Impact of protein/protein interactions on global intermolecular translocation rates of the transcription factors Sox2 and Oct1 between DNA cognate sites analyzed by z-exchange NMR spectroscopy

Abstract

Oct1 and Sox2 synergistically regulate developmental genes by binding to adjacent sites within promoters. We have investigated the kinetics of global intermolecular translocation of Sox2 and Oct1 between cognate sites located on different DNA molecules by z-exchange NMR spectroscopy. In the Hoxb1 promoter, the Sox2 and Oct1 sites are immediately adjacent to one another, and the intermolecular translocation rates are too slow to be measured by z-exchange spectroscopy. By introducing a 3-bp insertion between the Sox2 and Oct1 sites to mimic the spacing in the FGF4 enhancer, the interprotein contact surface is reduced, and the translocation rates are increased. Interaction between Sox2 and the POU-specific domain (POUS) of Oct1 does not affect the translocation mechanism but modulates the rates. Translocation involves only jumping (dissociation and reassociation) for Sox2, but both jumping and direct intersegment transfer (no dissociation into free solution) for Oct1. The dissociation (koff ∼1.5 s-1) and association (k on ∼5.1 × 109M-1s-1) rate constants for Sox2 are reduced 4-fold and increased 5-fold, respectively, in the presence of Oct1. koff (∼3.5 s-1) for Oct1 is unaffected by Sox2, whereas kon (∼1.3 × 10 9M-1s-1) is increased ∼13-fold. The direct intermolecular translocation rate (kinter ∼1.8 × 10 4 M-1s-1) for the POUS domain of Oct1 is reduced 2-fold by Sox2, whereas that for the POU homeodomain (POU HD) of Oct1 (kinter ∼1.7 × 104 M -1s-1) remains unaltered, consistent with the absence of contacts between Sox2 and POUHD. The data suggest a model for the sequence of binding events involved in synergistic gene regulation by Sox2 and Oct1.