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

Motivation: After 10-year investigations, the folding mechanismsof β-hairpins are still under debate. Experiments stronglysupport zip-out pathway, while most simulations prefer the hydrophobiccollapse model (including middle-out and zip-in pathways). Inthis article, we show that all pathways can occur during thefolding of β-hairpins but with different probabilities.The zip-out pathway is the most probable one. This is in agreementwith the experimental results. We came to our conclusions by38 100-ns room-temperature all-atom molecular dynamics simulationsof the β-hairpin trpzip2. Our results may help to clarifythe inconsistencies in the current pictures of β-hairpinfolding mechanisms. Contact: yxiao{at}mail.hust.edu.cn Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Anna Tramontano