Role of the hydrophobic effect in stability of site-specific protein-DNA complexes

Abstract

The site-specific binding interaction of lac repressor with a symmetric operator sequence and of EcoRI endonuclease with its specific recognition site both exhibit a characteristic dependence of equilibrium binding constant ( K obs) on temperature, in which K obs attains a relative maximum in the physiologically relevant temperature range. This behavior, which appears to be quite general for site-specific protein-DNA interactions, is indicative of a large negative standard heat capacity change ( ΔC P, obs 0) in the association process. By analogy with model compound transfer studies and protein folding data, we propose that this Δ P, obs 0 results primarily from the removal of non-polar surface from water in the association process. From ΔC P, obs 0 we obtain semiquantitative information regarding the change in water-exposed non-polar surface area ( ΔA np) and the corresponding hydrophobic driving force for association ( ΔG hyd 0): ΔG hyd 0 ≅ 8 (± 1) × 10 1 ΔC P, obs 0 ≅ −22(±5) ΔA np. We propose that removal of non-polar surface from water (the hydrophobic effect) and release of cations (the polyelectrolyte effect) drive the thermodynamically unfavorable processes (e.g. conformational distortions) necessary to achieve mutually complementary recognition surfaces (at a steric and functional-group level) in the specific complex.