Biomolecular Dynamics Simulations with Massively Parallel Molecular Dynamics Software       


Medical, Health Informatics and Computational Biology Accomplishment | 2008

IBM researchers: Ruhong Zhou, Robert Germain, Blake Fitch, Michael Pitman, Christopher Ward, Frank Suits, Jed PiteraWilliam Swope

Where the work was done: IBM T.J. Watson Research Center, IBM Almaden Lab

What we accomplishedProtein folding is one of the most fundamental problems in molecular biology. Recent advances in experimental techniques that probe proteins at different stages during the folding process have shed light on the nature of the physical mechanisms and relevant interactions that determine the kinetics of folding, binding, function and thermodynamic stability. To gain a deeper understanding of the protein folding pathways, we have carried out the first all-atom simulation to explore the free energy landscape of the  beta hairpin in explicit water since it is  one of the smallest naturally occurring systems, which exhibits many features of a full size protein. This same technique was also applied to study the folding free energy landscape in explicit water for Trg-cage, which is believed to be the fastest folder known so far and can serve to meet both ends of experimental and theoretical studies. Our rigorous studies of these proteins provide a foundation for investigating more complex proteins and suggest that more work needs to be done in the force field parameterization to yield the correct temperature dependence from simulations.

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Image credit: Biomedical Computation Review

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