Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model.
The internal motions of proteins may serve as a "gate" in some systems, which controls ligand-protein association. This study applies Brownian dynamics simulations in a coarse-grained model to study the gated association rate constants of HIV-1 proteases and drugs. The computed gated association rate constants of three protease mutants, G48V/V82A/I84V/L90M, G48V, and L90M with three drugs, amprenavir, indinavir, and saquinavir, yield good agreements with experiments. The work shows that the flap dynamics leads to "slow gating". The simulations suggest that the flap flexibility and the opening frequency of the wild-type, the G48V and L90M mutants are similar, but the flaps of the variant G48V/V82A/I84V/L90M open less frequently, resulting in a lower gated rate constant. The developed methodology is fast and provides an efficient way to predict the gated association rate constants for various protease mutants and ligands.
Chang
Chia-En
CE
Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA, USA. cchang@mccammon.ucsd.edu
Shen
Tongye
T
Trylska
Joanna
J
Tozzini
Valentina
V
McCammon
J Andrew
JA
D002219:Carbamates / Q000737:chemistry; D003198:Computer Simulation; D004789:Enzyme Activation; D005663:Furans; D016333:HIV Protease / Q000737:chemistry* / Q000235:genetics; D017320:HIV Protease Inhibitors / Q000737:chemistry*; D019469:Indinavir / Q000494:pharmacology; D008024:Ligands; D008958:Models, Molecular; D009154:Mutation; D019258:Saquinavir / Q000737:chemistry; D013449:Sulfonamides / Q000737:chemistry
D002219:Carbamates; D005663:Furans; D017320:HIV Protease Inhibitors; D008024:Ligands; D013449:Sulfonamides; C095108:amprenavir; D019469:Indinavir; D016333:HIV Protease; D019258:Saquinavir