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

• 批准号: 10665090
• 负责人: Lin X Chen
• 金额: $ 35.14万
• 依托单位: NORTHWESTERN UNIVERSITY
• 依托单位国家: 美国
• 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/10665090
• 关键词: Active Sites; Antineoplastic Agents; Binding; Biochemical Reaction; Biological; Biological Process; Calcium ion; Catalysis; Computing Methodologies; Consumption; Coupled; DNA Structure; Data; Data Analyses; Data Collection; Deposition; Drug Delivery Systems; Drug Design; Electromagnetic Fields; Environment; Enzymes; Evolution; Exclusion; 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; 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; innovation; insight; instrumentation; macromolecule; milligram; millisecond; molecular dynamics; nanocarrier; nanometer; novel; novel strategies; nucleic acid structure; oxidation; programs; protein data bank; protein folding; protein structure; response; simulation; structural determinants; three dimensional structure; time use; tool; x-ray free-electron laser

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.

总结/摘要 拟议研究的长期目标是开发一种能够 研究蛋白质/核酸结构动力学，与它们在时间尺度上的功能相关 从飞秒到毫秒，以获得对活性位点结构和 这些分子的全局构象。不同温度下溶液相分子结构的快照 空间尺度，从活性位点的亚微米到整体构象的几纳米， 使用时间分辨X射线光谱和散射捕获。这些结构研究将结合 先进的分子动力学模拟，将产生详细的原子动力学一致 具有在从飞秒到毫秒的宽范围的时间尺度上测量的散射轮廓。 该研究是对单晶X射线衍射的补充，旨在绘制反应图 通过三维结构的轨迹作为模拟生物介质中时间的函数 环境.为了检测系综中的结构变化，必须设计反应触发器， 产生突然的环境变化，使分子的动作与更长的时间同步， 分辨率比传统的混合。该方案有三个主要创新，从以前的研究：1）， 开发超越过去用于引发反应的直接光激发的触发源，以克服 ·与人类健康相关的生物系统很少被光激活以发挥其功能的局限性; 2)开发新型样品输送系统，将样品消耗量减少100倍， 使许多珍贵的实验室样品能够使用时间分辨X射线方法进行研究;以及3） 开发一种结合先进分子动力学模拟的数据分析方法， 时间相关的X射线散射数据，以提取具有改进的结构精度的结构， 对于那些共存的物种来说。上述方法的创新将使我们能够调查一些 对于酶促反应、信号传感、蛋白质/核酸 折叠/解折叠以及脂质相变。几个系统被选择为拟议的研究 为了捕获以下的瞬时结构：a）细胞色素c的局部金属中心和全局蛋白质构象 由抑制剂的光解离触发的氧化酶模型蛋白; B）由钙诱导的蛋白折叠 离子a浓度跳跃; c）温度诱导RNA构象变化感测信号 翻译; d）用于人类致癌基因调节的pH依赖性DNA结构和e）pH响应性脂质 用于抗癌药物递送的纳米载体组件。这些结构的结果与反应的结果相结合 来自光学瞬态光谱的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，这将对药物设计、酶功能 增强、催化以及理论计算。

项目成果

Direct Observation of Insulin Association Dynamics with Time-Resolved X-ray Scattering.

• DOI: 10.1021/acs.jpclett.7b01720
• 发表时间: 2017-09-21
• 期刊: The journal of physical chemistry letters
• 作者: Rimmerman D;Leshchev D;Hsu DJ;Hong J;Kosheleva I;Chen LX
• 通讯作者: Chen LX

Revealing Fast Structural Dynamics in pH-Responsive Peptides with Time-Resolved X-ray Scattering.

• DOI: 10.1021/acs.jpcb.9b00072
• 发表时间: 2019-02
• 期刊: The journal of physical chemistry. B
• 作者: Dolev Rimmerman;Denis Leshchev;Darren J. Hsu;Jiyun Hong;B. Abraham;R. Henning;I. Kosheleva;Lin X. Chen

Probing Cytochrome c Folding Transitions upon Phototriggered Environmental Perturbations Using Time-Resolved X-ray Scattering.

使用时间分辨的X射线散射探测在光触发环境扰动上进行细胞色素C折叠跃迁。

• DOI: 10.1021/acs.jpcb.8b03354
• 发表时间: 2018-05-24
• 期刊: The journal of physical chemistry. B
• 作者: Rimmerman D;Leshchev D;Hsu DJ;Hong J;Abraham B;Henning R;Kosheleva I;Chen LX
• 通讯作者: Chen LX

Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures.

• DOI: 10.1021/acs.jpcb.1c05820
• 发表时间: 2021-11-18
• 期刊: JOURNAL OF PHYSICAL CHEMISTRY B
• 影响因子: 3.3
• 作者: Nijhawan, Adam K.;Chan, Arnold M.;Hsu, Darren J.;Chen, Lin X.;Kohlstedt, Kevin L.
• 通讯作者: Kohlstedt, Kevin L.

Insulin hexamer dissociation dynamics revealed by photoinduced T-jumps and time-resolved X-ray solution scattering.

通过光诱导 T 跃迁和时间分辨 X 射线溶液散射揭示胰岛素六聚体解离动力学。

• DOI: 10.1039/c8pp00034d
• 发表时间: 2018
• 期刊: Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology
• 作者: Rimmerman,Dolev;Leshchev,Denis;Hsu,DarrenJ;Hong,Jiyun;Abraham,Baxter;Kosheleva,Irina;Henning,Robert;Chen,LinX
• 通讯作者: Chen,LinX