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，是研究酶中的原子运动。我们建议研究蛋白质的动力学性质如何影响酶的功能和酶的能量景观从酶-底物到酶上过渡态过渡态形成的概念。我们汇集了不同背景的熟练的研究小组，旨在了解酶的功能。重要的是，我们带来了独特的，先进的，有效的实验和理论方法敏感的蛋白质结构的演变在多个时间尺度上，从ps到分钟。有四个项目和两个核心。项目一：“Energy Landscapes Encoding Function in LDH Investigated Over Broad Time Scales”将（1）探索从皮秒到毫秒的构象运动如何有助于乳酸脱氢酶的过渡态形成，以及不同时间尺度上的运动如何相互关联，（2）探索促进振动对酶催化的贡献。项目二：“动力学和嘌呤核苷磷酸化酶的过渡态”研究（1）运动导致过渡态形成的PNP和（2）过渡态的性质PNP通过定位和表征动态促进振动和产生振动改变酶的局部和集体键动力学改变的概率达到过渡态。项目三：“绘制DHFR中催化的能量景观”旨在（1）确定二氢叶酸还原酶中底物结合和米氏复合物形成以及偶联蛋白质运动的动力学;（2）确定DHFR中质子转移的动力学;（3）确定促进振动在DHFR催化反应中的作用。项目四：“酶催化中的能量景观和运动时间尺度”研究了多个时间尺度上的酶动力学，并通过以下方式为其他项目提供理论支持：（1）研究更长时间的构象运动如何有助于酶功能，以及原子细节，不同时间尺度上的运动如何相互关联;（2）确定蛋白质结构如何导致酶中的振动能量“通道”，并研究突变如何影响这种结构;（3）阐明了过渡态紧束缚的概念，并说明了在特定反应中，过渡态是如何接近和过渡的。设备核心（核心A）支持该计划的专用综合仪器套件。管理核心（核心B）管理计划项目。

DESCRIPTION (provided by applicant): The goal of this Program Project, entitled Protein Dynamics in Enzymatic Catalysis, is to study atomic motion in enzymes. We propose to study concepts of how the dynamical nature of proteins affects enzymic function and the energy landscape of enzymes from enzyme-substrate to on-enzyme transition state transition state formation. We bring together a skilled research group of diverse backgrounds all aimed at understanding enzyme function. Importantly, we bring to bear unique, advanced, and effective experimental and theoretical approaches sensitive to the evolution of protein structure on multiple time scales, from ps to minutes. There are four projects and two cores. Project 1: 'Energy Landscapes Encoding Function in LDH Investigated Over Broad Time Scales' will (1) probe how conformational motion from picoseconds to milliseconds contributes transition state formation in lactate dehydrogenase and how motions on different timescales are related to each other and (2) probe the contribution of promoting vibrations to enzymic catalysis. Project 2: 'Dynamics and the Transition State of Purine Nucleoside Phosphorylase' studies (1) the motions leading to transition state formation in PNP and (2) the nature of the transition state in PNP by locating and characterizing dynamic promoting vibrations and by generating a vibrationally altered enzyme whose local and collective bond dynamics alter the probability of reaching the transition state. Project 3: 'Mapping the Energy Landscape of Catalysis in DHFR' aims to (1) determine the dynamics of substrate binding and Michaelis complex formation and coupled protein motions in dihydrofolate reductase; (2) determine the dynamics of proton transfer in DHFR; and (3) determine the role of promoting vibrations in the catalytic reaction of DHFR. Project 4: 'Energy Landscapes and Motional Timescales in Enzyme Catalysis' investigates dynamics in enzymes on multiple time scales and provides theoretical support to the other projects by (1) investigating how longer time conformational motion contributes to enzyme function, and in atomic detail, how motions at different timescales are related to each other; (2) determining how protein architecture results in vibrational energy "channeling" in enzymes and study how mutation effects this architecture; and (3) elucidating the concept of the tight binding of the transition state and show how, in a specific reaction, the transition state is approached and transited. The Equipment Core (Core A) supports the specialized comprehensive suite of instrumentation for the Program. The Administrative Core (Core B) administers the Program Project.