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.

  • Article
  • Published:

An engineered allosteric switch in leucine-zipper oligomerization

An Erratum to this article was published on 01 July 1996

Abstract

Controversy remains about the role of core side-chain packing in specifying protein structure. To investigate the influence of core packing on the oligomeric structure of a coiled coil, we engineered a GCN4 leucine zipper mutant that switches from two to three strands upon binding the hydrophobic ligands cyclohexane and benzene. In solution these ligands increased the apparent thermal stability and the oligomerization order of the mutant leucine zipper. The crystal structure of the peptide–benzene complex shows a single benzene molecule bound at the engineered site in the core of the trimer. These results indicate that coiled coils are well-suited to function as molecular switches and emphasize that core packing is an important determinant of oligomerization specificity.

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

Access options

Buy this article

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

Similar content being viewed by others

References

  1. Bryson, J.W. et al. Protein design: A hierarchic approach. Science 270, 935–941 (1995).

    Article  CAS  Google Scholar 

  2. Spencer, D.M., Wandless, T.J., Schreiber, S.L. & Crabtree, G.R. Controlling signal transduction with synthetic ligands. Science 262, 1019–1024 (1993).

    Article  CAS  Google Scholar 

  3. Landschulz, W.H., Johnson, P.F. & McKnight, S.L. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240, 1759–1764 (1988).

    Article  CAS  Google Scholar 

  4. Peteranderl, R. & Nelson, H.C.M. Trimerization of the heat shock transcription factor by a triple-stranded alpha-helical coiled-coil. Biochemistry 31, 12272–12276 (1992).

    Article  CAS  Google Scholar 

  5. Parry, D.A.D. & Steinert, P.M. Intermediate filament structure. Curr. Opin. Cell Biol. 4, 94–98 (1992).

    Article  CAS  Google Scholar 

  6. Hunter, I., Schulthess, T. & Engel, J. Laminin chain assembly by triple and double stranded coiled-coil structures. J. Biol. Chem. 267, 6006–6011 (1992).

    CAS  PubMed  Google Scholar 

  7. Kodama, T. et al. Type I macrophage scavenger receptor contains alpha-helical and collagen-like coiled coils. Nature 343, 531–535 (1990).

    Article  CAS  Google Scholar 

  8. Doi, T. et al. The histidine interruption of an alpha-helical coiled coil allosterically mediates a pH-dependent ligand dissociation from macrophage scavenger receptors. J. Biol. Chem. 269, 25598–25604 (1994).

    CAS  PubMed  Google Scholar 

  9. Carr, C.M. & Kim, P.S. A spring-loaded mechanism for the conformational change of influenza hemagglutinin. Cell 73, 823–832 (1993).

    Article  CAS  Google Scholar 

  10. Bullough, P.A., Hughson, F.M., Skehel, J.J. & Wiley, D.C. Structure of influenza haemagglutinin at the pH of membrane fusion. Nature 371, 37–43 (1994).

    Article  CAS  Google Scholar 

  11. Rabindran, S.K., Haroun, R.I., Clos, J., Wisniewski, J. & Wu, C. Regulation of heat shock factor trimer formation: role of a conserved leucine zipper. Science 259, 230–234 (1993).

    Article  CAS  Google Scholar 

  12. Oas, T.G. & Endow, S.A. Springs and hinges: dynamic coiled coils and discontinuities. Trends Biochem. Sci. 19, 51–54 (1994)

    Article  CAS  Google Scholar 

  13. Cohen, C. & Parry, D.A.D. Alpha-helical coiled coils and bundles: how to design an alpha-helical protein. Proteins 7, 1–15 (1990).

    Article  CAS  Google Scholar 

  14. Harbury, P.B., Kim, P.S. & Alber, T. Crystal structure of an isoleucine-zipper trimer. Nature 371, 80–83 (1994).

    Article  CAS  Google Scholar 

  15. Cohen, C. & Parry, D.A.D. Alpha-helical coiled coils: more facts and better predictions. Science 263, 488–489 (1994).

    Article  CAS  Google Scholar 

  16. Harbury, P.B., Zhang, T., Kim, P.S. & Alber, T. A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 262, 1401–1407 (1993).

