Non-Markovian Configurational Diffusion and Reaction Coordinates for Protein Folding

Abstract

The non-Markovian nature of polymer motions is accounted for in folding kinetics, using frequency-dependent friction. Folding, like many other problems in the physics of disordered systems, involves barrier crossing on a correlated energy landscape. A variational transition state theory (VTST) that reduces to the usual Bryngelson-Wolynes Kramers approach when the non-Markovian aspects are neglected is used to obtain the rate, without making any assumptions regarding the size of the barrier, or the memory time of the friction. The transformation to collective variables dependent on the dynamics of the system allows the theory to address the controversial issue of what are ``good'' reaction coordinates for folding.

9 pages RevTeX, 3 eps-figures included, submitted to PRL

References in corpus (4)

• Diffusive Dynamics of the Reaction Coordinate for Protein Folding Funnels
• Viscosity Dependence of the Folding Rates of Proteins
• Aging on Parisi's tree
• Statistical mechanics of a correlated energy landscape model for protein folding funnels

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