A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

ABSTRACT: Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solva

SUBMITTER: Marinelli F 

PROVIDER: S-EPMC2711228 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature