Solvent Viscosity Dependence of the Folding Rate of a Small Protein: Distributed Computing Study.

Bojan Zagrovic and Vijay S. Pande. Journal of Computational Chemistry (2003)

ABSTRACT: By using distributed computing techniques and a supercluster of more than 20,000 processors we simulated folding of a 20-residue Trp Cage miniprotein in atomistic detail with implicit GB/SA solvent at a variety of solvent viscosities (g). This allowed us to analyze the dependence of folding rates on viscosity. In particular, we focused on the low-viscosity regime (values below the viscosity of water). In accordance with Kramers’ theory, we observe approximately linear dependence of the folding rate on 1/g for values from 1-10^(-1) that of water viscosity. However, for the regime between 10^(-4) – 10^(-1) that of water viscosity we observe power-law dependence of the form k ~ g^(-1/5). These results suggest that estimating folding rates from molecular simulations run at low viscosity under the assumption of linear dependence of rate on inverse viscosity may lead to erroneous results.