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Protein Science (2004), 13:822-829. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Cooperativity in two-state protein folding kinetics

Thomas R. Weikl1,2, Matteo Palassini1,3 and Ken A. Dill1

1 Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
2 Max-Planck-Institut für Kolloid- und Grenzflächenforschung, 14424 Potsdam, Germany

(RECEIVED September 4, 2003; FINAL REVISION October 27, 2003; ACCEPTED October 27, 2003)



Abstract

We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure events that can be inferred from native structures. For CI2, the src SH3 domain, TNfn3, and protein L, the model reproduces two-state kinetics, and it predicts well the average {Phi}-values for secondary structures. The barrier to folding is the formation of predominantly local structures such as helices and hairpins, which are needed to bring nonlocal pairs of amino acids into contact.

Keywords: protein folding kinetics; two-state folding; folding cooperativity; {Phi}-value analysis; effective contact order; loop-closure entropy; master equation

Reprint requests to: Thomas Weikl, Max-Planck-Institut für Kolloid- und Grenzflächenforschung, 14424 Potsdam, Germany; e-mail: Thomas. Weikl{at}mpikg-golm.mpg.de; fax: +49-331-567-9612.

3 Present address: Laboratoire de Physique Théorique et Modéles Statistiques, Bêt 100, Universite Paris-Sud, 91405 Orsay, France.

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.03403604.


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