title: Dual DNA recognition codes of a short peptide derived from the basic leucine zipper protein EmBP1.
abstract: Sequence-specific DNA binding of short peptide dimers derived from a plant basic leucine zipper protein EmBP1 was studied. A homodimer of the EmBP1 basic region peptide recognized a palindromic DNA sequence, and a heterodimer of EmBP1 and GCN4 basic region peptides targets a non-palindromic DNA sequence when a beta-cyclodextrin/adamantane complex is utilized as a dimerization domain. A homodimer of the EmBP1 basic region peptide binds the native EmBP1 binding 5'-GCCACGTGGC-3' and the native GCN4 binding 5'-ATGACGTCAT-3' sequences with almost equal affinity in the alpha-helical conformation, indicating that the basic region of EmBP1 by itself has a dual recognition codes for the DNA sequences. The GCN4 basic region peptide binds 5'-ATGAC-3' in the alpha-helical conformation, but it neither shows affinity nor helix formation with 5'-GCCAC-3'. Because native EmBP1 forms 100 times more stable complex with 5'-GCCACGTGGC-3' over 5'-ATGACGTCAT-3', our results suggest that the sequence-selectivity of native EmBP1 is dictated by the structure of leucine zipper dimerization domain including the hinge region spanning between the basic region and the leucine zipper.
authors.affiliation: Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
authors.forename: Akiyoshi
authors.initials: A
authors.lastname: Hirata
authors.forename: Masaru
authors.initials: M
authors.lastname: Ueno
authors.forename: Yasunori
authors.initials: Y
authors.lastname: Aizawa
authors.forename: Katsutoshi
authors.initials: K
authors.lastname: Ohkubo
authors.forename: Takashi
authors.initials: T
authors.lastname: Morii
authors.forename: Susumu
authors.initials: S
authors.lastname: Yoshikawa
mesh_terms: D000595:Amino Acid Sequence; D050976:Basic-Leucine Zipper Transcription Factors; D002240:Carbohydrate Sequence; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D016172:DNA Fingerprinting / Q000379:methods; D004268:DNA-Binding Proteins / Q000138:chemical synthesis / Q000737:chemistry* / Q000502:physiology; D003850:Deoxyribonuclease I / Q000378:metabolism; D016350:Leucine Zippers / Q000502:physiology*; D008969:Molecular Sequence Data; D010455:Peptides / Q000138:chemical synthesis / Q000737:chemistry* / Q000502:physiology; D010940:Plant Proteins / Q000737:chemistry*; D017434:Protein Structure, Tertiary / Q000502:physiology; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D050976:Basic-Leucine Zipper Transcription Factors; D004268:DNA-Binding Proteins; D010455:Peptides; D010940:Plant Proteins; D014157:Transcription Factors; D004247:DNA; D003850:Deoxyribonuclease I