Protein Dynamics in Enzymatic Catalysis

项目描述（由申请人提供）：本项目名为“酶催化中的蛋白质动力学”，旨在研究酶的原子运动。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从酶-底物到酶上过渡态过渡态形成的能量景观的概念。我们汇集了一个不同背景的技术研究小组，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，对蛋白质结构在多个时间尺度上的进化敏感，从ps到分钟。有四个项目和两个核心。项目1：“宽时间尺度上LDH的能量景观编码功能研究”将(1)探索从皮秒到毫秒的构象运动如何促进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2：“嘌呤核苷磷酸化酶的动力学和过渡态”研究(1)PNP中导致过渡态形成的运动，(2)通过定位和表征动态促进振动，并通过产生振动改变的酶，其局部和集体键动力学改变了达到过渡态的可能性，研究PNP中过渡态的性质。项目3：“绘制DHFR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Michaelis复合物形成以及耦合蛋白质运动的动力学；(2)确定DHFR中质子转移动力学；(3)确定促进振动在DHFR催化反应中的作用。项目4：“酶催化中的能量景观和运动时间尺度”研究酶在多个时间尺度上的动力学，并通过(1)研究长时间构象运动对酶功能的贡献，以及在原子细节上，不同时间尺度上的运动如何相互关联，为其他项目提供理论支持；(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)阐明过渡态紧密结合的概念，并说明在具体反应中，过渡态是如何接近和过渡的。设备核心（Core A）支持该计划的专业综合仪器套件。行政核心（核心B）管理该计划项目。

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. PUBLIC HEALTH RELEVANCE: Enzymes are targets for a broad array of Pharmaceuticals. How atomic motion in proteins brings about enzymatic catalysis is very poorly understood. The detailed structure of the enzymatic transition state is a powerful target for drug design, and increased knowledge of how enzymes form this state is fundamental for all catalysts and specifically for designing new classes of drugs.