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

• Main Authors: Liubov Dadinova, Roman Kamyshinsky, Yury Chesnokov, Andrey Mozhaev, Vladimir Matveev, Andrey Gruzinov, Alexander Vasiliev, Eleonora Shtykova
• Format: Article
• Language: English
• Published: MDPI AG 2021-06-01
• Series: International Journal of Molecular Sciences
• Subjects: DNA–Dps co-crystals; DNA–protein interaction; small-angle X-scattering; cryo-electron microscopy
• Online Access: https://www.mdpi.com/1422-0067/22/11/6056

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.