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Bioinformatics Advance Access originally published online on January 23, 2008
Bioinformatics 2008 24(5):659-665; doi:10.1093/bioinformatics/btn029
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Observation of multiple folding pathways of β-hairpin trpzip2 from independent continuous folding trajectories

Changjun Chen and Yi Xiao *

Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China

*To whom correspondence should be addressed.


  Abstract

Motivation: After 10-year investigations, the folding mechanisms of β-hairpins are still under debate. Experiments strongly support zip-out pathway, while most simulations prefer the hydrophobic collapse model (including middle-out and zip-in pathways). In this article, we show that all pathways can occur during the folding of β-hairpins but with different probabilities. The zip-out pathway is the most probable one. This is in agreement with the experimental results. We came to our conclusions by 38 100-ns room-temperature all-atom molecular dynamics simulations of the β-hairpin trpzip2. Our results may help to clarify the inconsistencies in the current pictures of β-hairpin folding mechanisms.

Contact: yxiao{at}mail.hust.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Anna Tramontano

Received on October 26, 2007; revised on December 21, 2007; accepted on January 18, 2008

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