The role of water in CAP-DNA interactions

The formation of a protein-DNA complex in aqueous solution is accotnpanied by tile displacement of water from the interacting surfaces. I'he water stoichiometry of such a reaction can be evaluated from the dependence of the. observed equilibrium constant K(obs) on water activity. Measurements with low molecular weight osmolytes indicate that the binding of lhe I coil (?AP protein to lactose promoter DNA is accompanied by the displacement of 0 k 27 water molecules. Water is thus the dominant stoichiometric component of the binding reaction. If one water molecule occupies 9:i,2 of macromolecular surface, this stoichiometric difference is consistent with lhe loss of 720 :t- 2502-,2 of solvent-exposed surface. Isosteric surface area calculations pre diet a loss of 9,5&-2 on formation of the specific complex. This suggests that contbrmation changes accompanying binding occur with little net change in solvent-exposed surface area. Binding to non-specific DN:k results in the release of 20 water molecules. If these are displaced from interacting surfaces, the area of protein-DNA contact in the non-specific complex luust be l,q0J2. A smaller contact area could explain, in part, the substantial ditference in specific and non-specific binding affinities. Surface area estimates such as these provide a basis for evaluating the role of the hydrophobic elfbct in the stabilily of protein-DNA complexes.