title: Effective stochastic dynamics on a protein folding energy landscape.
abstract: We present an approach to protein folding kinetics using stochastic reaction-coordinate dynamics, in which the effective drift velocities and diffusion coefficients are determined from microscopic simulation data. The resultant Langevin equation can then be used to directly simulate the folding process. Here, we test this approach by applying it to a toy two-state dynamical system and to a funnellike structure-based (Go-type) model. The folding time predictions agree very well with full simulation results. Therefore, we have in hand a fast numerical tool for calculating the folding kinetic properties, even when full simulations are not feasible. In addition, the local drift and diffusion coefficients provide an alternative way to compute the free energy profile in cases where only local sampling can be achieved.
authors.affiliation: Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California 92093-0374, USA. syang@physics.ucsd.edu
authors.forename: Sichun
authors.initials: S
authors.lastname: Yang
authors.forename: José N
authors.initials: JN
authors.lastname: Onuchic
authors.forename: Herbert
authors.initials: H
authors.lastname: Levine
mesh_terms: D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D004058:Diffusion; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D015233:Models, Statistical; D008968:Molecular Conformation; D016011:Normal Distribution; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013269:Stochastic Processes; D013816:Thermodynamics
chemical_list: D011506:Proteins