CONFORMATIONAL DYNAMICS IN MYOSIN AND T7 RNA POLYMERASE

这个子项目是许多利用 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 将进行探索性和测试运行，以计划在BigBen平台上进行肌球蛋白和T7 RNA聚合酶蛋白动力学的计算研究。该项目是前一年项目的延续/扩展，其中使用伞形采样/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平台和本地集群环境中运行。将使用CHARMM在延伸阶段对具有结合ATP的扇贝肌球蛋白和T7 RNAP运行少量窗口。对于肌球蛋白，将使用相对RMSD作为反应坐标，并使用CONS RMSD模块进行约束。对于T7 RNAP，将使用易位反应坐标运行类似的约束动力学，这已经在PI的组中的CHARMM的修改版本中实现。缩放效率和模拟速度都将在新平台上进行评估。将根据测试结果编写完整的提案。

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.