Diffusive dynamics of protein folding studied by molecular dynamics simulations of an off-lattice model.
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.
Baumketner
A
A
Faculty of Science, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan. andrij@icmp.lviv.ua
Hiwatari
Y
Y
D055598:Chemical Phenomena; D002627:Chemistry, Physical; D004058:Diffusion; D007700:Kinetics; D008958:Models, Molecular; D017510:Protein Folding; D013269:Stochastic Processes; D013816:Thermodynamics