CONFORMATIONAL DYNAMICS IN MYOSIN AND T7 RNA POLYMERASE

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 将进行探索性和测试性运行，以计划在BigBen平台上进行肌球蛋白和T7 RNA聚合酶蛋白质动力学的计算研究。该项目将是前一年项目的延续/扩展，在前一年的项目中，使用伞状采样/自由能MD方法研究了肌球蛋白构象动力学，该方法部分在LeMieux平台上运行以及在本地集群环境中运行。使用CHARMM，在伸长阶段，将为结合了ATP的扇贝肌球蛋白和T7 RNAP运行少量的窗口。对于肌球蛋白，使用CONS RMSD模块将相对RMSD作为带有约束的反应坐标。对于T7 RNAP，将使用易位反应坐标运行类似的约束动力学，该坐标已在PI的组中的CHARMM的修改版本中实现。在新的平台上，将对缩放效率和模拟速度进行评估。将根据测试结果编写完整的建议书。

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.