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Bioinformatics Advance Access published online on January 23, 2008
Bioinformatics, 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 *

*To whom correspondence should be addressed. Yi Xiao, E-mail: yxiao{at}mail.hust.edu.cn, yxiao717{at}163.com


  Abstract

Motivation:After ten-year investigations, the folding mechanisms of beta-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 paper, we show that all pathways can occur during the folding of beta-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 thirty-eight 100-ns room-temperature all-atom molecular dynamics simulations of the beta-hairpin trpzip2. Our results may help to clarify the inconsistencies in the current pictures of β-hairpin folding mechanisms.

Associate Editor: Prof. Anna Tramontano

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

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