A molecular dynamics study of solvent behavior around a protein.

Abstract

The solvent structure and behavior around a protein were examined by analyzing a trajectory of molecular dynamics simulation of the trp-holorepressor in a periodic box of water. The calculated self diffusion coefficient indicated that the solvent within 10 A of the protein had lower mobility. Examination of the solvent diffusion around different atoms of different kinds of residues showed no general tendency. This fact suggested that the solvent mobility is not influenced significantly by the kind of the atom or residue they solvated. Distribution analysis around the protein revealed two peaks of water oxygen: a sharp one at 2.8 A around polar and charged atoms and a broad one at approximately 3.4 A around apolar atoms. The former was stabilized by water-protein hydrogen bonds, and the latter was stabilized by water-water hydrogen bonds, suggesting the existence of a hydrophobic shell. An analysis of protein atom-water radial distribution functions confirmed these shell structures around polar or charged atoms and apolar ones.