Dual DNA recognition codes of a short peptide derived from the basic leucine zipper protein EmBP1 Original Research Article

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 β-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 α-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 α-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.