Capturing Transient Protein and Nucleic Acid Structures During Their Functions on Multiple Spatial and Temporal Scales

捕获在多个空间和时间尺度上发挥作用期间的瞬时蛋白质和核酸结构

基本信息

批准号：
10264031
负责人：
Lin X Chen
金额：
$ 35.04万
依托单位：
NORTHWESTERN UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-07-01 至 2024-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10264031
关键词：
Active Sites Antineoplastic Agents Binding Biochemical Reaction Biological Biological Process Calcium ion Catalysis Computing Methodologies Consumption Coupled Crystallization DNA Structure Data Data Analyses Data Collection Deposition Diffusion Drug Delivery Systems Drug Design Electromagnetic Fields Environment Enzymes Evolution Future Health Human Investigation Kinetics Laboratories Laboratory Research Lasers Ligands Light Lipids Maps Measures Membrane Metabolism Metals Methodology Methods Microfluidic Microchips Modeling Modification Molecular Molecular Conformation Molecular Structure Motion Nucleic Acid Folding Nucleic Acids Oncogenes Optics Oxidation-Reduction Phase Phase Transition Physiologic pulse Physiological Processes Protein Conformation Protein Dynamics Proteins Pump RNA Conformation Reaction Regulation Research Resolution Respiration Roentgen Rays Sampling Scientist Signal Transduction Source Spectrum Analysis Stimulus Structure Synchrotrons System Temperature Time Translations Work X ray diffraction analysis X ray spectroscopy X-Ray Crystallography absorption biological systems biomacromolecule chromophore cytochrome c oxidase design emission spectroscopy environmental change improved inhibitor/antagonist innovation insight instrumentation macromolecule milligram millisecond molecular dynamics nanocarrier nanometer novel novel strategies nucleic acid structure programs protein data bank protein folding protein structure response simulation three dimensional structure time use tool x-ray free-electron laser

项目摘要

Summary/Abstract The long term objective of the proposed research is to develop an integrated instrumentation capable of studying protein/nucleic acid structural dynamics that are relevant to their functions on the time scales from femtosecond to millisecond in order to gain new insight into correlations of active site structures and global conformations of these molecules. Snapshots of solution phase molecular structures over different spatial scales, from sub-Ångström for active sites to several nanometers for overall conformation, will be captured using time-resolved X-ray spectroscopy and scattering. These structural studies will be combined with advanced molecular dynamics simulations that will generate detailed atomistic dynamics consistent with measured scattering profiles over a wide-range of temporal scales from femtosecond to millisecond. The proposed research is complementary to single crystal X-ray diffraction, and intends to map reaction trajectories through three-dimensional structures as a function time in media that mimic biological environments. In order to detect structural changes in an ensemble, reaction triggers must be designed to create sudden environmental changes that synchronize actions of the molecules with much higher time resolution than traditional mixing. The program has three main innovations from previous studies: 1) to develop triggering sources beyond direct light excitation used in the past to initiate reactions to overcome the limitation that very few biological systems related to human health are light activated for their function; 2) to develop novel sample delivery system that reduces the sample consumption by a factor of 100 and enables many precious laboratory samples to be studied using the time-resolved X-ray methods; and 3) to develop a combined approach in data analyses using advanced molecular dynamics simulation coupled to time-dependent X-ray scattering data to extract structures with improved structural accuracy especially for those coexisting species. The above innovation in methodology will allow us to investigate a number of systems that are biologically significant for enzymatic reactions, signal sensing, protein/nucleic acid folding/unfolding as well as lipids phase transitions. Several systems are chosen for the proposed studies to capture transient structures of, a) local metal center and global protein conformations of cytochrome c oxidase model proteins triggered by photodissociation of inhibitors; b) protein folding induced by calcium ion a concentration jump; c) temperature-induced RNA conformational changes sensing signal for translation; d) pH-dependent DNA structures for human oncogene regulation and e) pH-responsive lipid nanocarrier assembly for anticancer drug delivery. These structural results combined with those of reaction kinetics from optical transient spectroscopy will provide guidance for modulating protein and nucleic acid functions via structural modifications, which will lead to impacts in drug design, enzymatic function enhancement, catalysis, as well as theoretical calculations.

摘要/摘要拟议研究的长期目标是开发一种能够研究与其在时间尺度上的功能相关的蛋白质/核酸结构动力学从飞秒到毫秒，以获得对活性位点结构和这些分子的整体构象不同的溶液相分子结构的快照。空间尺度，从活性位点的亚埃级到整体构象的几纳米，将是使用时间分辨X射线光谱和散射捕获这些结构研究将被结合起来。通过先进的分子动力学模拟，将生成一致的详细原子动力学在从飞秒到毫秒的广泛时间尺度上测量散射剖面。拟议的研究是对单晶 X 射线衍射的补充，旨在绘制反应图谱通过三维结构的轨迹作为模仿生物的媒体中的功能时间为了检测整体的结构变化，反应触发器必须设计为产生突然的环境变化，使分子的行为与更长的时间同步与传统混合相比，该程序具有三个主要创新点：1）开发超越过去用于引发反应的直接光激发的触发源来克服与人类健康相关的生物系统很少有光激活其功能的局限性； 2) 开发新型样品输送系统，将样品消耗量减少 100 倍能够使用时间分辨 X 射线方法研究许多珍贵的实验室样品；3) 使用先进的分子动力学模拟耦合来开发数据分析的组合方法与时间相关的 X 射线散射数据可提取结构，特别是提高结构精度对于那些共存的物种，上述方法上的创新将使我们能够研究一些。对酶反应、信号传感、蛋白质/核酸具有生物学意义的系统折叠/展开以及脂质相变被选择用于拟议的研究。捕获 a) 细胞色素 c 的局部金属中心和全局蛋白质构象的瞬时结构抑制剂光解引发的氧化酶模型蛋白 b) 钙诱导的蛋白折叠； c) 温度诱导的RNA构象变化传感信号翻译；d) 用于人类癌基因调节的 pH 依赖性 DNA 结构和 e) pH 响应脂质用于抗癌药物递送的纳米载体组装。这些结构结果与反应结果相结合。光学瞬态光谱动力学将为调节蛋白质和核酸提供指导通过结构修饰发挥功能，这将影响药物设计、酶功能增强、催化以及理论计算。