Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
2187920 | Journal of Molecular Biology | 2007 | 8 Pages |
Abstract
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 β-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.
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Authors
Sichun Yang, José N. Onuchic, Angel E. García, Herbert Levine,