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arXiv · 1308.2388

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

Jacek Wabik·Sebastian Kmiecik·Dominik Gront·Maksim Kouza·Andrzej Kolinski
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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.

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Jacek Wabik, Sebastian Kmiecik, Dominik Gront, Maksim Kouza, Andrzej Kolinski. 2013-08-11. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics. https://doi.org/10.3390/ijms14059893

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