Stair motifs at protein-DNA interfaces: nonadditivity of H-bond, stacking, and cation-pi interactions.

At the interface between protein and double-stranded DNA, stair motifs simultaneously involve three different types of pairwise interactions: aromatic base stacking, hydrogen bonding, and cation-pi. The relative importance of these interactions is studied in the stair motif occurring in the 1TC3 crystal structure, which involves an arginine and two stacked guanines, by means of Hartree-Fock (HF) and Møller-Plesset energy and free energy calculations, including vibrational, rotational, translational contributions, both in a vacuum and various solvents. The results obtained show an anti-cooperative tendency of the HF energy and vibrational free energy terms, and the cooperativity of the rotational, translational, and solvation free energies. Hence, the cooperativity of the stair motif interactions, in the context of protein-DNA recognition, can be viewed as arising from the environment.