Diffusive dynamics of protein folding studied by molecular dynamics simulations of an off-lattice model
- 12 July 2002
- journal article
- Published by American Physical Society (APS) in Physical Review E
- Vol. 66 (1) , 011905
- https://doi.org/10.1103/physreve.66.011905
Abstract
We report the results of a molecular dynamics study on the kinetic properties of a small off-lattice model of proteins. The model consists of a linear chain of monomers interacting via a number of potentials. These include hydrophobic, bond-angle, and torsion potentials. The ground-state conformation of the studied model is a beta-sheet motif. Molecular dynamics simulations focused on the time evolution of the reaction coordinate measuring the similarity of a given conformation with the native state. Folding time for the studied model is calculated following the diffusive-rate formula of Bryngelson and Wolynes [J. Phys. Chem. 93, 6902 (1989)] by using a computed separately configurational diffusion coefficient. Comparison of the folding time with the mean-first passage time obtained directly from folding simulations shows that the approximation depicting the dynamics of the reaction coordinate in protein folding as a diffusive motion on a free-energy landscape is quantitatively correct for the studied model.Keywords
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