Falconi M, Gallimbeni R, Paci E
Department of Biology, University of Rome, Tor Vergata, Italy.
J Comput Aided Mol Des. 1996 Oct;10(5):490-8. doi: 10.1007/BF00124478.
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.
已进行了100皮秒的分子动力学（MD）模拟，以研究铜锌超氧化物歧化酶二聚体（SOD）在水中的活性位点行为。在整个模拟过程中，通过计算功能残基与催化铜之间的距离来监测每个亚基的活性位点。结果表明，每个活性位点的电荷取向保持不变，但溶剂可及性有所不同。使用原子位移协方差矩阵进行的MD模拟分析表明，两个单体的亚基内相关模式不同，且存在亚基间相关性。此处呈现的MD模拟表明两个活性位点存在不对称性，且两个SOD亚基的动态行为不同。
