Developing Infrared 'FRET' Analogs to Capture Molecular Snapshots through Non-equilibrium 2D IR Spectroscopy of Recognition and Self-Assembly in Biologically Relevant Systems

开发红外“FRET”类似物，通过生物相关系统中的非平衡二维红外光谱识别和自组装捕获分子快照

• 批准号: 9377685
• 负责人: Matthew J Tucker
• 金额: $ 34.96万
• 依托单位: UNIVERSITY OF NEVADA RENO
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2021-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9377685
• 关键词: Address; Alzheimer' s Disease; Amino Acids; Autoimmune Diseases; Biological; Biological Models; Biological Process; Complex; Coupled; Coupling; Crowding; Crystallization; Cytolysis; Disease; Electrostatics; Environment; Equilibrium; Event; Evolution; Fatty Acids; Fingers; Fluorescence Resonance Energy Transfer; Free Energy; Frequencies; Head; Hydrogen Bonding; Hydrophobicity; Individual; Kinetics; Label; Lead; Lipids; Location; Lupus; Lytic; Maps; Measurement; Measures; Medical; Membrane; Methods; Modeling; Molecular; Molecular Conformation; Monitor; Motion; Nucleic Acids; Pathway interactions; Peptides; Physiologic pulse; Play; Process; Proteins; RNA; RNA Folding; Reaction; Research; Resolution; Role; Rotation; Side; Site; Solubility; Solvents; Spectrum Analysis; Structure; System; Techniques; Testing; Time; Vertebral column; Virus Diseases; Water; Work; X ray diffraction analysis; X-Ray Crystallography; X-Ray Diffraction; analog; antimicrobial peptide; base; cancer cell; chemical bond; driving force; experimental study; innovation; insight; interest; molecular assembly/self assembly; molecular dynamics; molecular recognition; nanosecond; non-Native; peptide I; photolysis; prevent; protein aminoacid sequence; self assembly; simulation; single bond; spectroscopic survey; stem; temperature jump; therapeutic development; therapeutic target; three dimensional structure; tool; two-dimensional; vibration

Project Summary. Despite strong interest, the study of the 3D structures of biomolecules and their dynamics remain challenging by the inherent difficulty in growing 3D crystals suitable for X-ray diffraction and by their poor solubility for solution NMR studies. We propose a transient 2D IR approach that will address questions of conformational dynamics and structural change of backbone and side chain motions directly, especially when the biomolecule begins in a well-defined initial condition, and then upon short pulse photolysis, evolution of the resulting structure distributions can be tracked by 2D IR spectroscopy. In the course of this research, a spectroscopic tool will be developed to map out both structural motions while concurrently providing insight into the solvent dynamics at each labelled site and how their corresponding locations promote the molecular recognition and self-assembly through weak associative forces. The fast dynamics during the key structural events in RNA or antimicrobial peptide (AMP) action will be measured on time scales ranging from single bond rotational periods (fs-ps) to those required for significant conformational reorganization (ns-ms) by employing our transient 2D IR methods. Observations in real time of the non-equilibirum dynamics will provide an atomic level view of how chosen structures traverse reaction paths to stable final states. This information will then be used to challenge and test cutting edge non-equilibrium molecular dynamics simulations. The research outlined herein aims to combine techniques (eg. photo-initation, pH-jump, etc.) traditionally used to determine kinetics in linear spectroscopies with the information package that comes from probing with 2D IR spectroscopy. 2D IR spectroscopy will afford sufficient structural and time resolution to generate snapshots of molecular motions along the reaction pathway of specific biological events. In particular, we will simultaneously measure distances and angles within biomolecules and also detect the local vibrational dynamics, including H-bond exchange, coupled water dynamics and polar residue field fluctuations, around each individual probe. By harnessing the strengths of various initiation techniques, we will dissect the side chain motions and global structural changes responsible for molecular recognition, folding, and molecular assembly of AMP activity. Furthermore, we will disentangle the loss of hydrogen bonding, base stacking, and evolving compactness to uncover molecular details of the mechanistic pathway of RNA folding/unfolding. The broader objective is to obtain a chemical bond scale description of interactions that lead to productive conformational changes. Although RNA misfolds are believed to be responsible for autoimmune diseases such as lupus, they are not as well understood as protein misfolds leading to Alzheimer's disease for example. This work will help uncover the reasons for these non-native folds. Moreover, in regards to AMPs, some of these lytic peptides may hold the key to destroy cancer cells and mark the way for the development of therapeutics that can target specific lipid composition.

项目摘要。尽管人们对生物分子的 3D 结构及其动力学的研究抱有浓厚的兴趣 由于生长适合 X 射线衍射的 3D 晶体的固有困难及其 溶液 NMR 研究的溶解度较差。我们提出了一种瞬态 2D IR 方法，该方法将解决以下问题 直接主链和侧链运动的构象动力学和结构变化，特别是当 生物分子开始于明确的初始条件，然后通过短脉冲光解作用，进化出 由此产生的结构分布可以通过二维红外光谱进行跟踪。在本研究过程中，一个 将开发光谱工具来绘制两种结构运动，同时提供对 每个标记位点的溶剂动力学以及它们相应的位置如何促进分子 通过弱联合力进行识别和自组装。关键结构过程中的快速动态 RNA 或抗菌肽 (AMP) 作用中的事件将在单键范围内的时间尺度上进行测量 通过使用旋转周期（fs-ps）到显着构象重组（ns-ms）所需的周期 我们的瞬态二维红外方法。对非平衡动力学的实时观察将提供原子 所选结构如何穿越反应路径达到稳定最终状态的水平视图。该信息随后将被 用于挑战和测试尖端的非平衡分子动力学模拟。 本文概述的研究旨在将技术（例如光引发、pH 跳跃等）与 传统上用于确定线性光谱中的动力学，其信息包来自 2D IR 光谱探测。二维红外光谱将提供足够的结构和时间分辨率 沿着特定生物事件的反应途径生成分子运动的快照。尤其， 我们将同时测量生物分子内的距离和角度，并检测局部振动 动力学，包括氢键交换、耦合水动力学和极性残留场波动， 每个单独的探头。通过利用各种启动技术的优势，我们将剖析侧面 链运动和全局结构变化负责分子识别、折叠和分子 AMP 活性的组装。此外，我们将解开氢键的损失、碱基堆积和 不断发展的紧凑性以揭示 RNA 折叠/解折叠机制途径的分子细节。 更广泛的目标是获得相互作用的化学键尺度描述，从而导致 生产性构象变化。尽管 RNA 错误折叠被认为是导致自身免疫性疾病的原因 对于狼疮等疾病，人们对它们的了解不如对导致阿尔茨海默氏病的蛋白质错误折叠了解的多。 例子。这项工作将有助于揭示这些非原生折叠的原因。此外，关于 AMP， 其中一些裂解肽可能是摧毁癌细胞的关键，并为癌症的发展指明了道路。 可以针对特定脂质成分的疗法。