SOLUTION STRUCTURE OF THE ATF-2 RECOGNITION SITE AND ITS INTERACTION WITH THE ATF-2 PEPTIDE

The effect of leucine zipper proteins binding to the DNA recognition s ite is controversial. Results from crystallography, gel and solution m ethods have led to opposite conclusions about the conformation of the DNA in the complex, The role of the DNA binding site in the recognitio n process and in the gene induction mediated by transcription factors needs to be investigated further. In this article the self-complementa ry 16 bp oligodeoxynucleotide (CATGTGACGTCACATG)(2), which contains th e cAMP response element recognised by numerous transcription factors o f the leucine zipper family has been examined free from proteins and i n its interaction with the mammalian activating transcription factor 2 . The recognition process has been investigated by circular dichroism analysis, which has revealed conformational changes in both DNA and pr otein upon binding. The solution structure of the 16mer important in o rder to define the effects induced by binding of leucine zipper protei ns and the intrisic bending properties of DNA, has been determined fro m MMR data using direct refinement against NOE intensities, analysis o f scalar coupling constants and restrained molecular dynamics calculat ions. Final structures starting from the A and B forms of DNA agreed t o a pairwise roof mean square deviation (r.m.s.d.) of 1.04 +/- 0.3 Ang strom (0.7 +/- 0.2 Angstrom to the average) for all atoms, The termina l base pairs were less well determined, and the pairwise deviation of the 12 core bp was 0.83 +/- 0.27 Angstrom (0.55 +/- 0.19 Angstrom to t he average). The final structures are within the B-family with an aver age helical twist of 36 +/- 2 degrees. No significant intrinsic DNA be nd is shown in the activating transcription factor regulatory site. Ho wever, there are substantial deviations from the canonical B-DNA (r.m. s.d. = 3.6 Angstrom) in the core of the molecule, associated with rela tively large base inclinations.