    Article  CAS  Google Scholar 

  17. Zhu, B.Y., Zhou, N.E., Kay, C.M. & Hodges, R.S. Packing and hydrophobicity effects on protein folding and stability: effects of beta-branched amino acids, valine and isoleucine, on the formation and stability of two-stranded alpha-helical coiled coils/leucine zippers. Protein Science 2, 383–394 (1993).

    Article  CAS  Google Scholar 

  18. Woolfson, D.N. & Alber, T. Predicting oligomerization states of coiled coils. Protein Science 4, 1596–1607 (1995).

    Article  CAS  Google Scholar 

  19. O'Shea, E.K., Rutkowski, R. & Kim, P.S. Evidence that the leucine zipper is a coiled coil. Science 243, 538–542 (1989).

    Article  CAS  Google Scholar 

  20. O'Shea, E.K., Klemm, J.D., Kim, P.S. & Alber, T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254, 539–544 (1991).

    Article  CAS  Google Scholar 

  21. Hurst, H.C. Sequences of bZIP proteins. Protein Profile 1, 125–134 (1994).

    Google Scholar 

  22. Potekhin, S.A., Medvedkin, V.N., Kashparov, I.A. & Venyaminov, S.U. Synthesis and properties of the peptide corresponding to the mutant form of the leucine zipper of the transcriptional activator GCN4 from yeast. Protein Eng. 7, 1097–1101 (1994).

    Article  CAS  Google Scholar 

  23. Monod, J., Wyman, J. & Changeux, J.P. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12, 88–118 (1965).

    Article  CAS  Google Scholar 

  24. Eriksson, A.E., Baase, W.A., Wozniak, J.A. & Matthews, B.W. A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene. Nature 355, 371–373 (1992).

    Article  CAS  Google Scholar 

  25. Morton, A. & Matthews, B.W. Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity. Biochemistry 34, 8576–8588 (1995).

    Article  CAS  Google Scholar 

  26. Morton, A., Baase, W.A. & Matthews, B.W. Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry 34, 8564–8575 (1995).

    Article  CAS  Google Scholar 

  27. Connolly, M. L. Solvent-accessible surfaces of proteins and nucleic acids. Science 222, 709–713 (1983).

    Article  Google Scholar 

  28. Adamson, J.G., Zhou, N.E. & Hodges, R.S. Sucture, function and application of the coiled-coil protein folding motif. Curr. Opin. Biotechnol. 4, 428–437 (1993).

    Article  CAS  Google Scholar 

  29. Betz, S.F., Fairman, R., O'Neil, K.T. & DeGrado, W.F. Design of two-stranded and three-stranded coiled-coil peptides. Phil. Trans. Roy. Soc. Lond. B348, 81–88 (1995).

    Google Scholar 

  30. Lumb, K.J. & Kim, P.S. A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil. Biochemistry 33, 7361–7367 (1994).

    Article  CAS  Google Scholar 

  31. Laue, T.M., Shah, B.D., Ridgeway, T.M. & Pelletier, S.L. Computer-aided interpretation of analytical sedimentation data for proteins. Analytical Ultracentrifugation in Biochemistry and Polymer Science (Harding, S. E., Rowe, A. J. & Horton, J. C., Eds.) 90–125 (The Royal Society of Chemistry, Cambridge; 1992).

    Google Scholar 

  32. Johnson, M.L., Correia, J.J., Yphantis, D.A. & Halvorson, H.R. Analysis of data from the analytical ultracentrifuge by nonlinear least-squares techniques. Biophys. J. 36, 575–588 (1981).

    Article  CAS  Google Scholar 

  33. Brünger, A.T. X-PLOR, version 3.1: A system for X-ray crystallography and NMR. Yale University Press, New Haven, Connecticut (1992).

    Google Scholar 

  34. Tronrud, D.E. Conjugate-direction minimization: an improved method for the refinement of macromolecules. Acta Crystallogr. A48, 912–916 (1992).

    Article  CAS  Google Scholar 

  35. Creighton, T.E. Proteins, p. 339, W. H. Freeman and Company, New York (1993).

    Google Scholar 

  36. Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gonzalez, L., Plecs, J. & Alber, T. An engineered allosteric switch in leucine-zipper oligomerization. Nat Struct Mol Biol 3, 510–515 (1996). https://doi.org/10.1038/nsb0696-510

Download citation

  • Received:

  • Accepted:

  • Issue date:

  • DOI: https://doi.org/10.1038/nsb0696-510

This article is cited by

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