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:

Rational design of faster associating and tighter binding protein complexes

Nature Structural Biology volume 7, pages 537–541 (2000)Cite this article

Abstract

A protein design strategy was developed to specifically enhance the rate of association (kon) between a pair of proteins without affecting the rate of dissociation (koff). The method is based on increasing the electrostatic attraction between the proteins by incorporating charged residues in the vicinity of the binding interface. The contribution of mutations towards the rate of association was calculated using a newly developed computer algorithm, which predicted accurately the rate of association of mutant protein complexes relative to the wild type. Using this design strategy, the rate of association and the affinity between TEM1 β-lactamase and its protein inhibitor BLIP was enhanced 250-fold, while the dissociation rate constant was unchanged. The results emphasize that long range electrostatic forces specifically alter kon, but do not effect koff. The design strategy presented here is applicable for increasing rates of association and affinities of protein complexes in general.

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: Validating PARE for different proteins.
Figure 2: Surface representations of TEM1 and BLIP.
Figure 3: Rates of association of TEM1 with BLIP.
Figure 4: koff, affinity and activity of BLIP mutants.

Similar content being viewed by others

References

  1. Shoup, D. & Szabo, A. Biophys. J. 40, 33–39 (1982).

    Article  CAS  Google Scholar 

  2. Berg, O.G. & von Hippel, P.H. Annu. Rev. Biophys. Biophys. Chem. 14, 131–160 ( 1985).

    Article  CAS  Google Scholar 

  3. Schreiber, G. & Fersht, A.R. Nature Struct. Biol. 3, 427–431 (1996).

    Article  CAS  Google Scholar 

  4. Shi, Y.Y. et al. Protein Eng. 6, 289–295 (1993).

    Article  CAS  Google Scholar 

  5. Schreiber, G., Buckle, A.M. & Fersht, A.R. Structure. 2, 945– 951 (1994).

    Article  CAS  Google Scholar 

  6. Lee, F.S., Auld, D.S. & Vallee, B.L. Biochemistry. 28, 219– 224 (1989).

    Article  CAS  Google Scholar 

  7. Harel, M., Kleywegt, G.J., Ravelli, R.B., Silman, I. & Sussman, J.L. Structure. 3, 1355–1366 (1995).

    Article  CAS  Google Scholar 

  8. Radic, Z., Kirchhoff, P.D., Quinn, D.M., McCammon, A. & Taylor, P. J. Biol. Chem. 37, 23265–23277 (1997).

    Article  Google Scholar 

  9. Getzoff, E.D. et al. Nature 358, 347–351 (1992).

    Article  CAS  Google Scholar 

  10. Davis, M.E., Madura, J.D., Luty, B.A. & McCammon, A.J. Comput. Phys. Commun. 62, 187–197 ( 1991).

    Article  CAS  Google Scholar 

  11. Kozack, U.E., d'Mello, M.J. & Subramanian, S. Biophys. J. 68, 807–814 (1995).

    Article  CAS  Google Scholar 

  12. Madura, J.D. et al. Comput. Phys. Commun. 91, 57– 95 (1995).

    Article  CAS  Google Scholar 

  13. Gabdoulline, R.R. & Wade, R.C. Biophys. J. 72, 1917–1929 (1997).

    Article  CAS  Google Scholar 

  14. Zhou, H.X., Wong, K.Y. & Vijayakumar, M. Proc. Natl. Acad. Sci. USA 94, 12372–12377 (1997).

    Article  CAS  Google Scholar 

  15. Vijayakumar, M., et al. J. Mol. Biol. 278, 1015– 1024 (1998).

    Article  CAS  Google Scholar 

  16. Selzer, T. & Schreiber, G. J. Mol. Biol. 287, 409–419 (1999).

    Article  CAS  Google Scholar 

  17. Strynadka, N.C.J., Jensen, S.E., Alzari, P.M. & James, M.N. Nature Struct. Biol. 3, 290–297 (1996).

    Article  CAS  Google Scholar 

  18. Strynadka, N.C.J. et al. Nature. 368, 657–660 (1994).

    Article  CAS  Google Scholar 

  19. Albeck, S. & Schreiber, G. Biochemistry. 38, 11–21 (1999).

    Article  CAS  Google Scholar 

  20. Gilson, M.K. & Honig, B.A. Nature 330, 184–186 (1987).

    Article  Google Scholar 

  21. Schindler, P. & Huber, G. In Enzyme inhibitors. (ed. Brodbeck, U.) 169–176 (Verlag Chemie, Weinheim; 1980).

    Google Scholar 

  22. Guex, N. & Peitsch, M.C. Electrophoresis 18 , 2714–2723 (1997).

    Article  CAS  Google Scholar 

  23. Schreiber, G. & Fersht, A.R. Biochemistry 32, 11195–11203 (1993b).

    Article  CAS  Google Scholar 

  24. Stone, R.S., Dennis, S. & Hofsteenge, J. Biochemistry 28, 6857– 6863 (1989).

    Article  CAS  Google Scholar 

  25. Nicholls, A. GRASP: graphical representation and analysis of surface properties (Columbia University, New York; 1992).

    Google Scholar 

Download references

Acknowledgements

G.S. holds the Dewey David Stone and Harry Levine career development chair. This research was supported by a research grant from the Crown endowment fund for immunological research. We thank J. Sussman and A. Horovitz for their critical reading of the manuscript.

Author information

Authors and Affiliations

  1. Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel

    Tzvia Selzer, Shira Albeck & Gideon Schreiber

Authors
  1. Tzvia Selzer
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shira Albeck
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gideon Schreiber
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gideon Schreiber.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Selzer, T., Albeck, S. & Schreiber, G. Rational design of faster associating and tighter binding protein complexes . Nat Struct Mol Biol 7, 537–541 (2000). https://doi.org/10.1038/76744

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/76744

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