3 Dimensional Structure Of Macromolecules by NMR

通过 NMR 观察大分子的三维结构

• 批准号: 6983741
• 负责人: G. MARIUS CLORE
• 金额: --
• 依托单位: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6983741
• 关键词: AIDS; DNA; DNA binding protein; biological signal transduction; genetic transcription; human immunodeficiency virus; ligands; liquid crystal; macromolecule; method development; molecular dynamics; nuclear magnetic resonance spectroscopy; protein protein interaction; protein structure; solutions; structural biology; virus protein

Research in this laboratory is centered around solution studies on the structure and dynamics of proteins, protein-protein complexes and protein-nucleic acid complexes using multidimensional NMR spectroscopy, and on the development and application of novel NMR and computational methods to aid in these studies. Particular emphasis is being placed on complexes involved in signal transduction and transcriptional regulation, and on AIDS and AIDS-related proteins. Recent accomplishments include the extension of the applicability of the NMR method to structures larger than 40 kDa. Structures solved in the last year include phosphoryl transfer complexes of enzyme IIA(mannitol) + HPr, and enzyme IIA(glucose)enzyme IIB(glucose) of the PTS pathway, and a 42 kDa ternary Oct1-Sox2-DNA complex. Examples of methodological developments include the panoply of 3D and 4D heteronuclear NMR experiments that have been developed at the NIH and are essential for studying larger proteins whose overlapping resonances pose a formidable problem; methods that make use of anisotropy of the alignment tensor (e.g. residual dipolar couplings measured on macromolecules dissolved in dilute liquid crystalline media such as the nematic phases of rod-shaped virus particles) or the diffusion tensor (for highly non-spherical molecules) to provide long-range orientational information that is not available from other NMR parameters that rely entirely on close spatial proximity of atoms; and the development of fast and efficient algorithms for the analysis of NMR spectra and for the computation of three-dimensional structures based on all available experimental NMR restraints. Very recent developments include the use of rigid mody minimization and constrained/restrained simulated annealing to accurately dock protein-protein complexes on the basis of intermolecular NOE and dipolar coupling data, as well as chemical shift perturbation data, the development of new methods for solving structures of complexes based on paramagnetic relaxation enhancement measurements to derive long range (up to 35 ?) distance information), and the development of a novel approach for solving NMR structures directly from completely automatically peak-picked multidimensional NOE spectra using a highly error tolerant algorithm that permits up to 80% of the long-range NOE information to be incorrect.

该实验室的研究主要集中在利用多维核磁共振波谱对蛋白质、蛋白质-蛋白质复合体和蛋白质-核酸复合体的结构和动力学进行溶液研究，以及开发和应用新的核磁共振和计算方法来辅助这些研究。目前正在特别重视信号转导和转录调控的复合体，以及艾滋病和艾滋病相关蛋白。最近的成就包括将核磁共振方法的适用性扩展到大于40 kDa的结构。在过去的一年中解决的结构包括酶IIA(甘露醇)+HPR的磷酸转移络合物，PTS途径的酶IIA(葡萄糖)酶IIB(葡萄糖)，以及42 kDa的Oct1-Sox2-DNA三元复合体。方法学发展的例子包括美国国立卫生研究院开发的全套3D和4D异核核磁共振实验，这些实验对于研究较大的蛋白质来说是必不可少的，其重叠的共振构成了一个可怕的问题；方法利用排列张量的各向异性(例如，在溶解于稀释型液晶介质中的大分子上测量的残余偶极耦合)或扩散张量(对于高度非球形的分子)来提供远距离取向信息，这是其他完全依赖于原子空间接近的核磁共振参数所不能获得的；并根据所有可用的实验核磁共振限制条件，开发快速有效的算法来分析核磁共振谱并计算三维结构。最新的发展包括使用刚性Mody最小化和约束/约束模拟退火法，以分子间NOE和偶极耦合数据以及化学位移微扰数据为基础，精确对接蛋白质-蛋白质复合体，开发基于顺磁驰豫增强测量的求解复合体结构的新方法，以获得长程(高达35？)距离信息)，并开发了一种新的方法，用于直接从完全自动拾峰的多维NOE谱中解算核磁共振结构，使用高度容错的算法，允许高达80%的远程NOE信息是不正确的。