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: 10651833
• 负责人: Songi Han
• 金额: $ 37.39万
• 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/10651833
• 关键词: 2,4-Dinitrophenol; Affinity; Binding; Binding Sites; Biological; Characteristics; Chemistry; Code; Detection; Disease; Electron Spin Resonance Spectroscopy; 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; Rationalization; Resolution; Site; Solubility; Spectrum Analysis; Structure; Structure-Activity Relationship; Surface; Translating; Translations; Vision; Water; aggregation pathway; biochemical tools; design; globular protein; novel strategies; 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： 前所未有的高分辨率生物构件结构的出现正在彻底改变 我们可以使蛋白质机制合理化，但该结构仅提供了必要但不充分的起始点 旨在揭示蛋白质的特性、活性和功能。理解上存在基础知识差距 将蛋白质结构和表面化学转化为蛋白质特性和功能。即使是房产 广泛研究，因为蛋白质溶解度不能用我们目前的已知蛋白质结构先验预测 工具和知识，正如观察到许多单一突变调用最小的结构所强调的那样 变化的同时极大地改变了稳定性、属性和可聚集性。我们的愿景是揭开密码 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。汉人 实验室正在努力实现这种转化，除其他外，借助先进的光谱方法来探测 局部蛋白质动力学、位点特异性水合特性和构象集合。这些测量 通过现有最先进的工具实现，例如电子顺磁共振 (EPR) 线形 分析、脉冲偶极 EPR 和固态核磁共振 (NMR) 以及新方法 汉实验室开发的，如Overhauser动态核极化（ODNP）和其他DNP放大 核磁共振方法。这些方法的结合将能够检测蛋白质表面水合、拓扑结构 和相互作用，在生理条件下的稀溶液状态下具有增强的灵敏度。汉实验室 将系统地应用和完善研究蛋白质稳定性、相互作用、相分离的工具和方法， 低聚到聚集。五年目标重点关注以下选定类别的蛋白质。我们选择 球状蛋白 LOV 作为揭示结构与功能关系的模型，以帮助理性蛋白质 工程导致诸如增强的结合亲和力、变构、荧光特性和受控特性等特性 构象可塑性。我们选择 tau 蛋白来研究本质上无序的蛋白 (IDP)，其中 单点突变和微妙的伙伴相互作用显着调整其稳定性和聚集倾向 在疾病背景下。我们的目标是揭示其中的机制，例如通过水合扰动或构象 整体转变，突变和其他修饰通过这种转变调节聚集倾向。最后，我们 旨在揭示寡聚化的结构和机制基础以及功能后果 两种跨膜蛋白，PR 和 A2A。该提案的长期目标是破译设计规则 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-蛋白质组装的结合位点， 并选择或设计特定的聚合路径。

项目成果

Lipid membrane mimetics and oligomerization tune functional properties of proteorhodopsin

脂质膜模拟物和寡聚调节蛋白视紫红质的功能特性

• DOI: 10.1016/j.bpj.2022.11.012
• 发表时间: 2022
• 期刊: Biophysical Journal
• 影响因子: 3.4
• 作者: Han, Chung-Ta;Nguyen, Khanh Dinh;Berkow, Maxwell W.;Hussain, Sunyia;Kiani, Ahmad;Kinnebrew, Maia;Idso, Matthew N.;Baxter, Naomi;Chang, Evelyn;Aye, Emily
• 通讯作者: Aye, Emily