Understanding allostery from the perspective of protein dynamics and energy flows

项目摘要/摘要 变构是所有蛋白质固有的蛋白质功能的一个基本方面。它在以下方面具有重要影响 酶催化、信号转导、药物设计和蛋白质工程。对机制的理解 变构理论具有根本性的重要性。对其机理的严格理解具有根本性的意义。 重要性。变构的本质是效应器与变构位点的结合。 活性部位会改变活性部位的蛋白质功能(例如底物亲和力的增加)。两个基本原则 问题是核心。1)效应器结合引起的活性部位的改变是什么导致的 底物亲和力增强？这个问题涉及变构信号的性质。2)变化如何？ 在效应器结合引入的变构部位，传递到活性部位？这个问题涉及到 变构途径。我们提出了一种新的方法，在一个统一的 框架：变构信号是由效应器结合和变构引起的功能动力学变化 通路是功能动力学的过渡通路。我们开发的能量流理论为我们提供了 一种严格的方法来确定功能动力学的途径和机制，因此途径和 变构机制。 我们建议用能量流方法来理解两个典型体系中的变构。目标 1.鉴定PDZ结构域中的变构途径，并阐明其变构机制。PDZ结构域 都是“动态变构”的雏形，引起了人们的强烈关注。变构残留物的鉴定 然而，现有的方法不能在严格的基础上与PDZ域的信号转导联系在一起。 PDZ结构域中配体结合和能量驰豫的能流分析将使我们能够严格地 确定其变构和信号转导途径。目标2：确定变构途径 对HIV-1蛋白酶(HIV-PR)的非活性部位耐药突变负责，并阐明 变构机制。我们的初步结果确定这些残留物是襟翼中的重要参与者- 开放动力学，表明它们的抗药性是通过变构实现的。

Project Summary/Abstract Allostery is a fundamental aspect of protein function intrinsic to all proteins. It has important implications in enzyme catalysis, signal transduction, drug design and protein engineering. Understanding the mechanism of allostery is of fundamental importance. A rigorous understanding of its mechanism is of fundamental importance. The essence of allostery is that the binding of an effector to an allosteric site distal from the active site changes protein function (e.g. an increase in substrate affinity) at the active site. Two fundamental questions are central. 1) What is the change to the active site, induced by effector binding, that leads to the increased substrate affinity? This question concerns the nature of the allosteric signal. 2) How is the change at the allosteric site, introduced by effector binding, communicated to the active site? This question concerns the allosteric pathway. We propose a new approach to address both questions within a single unified framework: allosteric signal is a change in functional dynamics induced by effector-binding and allosteric pathway is the transition pathway of functional dynamics. The energy flow theory we developed provides us a rigorous approach to identify the pathway and mechanism of functional dynamics, hence the pathway and mechanism of allostery. We propose to apply the energy flow method to understand allostery in two representative systems. Aim 1: Identify the allosteric pathway in PDZ domain and elucidate its allosteric mechanism. PDZ domains are a prototype of “dynamic allostery” and attracted intensive attention. Allosteric residues identified by existing methods, however, cannot be identified with signal transduction of PDZ domain on a rigorous ground. Energy flow analysis on ligand-binding and energy relaxation in PDZ domain will enable us to rigorously determine its pathway for allostery and signal transduction. Aim 2: Identify the allosteric pathway responsible for non-active-site drug-resistant mutations in HIV-1 protease (HIV-PR) and elucidate the allosteric mechanism. Our Preliminary Results identified these residues as prominent players in the flap- opening dynamics, suggesting that their drug resistance is achieved via allostery.