Diffusive model of protein folding dynamics with Kramers turnover in rate

Phys Rev Lett. 2006 Jun 9;96(22):228104. doi: 10.1103/PhysRevLett.96.228104. Epub 2006 Jun 7.

Abstract

We study the folding kinetics of a three-helix bundle protein using a coarse polymer model. The folding dynamics can be accurately represented by one-dimensional diffusion along a reaction coordinate selected to capture the transition state. By varying the solvent friction, we show that position-dependent diffusion coefficients are determined by microscopic transitions on a rough energy landscape. A maximum in the folding rate at intermediate friction is explained by "Kramers turnover" in these microscopic dynamics that modulates the rate via the diffusion coefficient; overall folding remains diffusive even close to zero friction. For water friction, we find that the "attempt frequency" (or "speed limit") in a Kramers model of folding is about 2 micros-1, with an activation barrier of about 2kBT, and a folding transition path duration of approximately equal to 100 ns, 2 orders of magnitude less than the folding time of approximately equal to 10 micros.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Diffusion
  • Kinetics
  • Models, Chemical*
  • Protein Conformation
  • Protein Folding*
  • Proteins / chemistry*
  • Thermodynamics

Substances

  • Proteins