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:

Mg2+-dependent folding of a large ribozyme without kinetic traps

Nature Structural Biology volume 6, pages 1091–1095 (1999)Cite this article

Abstract

The folding kinetics of the catalytic domain of Bacillus subtilis ribonuclease P is analyzed here by fluorescence and catalytic activity. The folding pathway is apparently free of kinetic traps, as indicated by a decrease in folding rates upon the addition of urea. We apply Mg2+ and urea chevron analysis to fully describe the folding and unfolding kinetics of this ribozyme. A folding scheme containing two kinetic intermediates completely accounts for the free energy, the Mg2+ Hill coefficient and the surface buried in the equilibrium transition. At saturating Mg2+concentrations, folding is limited by a barrier that is independent of Mg2+ and urea. These results describe the first trap-free folding pathway of a large ribozyme and indicate that kinetic traps are not an obligate feature of RNA folding.

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: Folding kinetics of C-domain at 10 mM MgCl2.
Figure 2: Mg2+ and urea dependence of C-domain folding.
Figure 3: Population distribution as a function of Mg2+ concentration.
Figure 4: Predicted Mg2+ and urea chevron plots.

Similar content being viewed by others

References

  1. Zarrinkar, P.P. & Williamson, J.R. Science 265, 918–924 (1994).

    Article  CAS  Google Scholar 

  2. Banerjee, A.R. & Turner, D.H. Biochemistry 34, 6504–6512 (1995).

    Article  CAS  Google Scholar 

  3. Downs, W.D. & Cech, T.R. RNA 2, 718 –732 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Thirumalai, D. & Woodson, S.A. Acc. Chem. Res. 29 , 433–439 (1996).

    Article  CAS  Google Scholar 

  5. Draper, D.E. Nature Struct. Biol. 3, 397–400 (1996).

    Article  CAS  Google Scholar 

  6. Brion, P. & Westhof, E. Ann. Rev. Biophys. Biomol. Struct. 26, 113–137 ( 1997).

    Article  CAS  Google Scholar 

  7. Sclavi, B., Sullivan, M., Chance, M.R., Brenowitz, M. & Woodson, S.A. Science 279, 1940–1943 (1998).

    Article  CAS  Google Scholar 

  8. Pan, J., Thirumalai, D. & Woodson, S.A. J. Mol. Biol. 273, 7– 13 (1997).

    Article  CAS  Google Scholar 

  9. Pan, T. & Sosnick, T.R. Nature Struct. Biol. 4, 931–938 (1997).

    Article  CAS  Google Scholar 

  10. Treiber, D.K., Rook, M.S., Zarrinkar, P.P. & Williamson, J.R. Science 279, 1943–1946 ( 1998).

    Article  CAS  Google Scholar 

  11. Pan, J. & Woodson, S.A. J. Mol. Biol. 280, 597–609 (1998).

    Article  CAS  Google Scholar 

  12. Rook, M.S., Treiber, D.K. & Williamson, J.R. J. Mol. Biol. 281, 609– 620 (1998).

    Article  CAS  Google Scholar 

  13. Matthews, C.R. Methods Enzymol. 154, 498–511 (1987).

    Article  CAS  Google Scholar 

  14. Matouschek, A., Kellis Jr., J.T., Serrano, L., Bycroft, M. & Fersht, A.R. Nature 346, 440–445 (1990).

    Article  CAS  Google Scholar 

  15. Creighton, T.E. Nature Struct. Biol. 1, 135–138 (1994).

    Article  CAS  Google Scholar 

  16. Pan, J., Thirumalai, D. & Woodson, S.A. Proc. Natl. Acad. Sci. USA 96, 6149–6154 (1999).

    Article  CAS  Google Scholar 

  17. Zarrinkar, P.P., Wang, J. & Williamson, J.R. RNA 2, 564– 573 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Pan, T., Fang, X. & Sosnick, T.R. J. Mol. Biol. 286, 721– 731 (1999).

    Article  CAS  Google Scholar 

  19. Gluick, T.C., Gerstner, R.B. & Draper, D.E. J. Mol. Biol. 270, 451– 463 (1997).

    Article  CAS  Google Scholar 

  20. Milligan, J.F. & Uhlenbeck, O.C. Methods Enzymol. 180, 51–62 ( 1989).

    Article  CAS  Google Scholar 

  21. Pan, T. & Jakacka, M. EMBO J. 15, 2249–2255 (1996).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by a grant from NIH to T.P. and T.R.S. and from the Cancer Research Foundation to T.R.S. We thank J. Piccirilli, B. Golden, J. Williamson, S. Woodson and the reviewers for helpful discussions and comments on the manuscript.

Author information

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, 60637, Illinois, USA

    Xing-wang Fang, Tao Pan & Tobin R. Sosnick

Authors
  1. Xing-wang Fang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tao Pan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tobin R. Sosnick
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Tao Pan or Tobin R. Sosnick.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Fang, Xw., Pan, T. & Sosnick, T. Mg2+-dependent folding of a large ribozyme without kinetic traps. Nat Struct Mol Biol 6, 1091–1095 (1999). https://doi.org/10.1038/70016

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/70016

This article is cited by

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