Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Visualizing spatially correlated dynamics that directs RNA conformational transitions

Nature volume 450, pages 1263–1267 (2007)Cite this article

Abstract

RNAs fold into three-dimensional (3D) structures that subsequently undergo large, functionally important, conformational transitions in response to a variety of cellular signals1,2,3. RNA structures are believed to encode spatially tuned flexibility that can direct transitions along specific conformational pathways4,5. However, this hypothesis has proved difficult to examine directly because atomic movements in complex biomolecules cannot be visualized in 3D by using current experimental methods. Here we report the successful implementation of a strategy using NMR that has allowed us to visualize, with complete 3D rotational sensitivity, the dynamics between two RNA helices that are linked by a functionally important trinucleotide bulge over timescales extending up to milliseconds. The key to our approach is to anchor NMR frames of reference onto each helix and thereby directly measure their dynamics, one relative to the other, using ‘relativistic’ sets of residual dipolar couplings (RDCs)6,7. Using this approach, we uncovered super-large amplitude helix motions that trace out a surprisingly structured and spatially correlated 3D dynamic trajectory. The two helices twist around their individual axes by approximately 53° and 110° in a highly correlated manner (R = 0.97) while simultaneously (R = 0.81–0.92) bending by about 94°. Remarkably, the 3D dynamic trajectory is dotted at various positions by seven distinct ligand-bound conformations of the RNA. Thus even partly unstructured RNAs can undergo structured dynamics that directs ligand-induced transitions along specific predefined conformational pathways.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Measurement of RNA helix motions in 3D using helix-anchored frames and RDCs.
Figure 2: Helix motions from model-free order-tensor analysis of RDCs.
Figure 3: Visualizing TAR inter-helical motions in 3D.
Figure 4: Correlated TAR dynamics steer ligand-induced transitions.

Similar content being viewed by others

References

  1. Micura, R. & Hobartner, C. On secondary structure rearrangements and equilibria of small RNAs. ChemBioChem 4, 984–990 (2003)

    Article  CAS  Google Scholar 

  2. Schroeder, R., Barta, A. & Semrad, K. Strategies for RNA folding and assembly. Nature Rev. Mol. Cell Biol. 5, 908–919 (2004)

    Article  CAS  Google Scholar 

  3. Schwalbe, H. et al. Structures of RNA switches: insight into molecular recognition and tertiary structure. Angew. Chem. Int. Edn Engl. 46, 1212–1219 (2007)

    Article  CAS  Google Scholar 

  4. Leulliot, N. & Varani, G. Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 40, 7947–7956 (2001)

    Article  CAS  Google Scholar 

  5. Al-Hashimi, H. M. Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy. ChemBioChem 6, 1506–1519 (2005)

    Article  CAS  Google Scholar 

  6. Tjandra, N. & Bax, A. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278, 1111–1114 (1997)

    Article  ADS  CAS  Google Scholar 

  7. Tolman, J. R., Flanagan, J. M., Kennedy, M. A. & Prestegard, J. H. NMR evidence for slow collective motions in cyanometmyoglobin. Nature Struct. Biol. 4, 292–297 (1997)

    Article  CAS  Google Scholar 

  8. Furtig, B. et al. Time-resolved NMR studies of RNA folding. Biopolymers 86, 360–383 (2007)

    Article  Google Scholar 

  9. Blackledge, M. Recent progress in the study of biomolecular structure and dynamics in solution from residual dipolar couplings. Prog. Nucl. Magn. Reson. Spectrosc. 46, 23–61 (2005)

    Article  CAS  Google Scholar 

  10. Mittermaier, A. & Kay, L. E. New tools provide new insights in NMR studies of protein dynamics. Science 312, 224–228 (2006)

    Article  ADS  CAS  Google Scholar 

  11. Palmer, A. G. & Massi, F. Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700–1719 (2006)

    Article  CAS  Google Scholar 

  12. Bruschweiler, R. New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins. Curr. Opin. Struct. Biol. 13, 175–183 (2003)

    Article  CAS  Google Scholar 

  13. Zhang, Q., Sun, X., Watt, E. D. & Al-Hashimi, H. M. Resolving the motional modes that code for RNA adaptation. Science 311, 653–656 (2006)

    Article  ADS  CAS  Google Scholar 

  14. Zhang, Q. & Al-Hashimi, H. M. Extending the NMR spatial resolution limit by motional couplings. Nature Methods (submitted)

  15. Aboul-ela, F., Karn, J. & Varani, G. Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge. Nucleic Acids Res. 24, 3974–3981 (1996)

    Article  CAS  Google Scholar 

  16. Puglisi, J. D. et al. Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science 257, 76–80 (1992)

    Article  ADS  CAS  Google Scholar 

  17. Aboul-ela, F., Karn, J. & Varani, G. The structure of the human-immunodeficiency-virus type-1 Tar RNA reveals principles of RNA recognition by Tat protein. J. Mol. Biol. 253, 313–332 (1995)

    Article  CAS  Google Scholar 

  18. Ippolito, J. A. & Steitz, T. A. A 1.3-angstrom resolution crystal structure of the HIV-1 trans- activation response region RNA stem reveals a metal ion- dependent bulge conformation. Proc. Natl Acad. Sci. USA 95, 9819–9824 (1998)

    Article  ADS  CAS  Google Scholar 

  19. Faber, C., Sticht, H., Schweimer, K. & Rosch, P. Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B. J. Biol. Chem. 275, 20660–20666 (2000)

