The decrease in solvent density has been known to enhance intersolute attractive interactions. The drying flows can therefore induce the intersolute attractive interactions. Human lysozyme has a catalytic cleft on the protein surface. Large fluctuations of drying/wetting patterns were observed only around the cleft because the large fluctuations occur selectively around convex residues on the protein surface, to which large side-chain fluctuations of the protein are also assigned. The emergence of fair current patterns correlated well with the emergence of drying/wetting patterns. This correlation was found only near the protein surface. Near the protein surface, the vortex flow plane of rotation tended to be parallel to the surface. Current study suggests that the drying flows enhance the substrate approach to the catalytic cleft.
Umezawa
Koji
K
Laboratory of Protein Informatics, Graduate School of Frontier Biosciences, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
Morikawa
Ryota
R
Nakamura
Haruki
H
Higo
Junichi
J
D006801:Humans; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties; D014867:Water / Q000737:chemistry*
D011506:Proteins; D012997:Solvents; D014867:Water; D009113:Muramidase