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Updated: Jun 13, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
An analysis of 3D solvation structure in biomolecules: application to coiled coil serine and bacteriorhodopsin
Kenji Hirano1, Daisuke Yokogawa, Hirofumi Sato
1Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan.
Abstract:
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.
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