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

Int J Mol Sci. 2013 May 10;14(5):9893-905. doi: 10.3390/ijms14059893.

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 strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Molecular Dynamics Simulation*
  • Protein Folding
  • Protein Structure, Secondary
  • Proteins / chemistry*

Substances

  • Proteins