Abstract
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.
Highlights
It is well known that metal ions modulate various biological processes including interactions of polynucleotides with protein macromolecules, which are of particular importance [1]
Earlier [20], using small-angle X-ray scattering (SAXS), we showed that 10 mM MgCl2 almost completely destroys the Dps-DNA co-crystals, while the form-factor of the protein that exists independently of DNA can be clearly traced in solution
The iron clusters are elongated in one direction due to the reconstruction procedure (Figure 5B), the cryo-electron microscopy (cryo-EM) map unambiguously demonstrates that the iron clusters are stored inside the Dps cavity, close to the acidic
Summary
It is well known that metal ions modulate various biological processes including interactions of polynucleotides with protein macromolecules, which are of particular importance [1]. In the process of interaction with polycations (cationic protein and polyamines) DNAs can be tightly packaged inside cell nucleus, bacterial cytoplasm and viral capsids [4,5]. The presence of divalent metal cations such as Mg2+ and Fe2+ plays an important role in the formation and co-crystallization of the Dps-DNA complex, depending on the concentration of the cations in the cytoplasm of bacterial cells. The concentration of the ions in the nutrient medium decreases below the threshold value, and electrostatic interaction between negatively charged DNA bases and positively charged amino acids of the Dps dodecamers occurs, leading to well-known co-crystallization in living cells. When fresh nutrients containing divalent cations are supplied, the complex is destroyed [8]
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