Protein-directed DNA structure II. Raman spectroscopy of a leucine zipper bZIP complex

Mechanisms of transcription may involve protein-directed changes in DNA str ucture and DNA-directed changes in protein structure. We have employed Rama n spectroscopy to characterize vibrational signatures associated with such induced molecular fitting for two classes of transcription factors-the basi c leucine-zipper (bZIP) motif and the high-mobility-group (HMG) box-each wi th a DNA target site. Results for bZIP are described here; findings for the HMG-box are reported in the preceding paper in this issue [Benevides, J. M ., Chan, G., Lu, X.-J., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Biochemistry 39, 537-547]. The yeast activator GCN4 provides a well- studied example of bZIP recognition, wherein B-DNA serves essentially as a template for protein folding. Analysis of Raman spectra of the 57-residue G CN4 bZIP domain, its AP-1 binding site, and their specific complex confirms a DNA-induced increase in alpha-helicity, attributable to folding of GCN4 basic arms with virtually no change in B-DNA structure, consistent with pre vious X-ray and NMR structure determinations. The absence of DNA perturbati ons in the bZIP model contrasts sharply with the HMG box, where DNA structu re perturbations predominate. The bZIP and HMG-box models represent two opp osing extremes in a range of induced fits identifiable by Raman spectroscop y. Previously characterized lambda repressor/operator complexes [Benevides, J. M., Weiss, M. A., and Thomas, G. J. (1994) J. Biol. Chem. 269, 10869-10 878] occupy an intermediate position within this range. A comprehensive tab ulation of Raman markers proposed as diagnostic of different protein/DNA re cognition motifs is presented. The results are analyzed in terms of availab le DNA crystal structures (Nucleic Acid Database) to identify details of DN A conformation that correlate with specific Raman recognition markers.