Open AccessMolecular dynamics simulation of hydration in myoglobin
Author(s) -
Wei Gu,
Benno P. Schoenborn
Publication year - 1995
Language(s) - English
Resource type - Reports
DOI - 10.2172/104441
Subject(s) - myoglobin , molecular dynamics , neutron diffraction , molecule , hydrogen bond , chemistry , solvent , neutron , crystallography , rotational dynamics , bound water , chemical physics , materials science , computational chemistry , physics , crystal structure , organic chemistry , quantum mechanics
This study was carried out to evaluate the stability of the 89 bound water molecules that were observed in the neutron diffraction study of CO myoglobin. The myoglobin structure derived from the neutron analysis was used as the starting point in the molecular dynamics simulation using the software package CHARMM. After salvation of the protein, energy minimization and equilibration of the system, 50 pico seconds of Newtonian dynamics was performed. This data showed that only 4 water molecules are continously bound during the length of this simulation while the other solvent molecules exhibit considerable mobility and are breaking and reforming hydrogen bonds with the protein. At any instant during the simulation, 73 of the hydration sites observed in the neutron structure are occupied by water