Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method

The interaction between a single-stranded DNA (ssDNA) and a binding protein (Sulfolobus solfataricus ssDNA binding protein, SSB) were investigated by the ab initio fragment molecular orbital (FMO) method in explicit solvent. The calculated overall energy change upon complexation suggested that the ssDNA/SSB association is not strong. Nonetheless, more detailed analysis of interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) indicated that the ssDNA/SSB association is based upon a minute balance of various contributions of local structural parts of the molecules. The most stabilizing contribution was that by the electrostatic interaction between the sugarphosphate backbone of ssDNA and charged side chains of SSB, and the second was that by the stacking interaction between bases of ssDNA and aromatic side chains of SSB. Thus, though the overall association energy change was small, the local interactions were suggested to contribute to the association.