Sequence-specific DNA-binding dominated by dehydration

qFluorescence spectroscopy and isothermal titration calorimetry were used to study the thermodynamics of binding of the glucocorticoid receptor DNA-binding domain to four different, but similar, DNA-binding sites. The binding sites are two naturally occurring sites that differ in the composition of one base pair, i.e., A . T to G . C mutation, and two sites containing chemical intermediates of these base pairs. The calorimetrically determined heat capacity change (Delta C-p degrees(obs)) for glucocorticoid receptor DNA-binding domain binding agrees with that calculated for dehydration or solvent-accessible surface areas. A dominating effect of dehydration or solvent reorganization on the thermodynamics is also consistent with an observed linear relationship between observed enthalpy change (Delta H degrees(obs)) and observed entropy change (Delta S degrees(obs)) with a slope close to the experimental temperature. Comparisons with structural data allow us to rationalize individual differences between Delta H degrees(obs) (and Delta S degrees(obs)) for the four complexes. For instance, we find that the removal of a methyl group at the DNA-protein interface is enthalpically favorable but entropically unfavorable, which is consistent with a replacement by an ordered water molecule.