Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1993 Jun 1;90(11):4892–4896. doi: 10.1073/pnas.90.11.4892

Design superiority of palindromic DNA sites for site-specific recognition of proteins: tests using protein stitchery.

C Park 1, J L Campbell 1, W A Goddard 3rd 1
PMCID: PMC46619  PMID: 8506333

Abstract

Using protein stitchery with appropriate attachment of cysteines linking to either C or N termini of the basic region of the v-Jun leucine zipper gene-regulatory protein, we constructed three dimers--pCC, pCN, and pNN. All three bind specifically to the appropriately rearranged DNA recognition sites for v-Jun: ATGAcgTCAT, ATGAcgATGA, and TCATcgTCAT, respectively (Kd, approximately 4 nM at 4 degrees C). Results of DNase I footprinting provide strong support for bent recognition helices in leucine zipper protein-DNA complexes. Comparison of the results for pCC and pNN with those for pCN shows the design superiority of palindromic sequences for protein recognition.

Full text

PDF
4892

Images in this article

4892Fig. 1
on p.4892
4893Fig. 2
on p.4893
4894Fig. 3
on p.4894

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abate C., Luk D., Gagne E., Roeder R. G., Curran T. Fos and jun cooperate in transcriptional regulation via heterologous activation domains. Mol Cell Biol. 1990 Oct;10(10):5532–5535. doi: 10.1128/mcb.10.10.5532. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Agre P., Johnson P. F., McKnight S. L. Cognate DNA binding specificity retained after leucine zipper exchange between GCN4 and C/EBP. Science. 1989 Nov 17;246(4932):922–926. doi: 10.1126/science.2530632. [DOI] [PubMed] [Google Scholar]
  3. Bos T. J., Bohmann D., Tsuchie H., Tjian R., Vogt P. K. v-jun encodes a nuclear protein with enhancer binding properties of AP-1. Cell. 1988 Mar 11;52(5):705–712. doi: 10.1016/0092-8674(88)90408-4. [DOI] [PubMed] [Google Scholar]
  4. Corey D. R., Schultz P. G. Generation of a hybrid sequence-specific single-stranded deoxyribonuclease. Science. 1987 Dec 4;238(4832):1401–1403. doi: 10.1126/science.3685986. [DOI] [PubMed] [Google Scholar]
  5. Ellenberger T. E., Brandl C. J., Struhl K., Harrison S. C. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex. Cell. 1992 Dec 24;71(7):1223–1237. doi: 10.1016/s0092-8674(05)80070-4. [DOI] [PubMed] [Google Scholar]
  6. Gartenberg M. R., Ampe C., Steitz T. A., Crothers D. M. Molecular characterization of the GCN4-DNA complex. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6034–6038. doi: 10.1073/pnas.87.16.6034. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gentz R., Rauscher F. J., 3rd, Abate C., Curran T. Parallel association of Fos and Jun leucine zippers juxtaposes DNA binding domains. Science. 1989 Mar 31;243(4899):1695–1699. doi: 10.1126/science.2494702. [DOI] [PubMed] [Google Scholar]
  8. Kerppola T. K., Curran T. DNA bending by Fos and Jun: the flexible hinge model. Science. 1991 Nov 22;254(5035):1210–1214. doi: 10.1126/science.1957173. [DOI] [PubMed] [Google Scholar]
  9. 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. 1988 Jun 24;240(4860):1759–1764. doi: 10.1126/science.3289117. [DOI] [PubMed] [Google Scholar]
