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Folding rates and low-entropy-loss routes of two-state proteins
Authors:Weikl Thomas R  Dill Ken A
Institution:Department of Pharmaceutical Chemistry, University of California, Box 2240, San Francisco, CA 94143-2240, USA. thomas.weikl@mpikg-golm.mpg.de
Abstract:We develop a simple model for computing the rates and routes of folding of two-state proteins from the contact maps of their native structures. The model is based on the graph-theoretical concept of effective contact order (ECO). The model predicts that proteins fold by "zipping up" in a sequence of small-loop-closure events, depending on the native chain fold. Using a simple equation, with a few physical rate parameters, we obtain a good correlation with the folding rates of 24 two-state folding proteins. The model rationalizes data from Phi-value analysis that have been interpreted in terms of delocalized or polarized transition states. This model indicates how much of protein folding may take place in parallel, not along a single reaction coordinate or with a single transition state.
Keywords:protein folding kinetics  native state topology  effective contact order  loop-closure entropy  folding mechanism
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