Binding energy between lactose repressor protein and DNA: semiempirical molecular orbital calculations

Abstract

To elucidate the specific interaction between DNA-binding site of lactose repressor (Lac) and DNA, we investigated the binding energies between DNA and Lac as well as its amino-acid mutated ones by semiempirical molecular orbital calculations. By considering counter ions and solvent water molecules, we can obtain reliable binding energies for the Lac-DNA complexes. Furthermore, the effect of amino-acid mutation on the binding strength obtained by experiments was explained by the change in Lac-DNA hydrogen bonds bridged by solvent water molecules.