PROTEIN & DNA STRUCTURE DETERMINATION BY COMBINATION OF WAXS & SOLUTION NMR

蛋白质

• 批准号: 7601765
• 负责人: ALEXANDER V GRISHAEV
• 金额: $ 0.39万
• 依托单位: ILLINOIS INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-04-01 至 2008-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7601765
• 关键词: B-DNA; Binding; Calmodulin; Computer Retrieval of Information on Scientific Projects Database; Data; Disease; Funding; G-substrate; Goals; Grant; Institution; Investigation; Membrane Proteins; Methodology; Modeling; Motion; Muramidase; Positioning Attribute; Proteins; Research; Research Personnel; Resources; Roentgen Rays; Solutions; Solvents; Source; Structure; System; Tertiary Protein Structure; Ubiquitin; United States National Institutes of Health; Water; data modeling; improved; macromolecular assembly; macromolecule

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. Solution X-ray scattering has a promise of becoming very useful for structural investigation of systems such as large non-globular macromolecular assemblies, multi-domain proteins, or inherently flexible or disordered macromolecules. The central goal of this proposal is to create a methodology for a very accurate calculation of wide-angle scattering profiles from macromolecular atomic coordinates for a combined application with solution NMR for investigation of structure and dynamics. We are concentrating on macromolecular systems for which the highest quality structural solution NMR models are available, along with the extensive dynamical information, including protein G, ubiquitin, lysozyme, calmodulin and Dickerson dodecamer B-DNA. We are assuming that the average macromolecular geometry for these systems is known exactly and any discrepancies between the calculated and observed scattering profiles are to the deficiencies of the scattering data prediction. We will obtain explicitly calculated displaced solvent form factors from accurate bulk water distributions in place of the solvent-corrected atomic form factors which will afford us a more accurate prediction of the wide-angle scattering intensity. We will also incorporate a representation of the atomic motions in the macromolecule into the calculation of the scattering profile using extensive solution NMR data on the dynamics of the listed proteins. Finally, we will improve scattering data modeling by constructing inhomogeneous three-dimensional distributions of the solvent surrounding the macromolecule that reflect the compositions of the proteins surfaces and best-fit the scattering data. The methodology will be validated on Dickerson dodecamer B-DNA for which the positions of the bound waters are well known.

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。 溶液X射线散射有希望成为非常有用的系统，如大型非球形大分子组装，多结构域蛋白质，或固有的灵活或无序的大分子的结构研究。该提案的中心目标是创建一种方法，用于从大分子原子坐标中非常准确地计算广角散射分布，用于与溶液NMR结合应用，用于结构和动力学的研究。我们专注于大分子系统，其中最高质量的结构溶液NMR模型是可用的，沿着广泛的动力学信息，包括蛋白质G，泛素，溶菌酶，钙调蛋白和迪克森十二聚体B-DNA。我们假设这些系统的平均大分子几何形状是确切已知的，并且计算的和观察到的散射分布之间的任何差异都是散射数据预测的缺陷。我们将从准确的本体水分布中获得明确计算的置换溶剂形状因子， 溶剂校正的 原子形状因子，这将为我们提供更准确的预测广角散射强度。我们还将采用广泛的溶液NMR数据对所列蛋白质的动力学的散射配置文件的计算中的大分子中的原子运动的表示。最后，我们将通过构建反映蛋白质组成的大分子周围溶剂的非均匀三维分布来改进散射数据建模 曲面并最佳拟合散射数据。该方法将在Dickerson十二聚体B-DNA上进行验证，其结合沃茨的位置是众所周知的。