Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions

Physics-based potentials have been developed for the interactions between proteins and DNA for simulations with the UNRES + NARES-2P force field. The mean-field interactions between a protein and a DNA molecule can be divided into eight categories: (1) nonpolar side chain–DNA base, (2) polar uncharged side chain–DNA base, (3) charged side chain–DNA base, (4) peptide group–phosphate group, (5) peptide group–DNA base, (6) nonpolar side chain–phosphate group, (7) polar uncharged side chain–phosphate group, and (8) charged side chain–phosphate group. Umbrella-sampling molecular dynamics simulations in explicit TIP3P water using the AMBER force field were carried out to determine the potentials of mean force (PMF) for all 105 pairs of interacting components. Approximate analytical expressions for the mean-field interaction energy of each pair of the different kinds of interacting molecules were then fitted to the PMFs to obtain the parameters of the analytical expressions. These analytical expressions can reproduce satisfactorily the PMF curves corresponding to different orientations of the interacting molecules. The results suggest that the physics-based mean-field potentials of amino acid–nucleotide interactions presented here can be used in coarse-grained simulation of protein–DNA interactions.