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Molecular dynamics simulation of hydration in myoglobin
Author(s) -
Gu Wei,
Schoenborn Benno P.
Publication year - 1995
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340220104
Subject(s) - myoglobin , molecular dynamics , solvation , neutron diffraction , molecule , hydrogen bond , chemistry , rotational dynamics , chemical physics , solvent , neutron , bound water , materials science , crystallography , computational chemistry , physics , crystal structure , organic chemistry , nuclear physics
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 solvation of the protein, energy minimization and equilibration of the system, 50 ps 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. © 1995 Wiley‐Liss, Inc.