CONFORMATIONAL DYNAMICS IN MYOSIN AND T7 RNA POLYMERASE

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Exploratory and testing runs will be performed to plan for the computational study of myosin and T7 RNA polymerase protein dynamics on the BigBen platform. The project is to be a continuation/expansion of the previous year's project where myosin conformational dynamics was studied using umbrella sampling/free energy MD methods, which were partially run on LeMieux platform as well as local cluster environments. A small number of windows will be run both for scallop myosin with bound ATP and T7 RNAP in the elongation phase, using CHARMM. For myosin, relative RMSD will be used as reaction coordinate with constraints using CONS RMSD module. For T7 RNAP, similar constrained dynamics will be run with the translocation reaction coordinate, which has been implemented in a modified version of the CHARMM in the PI's group. Both the efficiency of scaling and simulation speed will be assessed on the new platform. A full proposal will be written based on the test results.