Protein Dynamics in Enzymatic Catalysis

酶催化中的蛋白质动力学

• 批准号: 9317648
• 负责人: Robert Callender
• 金额: $ 19.64万
• 依托单位: ALBERT EINSTEIN COLLEGE OF MEDICINE, INC
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-05-01 至 2019-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9317648
• 关键词: Active Sites; Allosteric Regulation; Area; Binding; Biological Preservation; Catalysis; Characteristics; Code; Complex; Coupled; Development; Drug effect disorder; Elements; Engineering; Enzyme Inhibitor Drugs; Enzyme Inhibitors; Enzyme Interaction; Enzymes; Foundations; Goals; Grant; Knowledge; Methods; Motion; Nature; Protein Dynamics; Proteins; Regulation; Research; Staging; Structure; Time; Ursidae Family; Work; base; bindin; design; inhibitor/antagonist; novel strategies; novel therapeutics; programs; protein function; protein structure; public health relevance; research study; small molecule; synthetic enzyme; theories; vibration

DESCRIPTION (provided by applicant): We propose to bring our Enzyme Dynamics Program into an uncharted area of inquiry with this renewal: bridging the gap from observation to design. Progress made thus far, developing powerful new approaches and a deep knowledge of the dynamical nature of enzymes, has set the stage for a fundamentally new approach to enzyme and inhibitor design based on dynamics. The overall objective of the research is the development of rational design principles based on dynamics for both 'allosteric' effectors and inhibitors for naturally occurring enzymes and rationally designed synthetic enzymes. The key to achieving this goal is to understand protein architectural design features that yield specific, functionally important dynamics. We bring together a skilled research group of diverse backgrounds all aimed at understanding enzyme function. This group has proven its ability to work closely in collaborative research over a decade. Importantly, we bring to bear unique, advanced, and effective experimental and theoretical approaches sensitive to the characteristics of protein structure and the dynamics this structure engenders on multiple time scales, from fs to ms or longer. This Program consists of four Projects with, collectively, two overall Aims: (1) To determine, via integrated application of experiment and theory, the elements of protein structure that create specific dynamics that are part of enzymatic catalysis on all relevant timescales. We will study how protein dynamics, particularly focused on the energy landscape of the Michaelis complex and motion of the promoting vibrations, is coupled to allostery and how this concept can be expanded to fully elucidate allosteric regulation of proteins. This presents a potential paradigm shift for protein and enzyme regulation via new drug action. In addition, a deeper understanding of transition state passage leaves us with the view that transition state inhibitors often do not function by "locking in" a specific structure, but rather by preserving dynamics at the transition state. We will investigate this new principle of strong inhibitor bindin via dynamic preservation as a paradigm for enzyme function and inhibition. (2) To use the understanding of how important functional dynamics are coded into the protein structure gained in (1) as a means to manipulate them in order to modify protein function. This objective comprises several parts. One is to design active site inhibitors against the dynamical nature of the enzyme. Another is to design small molecules to modify the dynamical nature through an 'allosteric' action which will either down or up-regulate activity and/or binding of substrate. The third is to develop methods to design rate controlling dynamics on a variety of timescales into engineered enzymes.

描述（由申请人提供）：我们建议将我们的酶动力学程序带入未知的调查领域，并通过此更新：弥合从观察到设计的差距。迄今为止取得的进步是，开发了强大的新方法以及对酶动力学性质的深入了解，为基于动态的酶和抑制剂设计的根本新方法奠定了基础。该研究的总体目的是基于“变构”效应子的动力学和自然存在的酶和合理设计的合成酶的抑制剂的制定理性设计原理。实现此目标的关键是了解蛋白质体系结构设计特征，这些特征会产生特定的，功能上重要的动态。我们汇集了一个熟练的研究小组，这些研究小组旨在了解酶功能。该小组已经证明了十年来其在协作研究中紧密工作的能力。重要的是，我们带来了对蛋白质结构的特征和动力学敏感的独特，先进和有效的实验和理论方法，这种结构在从FS到MS或更长的多个时间尺度上产生。该程序由四个项目组成，共同具有两个总体目的：（1）通过实验和理论的综合应用来确定蛋白质结构的要素，这些蛋白质结构的要素创建了特定动力学，这些动态是所有相关时间表上酶促催化的一部分。我们将研究蛋白质动力学，尤其是专注于迈克尔斯复合物的能量景观和促进振动的运动，与变构相结合，以及如何扩展该概念以完全阐明蛋白质的变构调节。这为蛋白质和酶调节的潜在范式转移带来了新的药物作用。此外，对过渡状态的更深入的了解使我们认为过渡状态抑制剂通常不会通过“锁定”特定结构，而是通过在过渡状态下保留动力学来起作用。我们将通过动态保存作为酶功能和抑制作用的范式来研究强抑制剂结合素的新原理。 （2）使用对如何将功能动力学编码为（1）中获得的蛋白质结构的理解来操纵它们以修改蛋白质功能。这个目标包括多个部分。一种是针对酶的动力学性质设计活性位点抑制剂。另一个是设计小分子来通过“变构”作用来修改动力学性质，该动作将降低或上调底物的活性和/或结合。这 第三是开发方法，将各种时间尺度上的动力学设计速率控制到工程酶中。