Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

Honglue Shi, Atul Rangadurai, Hala Abou Assi, Rohit Roy, David A. Case (), Daniel Herschlag (), Joseph D. Yesselman () and Hashim M. Al-Hashimi ()
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Honglue Shi: Duke University
Atul Rangadurai: Duke University School of Medicine
Hala Abou Assi: Duke University School of Medicine
Rohit Roy: Duke University School of Medicine
David A. Case: Rutgers University
Daniel Herschlag: Stanford University
Joseph D. Yesselman: University of Nebraska-Lincoln
Hashim M. Al-Hashimi: Duke University

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: Abstract Biomolecules form dynamic ensembles of many inter-converting conformations which are key for understanding how they fold and function. However, determining ensembles is challenging because the information required to specify atomic structures for thousands of conformations far exceeds that of experimental measurements. We addressed this data gap and dramatically simplified and accelerated RNA ensemble determination by using structure prediction tools that leverage the growing database of RNA structures to generate a conformation library. Refinement of this library with NMR residual dipolar couplings provided an atomistic ensemble model for HIV-1 TAR, and the model accuracy was independently supported by comparisons to quantum-mechanical calculations of NMR chemical shifts, comparison to a crystal structure of a substate, and through designed ensemble redistribution via atomic mutagenesis. Applications to TAR bulge variants and more complex tertiary RNAs support the generality of this approach and the potential to make the determination of atomic-resolution RNA ensembles routine.

Date: 2020
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DOI: 10.1038/s41467-020-19371-y

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