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

Nat Struct Biol. 2001 Jul;8(7):589-93. doi: 10.1038/89617.


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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Allosteric Site
  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Crystallography, X-Ray
  • DNA / genetics
  • DNA / metabolism*
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Dimerization
  • Homeodomain Proteins / chemistry
  • Homeodomain Proteins / metabolism
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Peptides / chemistry*
  • Peptides / genetics
  • Peptides / metabolism*
  • Protein Binding
  • Protein Conformation
  • Protein Engineering
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / metabolism
  • Sequence Alignment
  • Substrate Specificity
  • Zinc Fingers*


  • DNA-Binding Proteins
  • Homeodomain Proteins
  • Peptides
  • Recombinant Fusion Proteins
  • DNA

Associated data

  • PDB/1F2I