Superoxide dismutase: Fluctuations in the structure and solvation of the active site channel studied by molecular dynamics simulation
- 1 December 1989
- journal article
- research article
- Published by Wiley in Biopolymers
- Vol. 28 (12), 2085-2096
- https://doi.org/10.1002/bip.360281205
Abstract
The molecular dynamics (MD) simulation of superoxide dismutase (SOD) in water is carried out for a total of 23 ps. The simulation system is a 26 Å sphere centered at the active site of SOD, including 1602 atoms from SOD and 1761 water molecules. There is no gross deviation from the x-ray structure for the average MD structure. The structure and potential fluctuations around the active site are examined. The results provide new insight to the interactions between SOD and its substrate superoxide.This publication has 18 references indexed in Scilit:
- Simulation of the diffusion‐controlled reaction between superoxide and superoxide dismutase. II. Detailed modelsBiopolymers, 1988
- Electrostatic control of the rate-determining step of the copper, zinc, superoxide dismutase catalytic reactionBiochemistry, 1987
- Dynamic Simulations of Oxygen Binding to MyoglobinAnnals of the New York Academy of Sciences, 1986
- Simulation of the diffusion‐controlled reaction between superoxide and superoxide dismutase. I. Simple modelsBiopolymers, 1985
- Steady-state kinetic studies of superoxide dismutases: properties of the iron containing protein from Escherichia coliJournal of the American Chemical Society, 1985
- Dynamics of substrate binding to copper zinc superoxide dismutaseThe Journal of Physical Chemistry, 1985
- Determination and analysis of the 2 Å structure of copper, zinc superoxide dismutaseJournal of Molecular Biology, 1982
- Dynamics of ligand binding to heme proteinsJournal of Molecular Biology, 1979
- The protein data bank: A computer-based archival file for macromolecular structuresJournal of Molecular Biology, 1977
- The interpretation of protein structures: Estimation of static accessibilityJournal of Molecular Biology, 1971