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

谷氨酸中裂隙闭合转变和谷氨酸结合的能量

• 批准号: 7956194
• 负责人: MARIA G KURNIKOVA
• 金额: $ 0.08万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956194
• 关键词: Adopted; Binding; Biomedical Research; Cleaved cell; Computer Retrieval of Information on Scientific Projects Database; Computing Methodologies; Electrostatics; Environment; Free Energy; Funding; Glutamates; Grant; High Performance Computing; Institution; Ligands; Modeling; Molecular Conformation; Mutate; Mutation; Pathway interactions; Proteins; Research; Research Personnel; Resources; Running; Sampling; Source; Structure; Thermodynamics; United States National Institutes of Health; mutant; simulation

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

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。 通过MD模拟，我们证明了GluR2采用开放形式。为了估计两种构象之间的自由能差，我们使用了我们先前研究中确定的开放转变的路径。我们采用了联合的方法，其中包括热力学积分(TI)，其中蛋白质在一个构象中突变(TI)和伞状取样(US)，沿着我们先前研究中确定的开放转变的途径。为了得到从封闭到开放的自由能分布，我们在没有配基的情况下保持封闭构象，并在突变过程中将E705残基变为E705-0.75。然后进行伞状抽样MD模拟，以确定具有E705-0.75突变体的GluR2从封闭结构到开放结构的结构转变的自由能。接下来，将E705-0.75的开放GluR2突变为E705，以适应其先前的静电环境。计算方法的组合在这里被用来模拟打开转变和使用热力学循环计算自由能差