Differences in water release with DNA binding by ultrabithorax and deformed homeodomains

The amino acid sequences of the homeodomains (HD) within the Ultrabithorax (Ubx) and Deformed (Dfd) proteins from Drosophila melanogaster are highly conserved despite distinct genetic regulatory functions for these proteins in embryonic development. We reported recently that Ubx-HD binding to a single target site displayed significantly increased affinity and greater salt concentration dependence at lower pH; in contrast, Dfd-HD did not show pH dependence in its DNA binding properties [Li, L., et al. (1996) Biochemistry 35, 9832-9839]. We demonstrate in this study that water activity differentially affects Ubx-HD and Dfd-HD DNA binding affinity. The sensitivity of the protein-DNA binding constant to osmotic pressures generated by neutral solutes was measured, and the formation of the Ubx-HD-DNA complex is associated with significantly greater water release than that of the Dfd-HD-DNA complex. No influence of pH on water release was detected for either HD. Experiments with chimeric Ubx-Dfd homeodomains demonstrated that the C-terminal region of the Ubx-HD is the primary determinant for the greater water release associated with DNA binding for this protein. DNA sequences do not exert a significant effect on the magnitude of water release associated with protein-DNA binding for Ubx-HD and the chimeric HD, UDU.