Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model (Articolo in rivista)

Type
Label
  • Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model (Articolo in rivista) (literal)
Anno
  • 2006-01-01T00:00:00+01:00 (literal)
Alternative label
  • Chang, CE; Shen, T; Trylska, J; Tozzini, V; McCammon, JA (2006)
    Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model
    in Biophysical journal (Print)
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Chang, CE; Shen, T; Trylska, J; Tozzini, V; McCammon, JA (literal)
Pagina inizio
  • 3880 (literal)
Pagina fine
  • 3885 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume
  • 90 (literal)
Rivista
Note
  • ISI Web of Science (WOS) (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA 92093 USA; Univ Calif San Diego, Ctr Theoret Biol Phys, La Jolla, CA 92093 USA; Univ Calif San Diego, Howard Hughes Med Inst, La Jolla, CA 92093 USA; Univ Calif San Diego, Dept Pharmacol, La Jolla, CA 92093 USA; Warsaw Univ, Interdisciplinary Ctr Math & Computat Modelling, Warsaw, Poland; NEST Scuola Normale Super, Pisa, Italy (literal)
Titolo
  • Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model (literal)
Abstract
  • 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. (literal)
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