Adaptability at the protein-DNA interface is an important aspect of sequence recognition by bZIP proteins

The related AP-1 and ATF/CREB families of transcriptional regulatory proteins bind as dimers to overlapping or adjacent DNA half-sites by using a bZIP structural motif. Using genetic selections, we isolate derivatives of yeast GCN4 that affect DNA-binding specificity at particular positions of the AP-1 target sequence. In general, altered DNA-binding specificity results from the substitution of larger hydrophobic amino acids for GCN4 residues that contact base pairs. However, in several cases, DNA binding by the mutant proteins cannot be simply explained in terms of the GCN4-AP-1 structure; movement of the protein and/or DNA structural changes are required to accommodate the amino acid substitutions. The quintet of GCN4 residues that make basepair contacts do not entirely determine DNA-binding specificity because these residues are highly conserved in the bZIP family, yet many of the bZIP proteins bind to distinct DNA sites. The α-helical fork between the GCN4 DNA-binding and dimerization surfaces is important for half-site spacing preferences, because mutations in the fork alter the relative affinity for AP-1 and ATF/CREB sites. The basic region in the protein-DNA complex is a long isolated α-helix, with no constraints from other parts of a folded domain. From all of these considerations, we suggest that small shifts in position and orientation or local deformations in the α-helical backbone distinguish one bZIP complex from another.