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:

A residue-specific view of the association and dissociation pathway in protein–DNA recognition

Nature Structural Biology volume 9, pages 193–197 (2002)Cite this article

Abstract

Signal propagation in biological systems occurs through a series of inter- and intramolecular events, the precise pathways of which remain elusive in most cases. With respect to protein–DNA interactions in particular, little is known about the association and dissociation reaction pathways. Here we show that the exchange of amide protons detected by NMR can be used to characterize, at residue level, the mechanism, kinetics and thermodynamics of Lac headpiece (HP) interaction with DNA operators. Specific protein–DNA contacts responsible for the direct readout of the sequence are formed and broken at distinct time scales. Unfolding of the hinge helices triggers protein–DNA dissociation by progressive destabilization of distinct structural units, which is facilitated by the low stability of the protein in the uncomplexed state. Upon DNA binding, a dramatic alteration in the dynamics of the protein is observed, which may be used advantageously by the biological system to switch between functional states. Hydrogen-deuterium exchange can provide an unusually detailed view of the interaction mechanism of a protein–DNA complex and the associated energetics of DNA recognition with residue-level specificity.

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: The Lac operator sequences used for the present studies.
Figure 2: Protection factors (P) and opening rates of the dimeric Lac HP62-V52C plotted as a function of residue number.
Figure 3: Summary of the thermodynamic and kinetic data extracted from hydrogen exchange data.
Figure 4: Plot of equilibrium (observed) exchange rate, kobs, versus intrinsic exchange rate, kint.
Figure 5: Model of the dissociation pathway of the Lac repressor from the ideal SymL operator.

Similar content being viewed by others

References

  1. Freire, E. Proc. Natl. Acad. Sci. USA 96, 10118–10122 (1999).

    Article  CAS  Google Scholar 

  2. Dunker, A.K. et al. J. Mol. Graph. Model. 19, 26–59 (2001).

    Article  CAS  Google Scholar 

  3. Wright, P.E. & Dyson, H.J. J. Mol. Biol. 293, 321–331 (1999).

    Article  CAS  Google Scholar 

  4. Lefstin J.A. & Yamamoto, K.R. Nature 392, 885–888 (1998).

    Article  CAS  Google Scholar 

  5. Bell, C.E. & Lewis, M. Curr. Opin. Struct. Biol. 11, 19–25 (2001).

    Article  CAS  Google Scholar 

  6. Lewis, M. et al. Science 271, 1247–1254 (1996).

    Article  CAS  Google Scholar 

  7. Spronk, C.A.E.M. et al. Structure 7, 1483–1492 (1999).

    Article  CAS  Google Scholar 

  8. Spronk, C.A.E.M., Slijper, M., van Boom, J.H., Kaptein, R. & Boelens, R. Nature Struct. Biol. 3, 916–919 (1996).

    Article  CAS  Google Scholar 

  9. Bell, C.E. & Lewis, M. Nature Struct. Biol. 7, 209–214 (2000).

    Article  CAS  Google Scholar 

  10. Kalodimos, C.G., Folkers, G.E., Boelens, R. & Kaptein, R. Proc. Natl. Acad. Sci. USA 98, 6039–6044 (2001).

    Article  CAS  Google Scholar 

  11. Englander, S.W. & Krishna, M.M.G. Nature Struct. Biol. 8, 741–742 (2001).

    Article  CAS  Google Scholar 

  12. Englander, S.W. Annu. Rev. Biophys. Biomol. Struct. 29, 213–238 (2000).

    Article  CAS  Google Scholar 

  13. Xu, Y., Mayne, L. & Englander, S.W. Nature Struct. Biol. 5, 774–778 (1998).

    Article  CAS  Google Scholar 

  14. Chamberlain, A.K., Handel, T.M. & Marqusee, S. Nature Struct. Biol. 3, 782–787 (1996).

    Article  CAS  Google Scholar 

  15. Kiefhaber, T. & Baldwin, R.L. Proc. Natl. Acad. Sci. USA 92, 2657–2661 (1995).

    Article  CAS  Google Scholar 

  16. Zahn, R., Perrett, S., Stenberg, G. & Fersht, A.R. Science 271, 642–645 (1996).

    Article  CAS  Google Scholar 

  17. Parker, M.J., Dempsey, C.E., Hosszu, L.L.P., Waltho, J.P. & Clarke, A.R. Nature Struct. Biol. 5, 194–198 (1998).

    Article  CAS  Google Scholar 

  18. Hvidt, A. & Nielsen, S.O. Adv. Protein Chem. 21, 287–386 (1966).

    Article  CAS  Google Scholar 

  19. Bai, Y., Milne, J.S., Mayne, L. & Englander, S.W. Proteins 17, 75–86 (1993).

    Article  CAS  Google Scholar 

  20. Sivaraman, T., Arrington, C.B. & Robertson, A.D. Nature Struct. Biol. 8, 331–333 (2001).

    Article  CAS  Google Scholar 

  21. Sasmor, H.M. & Betz, J.L. Gene 89, 1–6 (1990).

    Article  CAS  Google Scholar 

  22. Spolar, R.S. & Record, M.T. Jr. Science 263, 777–784 (1994).

    Article  CAS  Google Scholar 

  23. Arrington, C.B. & Robertson, A.D. J. Mol. Biol. 300, 221–232 (2000).

    Article  CAS  Google Scholar 

  24. Falcon, C.M. & Matthews, K.S. Biochemistry 39, 11074–11083 (2000).

    Article  CAS  Google Scholar 

  25. Wintjens, R. & Rooman, M. J. Mol. Biol. 262, 294–313 (1996).

    Article  CAS  Google Scholar 

  26. Ciubotatu, M., Bright, F.V., Ingersoll, C.M. & Koudelka, G.B. J. Mol. Biol. 294, 859–873 (1999).

    Article  Google Scholar 

  27. van Tilborg, M.A. et al. J. Mol. Biol. 301, 947–958 (2000).

    Article  CAS  Google Scholar 

  28. Arrington, C.B. & Robertson, A.D. Biochemistry 36, 8686–8691 (1997).

    Article  CAS  Google Scholar 

  29. Koradi, R., Billeter, M. & Wüthrich, K. J. Mol. Graph. 14, 52–55 (1996).

    Article  Google Scholar 

  30. Riggs, A D., Bourgeois, S. & Cohn, M. J. Mol. Biol. 53, 401–417 (1970).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was financially supported by the Netherlands Foundation for Scientific Research (NOW-CW)

Author information

Authors and Affiliations

  1. Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, CH, 3584, Utrecht, The Netherlands

    Charalampos G. Kalodimos, Rolf Boelens & Robert Kaptein

Authors
  1. Charalampos G. Kalodimos
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rolf Boelens
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Robert Kaptein
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Robert Kaptein.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kalodimos, C., Boelens, R. & Kaptein, R. A residue-specific view of the association and dissociation pathway in protein–DNA recognition. Nat Struct Mol Biol 9, 193–197 (2002). https://doi.org/10.1038/nsb763

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb763

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