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

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。 溶液X射线散射有望成为非常有用的体系的结构研究，如大的非球状大分子组装，多结构域蛋白质，或固有的柔性或无序的大分子。这项建议的中心目标是创建一种方法，用于非常准确地计算从大分子原子坐标到广角散射轮廓的非常准确的计算，以便与溶液核磁共振结合应用于结构和动力学研究。我们专注于拥有最高质量结构溶液核磁共振模型的大分子体系，以及广泛的动力学信息，包括蛋白G、泛素、溶菌酶、钙调蛋白和Dickerson十二聚体B-DNA。我们假设这些体系的平均大分子几何形状是精确已知的，并且计算和观测的散射分布之间的任何差异都是散射数据预测的不足。我们将从准确的体积水分布中获得显式计算的置换溶剂形状因子，而不是溶剂校正的原子形状因子，这将给我们提供更准确的广角散射强度的预测。我们还将使用有关所列蛋白质动力学的大量溶液核磁共振数据，将大分子中原子运动的表示纳入散射分布的计算中。最后，我们将通过构建大分子周围溶剂的非均匀三维分布来改进散射数据建模，这些分布反映了蛋白质表面的组成并最佳地拟合了散射数据。该方法将在Dickerson十二聚体B-DNA上进行验证，该DNA的结合水的位置是众所周知的。

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.