Dynamic Networks and Mechanisms of Allosteric Communication in Proteins

蛋白质变构通讯的动态网络和机制

• 批准号: 7933132
• 负责人: Andrew L Lee
• 金额: $ 9.76万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2010-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7933132
• 关键词: Address; Allosteric Regulation; Behavior; Binding; Biological; Biological Process; Biology; Biotechnology; Cell division; Chemicals; Chemotaxis; Communication; Coupling; Data; Databases; Distal; Drug effect disorder; Drug resistance; Escherichia coli; Event; Fluorescence; Foundations; Free Energy; Funding; Goals; Heart; Heterogeneity; Individual; Industry; Lead; Ligand Binding; Ligands; Light; Maps; Measurement; Measures; Mediating; Metabolism; Methodology; Methods; Modeling; Modification; Motion; Motor; Mutation; Pathway interactions; Pattern; Peptides; Pharmaceutical Preparations; Phosphorylation; Play; Population Dynamics; Process; Property; Protein Dynamics; Proteins; Regulation; Relative (related person); Relaxation; Research; Role; Serine Proteinase Inhibitors; Side; Signal Pathway; Signal Transduction; Site; Solutions; Stimulus; Structure; Surface; Technology; Tertiary Protein Structure; Testing; Therapeutic; Therapeutic Intervention; Thermodynamics; Time; base; beryllium fluoride; density; design; drug discovery; engineering design; falls; genetic regulatory protein; globular protein; mutant; protein folding; protein function; public health relevance; research study; response; theories

DESCRIPTION (provided by applicant): How proteins regulate themselves is a fundamental question in biology. Regulation of protein activity drives cell division, metabolism, signal transduction, and therapeutic intervention. The most common and versatile regulatory proteins are allosteric proteins. Allosteric proteins are distinguished by their capacity to respond to ligand binding or chemical modification at one site, and alter ligand binding or activity at a distal site. Although many allosteric proteins have been characterized structurally, and models of allostery exist, most of the details of how allosteric transitions proceed remain unknown. The long-range goal of this research is to experimentally reveal the time-resolved structural processes that constitute allosteric function. Central to the approach to be taken is the idea that proteins are highly dynamic, especially allosteric proteins, and that dynamic motions are an essential component of allosteric conformational change. Classical oligomeric allosteric proteins are too large for in-depth studies of site-specific dynamics by NMR. Therefore, the monomeric, 14 kDa bacterial response regulator CheY protein will be used as a model allosteric domain. CheY is a chemotaxis signal transduction protein that, upon phosphorylation at Asp-57, undergoes a conformational change at a distal surface that modulates binding to the flagellar motor. The ps-ns and ¿s-ms timescale dynamics of CheY will be extensively characterized in the absence and presence of phosphoryl group mimic, BeF3-, using NMR relaxation methods. In separate experiments, long-range thermodynamic couplings will be mapped using high-throughput methodology. Because, recently, long-range communication has been observed in proteins that are not functionally allosteric, mechanisms similar to those in allosteric proteins may exist in non-allosteric proteins, albeit to a lesser extent. The serine protease inhibitor eglin c is a good example of this: conservative mutations in eglin c lead to long-range dynamic effects in the absence of structural change. In the proposed research, four Specific Aims fall into two main thrusts. In the first thrust, patterns of long-range coupling (or "communication") - both dynamic and thermodynamic - will be compared between the non-allosteric eglin c and the allosteric CheY. These comparisons will shed light on any basic differences in coupling networks between allosteric and non-allosteric proteins; they will also provide a test of the role of dynamics in mediating thermodynamic coupling. In the second thrust, the mechanism of intramolecular signal transduction in CheY will be investigated from an NMR dynamics perspective, using CheY's various biological states and mutations that modulate its activity. Overall, by increasing understanding of the biophysical properties and role of dynamics in allostery, this research will help to lay the foundation for the rational design of allosteric proteins and drugs. PUBLIC HEALTH RELEVANCE: Allosteric conformational change in proteins lies at the heart of regulatory processes such as cell division, metabolism, signal transduction, and drug action. This research seeks to understand the dynamic underpinnings of allostery by experimentally contrasting motional dynamics in non-allosteric and allosteric proteins. The small bacterial signal transduction protein CheY will serve as a model allosteric domain. A detailed understanding of allosteric mechanisms will be needed to rationally design proteins and drugs that take advantage of allosteric principles, as well as understand mechanisms of drug resistance.

描述（由申请人提供）：蛋白质如何调节自身是生物学中的一个基本问题。蛋白质活性的调节驱动细胞分裂、代谢、信号转导和治疗干预。最常见和最通用的调节蛋白是变构蛋白。变构蛋白的特征在于它们在一个位点响应配体结合或化学修饰，并在远端位点改变配体结合或活性的能力。虽然许多变构蛋白质已经在结构上得到了表征，并且存在变构模型，但是关于变构转变如何进行的大部分细节仍然是未知的。本研究的长期目标是通过实验揭示构成变构功能的时间分辨结构过程。该方法的核心思想是蛋白质是高度动态的，特别是变构蛋白质，并且动态运动是变构构象变化的重要组成部分。经典的寡聚变构蛋白太大，无法通过NMR深入研究位点特异性动力学。因此，单体的14 kDa细菌反应调节剂CheY蛋白将被用作模型变构域。CheY是一种趋化性信号转导蛋白，在Asp-57磷酸化后，其远端表面发生构象变化，调节与鞭毛马达的结合。ps-ns和使用NMR弛豫方法，CheY的s-ms时间尺度动力学将在磷酰基模拟物BeF 3-的存在和不存在下被广泛表征。在单独的实验中，远程热力学耦合将使用高通量方法进行映射。因为，最近，已观察到的远程通信的蛋白质，不是功能变构，类似的机制，在变构蛋白质中可能存在于非变构蛋白质，虽然在较小的程度。丝氨酸蛋白酶抑制剂eglin c就是一个很好的例子：eglin c中的保守突变在没有结构变化的情况下会导致长期的动态效应。在拟议的研究中，四个具体目标分为两个主要目标。在第一个推力，模式的远程耦合（或“通信”）-动力学和热力学-将比较之间的非变构eglin c和变构的CheY。这些比较将揭示任何基本的差异，耦合网络之间的变构和非变构蛋白质，他们也将提供一个测试的作用，动力学介导的热力学耦合。在第二个推力，在CheY的分子内信号转导的机制将从NMR动力学的角度进行研究，使用CheY的各种生物状态和突变，调节其活动。总体而言，通过增加对生物物理特性和动力学在变构中的作用的理解，这项研究将有助于为变构蛋白质和药物的合理设计奠定基础。公共卫生相关性：蛋白质的变构构象变化是细胞分裂、代谢、信号转导和药物作用等调控过程的核心。本研究试图通过实验对比非变构和变构蛋白质的运动动力学来理解变构的动力学基础。小的细菌信号转导蛋白CheY将作为模型变构域。需要对变构机制有详细的了解，以合理地设计利用变构原理的蛋白质和药物，以及了解耐药性机制。