THE ROLE OF A BASIC-AMINO-ACID CLUSTER IN TARGET SITE SELECTION AND NONSPECIFIC-BINDING OF BZIP PEPTIDES TO DNA

The ability of a transcription factor to locate and bind its cognate D NA site in the presence of closely related sites and a vast array of n on-specific DNA is crucial for cell survival, The CREB/ATF family of t ranscription factors is an important group of basic region leucine zip per (bZIP) proteins that display high affinity for the CRE site and lo w affinity for the closely related AP-1 site, Members of the CREB/ATF family share in common a cluster of basic amino acids at the N-terminu s of their bZIP element, This basic cluster is necessary and sufficien t to cause the CRE site to bend upon binding of a CREB/ATF protein, Th e possibility that DNA bending and CRE/AP-1 specificity were linked in CREB/ATF proteins was investigated using chimeric peptides derived fr om human CRE-BP1 (a member of the CREB/ATF family) and yeast GCN4, whi ch lacks both a basic cluster and CRE/AP-1 specificity, Gain of functi on and loss of function experiments demonstrated that the basic cluste r was not responsible for the CRE/AP-1 specificity displayed by all ch aracterized CREB/ATF proteins, The basic cluster was, however, respons ible for inducing very high affinity for nonspecific DNA, It was furth er shown that basic cluster-containing peptides bind non-specific DNA in a random coil conformation, We postulate that the high nonspecific DNA affinities of basic cluster-containing peptides result from cooper ative electrostatic interactions with the phosphate backbone that do n ot require peptide organization.