Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3

摘要: Time-correlated atomic motions were used to characterize protein domain boundaries from coordinates generated by molecular dynamics simulations. A novel application of the dynamical cross-correlation matrix (DCCM) analysis tool was help identify putative domains. In implementing this new approach, several DCCM maps calculated, each using a different coordinate reference frame which and residue constituents could be identified. Cytochrome P450BM-3, Bacillus megaterium, as model in study. The analyses indicated that simulated comprises three distinct regions; contrast, only two domains identified original crystal structure report. Specifically, showed F-G helix region separate entity not part alpha domain, previously designated. simulations demonstrated effected both size shape enzyme active site, possibly control access substrate binding pocket.