Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.

ABSTRACT: We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results stron

SUBMITTER: Wabik J 

PROVIDER: S-EPMC3676820 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature