EAGER: Methodology development for 3D atomic-scale structural dynamics movies of enzymes

EAGER：酶的 3D 原子尺度结构动力学电影的方法开发

• 批准号: 1842951
• 负责人: Shimon Weiss
• 金额: $ 30万
• 依托单位: University of California-Los Angeles
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2023-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1842951&HistoricalAwards=false
• 关键词: EAGER; Methodology; development; 3D; atomic

Capturing the dynamic structure of a biological machine performing its function remains the holy grail of biology. Conventional tools provide only structural "snapshots" of stable states along the reaction pathway. This project aims to develop methods that will capture a full movie of a macromolecule's structure as it works. The research tools developed will be applicable to a wide variety of biological systems, and will be disseminated by means of publications, tutorials, conference presentations and the like, to accelerate their adoption. The education component of the project will emphasize the use of single molecule biophysics and computational tools for dynamic structure determination. It will provide high school, undergraduate, graduate students and postdocs training in state-of-the-art single molecule biophysics research, and offer leadership experiences for graduate students and postdocs as well.Specifically, this project will study the structure of the transcription bubble in a simple bacterial transcription system during initiation as a test case for developing new technological concepts. The existence of certain intermediates in bacterial transcription suggests common features of the process exist across the different domains of life and reflects a conserved regulatory mechanism; thus, the findings will have broad utility. For the purpose of dynamic structure determination, the project will combine experimental and theoretical tools, including multi-spot single-molecule FRET measurements, fast single-molecule microfluidic mixing, molecular dynamics simulations and time-resolved single-photon detection to acquire data on- and perform molecular modeling of- the transcription bubble during initiation.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

捕捉生物机器执行其功能的动态结构仍然是生物学的圣杯。传统的工具只能提供沿着反应路径的稳定状态的结构“快照”。这个项目的目标是开发一种方法，在大分子结构工作时捕捉其完整的电影。开发的研究工具将适用于各种生物系统，并将通过出版物、教程、会议报告等方式传播，以加速采用这些工具。该项目的教育部分将强调使用单分子生物物理学和计算工具来确定动态结构。它将为高中、本科生、研究生和博士后提供最先进的单分子生物物理学研究方面的培训，并为研究生和博士后提供领导经验。具体地说，该项目将研究启动过程中简单细菌转录系统中转录泡泡的结构，作为开发新技术概念的测试案例。细菌转录中某些中间体的存在表明，该过程存在于生命的不同领域，并反映了一种保守的调控机制；因此，这一发现将具有广泛的实用价值。为了确定动态结构，该项目将结合实验和理论工具，包括多点单分子FRET测量、快速单分子微流控混合、分子动力学模拟和时间分辨单光子检测，以获取关于启动过程中转录气泡的数据并对其进行分子建模。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins.

• DOI: 10.1016/j.ymeth.2019.07.021
• 发表时间: 2019-10-01
• 期刊: Methods (San Diego, Calif.)
• 作者: Segal M;Ingargiola A;Lerner E;Chung S;White JA;Streets A;Weiss S;Michalet X
• 通讯作者: Michalet X

A user-friendly tool to convert photon counting data to the open-source Photon-HDF5 file format

一个用户友好的工具，可将光子计数数据转换为开源 Photon-HDF5 文件格式

• DOI: 10.1117/12.2608487
• 发表时间: 2022
• 期刊: Single Molecule Spectroscopy and Superresolution Imaging XV
• 作者: Ferschweiler, Donald;Segal, Maya;Weiss, Shimon;Michalet, Xavier
• 通讯作者: Michalet, Xavier