Mechanisms of influence of divalent Mg cation on DNA–Dps complex revealed by molecular modeling methods

The destructive effect of divalent cations Mg²⁺ on the crystal structure of the DNA–Dps complex was explored. It was shown using the classical molecular dynamics methods that this effect resulted from a decrease of interaction between the N-termini of the Dps protein and DNA when the concentration of Mg²⁺ in the system increases, and important Mg²⁺ binding sites in the protein and DNA molecules were determined. It is concluded that the preferential interaction of DNA and protein oxygen atoms with the Mg²⁺ cation leads to the weakening of their mutual bonds and destruction of the DNA–Dps complex.