Structural Rearrangement of Dps-DNA Complex Caused by Divalent Mg and Fe Cations

• Published in: International journal of molecular sciences 2021-06, Vol.22 (11), p.6056
• Main Authors: Dadinova, Liubov, Kamyshinsky, Roman, Chesnokov, Yury, Mozhaev, Andrey, Matveev, Vladimir, Gruzinov, Andrey, Vasiliev, Alexander, Shtykova, Eleonora
• Format: Article
• Language: English
• Subjects: cryo-electron microscopy; DNA–Dps co-crystals; DNA–protein interaction; small-angle X-scattering
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms22116056

Two independent, complementary methods of structural analysis were used to elucidate the effect of divalent magnesium and iron cations on the structure of the protective Dps-DNA complex. Small-angle X-ray scattering (SAXS) and cryo-electron microscopy (cryo-EM) demonstrate that Mg2+ ions block the N-terminals of the Dps protein preventing its interaction with DNA. Non-interacting macromolecules of Dps and DNA remain in the solution in this case. The subsequent addition of the chelating agent (EDTA) leads to a complete restoration of the structure of the complex. Different effect was observed when Fe cations were added to the Dps-DNA complex; the presence of Fe2+ in solution leads to the total complex destruction and aggregation without possibility of the complex restoration with the chelating agent. Here, we discuss these different responses of the Dps-DNA complex on the presence of additional free metal cations, investigating the structure of the Dps protein with and without cations using SAXS and cryo-EM. Additionally, the single particle analysis of Dps with accumulated iron performed by cryo-EM shows localization of iron nanoparticles inside the Dps cavity next to the acidic (hydrophobic) pore, near three glutamate residues.