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Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

Nature Methods volume 11, pages 413–416 (2014)Cite this article

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Abstract

Structured noncoding RNAs underlie fundamental cellular processes, but determining their three-dimensional structures remains challenging. We demonstrate that integrating 1H NMR chemical shift data with Rosetta de novo modeling can be used to consistently determine high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 'blind' targets, chemical-shift Rosetta for RNA (CS-Rosetta-RNA) recovered experimental structures with high accuracy (0.6–2.0 Å all-heavy-atom r.m.s. deviation) in 18 cases.

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Figure 1: CS-Rosetta-RNA illustrated on an UUAAGU hairpin.
Figure 2: Comparison of experimental and CS-Rosetta-RNA models for diverse RNA motifs.

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References

  1. Gesteland, R.F., Cech, T. & Atkins, J.F. The RNA World: The Nature of Modern RNA Suggests a Prebiotic RNA World. Vol. 43 (Cold Spring Harbor Lab Press, 2006).

  2. Scott, L.G. & Hennig, M. Methods Mol. Biol. 452, 29–61 (2008).

    Article  CAS  Google Scholar 

  3. Schmitz, U., James, T.L., Lukavsky, P. & Walter, P. Nat. Struct. Biol. 6, 634–638 (1999).

    Article  CAS  Google Scholar 

  4. Jovine, L. et al. Structure 8, 527–540 (2000).

    Article  CAS  Google Scholar 

  5. Nabuurs, S.B., Spronk, C.A.E.M., Vuister, G.W. & Vriend, G. PLoS Comput. Biol. 2, e9 (2006).

    Article  Google Scholar 

  6. Tolbert, B.S. et al. J. Biomol. NMR 47, 205–219 (2010).

    Article  CAS  Google Scholar 

  7. Cornilescu, G., Delaglio, F. & Bax, A. J. Biomol. NMR 13, 289–302 (1999).

    Article  CAS  Google Scholar 

  8. Clore, G.M. & Gronenborn, A.M. Proc. Natl. Acad. Sci. USA 95, 5891–5898 (1998).

    Article  CAS  Google Scholar 

  9. Cavalli, A., Salvatella, X., Dobson, C.M. & Vendruscolo, M. Proc. Natl. Acad. Sci. USA 104, 9615–9620 (2007).

    Article  CAS  Google Scholar 

  10. Shen, Y. et al. Proc. Natl. Acad. Sci. USA 105, 4685–4690 (2008).

    Article  CAS  Google Scholar 

  11. Case, D.A. J. Biomol. NMR 6, 341–346 (1995).

    Article  CAS  Google Scholar 

  12. Cromsigt, J.A., Hilbers, C.W. & Wijmenga, S.S. J. Biomol. NMR 21, 11–29 (2001).

    Article  CAS  Google Scholar 

  13. Girard, F.C., Ottink, O.M., Ampt, K.A., Tessari, M. & Wijmenga, S.S. Nucleic Acids Res. 35, 2800–2811 (2007).

    Article  CAS  Google Scholar 

  14. van der Werf, R.M., Tessari, M. & Wijmenga, S.S. J. Biomol. NMR 56, 95–112 (2013).

    Article  CAS  Google Scholar 

  15. Frank, A.T., Horowitz, S., Andricioaei, I. & Al-Hashimi, H.M. J. Phys. Chem. B 117, 2045–2052 (2013).

    Article  CAS  Google Scholar 

  16. Das, R., Karanicolas, J. & Baker, D. Nat. Methods 7, 291–294 (2010).

    Article  CAS  Google Scholar 

  17. Sripakdeevong, P., Kladwang, W. & Das, R. Proc. Natl. Acad. Sci. USA 108, 20573–20578 (2011).

    Article  CAS  Google Scholar 

  18. Fleishman, S.J. & Baker, D. Cell 149, 262–273 (2012).

    Article  CAS  Google Scholar 

  19. Deng, J., Xiong, Y., Pan, B. & Sundaralingam, M. Acta Crystallogr. D Biol. Crystallogr. 59, 1004–1011 (2003).

    Article  Google Scholar 

  20. Leontis, N.B. & Westhof, E. RNA 7, 499–512 (2001).

    Article  CAS  Google Scholar 

  21. Burkard, M.E. & Turner, D.H. Biochemistry 39, 11748–11762 (2000).

    Article  CAS  Google Scholar 

  22. Nozinovic, S., Furtig, B., Jonker, H.R., Richter, C. & Schwalbe, H. Nucleic Acids Res. 38, 683–694 (2010).

    Article  CAS  Google Scholar 

  23. Ennifar, E. et al. J. Mol. Biol. 304, 35–42 (2000).

    Article  CAS  Google Scholar 

  24. Wu, M. & Turner, D.H. Biochemistry 35, 9677–9689 (1996).

    Article  CAS  Google Scholar 

  25. Shankar, N. et al. Biochemistry 46, 12665–12678 (2007).

    Article  CAS  Google Scholar 

  26. Carter, A.P. et al. Nature 407, 340–348 (2000).

    Article  CAS  Google Scholar 

  27. Zhang, H., Fountain, M.A. & Krugh, T.R. Biochemistry 40, 9879–9886 (2001).

    Article  CAS  Google Scholar 

  28. Aboul-ela, F., Karn, J. & Varani, G. Nucleic Acids Res. 24, 3974–3981 (1996).

    Article  CAS  Google Scholar 

  29. Schweisguth, D.C. & Moore, P.B. J. Mol. Biol. 267, 505–519 (1997).

    Article  CAS  Google Scholar 

  30. Lerman, Y.V. et al. RNA 17, 1664–1677 (2011).

    Article  CAS  Google Scholar 

  31. Zhao, Q., Han, Q., Kissinger, C.R., Hermann, T. & Thompson, P.A. Acta Crystallogr. D Biol. Crystallogr. 64, 436–443 (2008).

