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。尽管有强烈的兴趣，生物分子的三维结构及其动力学的研究 由于生长适合于X射线衍射的3D晶体的固有困难以及其 对于溶液NMR研究，溶解度差。我们提出了一个瞬态二维红外方法，将解决的问题， 构象动力学和结构变化的主链和侧链运动直接，特别是当 生物分子在明确定义的初始条件下开始，然后在短脉冲光解时， 可以通过2DIR光谱法跟踪得到的结构分布。在这项研究中，A 将开发光谱工具，以绘制出两种结构运动，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 通过弱结合力进行识别和自组装。关键结构的快速动力学 RNA或抗菌肽（AMP）作用中的事件将在时间尺度上测量， 旋转周期（fs-ps）的显着构象重组所需的（ns-ms），通过采用 我们的瞬态二维红外方法。对非平衡动力学的真实的时间观测将提供一个原子 选择的结构如何遍历反应路径到稳定的最终状态的水平视图。这些信息将 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联合收割机技术（例如：光引发、pH跳变等） 传统上用于使用来自的信息包确定线性光谱中的动力学 用二维红外光谱进行探测。二维红外光谱将提供足够的结构和时间分辨率， 产生分子运动的快照，沿着特定生物事件的反应途径。特别是， 我们将同时测量生物分子内的距离和角度， 动力学，包括氢键交换，耦合水动力学和极性残留场波动，周围 每个单独的探针。通过利用各种启动技术的优势，我们将剖析侧面 链运动和整体结构变化负责分子识别，折叠和分子 AMP活性的组装。此外，我们将解开的损失氢键，基地堆叠， 进化的紧凑性，以揭示RNA折叠/解折叠的机制途径的分子细节。 更广泛的目标是获得一个化学键尺度的相互作用，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， 疾病，如狼疮，他们不像蛋白质错误折叠导致阿尔茨海默氏病， example.这项工作将有助于揭示这些非天然折叠的原因。此外，关于AMP， 其中一些裂解肽可能是破坏癌细胞的关键，并标志着癌细胞的发展。 可以靶向特定脂质组合物的治疗剂。