Large vortex-like structure of dipole field in computer models of liquid water and dipole-bridge between biomolecules.
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.
Higo
J
J
Biomolecular Engineering Research Institute (BERI), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan. higo@ls.toyaku.ac.jp
Sasai
M
M
Shirai
H
H
Nakamura
H
H
Kugimiya
T
T
D000596:Amino Acids / Q000737:chemistry*; D003198:Computer Simulation; D008958:Models, Molecular; D015394:Molecular Structure; D010316:Particle Size; D014867:Water / Q000737:chemistry*
D000596:Amino Acids; D014867:Water