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Asymmetric DNA binding by a homodimeric bHLH protein

Academic Article
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Overview

related to degree

  • Winston, Rachel Lynn, Ph.D. in Biology, Scripps Research 1995 - 1999

authors

  • Winston, Rachel Lynn
  • Ehley, J. A.
  • Baird, E. E.
  • Dervan, P. B.
  • Gottesfeld, Joel

publication date

  • August 2000

journal

  • Biochemistry  Journal

abstract

  • Protein-DNA interactions that lie outside of the core recognition sequence for the Drosophila bHLH transcription factor Deadpan (Dpn) were investigated using minor groove binding pyrrole-imidazole polyamides. Electrophoretic mobility shift assays and DNase I footprinting demonstrate that hairpin polyamides bound immediately upstream, but not immediately downstream of the Dpn homodimer selectively inhibit protein-DNA complex formation. Mutation of the Dpn consensus binding site from the asymmetric sequence 5'-CACGCG-3' to the palindromic sequence 5'-CACGTG-3' abolishes asymmetric inhibition. A Dpn mutant containing the unnatural amino acid norleucine in place of lysine at position 80 in the bHLH loop region is not inhibited by the polyamide, suggesting that the epsilon amino group at this position is responsible for DNA contacts outside the major groove. We conclude that the nonpalindromic Dpn recognition site imparts binding asymmetry by providing unique contacts to the basic region of each monomer in the bHLH homodimer.

subject areas

  • Amino Acid Substitution
  • Animals
  • Basic Helix-Loop-Helix Transcription Factors
  • Binding Sites
  • DNA
  • DNA-Binding Proteins
  • Deoxyribonuclease I
  • Dimerization
  • Drosophila
  • Drosophila Proteins
  • Helix-Loop-Helix Motifs
  • Kinetics
  • Lysine
  • Models, Molecular
  • Nuclear Proteins
  • Nylons
  • Oligonucleotide Probes
  • Peptide Fragments
  • Protein Binding
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Identity

International Standard Serial Number (ISSN)

  • 0006-2960

Digital Object Identifier (DOI)

  • 10.1021/bi000947d

PubMed ID

  • 10924102
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Additional Document Info

start page

  • 9092

end page

  • 9098

volume

  • 39

issue

  • 31

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