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Originally published as Biophys J. BioFAST on October 29, 2004.
doi:10.1529/biophysj.104.048744
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Biophysical Journal 88:50-61 (2005)
© 2005 The Biophysical Society

Kinetic Pathways of ß-Hairpin (Un)folding in Explicit Solvent

Peter G. Bolhuis

The van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands

Correspondence: Address reprint requests to Peter Bolhuis, University of Amsterdam, Chemistry Department, Nieuwe Achtergracht 166, 1019 JL Amsterdam, The Netherlands. Tel.: 020-525-6447; E-mail: bolhuis{at}science.uva.nl.

We examine the dynamical (un)folding pathways of the C-terminal ß-hairpin of protein G-B1 at room temperature in explicit solvent, by employing transition path sampling algorithms. The path ensembles contain information on the folding kinetics, including solvent motion. We determine the transition state ensembles for the two main transitions: 1), the hydrophobic collapse; and 2), the backbone hydrogen bond formation. In both cases the transition state ensembles are characterized by a layer (1) or a strip (2) of water molecules in between the two hairpin strands, supporting the hypothesis of the solvent as lubricant in the folding process. The transition state ensembles do not correspond with saddle points in the equilibrium free-energy landscapes. The kinetic pathways are thus not completely determined by the free-energy landscape. This phenomenon can occur if the order parameters obey different timescales. Using the transition interface sampling technique, we calculate the rate constants for (un)folding and find them in reasonable agreement with experiments, thus supporting the validation of using all-atom force fields to study protein folding.




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