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Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12129-34. Epub 2003 Oct 1.

Transition-path sampling of beta-hairpin folding.

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1
Department of Chemical Engineering, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands. bolhuis@science.uva.nl

Abstract

We examine the dynamical folding pathways of the C-terminal beta-hairpin of protein G-B1 in explicit solvent at room temperature by means of a transition-path sampling algorithm. In agreement with previous free-energy calculations, the resulting path ensembles reveal a folding mechanism in which the hydrophobic residues collapse first followed by backbone hydrogen-bond formation, starting with the hydrogen bonds inside the hydrophobic core. In addition, the path ensembles contain information on the folding kinetics, including solvent motion. Using the recently developed transition interface sampling technique, we calculate the rate constant for unfolding of the protein fragment and find it to be in reasonable agreement with experiments. The results support the validation of using all-atom force fields to study protein folding.

PMID:
14523242
PMCID:
PMC218724
DOI:
10.1073/pnas.1534924100
[Indexed for MEDLINE]
Free PMC Article
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