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

Publication ,  Journal Article
Shi, H; Rangadurai, A; Abou Assi, H; Roy, R; Case, DA; Herschlag, D; Yesselman, JD; Al-Hashimi, HM
Published in: Nat Commun
November 2, 2020

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.

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Published In

Nat Commun

DOI

EISSN

2041-1723

Publication Date

November 2, 2020

Volume

11

Issue

1

Start / End Page

5531

Location

England

Related Subject Headings

  • RNA, Viral
  • RNA Folding
  • Nuclear Magnetic Resonance, Biomolecular
  • Molecular Dynamics Simulation
  • Models, Chemical
  • HIV-1
  • HIV Long Terminal Repeat
  • Cheminformatics
 

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Shi, H., Rangadurai, A., Abou Assi, H., Roy, R., Case, D. A., Herschlag, D., … Al-Hashimi, H. M. (2020). Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction. Nat Commun, 11(1), 5531. https://doi.org/10.1038/s41467-020-19371-y
Shi, Honglue, Atul Rangadurai, Hala Abou Assi, Rohit Roy, David A. Case, Daniel Herschlag, Joseph D. Yesselman, and Hashim M. Al-Hashimi. “Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction.Nat Commun 11, no. 1 (November 2, 2020): 5531. https://doi.org/10.1038/s41467-020-19371-y.
Shi H, Rangadurai A, Abou Assi H, Roy R, Case DA, Herschlag D, et al. Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction. Nat Commun. 2020 Nov 2;11(1):5531.
Shi, Honglue, et al. “Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction.Nat Commun, vol. 11, no. 1, Nov. 2020, p. 5531. Pubmed, doi:10.1038/s41467-020-19371-y.
Shi H, Rangadurai A, Abou Assi H, Roy R, Case DA, Herschlag D, Yesselman JD, Al-Hashimi HM. Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction. Nat Commun. 2020 Nov 2;11(1):5531.

Published In

Nat Commun

DOI

EISSN

2041-1723

Publication Date

November 2, 2020

Volume

11

Issue

1

Start / End Page

5531

Location

England

Related Subject Headings

  • RNA, Viral
  • RNA Folding
  • Nuclear Magnetic Resonance, Biomolecular
  • Molecular Dynamics Simulation
  • Models, Chemical
  • HIV-1
  • HIV Long Terminal Repeat
  • Cheminformatics