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Molecules 2017, 22(11), 1904; doi:10.3390/molecules22111904

The Oligomeric Form of the Escherichia coli Dps Protein Depends on the Availability of Iron Ions

1
School of Life Sciences, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia
2
Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
3
Department of Biophysics and Biotechnology, Voronezh State University, 394018 Voronezh, Russia
4
Department of Cell Biology, Pushchino State Institute of Natural Sciences, 142290 Pushchino, Russia
5
Department of Structural and Functional genomics, Pushchino Scientific Center, 142290 Pushchino, Russia
*
Author to whom correspondence should be addressed.
Received: 13 October 2017 / Revised: 29 October 2017 / Accepted: 2 November 2017 / Published: 5 November 2017
(This article belongs to the Special Issue Metallopeptides)
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Abstract

The Dps protein of Escherichia coli, which combines ferroxidase activity and the ability to bind DNA, is effectively used by bacteria to protect their genomes from damage. Both activities depend on the integrity of this multi-subunit protein, which has an inner cavity for iron oxides; however, the diversity of its oligomeric forms has only been studied fragmentarily. Here, we show that iron ions stabilize the dodecameric form of Dps. This was found by electrophoretic fractionation and size exclusion chromatography, which revealed several oligomers in highly purified protein samples and demonstrated their conversion to dodecamers in the presence of 1 mM Mohr’s salt. The transmission electron microscopy data contradicted the assumption that the stabilizing effect is given by the optimal core size formed in the inner cavity of Dps. The charge state of iron ions was evaluated using Mössbauer spectroscopy, which showed the presence of Fe3O4, rather than the expected Fe2O3, in the sample. Assuming that Fe2+ can form additional inter-subunit contacts, we modeled the interaction of FeO and Fe2O3 with Dps, but the binding sites with putative functionality were predicted only for Fe2O3. The question of how the dodecameric form can be stabilized by ferric oxides is discussed. View Full-Text
Keywords: Escherichia coli; Dps proteins; oligomerization; ferroxidase; transmission electron microscopy; Mössbauer spectroscopy; molecular docking Escherichia coli; Dps proteins; oligomerization; ferroxidase; transmission electron microscopy; Mössbauer spectroscopy; molecular docking
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Antipov, S.; Turishchev, S.; Purtov, Y.; Shvyreva, U.; Sinelnikov, A.; Semov, Y.; Preobrazhenskaya, E.; Berezhnoy, A.; Shusharina, N.; Novolokina, N.; Vakhtel, V.; Artyukhov, V.; Ozoline, O. The Oligomeric Form of the Escherichia coli Dps Protein Depends on the Availability of Iron Ions. Molecules 2017, 22, 1904.

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