Determination of solution structures by NMR

通过 NMR 测定溶液结构

• 批准号: 7367231
• 负责人: David A Case
• 金额: $ 18.16万
• 依托单位: SCRIPPS RESEARCH INSTITUTE, THE
• 依托单位国家: 美国
• 财政年份: 1991
• 资助国家: 美国
• 起止时间: 1991-04-01 至 2008-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7367231
• 关键词: Accounting; Algorithms; Amber; Anisotropy; Attention; Biochemical Process; Biomolecular Nuclear Magnetic Resonance; Cell Nucleus; Cells; Chemicals; Chemotherapy-Oncologic Procedure; Classification; Code; Collaborations; Condition; Coupling; Data; Development; Diffusion; Dihydrofolate Reductase; Disease; Error Sources; Foundations; Funding; G-substrate; Generations; Goals; Kinetics; Lead; Life; Light; Measurement; Measures; Methods; Minor; Modeling; Molecular Conformation; Monitor; Motion; NMR Spectroscopy; Nature; Nuclear Magnetic Resonance; Nucleic Acids; Pancreatic ribonuclease; Pathway interactions; Property; Proteins; Rate; Relaxation; Rest; Ribonucleases; Rotation; Sampling; Simulate; Solutions; Solvents; Structural Models; Structure; Testing; Time; Update; Water; Work; base; computer code; computerized tools; conformer; dihydrofolate; experimental analysis; macromolecule; millisecond; molecular dynamics; molecular modeling; novel; research study; simulation; sound; tool

DESCRIPTION (provided by applicant): The principal goals of this project are the development of algorithms that allow one to make the best use of NMR data to determine solution structures of biomolecules, to assess in a systematic fashion their accuracy and precision, and to explore the extent to which dynamical information can be extracted from NMR data. This will involve the following components: Updated refinement methods. Refinement models will be developed that use modern protein and nucleic acid force fields in combination with generalized Born or explicit solvation models, and which incorporate conformational disorder through the "locally enhanced sampling" model that uses multiple copies of portions of the macromolecule. Studies on protein and nucleic acid dynamics. Long-time scale molecular dynamics simulations will be used to model NMR relaxation, with attention paid to anisotropic tumbling, to the correlation between internal and overall motions, and to conformational disorder. This will include an analysis of contributions from internal motions to chemical shift anisotropy (CSA) relaxation and to CSA-dipolar cross-correlated relaxation. Slower, microsecond to millisecond motions uncovered by relaxation dispersion experiments will be studied using novel models to identify minor conformers and to estimate their rates of interconversion with other conformations. Initial applications will be to protein G, ribonuclease A, and dihydrofolate reducatase. Nuclear magnetic resonance (NMR) spectroscopy provides a powerful tool for probing the properties of proteins and nucleic acids under conditions like those in living cells. The project uses computational tools to help gain the most information from NMR, promoting our understanding of basic biochemical processes that underlie both healthy and diseased cells. Two of the proteins studied here (ribonuclease and dihydrofolate reductase) are important targets for cancer chemotherapy.

描述（由申请人提供）：该项目的主要目标是开发算法，使人们能够最好地利用NMR数据来确定生物分子的溶液结构，以系统的方式评估其准确性和精度，并探索从NMR数据中提取动态信息的程度。这将涉及以下组成部分：更新完善方法。将开发使用现代蛋白质和核酸力场与广义玻恩或显式溶剂化模型相结合的精细模型，并通过使用大分子部分的多个拷贝的“局部增强采样”模型将构象紊乱纳入其中。蛋白质和核酸动力学研究。长时间尺度的分子动力学模拟将被用来模拟NMR弛豫，注意各向异性翻滚，内部和整体运动之间的相关性，以及构象紊乱。这将包括从内部运动化学位移各向异性（CSA）松弛和CSA偶极交叉相关松弛的贡献的分析。较慢，微秒到毫秒的运动发现的松弛分散实验将使用新的模型进行研究，以确定未成年人的构象，并估计其与其他构象的相互转化率。最初的应用将是蛋白G，核糖核酸酶A，和二氢叶酸还原酶。核磁共振（NMR）光谱学提供了一个强大的工具，用于探测蛋白质和核酸在活细胞等条件下的性质。该项目使用计算工具来帮助从NMR中获得最多的信息，促进我们对健康和患病细胞基础的基本生化过程的理解。这里研究的两种蛋白质（核糖核酸酶和二氢叶酸还原酶）是癌症化疗的重要靶点。