biostudies-literatureUnknown107(11)Abrams CFWe 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 dynaProceedings of the National Academy of Sciences of the United States of America4961-6https://www.ebi.ac.uk/biostudies/studies/S-EPMC2841907biostudies-literatureLarge-scale conformational sampling of proteins using temperature-accelerated molecular dynamics.PMC2841907Abrams CFVanden-Eijnden EfalseLarge-scale conformational sampling of proteins using temperature-accelerated molecular dynamics.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 dyna2010-01-01T00:00:00Z2010 Mar2025-04-22T20:17:12.532Z2019-03-27T00:29:33ZS-EPMC28419072019478510.1073/pnas.0914540107