title: Double-stranded DNA templates can induce alpha-helical conformation in peptides containing lysine and alanine: functional implications for leucine zipper and helix-loop-helix transcription factors.
abstract: Transcription factors of the basic-leucine zipper and basic-helix-loop-helix families specifically recognize DNA by means of intrinsically flexible peptide domains that assume an alpha-helical conformation upon binding to target DNA sequences. We have investigated the nonspecific interactions that underlie specific DNA recognition. Circular dichroism measurements showed that 20-bp double-stranded DNA oligonucleotides can act as templates to promote random coil-->alpha-helix transitions in short peptides containing alanine and lysine. This conformational change takes place without altering the structure of the DNA, and neither specific peptide-DNA contacts nor cooperative interactions between peptides are necessary. The conformational change does require (i) double-stranded (but not single-stranded) oligodeoxynucleotides in either the B or the B' conformation and (ii) peptides that can form positively charged amphipathic alpha-helices. In 10 mM Na2HPO4 (pH 7.5; 10 degrees C), the excess free-energy contribution of the DNA template to the stability of the alpha-helical form of the oligopeptides tested was delta Gex = -0.15 (+/- 0.07) kcal/mol per lysine residue. The implications of these results for the thermodynamics and kinetics of DNA target site selection by basic-leucine zipper and basic-helix-loop-helix regulatory proteins are discussed.
authors.affiliation: Institute of Molecular Biology, University of Oregon, Eugene 97403.
authors.forename: N P
authors.initials: NP
authors.lastname: Johnson
authors.forename: J
authors.initials: J
authors.lastname: Lindstrom
authors.forename: W A
authors.initials: WA
authors.lastname: Baase
authors.forename: P H
authors.initials: PH
authors.lastname: von Hippel
mesh_terms: D000409:Alanine / Q000737:chemistry; D000595:Amino Acid Sequence; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000378:metabolism*; D018257:Helix-Loop-Helix Motifs; D016350:Leucine Zippers; D008239:Lysine / Q000737:chemistry; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D013698:Templates, Genetic; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism
chemical_list: D014157:Transcription Factors; D004247:DNA; D008239:Lysine; D000409:Alanine