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We describe a combination of all-atom simulations with CABS, awell-established coarse-grained protein modeling tool, into a single multiscaleprotocol. The simulation method has been tested on the C-terminal beta hairpinof protein G, a model system of protein folding. After reconstructing atomisticdetails, conformations derived from the CABS simulation were subjected toreplica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sbforce fields in explicit solvent. Such a combination accelerates systemconvergence several times in comparison with all-atom simulations starting fromthe extended chain conformation, demonstrated by the analysis of meltingcurves, the number of native-like conformations as a function of time andsecondary structure propagation. The results strongly suggest that the proposedmultiscale method could be an efficient and accurate tool for high-resolutionstudies of protein folding dynamics in larger systems.

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