Studies on the formation of DNA•protein interfaces: DNA specificity and straightening by CREB

Transcriptional regulation by bZIP proteins in the CREB/ATF family requires that these proteins discriminate between the CRE and AP-1 target sites, two DNA sequences that differ by a single G•C base pair. We reported recently that CRE-BP1, one member of the CREB/ATF family, prefers the CRE target site to the AP-1 target site by 2.3 kcal•mol−1 and straightens the intrinsic bend in its specific CRE target site upon binding. Of all well-characterized members of the CREB/ATF family, the cyclic-AMP response-element binding protein (CREB) is among the most divergent from CRE-BP1 in primary sequence. Here we show that CREB, like CRE-BP1, (1) displays high selectivity (ΔΔG0obs= 1.5 kcal•mol−1) for the CRE target site and (2) straightens the intrinsically bent CRE target site upon binding. Although the effect of CREB on DNA conformation is comparable to that of CRE-BP1, the relative affinities of these two proteins for the CRE and AP-1 target sites are not. These results indicate that CRE/AP-1 specificity, the hallmark of the CREB/ATF transcription factor family, cannot be explained solely on the basis of differential DNA flexibility.