title: Interaction of a bZip oligopeptide model with oligodeoxyribonucleotides modelling DNA binding sites. The effect of flanking sequences.
abstract: A leucine zipper (bZip) binding peptide BP1 was constructed based on the DNA binding sequence of the GCN4 protein, slightly modified to make it more similar to the sequence of other bZip proteins (Jun) with related DNA binding specificity. Self-complementary DNA hexadecanucleotides containing ATF/CRE, AP-1 and C/EPB target sites were used to study peptide-DNA complex formation. Conformation changes in both components that occur on complex formation were studied by circular dichroism (CD) spectroscopy. The results show that the amount of alpha-helix formed in the peptide strongly depends not only on the target site present, but also on the type of the sequence flanking the ATF/CRE target site. Highest amount of the alpha-helix induced in the peptide was observed when homopurine homopyrimidine flanking sequences were present, whereas the presence of alternating sequences, especially of the CA/TG type, showed considerably lower effects. The change in DNA conformation on complex formation was generally small, but also depended on the type of the flanking sequence. It appears that the sequences flanking the target site can considerably modify the ability of the target sequence to bind specifically the bZip peptide, probably by slightly varying the overall DNA conformation.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Praha, Czech Republic. hanka@marilyn.uochb.cas.cz
authors.forename: H
authors.initials: H
authors.lastname: Votavová
authors.forename: K
authors.initials: K
authors.lastname: Hodanová
authors.forename: L
authors.initials: L
authors.lastname: Arnold
authors.forename: J
authors.initials: J
authors.lastname: Sponar
mesh_terms: D051698:Activating Transcription Factor 2; D000595:Amino Acid Sequence; D001665:Binding Sites; D022762:CCAAT-Enhancer-Binding Proteins; D002942:Circular Dichroism; D017362:Cyclic AMP Response Element-Binding Protein / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D005656:Fungal Proteins / Q000737:chemistry* / Q000378:metabolism; D016350:Leucine Zippers; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000378:metabolism; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism; D011494:Protein Kinases / Q000737:chemistry* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins; D012996:Solutions; D018808:Transcription Factor AP-1 / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D051698:Activating Transcription Factor 2; C083058:C-EPB transcription factor; D022762:CCAAT-Enhancer-Binding Proteins; D017362:Cyclic AMP Response Element-Binding Protein; D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D009838:Oligodeoxyribonucleotides; D009842:Oligopeptides; D029701:Saccharomyces cerevisiae Proteins; D012996:Solutions; D018808:Transcription Factor AP-1; D014157:Transcription Factors; D004247:DNA; D011494:Protein Kinases