title: Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.
abstract: It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution.
authors.affiliation: Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Michal
authors.initials: M
authors.lastname: Jamroz
authors.affiliation: IRB - BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine , Josep Samitier 1-5, Barcelona 08028, Spain.|Department of Biochemistry, Universitat of Barcelona , Gran Via de les Corts Catalanes, 585 08007 Barcelona, Spain.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
authors.affiliation: Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kolinski
authors.affiliation: Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kmiecik