Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 14, Issue 5, Pages 9893-9905Publisher
MDPI
DOI: 10.3390/ijms14059893
Keywords
CABS; replica-exchange molecular dynamics; multiscale modeling; protein folding
Funding
- Foundation for Polish Science TEAM project [TEAM/2011-7/6]
- Interdisciplinary Center for Mathematical and Computational Modeling (ICM) of the University of Warsaw [G43-9]
- European Regional Development Fund
- Polish National Science Center [NN301071140]
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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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