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Selected peptide extension contacts hydrophobic patch on neighboring zinc finger and mediates dimerization on DNA

Nature Structural Biology volume 8, pages 589–593 (2001)Cite this article

Abstract

Protein–protein interactions often play a crucial role in stabilizing protein–DNA complexes and thus facilitate site-specific DNA recognition. We have worked to incorporate such protein–protein contacts into our design and selection strategies for short peptide extensions that promote cooperative binding of zinc finger proteins to DNA. We have determined the crystal structure of one of these fusion protein–DNA complexes. The selected peptide extension was found to mediate dimerization by reaching across the dyad axis and contacting a hydrophobic patch on the surface of the zinc finger bound to the adjacent DNA site. The peptide–zinc finger protein interactions observed in this structure are similar to those of some homeodomain heterodimers. We also find that the region of the zinc finger surface contacted by the selected peptide extension corresponds to surfaces that also make key interactions in the zinc finger proteins GLI and SWI5.

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Figure 1: a, Sequence of the fusion protein and DNA used for crystallization.
Figure 2: The dimer interface.
Figure 3: Comparison of our complex with peptide–protein interactions in homeodomain heterodimeric complexes.
Figure 4: Comparison of the contact surfaces of various zinc fingers, showing Zif268 finger 1 from our complex (red), GLI finger 1 (green, ref. 12), GLI finger 2 (cyan, ref. 12) and SWI5 finger 1 (yellow, ref. 13).

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References

  1. Ptashne, M. A genetic switch: phage lambda and higher organisms (Cell Press, Cambridge, MA; 1992).

  2. Wolberger, C. Annu. Rev. Biophys. Biomol. Struct. 28, 29–56 (1999).

    Article  CAS  Google Scholar 

  3. Wang, B.S. & Pabo, C.O. Proc. Natl. Acad. Sci. USA 96, 9568–9573 (1999).

    Article  CAS  Google Scholar 

  4. Wolfe, S.A., Nekludova L. & Pabo, C.O. Annu. Rev. Biophy. Biomol. Struct. 29, 183–212 (2001).

    Article  Google Scholar 

  5. Christy, B.A., Lau, L.F. & Nathans, D. Proc. Natl. Acad. Sci. USA 85, 7857–7861 (1988).

    Article  CAS  Google Scholar 

  6. Pavletich, N.P. & Pabo, C.O. Science 252, 809–817 (1991).

    Article  CAS  Google Scholar 

  7. Elrod-Erickson, M., Rould, M.A., Nekludova, L. & Pabo, C.O. Structure 4, 1171–1180 (1996).

    Article  CAS  Google Scholar 

  8. Li, T., Stark, M.R., Johnson, A.D. & Wolberger, C. Science 270, 262–269 (1995).

    Article  CAS  Google Scholar 

  9. Passner, J.M., Ryoo, H.D., Shen, L., Mann, R.S. & Aggarwal, A.K. Nature 397, 714–719 (1999).

    Article  CAS  Google Scholar 

  10. Piper, D.E., Batchelor, A.H., Chang, C.-P., Cleary, M.L. & Wolberger, C. Cell 96, 587–597 (1999).

    Article  CAS  Google Scholar 

  11. MacKay, J.P. & Crossley, M. Trends Biochem. Sci. 23, 1–4 (1998).

    Article  CAS  Google Scholar 

  12. Pavletich, N.P. & Pabo, C.O. Science 261, 1701–1707 (1993).

    Article  CAS  Google Scholar 

  13. Dutnall, R.N., Neuhaus, D. & Rhodes, D. Structure 4, 599–611 (1996).

    Article  CAS  Google Scholar 

  14. Livnah, O. et al. Science 273, 464–471 (1996).

    Article  CAS  Google Scholar 

  15. Fairbrother, W.J. et al. Biochemistry 37, 17754–17764 (1998).

    Article  CAS  Google Scholar 

  16. DeLano, W.L., Ultsch, M.H., Vos, A.M.D. & Wells, J.A. Science 287, 1279–1283 (2000).

    Article  CAS  Google Scholar 

  17. Liu, Q., Segal, D.J., Ghiara, J.B., Barbas, C.F., III. Proc. Natl. Acad. Sci. USA 94, 5525–5530 (1997).

    Article  CAS  Google Scholar 

  18. Kim, J.-S. & Pabo, C.O. Proc. Natl. Acad. Sci. USA 95, 2812–2817 (1998).

    Article  CAS  Google Scholar 

  19. Pomerantz, J.L., Wolfe, S.A. & Pabo, C.O. Biochemistry 37, 965–970 (1998).

    Article  CAS  Google Scholar 

  20. Wolfe, S.A., Ramm, E.I. & Pabo, C.O. Structure Fold. Des. 8, 739–750 (2000).

    Article  CAS  Google Scholar 

  21. Elrod-Erickson, M., Benson, T.E. & Pabo, C.O. Structure 6, 451–464 (1998).

    Article  CAS  Google Scholar 

  22. Klemm, J.D., Rould, M.A., Aurora, R., Herr, W. & Pabo, C.O. Cell 77, 21–32 (1994).

    Article  CAS  Google Scholar 

  23. Otwinowski, Z. & Minor, W. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  24. Yeates, T.O. Methods Enzymol. 276, 344–358 (1997).

    Article  CAS  Google Scholar 

  25. Collaborative Computational Project, Number 4. Acta Crystallogr. D 50, 760–763 (1994).

  26. Terwilliger, T. & Berendzen, J. Acta Crystallogr. D 55, 849–861 (1999).

    Article  CAS  Google Scholar 

  27. Jones, T.A., Zou, J.-Y., Cowan, S.W. & Kjeldgaard, M. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

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

    Google Scholar 

  29. Hodel, A., Kim, S.H. & Brunger, A.T. Acta Crystallogr. A 48, 851–859 (1992).

    Article  Google Scholar 

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Acknowledgements

Supported by the Howard Hughes Medical Institute. We thank the staff at NSLS Beamline X4A — especially, C. Ogata — for the use of their facility; E. Peisach for assistance with data collection; and E. Peisach, S. Fay-Richard, S. Wolfe and T. Yeates for helpful discussions. B.S.W. was a Howard Hughes Medical Institute predoctoral fellow.

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Author notes

  1. Bryan S. Wang

    Present address: Praecis Pharmaceuticals Incorporated, 830 Winter Street, Waltham, Massachusetts, 02451, USA

Authors and Affiliations

  1. Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Bryan S. Wang, Robert A. Grant & Carl O. Pabo

  2. Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Robert A. Grant & Carl O. Pabo

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  1. Bryan S. Wang
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  2. Robert A. Grant
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  3. Carl O. Pabo
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Correspondence to Carl O. Pabo.

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Wang, B., Grant, R. & Pabo, C. Selected peptide extension contacts hydrophobic patch on neighboring zinc finger and mediates dimerization on DNA. Nat Struct Mol Biol 8, 589–593 (2001). https://doi.org/10.1038/89617

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