Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study.
Effects of the macromolecular solute on the translational mobility of surrounding solvent water, and Na+ and Cl- ions are investigated by molecular dynamics (MD) simulation. Using MD trajectories of myoglobin and d(C5T5) . d(G5A5) DNA decamer of high quality and length, we determine the average diffusion coefficients for all solvent species as a function of distance from the closest solute atom. We examine solvent mobility in the directions parallel and perpendicular to the solute surface and in proximity to three different classes of solute atoms (oxygens, nitrogens, and carbons). The nature and the magnitude of the solute effects on water diffusion appear to be very similar for protein and DNA decamer. The overall diffusion rate at the interface is lower than in the bulk. The rate is higher than the average in the direction parallel to the solute surface, and lower in the direction normal to the surface, up to 15 A away from the solute. The rate is also lower in the solvation shells of the macromolecules, producing characteristic depressions in the radial profiles of the diffusion coefficient that can be correlated with peaks in the corresponding radial distribution functions. The magnitude of these depressions is small compared to the overall change in solvent mobility at the interface. Similar features are observed in the radial profiles of the diffusion coefficient of sodium and chlorine ions as well.
Makarov
V A
VA
Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.
Feig
M
M
Andrews
B K
BK
Pettitt
B M
BM
D055592:Biophysical Phenomena; D001703:Biophysics; D004058:Diffusion; D007477:Ions; D046911:Macromolecular Substances; D008956:Models, Chemical; D012996:Solutions; D012997:Solvents; D055672:Static Electricity; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D007477:Ions; D046911:Macromolecular Substances; D012996:Solutions; D012997:Solvents; D014867:Water