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

@article{citeulike:1487791, abstract = {Time-correlated atomic motions were used to characterize protein domain boundaries from atomic coordinates generated by molecular dynamics simulations. A novel application of the dynamical cross-correlation matrix (DCCM) analysis tool was used to help identify putative protein domains. In implementing this new approach, several DCCM maps were calculated, each using a different coordinate reference frame from which protein domain boundaries and protein domain residue constituents could be identified. Cytochrome P450BM-3, from Bacillus megaterium, was used as the model protein in this study. The analyses indicated that the simulated protein comprises three distinct domain regions; in contrast, only two protein domains were identified in the original crystal structure report. Specifically, the DCCM analyses showed that the F-G helix region was a separate domain entity and not a part of the alpha domain, as previously designated. The simulations demonstrated that the domain motions of the F-G helix region effected both the size and shape of the enzyme active site, and that the dynamics of the F-G helix domain could possibly control access of substrate to the binding pocket.}, author = {Arnold, G. E. and Ornstein, R. L. }, citeulike-article-id = {1487791}, journal = {Biophys. J.}, keywords = {correlated\_motions, distance\_matrices, md\_simulation, protein\_sequence}, month = {September}, number = {3}, pages = {1147--1159}, posted-at = {2007-07-26 02:46:16}, priority = {2}, title = {Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3.}, url = {http://www.biophysj.org/cgi/content/abstract/73/3/1147}, volume = {73}, year = {1997} }

TY - JOUR ID - citeulike:1487791 L3 - citeulike-article-id:1487791 TI - Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3. JF - Biophys. J. VL - 73 IS - 3 SP - 1147 EP - 1159 N2 - Time-correlated atomic motions were used to characterize protein domain boundaries from atomic coordinates generated by molecular dynamics simulations. A novel application of the dynamical cross-correlation matrix (DCCM) analysis tool was used to help identify putative protein domains. In implementing this new approach, several DCCM maps were calculated, each using a different coordinate reference frame from which protein domain boundaries and protein domain residue constituents could be identified. Cytochrome P450BM-3, from Bacillus megaterium, was used as the model protein in this study. The analyses indicated that the simulated protein comprises three distinct domain regions; in contrast, only two protein domains were identified in the original crystal structure report. Specifically, the DCCM analyses showed that the F-G helix region was a separate domain entity and not a part of the alpha domain, as previously designated. The simulations demonstrated that the domain motions of the F-G helix region effected both the size and shape of the enzyme active site, and that the dynamics of the F-G helix domain could possibly control access of substrate to the binding pocket. KW - correlated_motions KW - distance_matrices KW - md_simulation KW - protein_sequence AU - Arnold, GE AU - Ornstein, RL PY - 1997/09/01/ UR - http://www.biophysj.org/cgi/content/abstract/73/3/1147 ER -