Macromolecular dynamics and conformational changes in biological function

生物功能中的大分子动力学和构象变化

• 批准号: 10318591
• 负责人: ARTHUR G PALMER
• 金额: $ 55.91万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10318591
• 关键词: Address; Biological Process; Biophysics; Breathing; Cadherins; Catalysis; Cell Adhesion Molecules; Core Protein; Coupled; Coupling; DNA Repair Gene; Development; Dimerization; Disease; Enzyme Inhibition; Enzymes; Equilibrium; Event; Feedback; Future; Goals; Health; Human; Investigation; Kinetics; Laboratories; Ligand Binding; Ligands; Measurement; Modification; Molecular; Molecular Conformation; Motion; Mutation; NMR Spectroscopy; Nucleic Acids; Pathology; Pharmacologic Substance; Process; Property; Protein Dynamics; Proteins; Psychological Techniques; RNA; Reaction; Regulation; Relaxation; Research; Resolution; Role; Site; Structure; Techniques; biological systems; conformational conversion; design; exosome; experimental study; gain of function; improved; macromolecule; member; molecular dynamics; molecular recognition; non-Native; novel; nucleic acid binding protein; nucleotidyltransferase; programs; protein activation; protein function; protein protein interaction; ribonuclease H1; theories; transcription factor

Conformational changes of proteins are required for nearly all biological functions and inappropriate conformational transitions are associated with numerous pathologies. Comprehensive experimental information on the essential contributions of intramolecular dynamics and intermolecular kinetics to biological functions of proteins is critical for biophysical theories of equilibrium properties, such as heat capacity and thermal stability; for mechanistic interpretations of kinetic processes, such as enzyme catalysis and ligand recognition; for understanding “action at a distance” in allostery or regulation; and for design of novel proteins and protein ligands, including pharmaceutical agents. Conformational changes in proteins, including local librations, loop motions, relative motions between domains, collective “breathing” of protein cores, ligand- binding or oligomerization reactions, and overall folding-unfolding events, may be closely coupled, and in some instances rate-limiting, to biological functions such as molecular recognition, transitions along the catalytic cycle of enzymes, and inhibition or activation of proteins through intra- or inter-molecular protein- protein interactions. Mutations that perturb dynamical processes and conformational equilibria are associated with significant pathology, including loss or gain of function and misfolding. Recent developments, including those from the PI laboratory, have opened new opportunities for investigation of conformational dynamic processes using NMR spin relaxation measurements (and other NMR observables) at equilibrium in solution and with atomic site resolution, without potential complications introduced by non-native modifications necessary for other solution-state spectroscopic techniques. In addition, close coupling between experimental measurements and molecular dynamics (MD) simulations or other theoretical approaches allow feedback between theory and experiment in interpreting results, formulating hypotheses for on-going investigation, and improving both experimental and theoretical techniques. The present proposal will use these approaches to explicate the functional roles of conformational transistions in enzymes, including ribonuclease HI (and other members of the nucleotidyl-transferase superfamily), the DNA-repair protein AlkB, and the RNA exosome; Hox transcription factors and other nucleic acid binding proteins; and protein-protein interactions, including strand-swapping and dimerization by cadherin cell-adhesion proteins. These objectives are supported by development of improved approaches for characterizing protein dynamics by NMR spectroscopy and MD simulation. This research program will explicate at a level of unprecedented detail molecular features and principles underlying conformational changes, dynamics, and kinetics that are critical for understanding normal and abnormal biological functions of proteins and other macromolecules. Completion of these goals will enable additional future applications to a wide range of macromolecular systems of biological importance.

蛋白质的构象变化几乎是所有生物功能所必需的，而且是不适当的 构象转变与许多病理现象有关。综合实验 关于分子内动力学和分子间动力学对生物学的基本贡献的信息 蛋白质的功能对于平衡性质的生物物理理论来说是至关重要的，例如热容和 热稳定性；用于动力学过程的机械解释，如酶催化和配基 识别；理解变构或调节中的“远距离作用”；以及设计新的蛋白质 和蛋白质配体，包括药剂。蛋白质的构象变化，包括局部的 振动、环运动、结构域之间的相对运动、蛋白质核心的集体“呼吸”、配体-- 结合或寡聚反应以及整个折叠-展开事件可以紧密耦合，并且在 一些实例限制了生物功能，如分子识别，沿 酶的催化循环，以及通过分子内或分子间蛋白质抑制或激活蛋白质- 蛋白质的相互作用。扰乱动力学过程和构象平衡的突变是相关的 有明显的病理改变，包括功能丧失或获得以及折叠错误。最近的事态发展，包括 来自PI实验室的那些人为构象动力学的研究打开了新的机会 在溶液中平衡时使用核磁共振自旋弛豫测量(和其他核磁共振观测数据)的过程 并具有原子站点分辨率，不会因非本地修改而导致潜在的复杂情况 对于其他溶液状态光谱技术来说是必要的。此外，实验之间的紧密耦合 测量和分子动力学(MD)模拟或其他理论方法允许反馈 在解释结果、为持续研究制定假设方面的理论和实验之间的差距，以及 改进实验和理论技术。本提案将利用这些办法 阐述构象转换在酶中的功能作用，包括核糖核酸酶HI(和其他 核苷酸转移酶超家族的成员)、DNA修复蛋白AlkB和RNA外切体； HOX转录因子和其他核酸结合蛋白；以及蛋白质-蛋白质相互作用，包括 钙粘附素细胞黏附蛋白的链交换和二聚化。这些目标得到以下支持 核磁共振波谱和分子动力学表征蛋白质动力学的改进方法研究进展 模拟。这项研究计划将以前所未有的详细程度阐述分子特征和 构象变化、动力学和动力学的基本原理对理解 蛋白质和其他大分子的正常和异常生物功能。完成这些目标 将使更多的未来应用于具有生物重要性的广泛的大分子系统。