title: Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation.
abstract: Molecular dynamics (MD) simulations of 100 ps have been carried out to study the active-site behaviour of the Cu,Zn superoxide dismutase dimer (SOD) in water. The active site of each subunit was monitored during the whole simulation by calculating the distances between functional residues and the catalytic copper. The results indicate that charge orientation is maintained at each active site but the solvent accessibility varies. Analysis of the MD simulation, carried out by using the atomic displacement covariance matrix, has shown a different intra-subunit correlation pattern for the two monomers and the presence of inter-subunit correlations. The MD simulation presented here indicates an asymmetry in the two active sites and different dynamic behaviour of the two SOD subunits.
authors.affiliation: Department of Biology, University of Rome, Tor Vergata, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Falconi
authors.forename: R
authors.initials: R
authors.lastname: Gallimbeni
authors.forename: E
authors.initials: E
authors.lastname: Paci
mesh_terms: D000818:Animals; D001665:Binding Sites; D002417:Cattle; D003198:Computer Simulation; D017076:Computer-Aided Design; D019281:Dimerization; D015195:Drug Design; D008958:Models, Molecular; D015394:Molecular Structure; D011487:Protein Conformation; D012997:Solvents; D013482:Superoxide Dismutase / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water
chemical_list: D012997:Solvents; D014867:Water; D013482:Superoxide Dismutase