Lei Ye, Huajun Chen, et al.
Journal of Bioinformatics and Computational Biology
The folding free energy landscape of the C-terminal β 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 β 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 β 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.
Lei Ye, Huajun Chen, et al.
Journal of Bioinformatics and Computational Biology
Payel Das, Ruhong Zhou
Journal of Physical Chemistry B
Toshikazu Ebisuzaki, Robert Germain, et al.
Communications of the ACM
Zonglin Gu, Zaixing Yang, et al.
Scientific Reports