Molecular dynamics simulation of hydration in myoglobin.
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 continuously 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.
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Department of Biochemistry, University of New Mexico, Albuquerque 87545, USA.
Schoenborn
B P
BP
D003198:Computer Simulation; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry*; D009502:Neutrons; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D009211:Myoglobin; C018013:carboxymyoglobin; D014867:Water