Solvent site-dipole field accompanying protein-ligand approach process

Abstract

We did a molecular dynamics simulation of a system consisting of a peptide and a protein in explicit solvent to study biomolecular approach process. In the initial structure of simulation, the minimum inter-biomolecular distance was 30 Å. During the simulation, the biomolecules approached and contacted to each other. In spite of diffusive motions of water molecules, the orientations of water molecules tended to order in the inter-biomolecular zone showing coherent spatial patterns (solvent site-dipole field) of the ordering. The degree of ordering was synchronized well with the inter-biomolecular distance. This result strongly suggests that the biomolecules distant to each other can interact via the solvent site-dipole field. The effective range for the coherent ordering (i.e., the interaction range via the solvent site-dipole field) was larger than 20 Å. A bridge-like structure of the solvent orientational ordering connected the two biomolecules. Biological and physicochemical significance of the ordering is discussed. Copyright 2008 Chem-Bio Informatics Society.