  10. Maki Y., Bos T. J., Davis C., Starbuck M., Vogt P. K. Avian sarcoma virus 17 carries the jun oncogene. Proc Natl Acad Sci U S A. 1987 May;84(9):2848–2852. doi: 10.1073/pnas.84.9.2848. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Neuberg M., Adamkiewicz J., Hunter J. B., Müller R. A Fos protein containing the Jun leucine zipper forms a homodimer which binds to the AP1 binding site. Nature. 1989 Sep 21;341(6239):243–245. doi: 10.1038/341243a0. [DOI] [PubMed] [Google Scholar]
  12. Neuberg M., Schuermann M., Hunter J. B., Müller R. Two functionally different regions in Fos are required for the sequence-specific DNA interaction of the Fos/Jun protein complex. Nature. 1989 Apr 13;338(6216):589–590. doi: 10.1038/338589a0. [DOI] [PubMed] [Google Scholar]
  13. O'Neil K. T., Hoess R. H., DeGrado W. F. Design of DNA-binding peptides based on the leucine zipper motif. Science. 1990 Aug 17;249(4970):774–778. doi: 10.1126/science.2389143. [DOI] [PubMed] [Google Scholar]
  14. Pabo C. O., Sauer R. T. Protein-DNA recognition. Annu Rev Biochem. 1984;53:293–321. doi: 10.1146/annurev.bi.53.070184.001453. [DOI] [PubMed] [Google Scholar]
  15. Park C., Campbell J. L., Goddard W. A., 3rd Protein stitchery: design of a protein for selective binding to a specific DNA sequence. Proc Natl Acad Sci U S A. 1992 Oct 1;89(19):9094–9096. doi: 10.1073/pnas.89.19.9094. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Patel L., Abate C., Curran T. Altered protein conformation on DNA binding by Fos and Jun. Nature. 1990 Oct 11;347(6293):572–575. doi: 10.1038/347572a0. [DOI] [PubMed] [Google Scholar]
  17. Ransone L. J., Visvader J., Wamsley P., Verma I. M. Trans-dominant negative mutants of Fos and Jun. Proc Natl Acad Sci U S A. 1990 May;87(10):3806–3810. doi: 10.1073/pnas.87.10.3806. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Ransone L. J., Wamsley P., Morley K. L., Verma I. M. Domain swapping reveals the modular nature of Fos, Jun, and CREB proteins. Mol Cell Biol. 1990 Sep;10(9):4565–4573. doi: 10.1128/mcb.10.9.4565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Ryseck R. P., Bravo R. c-JUN, JUN B, and JUN D differ in their binding affinities to AP-1 and CRE consensus sequences: effect of FOS proteins. Oncogene. 1991 Apr;6(4):533–542. [PubMed] [Google Scholar]
  20. Schüle R., Umesono K., Mangelsdorf D. J., Bolado J., Pike J. W., Evans R. M. Jun-Fos and receptors for vitamins A and D recognize a common response element in the human osteocalcin gene. Cell. 1990 May 4;61(3):497–504. doi: 10.1016/0092-8674(90)90531-i. [DOI] [PubMed] [Google Scholar]
  21. Talanian R. V., McKnight C. J., Kim P. S. Sequence-specific DNA binding by a short peptide dimer. Science. 1990 Aug 17;249(4970):769–771. doi: 10.1126/science.2389142. [DOI] [PubMed] [Google Scholar]
  22. Vinson C. R., Sigler P. B., McKnight S. L. Scissors-grip model for DNA recognition by a family of leucine zipper proteins. Science. 1989 Nov 17;246(4932):911–916. doi: 10.1126/science.2683088. [DOI] [PubMed] [Google Scholar]
  23. Weiss M. A. Thermal unfolding studies of a leucine zipper domain and its specific DNA complex: implications for scissor's grip recognition. Biochemistry. 1990 Sep 4;29(35):8020–8024. doi: 10.1021/bi00487a004. [DOI] [PubMed] [Google Scholar]
  24. Zuckermann R., Corey D., Schultz P. Efficient methods for attachment of thiol specific probes to the 3'-ends of synthetic oligodeoxyribonucleotides. Nucleic Acids Res. 1987 Jul 10;15(13):5305–5321. doi: 10.1093/nar/15.13.5305. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES