The free energy landscape for β hairpin folding in explicit water

被引:442
作者
Zhou, RH
Berne, BJ
Germain, R
机构
[1] Columbia Univ, Ctr Biomol Simulat, New York, NY 10027 USA
[2] IBM Corp, Thomas J Watson Res Ctr, Yorktown Hts, NY 10598 USA
关键词
D O I
10.1073/pnas.201543998
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The folding free energy landscape of the C-terminal beta hairpin of protein G has been explored in this study with explicit solvent under periodic boundary condition and OPLSAA force field. A highly parallel replica exchange method that combines molecular dynamics trajectories with a temperature exchange Monte Carlo process is used for sampling with the help of a new efficient algorithm P3ME/RESPA. The simulation results show that the hydrophobic core and the beta strand hydrogen bond form at roughly the same time. The free energy landscape with respect to various reaction coordinates is found to be rugged at low temperatures and becomes a smooth funnel-like landscape at about 360 K. In contrast to some very recent studies, no significant helical content has been found in our simulation at all temperatures studied. The beta hairpin population and hydrogen-bond probability are in reasonable agreement with the experiment at biological temperature, but both decay more slowly than the experiment with temperature.
引用
收藏
页码:14931 / 14936
页数:6
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