Formation of a Wrapped DNA–Protein Interface: Experimental Characterization and Analysis of the Large Contributions of Ions and Water to the Thermodynamics of Binding IHF to H′ DNA

To characterize driving forces and driven processes in formation of a large-interface, wrapped protein–DNA complex analogous to the nucleosome, we have investigated the thermodynamics of binding the 34-base pair (bp) H′ DNA sequence to the Escherichia coli DNA-remodeling protein integration host factor (IHF). Isothermal titration calorimetry and fluorescence resonance energy transfer are applied to determine effects of salt concentration [KCl, KF, K glutamate (KGlu)] and of the excluded solute glycine betaine (GB) on the binding thermodynamics at 20 °C. Both the binding constant Kobs and enthalpy ΔH°obs depend strongly on [salt] and anion identity. Formation of the wrapped complex is enthalpy driven, especially at low [salt] (e.g., ΔHoobs = − 20.2 kcal·mol− 1 in 0.04 M KCl). ΔH°obs increases linearly with [salt] with a slope (dΔH°obs/d[salt]), which is much larger in KCl (38 ± 3 kcal·mol− 1 M− 1) than in KF or KGlu (11 ± 2 kcal·mol− 1 M− 1). At 0.33 M [salt], Kobs is approximately 30-fold larger in KGlu or KF than in KCl, and the [salt] derivative SKobs = dlnKobs/dln[salt] is almost twice as large in magnitude in KCl (− 8.8 ± 0.7) as in KF or KGlu (− 4.7 ± 0.6).A novel analysis of the large effects of anion identity on Kobs, SKobs and on ΔH°obs dissects coulombic, Hofmeister, and osmotic contributions to these quantities. This analysis attributes anion-specific differences in Kobs, SKobs, and ΔH°obs to (i) displacement of a large number of water molecules of hydration [estimated to be 1.0(± 0.2) × 103] from the 5340 Å2 of IHF and H′ DNA surface buried in complex formation, and (ii) significant local exclusion of F− and Glu− from this hydration water, relative to the situation with Cl−, which we propose is randomly distributed. To quantify net water release from anionic surface (22% of the surface buried in complexation, mostly from DNA phosphates), we determined the stabilizing effect of GB on Kobs: dlnKobs/d[GB]  = 2.7 ± 0.4 at constant KCl activity, indicating the net release of ca. 150 H2O molecules from anionic surface.