title: Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations.
abstract: We show that our accelerated molecular-dynamics (MD) approach can extend the time scale in all-atom MD simulations of biopolymers. We also show that this technique allows for the kinetic rate information to be recaptured. In deducing the kinetic rates, the relationship between the local energetic roughness of the potential-energy landscape and the effective diffusion coefficient is established. These are demonstrated on a very slow but important biomolecular process: the dynamics of cis-trans-isomerization of Ser-Pro motifs. We do not only recapture the slow kinetic rates, which is difficult in traditional MD, but also obtain the underlying roughness of the energy landscape of proteins at atomistic resolution.
authors.affiliation: Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, 92093-0365, USA. dhamelbe@mccammon.ucsd.edu
authors.forename: Donald
authors.initials: D
authors.lastname: Hamelberg
authors.forename: Tongye
authors.initials: T
authors.lastname: Shen
authors.forename: J
authors.initials: J
authors.lastname: Andrew McCammon
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D004058:Diffusion; D007536:Isomerism; D007700:Kinetics; D011392:Proline / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D012694:Serine / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D001704:Biopolymers; D012694:Serine; D011392:Proline