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Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Faculty of Chemistry, University of Warsaw, L. Pasteura 1, Warsaw 02-093, Poland
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Received: 7 March 2013; in revised form: 9 April 2013 / Accepted: 24 April 2013 / Published: 10 May 2013
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.
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.
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.