Folding time predictions from all-atom replica exchange simulations.
We present an approach to predicting the folding time distribution from all-atom replica exchange simulations. This is accomplished by approximating the multidimensional folding process as stochastic reaction-coordinate dynamics for which effective drift velocities and diffusion coefficients are determined from the short-time replica exchange simulations. Our approach is applied to the folding of the second beta-hairpin of the B domain of protein G. The folding time prediction agrees quite well with experimental measurements. Therefore, we have in hand a fast numerical tool for calculating the folding kinetic properties from all-atom "first-principles" models.
Institute for Molecular Pediatric Sciences and Department of Pediatrics, Gordon Center for Integrative Science, The University of Chicago, Chicago, IL 60637, USA.
Sichun
S
Yang
José N
JN
Onuchic
Angel E
AE
García
Herbert
H
Levine
D003198:Computer Simulation; D004058:Diffusion; D019204:GTP-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013696:Temperature; D013997:Time Factors
D019204:GTP-Binding Proteins