An Interpretation of Small-Ion Effects on the Electrostatics of the λ Repressor DNA Complex

Abstract

Monte Carlo simulations of the interactions of Na+ and Cl- ions with λ repressor protein and its DNA operator site have revealed an interesting effect [Jayaram, B.; DiCapua, F. M.; Beveridge, D. L. J. Am. Chem. Soc. 1991, 113, 5211−5215]. When the protein is close to its binding site on DNA, the presence of the small ions strengthens the electrostatic net attractive force between the formally charged protein residues and the phosphate groups on DNA. The effect has been interpreted as a manifestation of the release of counterions condensed on DNA. We show that although counterions are indeed released, the enhancement of the attractive force at short distances has a different origin. There is a direct attraction between DNA phosphates and positively charged protein residues, and a direct repulsion between DNA phosphates and negatively charged protein residues. Close to the DNA, the net direct force is attractive. By weakening the direct repulsion between DNA phosphates and the negatively charged glutamate and aspartate residues on the protein, the presence of small ions increases the net attraction. A complete understanding of protein−DNA electrostatics thus involves consideration of the interaction of DNA phosphates with anionic as well as cationic protein residues. As a side result of our calculations, we estimate the effect of small ions on the binding free energy of the repressor−operator complex (from the isolated species) as unfavorable at about 40−45 kcal/mol.