Molecular dynamics and protein function.
A fundamental appreciation for how biological macromolecules work requires knowledge of structure and dynamics. Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled with improvements in methodology makes this an exciting time for the application of simulation to structural biology. In this Perspective we survey two areas, protein folding and enzymatic catalysis, in which simulations have contributed to a general understanding of mechanism. We also describe results for the F(1) ATPase molecular motor and the Src family of signaling proteins as examples of applications of simulations to specific biological systems.
Karplus
M
M
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA. marci@tammy.harvard.edu
Kuriyan
J
J
D000818:Animals; D000970:Antineoplastic Agents / Q000494:pharmacology; D001549:Benzamides; D001703:Biophysics / Q000379:methods*; D002384:Catalysis; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004798:Enzymes / Q000737:chemistry; D006801:Humans; D006859:Hydrogen / Q000737:chemistry; D000068877:Imatinib Mesylate; D008958:Models, Molecular; D009010:Monte Carlo Method; D010100:Oxygen / Q000737:chemistry; D010879:Piperazines / Q000494:pharmacology; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016315:Proto-Oncogene Proteins c-abl / Q000737:chemistry; D006180:Proton-Translocating ATPases / Q000737:chemistry; D011743:Pyrimidines / Q000494:pharmacology; D012984:Software; D013816:Thermodynamics; D013997:Time Factors; D019061:src-Family Kinases / Q000737:chemistry
D000970:Antineoplastic Agents; D001549:Benzamides; D004798:Enzymes; D010879:Piperazines; D011506:Proteins; D011743:Pyrimidines; D006859:Hydrogen; D000068877:Imatinib Mesylate; D016315:Proto-Oncogene Proteins c-abl; D019061:src-Family Kinases; D006180:Proton-Translocating ATPases; D010100:Oxygen