Int. J. Mol. Sci. 2013, 14(5), 9893-9905; doi:10.3390/ijms14059893
Article

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

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Received: 7 March 2013; in revised form: 9 April 2013 / Accepted: 24 April 2013 / Published: 10 May 2013
(This article belongs to the Special Issue Protein Folding 2013)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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.
Keywords: CABS; replica-exchange molecular dynamics; multiscale modeling; protein folding
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MDPI and ACS Style

Wabik, J.; Kmiecik, S.; Gront, D.; Kouza, M.; Koliński, A. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics. Int. J. Mol. Sci. 2013, 14, 9893-9905.

AMA Style

Wabik J, Kmiecik S, Gront D, Kouza M, Koliński A. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics. International Journal of Molecular Sciences. 2013; 14(5):9893-9905.

Chicago/Turabian Style

Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej. 2013. "Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics." Int. J. Mol. Sci. 14, no. 5: 9893-9905.

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