title: Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion.
abstract: Theoretical models have often modeled protein folding dynamics as diffusion on a low-dimensional free energy surface, a remarkable simplification. However, the accuracy of such an approximation and the number of dimensions required were not clear. For all-atom folding simulations of ten small proteins in explicit solvent we show that the folding dynamics can indeed be accurately described as diffusion on just a single coordinate, the fraction of native contacts (Q). The diffusion models reproduce both folding rates, and finer details such as transition-path durations and diffusive propagators. The Q-averaged diffusion coefficients decrease with chain length, as anticipated from energy landscape theory. Although the Q-diffusion model does not capture transition-path durations for the protein NuG2, we show that this can be accomplished by designing an improved coordinate Qopt. Overall, one-dimensional diffusion on a suitable coordinate turns out to be a remarkably faithful model for the dynamics of the proteins considered.
authors.affiliation: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States.
authors.forename: Wenwei
authors.initials: W
authors.lastname: Zheng
authors.affiliation: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States.
authors.forename: Robert B
authors.initials: RB
authors.lastname: Best
mesh_terms: D004058:Diffusion; D008956:Models, Chemical; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins