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Role of magnesium ions in the reaction mechanism at the interface between Tm1631 protein and its DNA ligand
Mitja Ogrizek, Janez Konc, Urban Bren, Milan Hodošček, Dušanka Janežič, 2016, original scientific article

Abstract: A protein, Tm1631 from the hyperthermophilic organism Thermotoga maritima belongs to a domain of unknown function protein family. It was predicted that Tm1631 binds with the DNA and that the Tm1631–DNA complex is an endonuclease repair system with a DNA repair function (Konc et al. PLoS Comput Biol 9(11): e1003341, 2013). We observed that the severely bent, strained DNA binds to the protein for the entire 90 ns of classical molecular dynamics (MD) performed; we could observe no significant changes in the most distorted region of the DNA, where the cleavage of phosphodiester bond occurs. In this article, we modeled the reaction mechanism at the interface between Tm1631 and its proposed ligand, the DNA molecule, focusing on cleavage of the phosphodiester bond. After addition of two Mg2+ ions to the reaction center and extension of classical MD by 50 ns (totaling 140 ns), the DNA ligand stayed bolted to the protein. Results from density functional theory quantum mechanics/molecular mechanics (QM/MM) calculations suggest that the reaction is analogous to known endonuclease mechanisms: an enzyme reaction mechanism with two Mg2+ ions in the reaction center and a pentacovalent intermediate. The minimum energy pathway profile shows that the phosphodiester bond cleavage step of the reaction is kinetically controlled and not thermodynamically because of a lack of any energy barrier above the accuracy of the energy profile calculation. The role of ions is shown by comparing the results with the reaction mechanisms in the absence of the Mg2+ ions where there is a significantly higher reaction barrier than in the presence of the Mg2+ ions.
Keywords: methods of analysis, computer science, magnesium ions, preteins, DNA
Published: 26.06.2017; Views: 154; Downloads: 67
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A silver/silver sulphide selective electrode prepared by means of chemical treatments of silver wire
Danilo Dobčnik, Igor Gros, Mitja Kolar, 1998, original scientific article

Abstract: The preparation and usability of a sulphide ion selective electrode, prepared by means of chemical pretreatment of silver wire with an ammonium perdisulphate solution, and the sulphidization in an alkaline sulphide solution are described. The electrode is suitable for direct potentiometric measuring of sulphide in alkaline solutions of concentrations down to ▫$1 X 10^{-6} mol/L$▫. The 45 min required for each chemical treatment are enough for the preparation of the described electrode.
Keywords: analytical chemistry, ion selective electrode, preparation, silver wire, potentiometric measurements, sulphide ions
Published: 17.08.2017; Views: 187; Downloads: 38
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