An analysis of 3D solvation structure in biomolecules: application to coiled coil serine and bacteriorhodopsin.
Three-dimensional (3D) solvation structure around coiled coil serine (Coil-Ser) and inner 3D hydration structure in bacteriorhodopsin (bR) were studied using a recently developed method named multicenter molecular Ornstein-Zernike equation (MC-MOZ) theory. In addition, a procedure for analyzing the 3D solvent distribution was proposed. The method enables us to calculate the coordination number of solvent water as well as the strength of hydrogen bonding between the water molecule and the protein. The results for Coil-Ser and bR showed very good agreement with the experimental observations.
Hirano
Kenji
K
Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan.
Yokogawa
Daisuke
D
Sato
Hirofumi
H
Sakaki
Shigeyoshi
S
D001436:Bacteriorhodopsins / Q000737:chemistry*; D006860:Hydrogen Bonding; D012694:Serine / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D012997:Solvents; D014867:Water; D012694:Serine; D001436:Bacteriorhodopsins