MIRA: Uncover Design Rules for Interaction and Assembly of Nature's Molecular Machines

MIRA：揭示自然分子机器相互作用和组装的设计规则

• 批准号: 10205773
• 负责人: Songi Han
• 金额: $ 9.41万
• 依托单位: UNIVERSITY OF CALIFORNIA SANTA BARBARA
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10205773
• 关键词: 2,4-Dinitrophenol; Affinity; Binding; Binding Sites; Biological; Characteristics; Chemistry; Code; Detection; Disease; Electron Spin Resonance Spectroscopy; Funding; Goals; Hydration status; Integral Membrane Protein; Knowledge; Learning; Measurement; Membrane Proteins; Methods; Modeling; Modification; Molecular; Molecular Conformation; Molecular Machines; Mutation; Nature; Nuclear; Nuclear Magnetic Resonance; Phase; Physiologic pulse; Physiological; Point Mutation; Property; Protein Conformation; Protein Dynamics; Protein Engineering; Proteins; Resolution; Site; Solubility; Spectrum Analysis; Structure; Structure-Activity Relationship; Surface; Translating; Translations; Vision; Water; aggregation pathway; biochemical tools; design; globular protein; novel strategies; parent grant; protein structure; solid state nuclear magnetic resonance; tau Proteins; tool

Project Summary/Abstract: The emergence of unprecedented high-resolution structures of biological building blocks is revolutionizing the way we can rationalize the protein machinery, yet the structure only offers a necessary, but insufficient, starting point to uncover protein property, activity and function. There is a fundamental knowledge gap in understanding the translation of protein structure and surface chemistry into protein property and function. Even a property as widely studied as protein solubility cannot be a priori predicted from a known protein structure with our current tools and knowledge, as underscored by the observation that many single mutations invoke minimal structural changes while dramatically changing the stability, property and aggregability. Our vision is to uncover the code for translating protein surface structural properties into protein surface activity, interaction and function. The Han lab is working on achieving such translation, among others, aided by advanced spectroscopy methods that probe local protein dynamics, site-specific hydration properties and conformational ensembles. These measurements are enabled by existing state-of-the-art tools, such as electron paramagnetic resonance (EPR) lineshape analysis, pulsed dipolar EPR and solid-state nuclear magnetic resonance (NMR), as well as novel approaches developed by the Han lab, such as Overhauser dynamic nuclear polarization (ODNP) and other DNP-amplified NMR methods. The combination of these methods will enable the detection of protein surface hydration, topology and interaction, in dilute solution state under physiological conditions and with enhanced sensitivity. The Han lab will systematically apply and refine the tools and methods to study protein stability, interaction, phase separation, oligomerization to aggregation. The five-year goals focus on the following select classes of proteins. We choose the globular protein LOV as a model to uncover the structure-function relationship to aid in rational protein engineering leading to properties such as enhanced binding affinity, allostery, fluorescent property and controlled conformational plasticity. We choose the protein tau to study an intrinsically disordered protein (IDP) for which single-point mutations and subtle partner interactions significantly tune its stability and aggregation propensity in disease contexts. Our goal will be to reveal the mechanisms, e.g. by hydration perturbation or conformational ensemble shifts, through which mutations and other modifications modulate aggregation propensity. Finally, we aim to uncover the structural and mechanistic basis, as well as functional consequences, of oligomerization of two trans-membrane proteins, PR and A2A. The long-term goal of this proposal is to decipher the design rules for interactions and active surfaces of proteins, so that from the protein surface structure and topology one can predict where the binding site is, or learn how to design one that rationally modulates protein-protein assembly, and select or design specific aggregation pathways.

项目摘要/摘要： 生物构建基础前所未有的高分辨率结构的出现正在革新 我们可以合理化蛋白质机械的方式，但是该结构只提供了必要但不足的开始 指出发现蛋白质特性，活性和功能。理解有根本的知识差距 蛋白质结构和表面化学的翻译成蛋白质特性和功能。甚至是财产 被广泛研究为蛋白质溶解度不能是从已知蛋白质结构中预测的先验 工具和知识，这是由于许多单一突变调用最小结构的观察结果所强调的 在大幅度改变稳定性，属性和汇总性的同时变化。我们的愿景是发现代码 用于将蛋白质表面结构特性转化为蛋白质表面活性，相互作用和功能。汉 实验室正在努力实现这种翻译，以及通过探测的高级光谱法帮助 局部蛋白质动力学，位点特异性水合特性和构象合奏。这些测量值 由现有的最新工具启用，例如电子顺磁共振（EPR）lineShape 分析，脉冲偶极EPR和固态核磁共振（NMR）以及新的接近 由HAN实验室开发的 NMR方法。这些方法的组合将使蛋白质表面水合检测，拓扑 和相互作用，在生理条件下稀释溶液状态，并具有增强的敏感性。汉实验室 将系统地应用并完善研究蛋白质稳定性，相互作用，相分离的工具和方法， 将聚集的寡聚化。五年目标集中于以下精选类别的蛋白质。我们选择 球状蛋白LOV是一个模型，以发现结构功能关系以帮助有助于理性蛋白 工程导致属性，例如增强的结合亲和力，变构，荧光特性和受控 构象可塑性。我们选择蛋白质tau来研究本质上无序的蛋白（IDP） 单点突变和微妙的伴侣相互作用显着调整其稳定性和聚合倾向 在疾病的情况下。我们的目标是揭示机制，例如通过水合扰动或构象 合奏转移，突变和其他修饰通过这些变化调节聚集倾向。最后，我们 旨在揭示结构和机械基础以及功能后果 两个跨膜蛋白，PR和A2A。该提议的长期目标是破译设计规则 对于蛋白质的相互作用和活性表面，因此从蛋白质表面结构和拓扑结构中可以 预测结合位点在哪里，或者学习如何设计一个合理调节蛋白质蛋白质组件的结合位点， 并选择或设计特定的聚合途径。