title: Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.
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.
authors.affiliation: Faculty of Chemistry, University of Warsaw, L. Pasteura 1, Warsaw 02-093, Poland. mkouza@chem.uw.edu.pl.
authors.forename: Jacek
authors.initials: J
authors.lastname: Wabik
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kmiecik
authors.forename: Dominik
authors.initials: D
authors.lastname: Gront
authors.forename: Maksim
authors.initials: M
authors.lastname: Kouza
authors.forename: Andrzej
authors.initials: A
authors.lastname: Koliński
mesh_terms: D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins