The free energy landscape for beta hairpin folding in explicit water.
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.
Zhou
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IBM Thomas J. Watson Research Center, Route 134 and P.O. Box 218, Yorktown Heights, NY 10598, USA.
Berne
B J
BJ
Germain
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R
D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D017510:Protein Folding; D013696:Temperature; D014867:Water / Q000737:chemistry*
C029152:G-substrate; D009419:Nerve Tissue Proteins; D014867:Water