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.

  • Correspondence
  • Published:

Aromatic hydrogen bond in sequence-specific protein DNA recognition

Nature Structural Biology volume 3, pages 837–841 (1996)Cite this article

An aromatic hydrogen bond—an interaction between the π-electron cloud of an aromatic ring and a hydrogen-bond donor—can substitute for a conventional hydrogen bond in sequence-specific protein—DNA interactions and can contribute 0.5–1 kcal mol−1 to binding and 1–2 kcal mol−1 to specificity.

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

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to the full article PDF.

USD 39.95

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

References

  1. Kolb, A., Busby, S., Buc, H., Garges, S. & Adhya, S. Ann. Rev. Biochem. 62, 749–795 (1993).

    Article  CAS  Google Scholar 

  2. Schultz, S., Shields, G. & Steitz, T. Science 253, 1001–1007 (1991).

    Article  CAS  Google Scholar 

  3. Parkinson, G. et al. J. Mol. Biol. 260, 395–408 (1996).

    Article  CAS  Google Scholar 

  4. Ebright, R., Cossart, P., Gicquel-Sanzey, B. & Beckwith, J. Nature 311, 232–235 (1984).

    Article  CAS  Google Scholar 

  5. Ebright, R., Cossart, P., Gicquel-Sanzey, B. & Beckwith, J. J. Proc. Natl. Acad. Sci. USA 81, 7274–7278 (1984).

    Article  CAS  Google Scholar 

  6. Ebright, R. et al. Proc. Natl. Acad. Sci. USA 84, 6083–6087 (1987).

    Article  CAS  Google Scholar 

  7. Ebright, R. Meths. Enzymol. 208, 620–640 (1991).

    Article  CAS  Google Scholar 

  8. Berg, O. & von Hippel, P. J. Mol. Biol. 200, 709–723 (1988).

    Article  CAS  Google Scholar 

  9. Ebright, R., Ebright, Y. & Gunasekera, A. Nucl. Acids Res. 17, 10295–10305 (1989).

    Article  CAS  Google Scholar 

  10. Gunasekera, A., Ebright, Y. & Ebright, R. J. Biol. Chem. 267, 14713–14720 (1992).

    CAS  PubMed  Google Scholar 

  11. Burley, S. & Petsko, G. FEBS Letts. 203, 139–143 (1986).

    Article  CAS  Google Scholar 

  12. Burley, S. & Petsko, G. Adv. Protein Chem. 39, 125–189 (1988).

    Article  CAS  Google Scholar 

  13. Levitt, M. & Perutz, M. J. Mol. Biol. 201, 751–754 (1988).

    Article  CAS  Google Scholar 

  14. Perutz, M. in The Chemical Bond (ed Zewail, E.) 17–30 (Academic Press, New York, 1992).

    Book  Google Scholar 

  15. Jorgensen, W. & Severance, D. J. Amer. Chem. Soc. 112, 4768–4774 (1990).

    Article  CAS  Google Scholar 

  16. Suzuki, S. et al. Science 257, 942–945 (1992).

    Article  CAS  Google Scholar 

  17. Rodham, D. et al. Nature 362, 735–737 (1993).

    Article  CAS  Google Scholar 

  18. Atwood, J., Hamada, F., Robinson, K., Orr, G.W. & Vincent, R. Nature 349, 683–684 (1991).

    Article  CAS  Google Scholar 

  19. Bakshi, P. et al. Can. J. Chem. 72, 1273–1293 (1993).

    Article  Google Scholar 

  20. Warshel, A. & Levitt, M. J. Mol. Biol. 103, 227–249 (1976).

    Article  CAS  Google Scholar 

  21. Mitchell, J., Nandi, C.L., McDonald, I. & Thornton, J. J. Mol. Biol. 239, 315–331 (1994).

    Article  CAS  Google Scholar 

  22. Jamison, R., Kakkad, B., Ebert, D., Newcomer, M. & Ong, D. Biochem. 34, 11128–11132 (1995).

    Article  CAS  Google Scholar 

  23. Zhang, X., Gunasekera, A., Ebright, Y. & Ebright, R. J. Biomol. Struct. Dyn. 9, 463–473 (1991).

    Article  CAS  Google Scholar 

  24. Kunkel, T., Bebenek, K. & McClary, J. Meths. Enzymol. 204, 125–138 (1991).

    Article  CAS  Google Scholar 

  25. Zhang, X. & Ebright, R. Proc. Natl. Acad. Sci. USA 87, 4717–4721 (1990).

    Article  CAS  Google Scholar 

  26. Brünger, A. X-PLOR Manual, Version 3.1 (Yale University Press, New Haven, 1992).

    Google Scholar 

  27. Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. & Berman, H. Acta Cryst. D52, 57–64 (1996).

    CAS  Google Scholar 

  28. Kraulis, P. J. Appl. Cryst. 24, 946–950 (1991).

    Article  Google Scholar 

Download references

Author information

Author notes

  1. Angelo Gunasekera

    Present address: Abbott Laboratories, Abbott Park, Illinois, 60064, USA

  2. Xiaoping Zhang

    Present address: Division of Infectious Disease, New England Medical Center, Boston, Massachusetts, 02111, USA

Authors and Affiliations

  1. Department of Chemistry and Waksman Institute, Rutgers University, New Brunswick, New Jersey, 08855, USA

    Gary Parkinson, Angelo Gunasekera, Jaroslav Vojtechovsky, Xiaoping Zhang, Helen Berman & Richard H. Ebright

  2. NIH-NIEHS, Research Triangle Park, North Carolina, 27709, USA

    Thomas A. Kunkel

Authors
  1. Gary Parkinson
    View author publications

    Search author on:PubMed Google Scholar

  2. Angelo Gunasekera
    View author publications

    Search author on:PubMed Google Scholar

  3. Jaroslav Vojtechovsky
    View author publications

    Search author on:PubMed Google Scholar

  4. Xiaoping Zhang
    View author publications

    Search author on:PubMed Google Scholar

  5. Thomas A. Kunkel
    View author publications

    Search author on:PubMed Google Scholar

  6. Helen Berman
    View author publications

    Search author on:PubMed Google Scholar

  7. Richard H. Ebright
    View author publications

    Search author on:PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Parkinson, G., Gunasekera, A., Vojtechovsky, J. et al. Aromatic hydrogen bond in sequence-specific protein DNA recognition. Nat Struct Mol Biol 3, 837–841 (1996). https://doi.org/10.1038/nsb1096-837

Download citation

  • Received:

  • Accepted:

  • Issue date:

  • DOI: https://doi.org/10.1038/nsb1096-837

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