Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study

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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 (γ). 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/γ 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 ∼ γ−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. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1432–1436, 2003

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