Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data.

ABSTRACT: Protein dynamics on the atomic level and on the microsecond timescale has recently become accessible from both computation and experiment. To validate molecular dynamics (MD) at the submicrosecond timescale against experiment we present microsecond MD simulations in 10 different force-field configurations for two globular proteins, ubiquitin and the gb3 domain of protein G, for which extensive NMR data is available. We find that the reproduction of the measured NMR data strongly depends on the chosen force field and electrostatics treatment. Generally, particle-mesh Ewald outperforms cut-off and reaction-field approaches. A comparison to measured J-couplings across hydrogen bonds suggests that there is room for improvement in the force-field description of hydrogen bonds in most modern for

SUBMITTER: Lange OF 

PROVIDER: S-EPMC2905107 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature