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

基本信息

批准号：
10546431
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
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-01-01 至 2024-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10546431
关键词：
Address Biological Process Biophysics Breathing Cadherins Catalysis Cell Adhesion Molecules Core Protein Coupled Coupling DNA Repair Gene Development Dimerization Disease 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

Address Biological Process Biophysics Breathing Cadherins Catalysis Cell Adhesion Molecules Core Protein Coupled Coupling DNA Repair Gene Development Dimerization Disease 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

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项目摘要

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.

几乎所有生物学功能都需要蛋白质的构象变化和不适当构象转变与许多病理有关。全面的实验有关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特性的生物物理理论至关重要，例如热容量和热稳定性；用于动力学过程的机械解释，例如酶催化和配体认出;理解变构或法规中的“距离行动”；以及用于新型蛋白质的设计和蛋白质配体，包括药剂剂。蛋白质的合法变化，包括局部图书馆，循环运动，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总体上折叠的事件可以紧密耦合，并在某些实例限制速率限制到生物学功能，例如分子识别，沿着酶的催化循环，以及通过分子内或分子间蛋白质抑制或激活蛋白蛋白质相互作用。扰动动态过程和构象等效物的突变是相关的具有重大病理，包括功能丧失或增加和错误折叠。最近的发展，包括来自PI实验室的人为投资构象动态提供了新的机会在溶液中使用NMR自旋松弛测量（和其他NMR可观测值）的过程并通过原子位点分辨率，没有非本性修改引入的潜在并发症对于其他溶液状态光谱技术所必需的。此外，在实验之间关闭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的理论和实验之间，为正在进行的研究制定假设以及改进实验和理论技术。本提案将使用这些方法来解释酶在酶中的构型晶体源的功能作用，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外泌体； HOX转录因子和其他核酸结合蛋白；和蛋白质 - 蛋白质相互作用，包括钙粘蛋白细胞粘附蛋白的链链和二聚化。这些目标得到了开发通过NMR光谱和MD来表征蛋白质动力学的改进方法模拟。该研究计划将以前所未有的细节分子特征和会议变化，动力学和动力学的原则对于理解至关重要蛋白质和其他大分子的正常和异常生物学功能。完成这些目标将使将来的其他应用适用于各种生物学重要性的大分子系统。