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 mo lecular dynamics (MD) simulation. Using MD trajectories of myoglobin a nd d(C5T5).d(G(5)A(5)) DNA decamer of high quality and length, we dete rmine 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 su rface and in proximity to three different classes of solute atoms (oxy gens, nitrogens, and carbons). The nature and the magnitude of the sol ute effects on water diffusion appear to be very similar for protein a nd DNA decamer. The overall diffusion rate at the interface is lower t han 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 t he surface, up to 15 Angstrom away from the solute. The rate is also l ower in the solvation shells of the macromolecules, producing characte ristic depressions in the radial profiles of the diffusion coefficient that can be correlated with peaks in the corresponding radial distrib ution functions. The magnitude of these depressions is small compared to the overall change in solvent mobility at the interface. Similar fe atures are observed in the radial profiles of the diffusion coefficien t of sodium and chlorine ions as well.