Protein Dynamics in Enzymatic Catalysis

描述(由申请人提供)：我们建议将我们的酶动力学项目带入一个未知的研究领域：弥合从观察到设计的差距。到目前为止所取得的进展，开发了强大的新方法和对酶的动力学性质的深入了解，为基于动力学的酶和抑制剂设计的根本新方法奠定了基础。这项研究的总体目标是开发基于动力学的合理设计原则，用于自然产生的酶的‘变构’效应器和抑制剂以及合理设计的合成酶。实现这一目标的关键是了解产生特定的、功能重要的动力学的蛋白质结构设计特征。我们聚集了一个具有不同背景的熟练研究小组，他们都是为了了解酶的功能。这个小组已经证明了它在十多年的合作研究中密切合作的能力。重要的是，我们带来了独特的、先进的和有效的实验和理论方法，这些方法对蛋白质结构的特征和这种结构在从fS到ms或更长时间的多个时间尺度上产生的动力学敏感。该计划由四个项目组成，总体目标有两个：(1)通过实验和理论的综合应用，确定在所有相关时间尺度上产生特定动力学的蛋白质结构元素，这些元素是酶催化的一部分。我们将研究蛋白质动力学，特别是米氏复合体的能量景观和促进振动的运动，是如何与变构耦合的，以及如何扩展这一概念以充分阐明蛋白质的变构调节。这为通过新药作用调节蛋白质和酶提供了一种潜在的范式转变。此外，对过渡态途径的更深层次的理解给我们留下了这样的观点，即过渡态抑制物通常不是通过“锁定”特定结构发挥作用的，而是通过保持过渡态的动力学来发挥作用的。我们将通过动态保存来研究这种强抑制物结合的新原理，作为酶功能和抑制的范例。(2)利用对(1)中所获得的蛋白质结构如何编码的重要功能动力学的理解作为操纵它们以改变蛋白质功能的一种手段。这一目标包括几个部分。一种是针对酶的动态性质设计活性部位抑制剂。另一种是设计小分子，通过‘变构’作用来改变动力学性质，这种作用将下调或上调底物的活性和/或结合。这个 第三是开发方法，将各种时间尺度上的速率控制动力学设计成工程酶。

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.