ENERGETICS OF THE CLEFT CLOSING TRANSITION AND GLUTAMATE BINDING IN THE GLUTAMA

这个子项目是许多研究子项目中的一个 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。 通过MD模拟，我们证明了GluR 2采用开放形式。为了估计两种构象之间的自由能差异，我们使用了在我们以前的研究中已经确定的开放过渡的途径。我们采用了结合的方法，其中包括热力学积分（TI），其中蛋白质是突变的一种构象和伞采样（US），沿着的开放过渡的途径，已经确定在我们以前的研究。为了获得从封闭到开放形式的自由能曲线，我们在不存在配体的情况下保持封闭构象，在将E705残基突变为E705-0.75期间具有谐波约束。然后进行伞形采样MD模拟以确定具有E705-0.75突变体的GluR 2从封闭结构到开放结构的结构转变的自由能。接下来，将具有E705-0.75的开放GluR 2突变为E705以采用其先前的静电环境。一个计算方法的组合已被采用在这里模拟开放过渡和计算自由能差使用热力学循环

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. By running MD simulations, we demonstrated that GluR2 adopts the open form. To estimate the free energy differences between two conformations we used the pathway of the opening transition as has been determined in our previous study. We employed the combined approach, which includes Thermodynamics integration (TI) in which the protein is mutated in one conformation and Umbrella Sampling (US), along the pathway of the opening transition as has been determined in our previous study. To get the free energy profile from the closed to the open form we kept the closed conformation in the absence of ligand with harmonic constrains during mutation the E705 residue to E705-0.75. Then umbrella sampling MD simulations were performed to determine free energy of the structural transition from the closed to open structure for GluR2 with the E705-0.75 mutant. Next the open GluR2 with E705-0.75 was mutated to E705 to adopt its previous electrostatic environment. A combination of computational methods has been employed here to model the opening transition and compute the free energy differences using a thermodynamic cycle