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

Stanford University, Stanford CA

Investigators

Abstract

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.