Modern protein force fields behave comparably in molecular dynamics simulations.
Several molecular dynamics simulations were performed on three proteins--bovine apo-calbindin D9K, human interleukin-4 R88Q mutant, and domain IIA of bacillus subtilis glucose permease--with each of the AMBER94, CHARMM22, and OPLS-AA force fields as implemented in CHARMM. Structural and dynamic properties such as solvent-accessible surface area, radius of gyration, deviation from their respective experimental structures, secondary structure, and backbone order parameters are obtained from each of the 2-ns simulations for the purpose of comparing the protein portions of these force fields. For one of the proteins, the interleukin-4 mutant, two independent simulations were performed using the CHARMM22 force field to gauge the sensitivity of some of these properties to the specific trajectory. In general, the force fields tested performed remarkably similarly with differences on the order of those found for the two independent trajectories of interleukin-4 with CHARMM22. When all three proteins are considered together, no force field showed any consistent trend in variations for most of the properties monitored in the study.
Department of Molecular Biology, TPC6, The Scripps Research Institute, 10550 North Torrey-Pines Road, La Jolla, California 92037, USA.
Daniel J
DJ
Price
Charles L
CL
Brooks
D000818:Animals; D001412:Bacillus subtilis / Q000737:chemistry; D002417:Cattle; D003198:Computer Simulation; D006801:Humans; D006860:Hydrogen Bonding; D015847:Interleukin-4 / Q000737:chemistry; D008956:Models, Chemical; D019906:Nuclear Magnetic Resonance, Biomolecular; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins; D015847:Interleukin-4; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C031629:phosphoenolpyruvate-glucose phosphotransferase