期刊
JOURNAL OF COMPUTATIONAL BIOLOGY
卷 16, 期 12, 页码 1719-1730出版社
MARY ANN LIEBERT, INC
DOI: 10.1089/cmb.2008.0070
关键词
beta-hairpin; folding mechanism; trpzip2; united-residue force field
类别
资金
- NSFC [30525037]
The folding mechanism of beta-hairpins might provide fundamental knowledge that helps us to understand how large proteins fold. However, all-atom molecular dynamics is difficult to do large-scale and long-time simulations, even for small peptides. In this article, we report a large-scale simulation of the beta-hairpin trpzip2 by Langevin dynamics with united-residue (UNRES) force field. We obtained 374 successfully folding trajectories of trpzip2. The results show that trpzip2 can fold into the native structure by adopting two different mechanisms: (1) zipper, and (2) simultaneous zipper and collapse. The former occurs with a larger probability. Furthermore, the folding of trpzip2 is heterogeneous. Our results clarify the inconsistencies in the current picture of the folding mechanisms of trpzip2 and other similar beta-hairpins.
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