FOLDING TRANSITION IN THE DNA-BINDING DOMAIN OF GCN4 ON SPECIFIC BINDING TO DNA

PROTEIN-DNA recognition is often mediated by a small domain containing a recognizable structural motif, such as the helix-turn-helix1 or the zinc-finger2. These motifs are compact structures that dock against the DNA double helix. Another DNA recognition motif, found in a highly conserved family of eukaryotic transcription factors including C/EPB, Fos, Jun and CREB, consists of a coiled-coil dimerization element - the leucine-zipper - and an adjoining basic region which mediates DNA binding3. Here we describe circular dichroism and 1NMR spectroscopic studies of another family member, the yeast transcriptional activator GCN44,5. The 58-residue DNA-binding domain of GCN4, GCN4-p, exhibits a concentration-dependent α-helical transition, in accord with previous studies of the dimerization properties of an isolated leucine-zipper peptide6. The GCN4-p dimer is ∼70% helical at 25°C, implying that the basic region adjacent to the leucine zipper is largely unstructured in the absence of DNA. Strikingly, addition of DNA containing a GCN4 binding site (AP-1 site) increases the α-helix content of GNC4-p to at least 95%. Thus, the basic region acquires substantial α-helical structure when it binds to DNA. A similar folding transition is observed on GCN4-p binding to the related ATF/CREB site, which contains an additional central base pair. The accommodation of DNA target sites of different lengths clearly requires some flexibility in the GCN4 binding domain, despite its high α-helix content. Our results indicate that the GCN4 basic region is significantly unfolded at 25°C and that its folded, α-helical conformation is stabilized by binding to DNA. © 1990 Nature Publishing Group.