Role of magnesium ions in the reaction mechanism at the interface between Tm1631 protein and its DNA ligand

摘要: A protein, Tm1631 from the hyperthermophilic organism Thermotoga maritima belongs to a domain of unknown function protein family. It was predicted that binds with DNA and Tm1631–DNA complex is an endonuclease repair system (Konc et al. PLoS Comput Biol 9(11): e1003341, 2013). We observed severely bent, strained for entire 90 ns classical molecular dynamics (MD) performed; we could observe no significant changes in most distorted region DNA, where cleavage phosphodiester bond occurs. In this article, modeled reaction mechanism at interface between its proposed ligand, molecule, focusing on bond. After addition two Mg2+ ions center extension MD by 50 ns (totaling 140 ns), ligand stayed bolted protein. Results density functional theory quantum mechanics/molecular mechanics (QM/MM) calculations suggest analogous known mechanisms: enzyme pentacovalent intermediate. The minimum energy pathway profile shows step kinetically controlled not thermodynamically because lack any barrier above accuracy calculation. role shown comparing results mechanisms absence there significantly higher than presence ions.