MFB: Evaluating and Advancing Cryo-EM for RNA Conformational Ensembles

MFB：评估和推进 RNA 构象整体的冷冻电镜

• 批准号: 2330652
• 负责人: Rhiju Das
• 金额: $ 150万
• 依托单位: Stanford University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2024
• 资助国家: 美国
• 起止时间: 2024-03-01 至 2027-02-28
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2330652&HistoricalAwards=false
• 关键词: MFB; Evaluating; Advancing; Cryo; EM

In this Molecular Foundations for Biotechnology project, Stanford faculty Rhiju Das and Wah Chiu will coordinate a team of expert collaborators to acquire foundational data sets and organize world-wide blind prediction challenges needed to resolve RNA motions. RNA molecules underlie the origin of life on Earth and fundamental processes across all modern life forms, ranging from viruses to humans to the microorganisms that dominate the planet’s fixation of carbon. Researchers currently imagine that most RNA molecules wiggle and shift shapes to carry out their functions, but experimentally visualizing the many conformations of any RNA has been difficult. The broader impacts of the proposed research include establishing standardized data sets and methods disseminated through challenges, publications, public data, and code to the broad community of scientists who are now focusing on RNA, including experts, biotechnology companies, academic trainees from underrepresented backgrounds, and citizen scientists who engage in RNA research through a long-standing video game called Eterna. If successful, this work will drive the development of methods that could be applied to visualize and dissect many RNA-based machines of biological or biotechnological interest. The proposed research has two aims: (1) to design, model, and experimentally probe RNA systems with discrete conformational states whose populations can be intentionally tuned, and (2) to characterize and challenge the broader artificial intelligence and computational communities to predict the continuous conformational ensembles of ribozymes, riboswitches, and synthetic RNAs. In both aims, the research will evaluate accuracy through double-blind studies in which predictions from one set of personnel – including independent labs, Eterna citizen scientists, and predictors in the biennial Critical Assessment of Structure Prediction – will be tested through experimental data collected by an independent set of personnel. The research will advance innovative interdisciplinary approaches, bringing together high-throughput RNA biochemistry, crowdsourcing, computer modeling, and cutting-edge cryogenic electron microscopy (cryo-EM) in the labs of the principal investigators, as well as the state of the art in deep learning research, molecular dynamics simulations, and sociology through collaborators and community-wide open science challenges. The research seeks to attain generality beyond any specific system through analysis of molecules drawn from viruses, bacteria, protozoans, metazoans, and from the imaginations of RNA nanotechnologists and citizen scientists. Finally, the research has the potential to benefit society through broader impacts in biotechnology and through educational opportunities involving direct mentorship of trainees from underrepresented racial and ethnic backgrounds and active learning through the Eterna citizen science platform and an Eterna Academy massive open online course.This project is supported by the Division of Chemistry in the Directorate for Mathematical and Physical Sciences, and by the Chemistry of Life Processes program in the Division of Chemistry.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.

在这个生物技术项目的分子基础中，斯坦福大学教职员工Rhiju Das和Wah Chiu将协调一个专家合作者团队，以获取基础数据集并组织全球范围内的盲目预测挑战，以解决RNA运动所需的挑战。 RNA分子是地球生命的起源和所有现代生命形式的基本过程，从病毒到人类到主导地球固定碳的微生物。研究人员目前可以想象，大多数RNA分子都会摆动和移动形状以执行其功能，但是实验可视化任何RNA的许多构象很困难。拟议研究的更广泛的影响包括建立通过挑战，出版物，公共数据和代码传播的标准化数据集和方法，这些科学家们现在专注于RNA，包括专家，生物技术公司，来自代表性不足的背景的学术学员以及通过RNA从事RNA研究的长期以来的视频游戏ETERNA参与RNA研究的公民科学家。如果成功的话，这项工作将推动可用于可视化和剖析许多基于RNA的生物学或生物技术兴趣的方法的开发。拟议的研究具有两个目的：（1）设计，模型和实验探测RNA系统具有离散构象状态，其种群可以被故意调整，（2）以表征和挑战更广泛的人工智能和计算社区，以预测核酶，核糖开关，核糖开关和合成RNA的连续构象的构象。在这两个目标中，该研究将通过双盲研究评估准确性，其中一组人员的预测（包括独立的实验室，Eterna公民科学家）以及对结构预测的两年一次批判性评估的预测因素 - 将通过一组独立人员收集的实验数据进行测试。这项研究将推进创新的跨学科方法，将高通量RNA生物化学，人群，计算机建模和尖端的低温电子显微镜（Cryo-EM）组合到主要研究者的实验室中，以及在深度学习研究，分子动力学模拟和社会上通过协作和社区挑战的艺术中的状况，以及社区挑战和社区的研究。该研究试图通过分析从病毒，细菌，原生动物，后生动物以及RNA纳米技术医生和公民科学家的想象中的分子来分析任何特定系统以外的通用性。最后，这项研究具有通过对生物技术的更广泛影响以及通过涉及教育者直接思想的教育机会受益于社会的潜力奖项反映了NSF的法定任务，并通过使用基金会的智力优点和更广泛的影响审查标准评估值得支持。