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      The free energy landscape for beta hairpin folding in explicit water.

      Proceedings of the National Academy of Sciences of the United States of America
      Amino Acid Sequence, Molecular Sequence Data, Nerve Tissue Proteins, chemistry, Nuclear Magnetic Resonance, Biomolecular, Protein Folding, Temperature, Water

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          Abstract

          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.

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          Author and article information

          Journal
          11752441
          64961
          10.1073/pnas.201543998

          Chemistry
          Amino Acid Sequence,Molecular Sequence Data,Nerve Tissue Proteins,chemistry,Nuclear Magnetic Resonance, Biomolecular,Protein Folding,Temperature,Water

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