title: HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state.
abstract: We report unrestrained, all-atom molecular dynamics simulations of HIV-1 protease (HIV-PR) with a continuum solvent model that reproducibly sample closing of the active site flaps following manual placement of a cyclic urea inhibitor into the substrate binding site of the open protease. The open form was obtained from the unbound, semi-open HIV-PR crystal structure, which we recently reported (Hornak, V.; et al. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 915-920.) to have spontaneously opened during unrestrained dynamics. In those simulations, the transiently open flaps always returned to the semi-open form that is observed in all crystal structures of the free protease. Here, we show that manual docking of the inhibitor reproducibly induces spontaneous conversion to the closed form as seen in all inhibitor-bound HIV-PR crystal structures. These simulations reproduced not only the greater degree of flap closure, but also the striking difference in flap "handedness" between bound and free enzyme. In most of the simulations, the final structures were highly accurate. Root-mean-square deviations (RMSD) from the crystal structure of the complex were approximately 1.5 A (averaged over the last 100 ps) for the inhibitor and each flap despite initial RMSD of 2-5 A for the inhibitors and 6-11 A for the flaps. Key hydrogen bonds were formed between the flap tips and between flaps and inhibitor that match those seen in the crystal structure. The results demonstrate that all-atom simulations have the ability to significantly improve poorly docked ligand conformations and reproduce large-scale receptor conformational changes that occur upon binding.
authors.affiliation: Department of Chemistry, Department of Applied Mathematics and Statistics, and Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794, USA.
authors.forename: Viktor
authors.initials: V
authors.lastname: Hornak
authors.forename: Asim
authors.initials: A
authors.lastname: Okur
authors.forename: Robert C
authors.initials: RC
authors.lastname: Rizzo
authors.forename: Carlos
authors.initials: C
authors.lastname: Simmerling
mesh_terms: D001381:Azepines / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D016333:HIV Protease / Q000737:chemistry* / Q000378:metabolism; D017320:HIV Protease Inhibitors / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D015497:HIV-1 / Q000201:enzymology*; D008956:Models, Chemical; D008958:Models, Molecular; D017510:Protein Folding; D014508:Urea / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D014867:Water / Q000737:chemistry / Q000378:metabolism
chemical_list: D001381:Azepines; D017320:HIV Protease Inhibitors; C104713:XK 263; D014867:Water; D014508:Urea; D016333:HIV Protease