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• W2000545830 abstract "We show how to apply the method of temperature-accelerated molecular dynamics (TAMD) in collective variables [Maragliano L, Vanden-Eijnden E (2006) Chem Phys Lett 426:168–175] to sample the conformational space of multidomain proteins in all-atom, explicitly solvated molecular dynamics simulations. The method allows the system to hyperthermally explore the free-energy surface in a set of collective variables computed at the physical temperature. As collective variables, we pick Cartesian coordinates of centers of contiguous subdomains. The method is applied to the GroEL subunit, a 55-kDa, three-domain protein, and HIV-1 gp120. For GroEL, the method induces in about 40 ns conformational changes that recapitulate the t → r ′′ transition and are not observed in unaccelerated molecular dynamics: The apical domain is displaced by 30 Å, with a twist of 90° relative to the equatorial domain, and the root-mean-squared deviation relative to the r ′′ conformer is reduced from 13 to 5 Å, representing fairly high predictive capability. For gp120, the method predicts both counterrotation of inner and outer domains and disruption of the so-called bridging sheet. In particular, TAMD on gp120 initially in the CD4-bound conformation visits conformations that deviate by 3.6 Å from the gp120 conformer in complex with antibody F105, again reflecting good predictive capability. TAMD generates plausible all-atom models of the so-far structurally uncharacterized unliganded conformation of HIV-1 gp120, which may prove useful in the development of inhibitors and immunogens. The fictitious temperature employed also gives a rough estimate of 10 kcal/mol for the free-energy barrier between conformers in both cases." @default.
• W2000545830 created "2016-06-24" @default.
• W2000545830 creator A5038508476 @default.
• W2000545830 creator A5044193587 @default.
• W2000545830 date "2010-03-01" @default.
• W2000545830 modified "2023-10-17" @default.
• W2000545830 title "Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics" @default.
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• W2000545830 doi "https://doi.org/10.1073/pnas.0914540107" @default.
• W2000545830 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2841907" @default.
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