Molecular Mechanics And Molecular Orbital Simulations On The Specific Interactions Between Lactose Repressor Protein And Its Inducer And Anti-Inducer Molecules

To elucidate the specific interactions between lactose repressor (LacR) and its inducer (IPTG) as well as anti-inducer (ONPF) ligand molecules, we investigated the stable structures and electronic properties of the LacR + IPTG and LacR + ONPF complexes including DNA and solvating water molecules, by the molecular simulations based on classical molecular mechanics and semiempirical molecular orbital methods. The results clarified that the specific water molecules bridging between the amino acid of ligand binding-site of LacR and ligand molecules are essential for the specific interactions between LacR and IPTG or ONPF. Moreover, it was found that the binding energy between the DNA-binding domain of LacR and DNA are affected largely by the binding of IPTG and ONPF to LacR.