Macromolecular dynamics and conformational changes in biological function

蛋白质的构象变化是几乎所有生物功能所必需的， 构象转变与许多病理学有关。综合实验 分子内动力学和分子间动力学对生物学的重要贡献的信息 蛋白质的功能对于平衡性质的生物物理理论至关重要，例如热容和 热稳定性;用于动力学过程的机械解释，如酶催化和配体 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 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- 结合或寡聚化反应，以及整个折叠-解折叠事件，可能是密切相关的， 在某些情况下，对生物学功能如分子识别的速率限制，沿着沿着 酶的催化循环，以及通过分子内或分子间的蛋白质- 蛋白质相互作用扰乱动力学过程和构象平衡的突变与 具有显著病理学，包括功能丧失或获得以及错误折叠。最近的事态发展，包括 这些来自PI实验室，为构象动力学的研究开辟了新的机会 在溶液中平衡时使用NMR自旋弛豫测量（和其他NMR可观测值）的方法 并且具有原子位置分辨率，而没有由非原生修改引入的潜在复杂性 其他溶液态光谱技术所必需的。此外，实验之间的紧密耦合 测量和分子动力学（MD）模拟或其它理论方法允许反馈 理论和实验之间的解释结果，制定假设正在进行的调查， 改进实验和理论技术。本提案将利用这些办法， 解释酶中构象转换的功能作用，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;以及蛋白质-蛋白质相互作用，包括 通过钙粘蛋白细胞粘附蛋白的链交换和二聚化。这些目标得到以下方面的支持： 开发了通过NMR光谱和MD表征蛋白质动力学的改进方法 仿真这项研究计划将在前所未有的详细水平上解释分子特征， 构象变化、动力学和动力学的基本原理，对于理解 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生物重要性的大分子系统的广泛范围。

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.