title: Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules.
abstract: We propose a framework to describe the cooperative orientational motions of water molecules in liquid water and around solute molecules in water solutions. From molecular dynamics (MD) simulation a new quantity "site-dipole field" is defined as the averaged orientation of water molecules that pass through each spatial position. In the site-dipole field of bulk water we found large vortex-like structures of more than 10 A in size. Such coherent patterns persist more than 300 ps although the orientational memory of individual molecules is quickly lost. A 1-ns MD simulation of systems consisting of two amino acids shows that the fluctuations of site-dipole field of solvent are pinned around the amino acids, resulting in a stable dipole-bridge between side-chains of amino acids. The dipole-bridge is significantly formed even for the side-chain separation of 14 A, which corresponds to five layers of water. The way that dipole-bridge forms sensitively depends on the side-chain orientations and thereby explains the specificity in the solvent-mediated interactions between biomolecules.
authors.affiliation: Biomolecular Engineering Research Institute (BERI), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan. higo@ls.toyaku.ac.jp
authors.forename: J
authors.initials: J
authors.lastname: Higo
authors.forename: M
authors.initials: M
authors.lastname: Sasai
authors.forename: H
authors.initials: H
authors.lastname: Shirai
authors.forename: H
authors.initials: H
authors.lastname: Nakamura
authors.forename: T
authors.initials: T
authors.lastname: Kugimiya
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D003198:Computer Simulation; D008958:Models, Molecular; D015394:Molecular Structure; D010316:Particle Size; D014867:Water / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D014867:Water