Molecular dynamics simulation of hydration in myoglobin
- Univ. of New Mexico, Albuquerque, NM (United States). Dept. of Biochemistry
- Los Alamos National Lab., NM (United States). Life Science Division
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. These 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.
- Sponsoring Organization:
- USDOE
- OSTI ID:
- 136716
- Journal Information:
- Proteins, Journal Name: Proteins Vol. 22; ISSN 0887-3585; ISSN PSFGEY
- Country of Publication:
- United States
- Language:
- English
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