Direct NMR Methods for Protein Structures and Assignment

蛋白质结构和分配的直接 NMR 方法

• 批准号: 6794063
• 负责人: Rafael Bruschweiler
• 金额: $ 18.25万
• 依托单位: FLORIDA STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-09-01 至 2008-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6794063
• 关键词: DNA binding protein; X ray crystallography; computer program /software; computer simulation; fungal proteins; ligands; mathematics; method development; molecular biology information system; nuclear magnetic resonance spectroscopy; peptide library; protein structure; protein structure function; proteomics

DESCRIPTION (provided by applicant): In nuclear magnetic resonance (NMR) studies of proteins, the assignment of nuclear spin resonances to individual atoms is a prerequisite for all subsequent biomedical applications, such as studies of ligand binding, protein-DNA interactions, and dynamics. Resonance assignment is one of the most time consuming and labor intensive steps even when the 3D xray structure of the protein is available. A new strategy is proposed to find resonance assignments that makes optimal use of the x-ray structure, residual dipolar coupling measurements, and chemical shifts. In this way, the complementary strengths of NMR, x-ray crystallography, and quantum chemistry are synergetically used. In contrast to standard assignment protocols, no NMR information about sequential connectivities is required. The assignment problem is mathematically formulated in terms of a weighted matching problem that can be solved using a computationally efficient combinatorial optimization algorithm. The chemical shift information provided by the assignment can be directly used for a wide variety of NMR applications including ligand binding studies that help to characterize binding sites, strengths, and specificity that will help to rationally guide drug design. The proposed work will make a large number of proteins, whose structure is deposited in the protein database (PDB), amenable to detailed biomedical NMR investigations. Structural genomics, which aims at the derivation of protein function from its 3D structure, requires rapid structure determination methods. For proteins whose structure is not determined by x-ray crystallography, an efficient method is proposed for the simultaneous structure determination and resonance assignment using NMR residual dipolar coupling information, incomplete sequential connnectivities, and modeling techniques. The method avoids the slow assignment step by directly building a library of 3D protein fragments that are consistent with residual dipolar couplings, amino-acid type specific chemical shifts, and sparse sequential backbone connectivity information. The individual fragments have good resolution and they are not biased towards known structures deposited in the PDB. The protein fragments are then assembled to complete 3D protein structures by high-performance computional methods using database derived penalty functions. In contrast to standard NMR methods, this approach does not rely on NOESY-derived distance constraints. The method, which promises a significant speed-up over standard NMR methods, will be tested and refined on model proteins and then applied to biologically relevant proteins.

描述（由申请人提供）：在蛋白质的核磁共振（NMR）研究中，核自旋共振分配到单个原子是所有后续生物医学应用的先决条件，例如配体结合，蛋白质- dna相互作用和动力学的研究。即使蛋白质的3D x射线结构可用，共振分配也是最耗时和劳动密集型的步骤之一。提出了一种新的策略来寻找共振分配，使x射线结构，残余偶极耦合测量和化学位移的最佳利用。这样，核磁共振、x射线晶体学和量子化学的互补优势被协同使用。与标准分配协议相比，不需要有关顺序连接的NMR信息。分配问题的数学形式是一个加权匹配问题，可以用计算效率高的组合优化算法来解决。指派所提供的化学位移信息可直接用于各种核磁共振应用，包括配体结合研究，有助于表征结合位点、强度和特异性，从而有助于合理指导药物设计。这项工作将使大量的蛋白质，其结构沉积在蛋白质数据库（PDB），适合于详细的生物医学核磁共振研究。