    Article  CAS  Google Scholar 

  32. Lukavsky, P.J., Kim, I., Otto, G.A. & Puglisi, J.D. Nat. Struct. Biol. 10, 1033–1038 (2003).

    Article  CAS  Google Scholar 

  33. Ye, J.D. et al. Proc. Natl. Acad. Sci. USA 105, 82–87 (2008).

    Article  CAS  Google Scholar 

  34. Davis, J.H. et al. J. Mol. Biol. 351, 371–382 (2005).

    Article  CAS  Google Scholar 

  35. Donghi, D., Pechlaner, M., Finazzo, C., Knobloch, B. & Sigel, R.K. Nucleic Acids Res. 41, 2489–2504 (2013).

    Article  CAS  Google Scholar 

  36. Zhao, Q. et al. Biopolymers 97, 617–628 (2012).

    Article  CAS  Google Scholar 

  37. Ziegeler, M., Cevec, M., Richter, C. & Schwalbe, H. ChemBioChem 13, 2100–2112 (2012).

    Article  CAS  Google Scholar 

  38. Chang, A.T. & Nikonowicz, E.P. Biochemistry 51, 3662–3674 (2012).

    Article  CAS  Google Scholar 

  39. Kennedy, S.D., Kierzek, R. & Turner, D.H. Biochemistry 51, 9257–9259 (2012).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank H. Al-Hashimi for suggesting the problem and the Rosetta community for sharing code, and G. Varani and J.D. Puglisi for providing experimental 1H chemical shift data (for HIV-1 TAR apical loop and hepatitis C virus IRES subdomain IIa, respectively). Calculations were carried out on the BioX2 cluster (US National Science Foundation award CNS-0619926) and Extreme Science and Engineering Discovery Environment (XSEDE) (allocation MCB090153). We acknowledge financial support from a Burroughs Wellcome Career Award at the Scientific Interface (to R.D.), US National Institutes of Health (NIH) grant R21 GM102716 (to R.D.), a C.V. Starr Asia/Pacific Stanford Graduate Fellowship (to P.S.), NIH grant GM73969 (to E.P.N.), NIH grant GM22939 (to D.H.T.), the Swiss National Science Foundation and the European Commission (BIO-NMR, ERC-Starting Grant, Marie Curie Fellowship; to M.C.E. and R.K.O.S.), and the Deutsche Forschungsgemeinschaft (Cluster of Excellence) and the European Commission (Bio-NMR, WeNMR, Marie Curie Fellowship; to M.C., M.Z. and H.S.).

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Authors and Affiliations

  1. Biophysics Program, Stanford University, Stanford, California, USA

    Parin Sripakdeevong & Rhiju Das

  2. Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany

    Mirko Cevec, Melanie Ziegeler & Harald Schwalbe

  3. Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, USA

    Andrew T Chang & Edward P Nikonowicz

  4. Department of Biochemistry, University of Oxford, Oxford, UK

    Michèle C Erat

  5. Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland

    Michèle C Erat & Roland K O Sigel

  6. Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA

    Qin Zhao

  7. Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA

    George E Fox & Xiaolian Gao

  8. Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA

    Scott D Kennedy

  9. Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland

    Ryszard Kierzek

  10. Department of Chemistry, University of Rochester, Rochester, New York, USA

    Douglas H Turner

  11. Department of Biochemistry, Stanford University, Stanford, California, USA

    Rhiju Das

  12. Department of Physics, Stanford University, Stanford, California, USA

    Rhiju Das

Authors
  1. Parin Sripakdeevong
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Contributions

P.S. and R.D. designed the research. P.S. implemented the method, generated the data, analyzed the results, and wrote the paper. R.D. assisted in analyzing the data and writing the paper. M.C., A.T.C., M.C.E., M.Z., Q.Z., G.E.F., X.G., S.D.K., R.K., E.P.N., H.S., R.K.O.S. and D.H.T. provided NMR spectroscopy data for the 11 blind targets and participated in evaluating the blinded trials. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Rhiju Das.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11, Supplementary Tables 1–3, Supplementary Results and Supplementary Note (PDF 25475 kb)

Supplementary Data

Data files for the top five CS-Rosetta-RNA models, the reference experimental structures, and the experimental 1H chemical shift data for each of the 23 RNA motifs in the benchmark (included readme file provides details about the contents). (ZIP 929 kb)

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Sripakdeevong, P., Cevec, M., Chang, A. et al. Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts. Nat Methods 11, 413–416 (2014). https://doi.org/10.1038/nmeth.2876

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