    Article  CAS  Google Scholar 

  20. Du, Z., Lind, K. E. & James, T. L. Structure of TAR RNA complexed with a Tat–TAR interaction nanomolar inhibitor that was identified by computational screening. Chem. Biol. 9, 707–712 (2002)

    Article  CAS  Google Scholar 

  21. Davis, B. et al. Rational design of inhibitors of HIV-1 TAR RNA through the stabilisation of electrostatic ‘hot spots’. J. Mol. Biol. 336, 343–356 (2004)

    Article  CAS  Google Scholar 

  22. Murchie, A. I. et al. Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA. J. Mol. Biol. 336, 625–638 (2004)

    Article  CAS  Google Scholar 

  23. Hansen, M. R., Mueller, L. & Pardi, A. Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nature Struct. Biol. 5, 1065–1074 (1998)

    Article  CAS  Google Scholar 

  24. Meiler, J. et al. Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins. J. Am. Chem. Soc. 123, 6098–6107 (2001)

    Article  CAS  Google Scholar 

  25. Tolman, J. R., Al-Hashimi, H. M., Kay, L. E. & Prestegard, J. H. Structural and dynamic analysis of residual dipolar coupling data for proteins. J. Am. Chem. Soc. 123, 1416–1424 (2001)

    Article  CAS  Google Scholar 

  26. Musselman, C. et al. Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings. J. Biomol. NMR 36, 235–249 (2006)

    Article  CAS  Google Scholar 

  27. Saupe, A. Recent results in the field of liquid crystals. Angew. Chem. Int. Edn Engl. 7, 97–112 (1968)

    Article  CAS  Google Scholar 

  28. Clore, G. M. & Schwieters, C. D. Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements. Biochemistry 43, 10678–10691 (2004)

    Article  CAS  Google Scholar 

  29. Al-Hashimi, H. M. et al. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. J. Mol. Biol. 315, 95–102 (2002)

    Article  CAS  Google Scholar 

  30. Meissner, A. & Sorensen, O. W. The role of coherence transfer efficiency in design of TROSY- type multidimensional NMR experiments. J. Magn. Reson. 139, 439–442 (1999)

    Article  ADS  CAS  Google Scholar 

  31. Cornilescu, G., Marquardt, J. L., Ottiger, M. & Bax, A. Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J. Am. Chem. Soc. 120, 6836–6837 (1998)

    Article  CAS  Google Scholar 

  32. Bailor, M. H. et al. Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings. Nature Protoc. 2, 1536–1546 (2007)

    Article  CAS  Google Scholar 

  33. Saenger, W. Principles of Nucleic Acid Structure (Springer-Verlag, New York, New York, 1984)

    Book  Google Scholar 

  34. Zweckstetter, M. & Bax, A. Prediction of sterically induced alignment in a dilute liquid crystalline phase; aid to protein structure determination by NMR. J. Am. Chem. Soc. 122, 3791–3792 (2000)

    Article  CAS  Google Scholar 

  35. Clore, G. M. et al. Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J. Am. Chem. Soc. 112, 4989–4991 (1990)

    Article  CAS  Google Scholar 

  36. Mandel, A. M., Akke, M. & Palmer, A. G. Backbone dynamics of Escherichia coli ribonuclease Hi: correlations with structure and function in an active enzyme. J. Mol. Biol. 246, 144–163 (1995)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank A. Kurochkin for NMR expertise. We acknowledge the Michigan Economic Development Cooperation and the Michigan Technology Tri-Corridor for the support of the purchase of a 600 MHz spectrometer, and the W. F. Keck Foundation, National Science Foundation (NSF) and National Institutes of Health (NIH) for funds for the purchase of an 800 MHz spectrometer. Supported by an NIH and NSF grant.

Author Contributions H.M.A. conceived the technique, Q.Z. and H.M.A. analysed the data and wrote the paper. Q.Z., C.K.F. and H.M.A. analysed the HIV-2 TAR data. Q.Z., A.C.S. and C.K.F. prepared the samples and performed the NMR experiments.

Author information

Authors and Affiliations

  1. Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA,

    Qi Zhang, Andrew C. Stelzer, Charles K. Fisher & Hashim M. Al-Hashimi

Authors
  1. Qi Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Andrew C. Stelzer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Charles K. Fisher
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hashim M. Al-Hashimi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hashim M. Al-Hashimi.

Additional information

Supplementary Movies are hosted at the publicly accessible Database of Macromolecular Movements (http://www.molmovdb.org/).

Supplementary information

Supplementary Information

This file contains Supplementary Discussion; Supplementary Tables S1-S4; Supplementary Figures S1-S5 with Legends; Legends to Supplementary Movies 1-2; and additional references. (PDF 3655 kb)

Supplementary Movie 1

This file contains Supplementary Movie 1 showing the TAR inter-helix motional trajectory. Shown are transitions 1→2, 2→3, and 3→1 between conformers in ensemble A via the linear conformational pathway in 3D inter-helix Euler space (see green lines in Fig. 4a of the main manuscript). HI and HII are shown in black and orange and are elongated in gray for clarity. (MOV 2411 kb)

Supplementary Movie 2

This file contains Supplementary Movie 2 showing how the TAR inter-helix motional trajectory encapsulates ligand-bound conformations. The TAR inter-helical motional trajectory is shown (in green) together with the ligand bound TAR conformations (in gray). Helix HI was used to superimpose all structures, which are represented using idealized A-form helices. (MOV 10611 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhang, Q., Stelzer, A., Fisher, C. et al. Visualizing spatially correlated dynamics that directs RNA conformational transitions. Nature 450, 1263–1267 (2007). https://doi.org/10.1038/nature06389

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature06389

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing