United-residue (UNRES) Langevin dynamics simulations of trpzip2 folding.
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.
He
Yi
Y
Biomolecular Physics and Molecular Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China. yxiaogmai@gmail.com
Chen
Changjun
C
Xiao
Yi
Y
D000596:Amino Acids / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics
D000596:Amino Acids; D011506:Proteins; C539234:Trpzip2 protein