Figure 5.

Proposed energetics of Pho4 variant binding and DNA bending. (A) Sketches based on the structures of Pho4 and Gcn4 bound to DNA. The red DNA resembles the DNA in the original structures, proposed to be the DNA shape for neutral appended residues. Steric interactions due to bulky loop residues of Pho4p allow appended cations (KKK charge variant) to cause DNA bending toward the minor groove (green), but do not allow substantial anion-mediated DNA bending (EEE charge variant) toward the major groove (blue). The bZIP charge variants have less steric hindrance and allow DNA bending in either direction. (B) Speculative energy balance for Pho4 EEE and KKK variants. ΔΔG° values relative to the SAA variant are shown. The values for protein folding, DNA-bending energy and the total ΔΔG° are calculated as described in Materials and Methods. The other ΔΔG° values, for the disruption of H1 contacts upon substitution, the formation of H1 contacts upon DNA bending and the disruption of loop contacts upon DNA bending, are reasonable guesses that rationalize bending only for the KKK variant and sum to the correct total ΔΔG°.