Protein Dynamics in Enzymatic Catalysis

描述（由申请人提供）：该计划项目的目标，题为酶催化中的蛋白质动力学，是了解原子运动如何影响酶催化。我们建议研究蛋白质-配体复合物的结构演变的系统沿着酶-底物和酶-产物之间的反应坐标。在这项研究中，蛋白质的动力学性质如何影响酶的功能的概念进行了探讨。我们汇集了一个研究小组，由专门从事动力学理论，计算化学，光谱与广泛的时间分辨率，酶化学机制，蛋白质化学和标记，合成有机化学家，过渡态形成和结构的研究人员组成。有四个项目和三个核心。 项目一：LDH和DHFR催化中的蛋白质动力学（Callender，PI）将研究底物和辅因子如何与重要的蛋白质残基结合在一起的运动和时间尺度，以乳酸脱氢酶和二氢叶酸还原酶为模型酶，在NAD（P）连接的酶中实现氢化物和质子转移。 项目二：PNP（Schramm）中蛋白质动力学和化学的协调研究嘌呤核苷磷酸化酶，该程序旨在表征底物-酶系统的动力学，因为它沿着从米氏复合物到过渡态的反应途径发展。 项目三：血红素铜氧化酶（Dyer）中的质子转移动力学是对蛋白质结构以及当血红素铜氧化酶引起氧化还原驱动的质子泵送时这些结构的演变的研究。 项目四：促进LDH和PNP中的振动（Schwartz）通过研究促进振动的快速运动如何以及在多大程度上与LDH和PNP的酶催化反应中的反应动力学耦合，研究蛋白质动力学是否在键形成和裂解的催化中具有直接作用。研究结果将接受实验研究。化学核心（核心A）旨在提供实验研究所需的蛋白质、突变体和位点特异性同位素标记的蛋白质和小分子。设备核心（核心B）支持大多数实验研究所需的温度跃变弛豫和差分光谱仪，以在原子水平上表征蛋白质-配体复合物的运动。

DESCRIPTION (provided by applicant): The goal of this Program Project, entitled Protein Dynamics in Enzymatic Catalysis, is to understand how atomic motion affects enzymatic catalysis. We propose to study the evolution of structure of protein-ligand complexes as the system moves along the reaction coordinate between enzyme-substrate and enzyme-product. In this study, concepts of how the dynamical nature of proteins affects enzymic function are explored. We bring together a research group consisting of researchers specializing in the theory of dynamics, computational chemistry, spectroscopy with broad time-resolution, enzymatic chemical mechanisms, protein chemistry and labeling, synthetic organic chemists, and transition state formation and structure. There are four projects and three cores. Project 1: Protein Dynamics in Catalysis by LDH and DHFR (Callender, PI) will examine the motions and time scales of how substrates and cofactors are brought together with important protein residues to bring about hydride and proton transfer in NAD(P)-linked enzymes using lactate dehydrogenase and dihydrofolate reductase as model enzymes. Project 2: Coordination of Protein Dynamics and Chemistry in PNP (Schramm) studies purine nucleoside phosphorylase in a program aimed at characterizing the dynamics of the substrate-enzyme system as it develops along the reaction pathway from Michaelis complex to transition state. Project 3: Proton Transfer Dynamics in Heme-Copper Oxidases (Dyer) is an investigation of the protein structures and evolution of these structures as the heme-copper oxidases bring about redox driven proton pumping. Project 4: Promoting Vibrations in LDH and PNP (Schwartz) examines whether or not protein dynamics has a direct role in the catalysis of bond formation and cleavage by studying how and to what extent the rapid motion of promoting vibrations couple to reaction dynamics in the enzyme-catalyzed reactions of LDH and PNP. The findings will be subjected to experimental investigation. The Chemistry Core (Core A) is designed to supply the proteins, mutants, and site specific isotopic labeled proteins and small molecules needed by the experimental studies. The Equipment Core (Core B) supports the temperature jump relaxation and difference spectrometers required of most of the experimental studies to characterize protein-ligand complex motion at the atomic level.