The Conformation of the N-Terminal Tails of <i>Deinococcus grandis</i> Dps Is Modulated by the Ionic Strength
DNA-binding proteins from starved cells (Dps) are homododecameric nanocages, with N- and C-terminal tail extensions of variable length and amino acid composition. They accumulate iron in the form of a ferrihydrite mineral core and are capable of binding to and compacting DNA, forming low- and high-o...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-04-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/9/4871 |
| _version_ | 1797504503148183552 |
|---|---|
| author | João P. L. Guerra Clement E. Blanchet Bruno J. C. Vieira Ana V. Almeida João C. Waerenborgh Nykola C. Jones Søren V. Hoffmann Pedro Tavares Alice S. Pereira |
| author_facet | João P. L. Guerra Clement E. Blanchet Bruno J. C. Vieira Ana V. Almeida João C. Waerenborgh Nykola C. Jones Søren V. Hoffmann Pedro Tavares Alice S. Pereira |
| author_sort | João P. L. Guerra |
| collection | DOAJ |
| description | DNA-binding proteins from starved cells (Dps) are homododecameric nanocages, with N- and C-terminal tail extensions of variable length and amino acid composition. They accumulate iron in the form of a ferrihydrite mineral core and are capable of binding to and compacting DNA, forming low- and high-order condensates. This dual activity is designed to protect DNA from oxidative stress, resulting from Fenton chemistry or radiation exposure. In most Dps proteins, the DNA-binding properties stem from the N-terminal tail extensions. We explored the structural characteristics of a Dps from <i>Deinococcus grandis</i> that exhibits an atypically long N-terminal tail composed of 52 residues and probed the impact of the ionic strength on protein conformation using size exclusion chromatography, dynamic light scattering, synchrotron radiation circular dichroism and small-angle X-ray scattering. A novel high-spin ferrous iron-binding site was identified in the N-terminal tails, using Mössbauer spectroscopy. Our data reveals that the N-terminal tails are structurally dynamic and alter between compact and extended conformations, depending on the ionic strength of the buffer. This prompts the search for other physiologically relevant modulators of tail conformation and hints that the DNA-binding properties of Dps proteins may be affected by external factors. |
| first_indexed | 2024-03-10T04:05:30Z |
| format | Article |
| id | doaj.art-8af7ee7082a14e9d855ee0648422a0d0 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T04:05:30Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-8af7ee7082a14e9d855ee0648422a0d02023-11-23T08:23:31ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-04-01239487110.3390/ijms23094871The Conformation of the N-Terminal Tails of <i>Deinococcus grandis</i> Dps Is Modulated by the Ionic StrengthJoão P. L. Guerra0Clement E. Blanchet1Bruno J. C. Vieira2Ana V. Almeida3João C. Waerenborgh4Nykola C. Jones5Søren V. Hoffmann6Pedro Tavares7Alice S. Pereira8Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, PortugalEuropean Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, GermanyCentro de Ciências e Tecnologias Nucleares, DECN, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066 Bobadela, PortugalAssociate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, PortugalCentro de Ciências e Tecnologias Nucleares, DECN, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066 Bobadela, PortugalISA, Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, DenmarkISA, Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, DenmarkAssociate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, PortugalAssociate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, PortugalDNA-binding proteins from starved cells (Dps) are homododecameric nanocages, with N- and C-terminal tail extensions of variable length and amino acid composition. They accumulate iron in the form of a ferrihydrite mineral core and are capable of binding to and compacting DNA, forming low- and high-order condensates. This dual activity is designed to protect DNA from oxidative stress, resulting from Fenton chemistry or radiation exposure. In most Dps proteins, the DNA-binding properties stem from the N-terminal tail extensions. We explored the structural characteristics of a Dps from <i>Deinococcus grandis</i> that exhibits an atypically long N-terminal tail composed of 52 residues and probed the impact of the ionic strength on protein conformation using size exclusion chromatography, dynamic light scattering, synchrotron radiation circular dichroism and small-angle X-ray scattering. A novel high-spin ferrous iron-binding site was identified in the N-terminal tails, using Mössbauer spectroscopy. Our data reveals that the N-terminal tails are structurally dynamic and alter between compact and extended conformations, depending on the ionic strength of the buffer. This prompts the search for other physiologically relevant modulators of tail conformation and hints that the DNA-binding properties of Dps proteins may be affected by external factors.https://www.mdpi.com/1422-0067/23/9/4871DNA-binding protein from starved cells (Dps)<i>Deinococcus grandis</i>N-terminal tail extensionsmini-ferritinsbiological small-angle X-ray scatteringconformational changes |
| spellingShingle | João P. L. Guerra Clement E. Blanchet Bruno J. C. Vieira Ana V. Almeida João C. Waerenborgh Nykola C. Jones Søren V. Hoffmann Pedro Tavares Alice S. Pereira The Conformation of the N-Terminal Tails of <i>Deinococcus grandis</i> Dps Is Modulated by the Ionic Strength International Journal of Molecular Sciences DNA-binding protein from starved cells (Dps) <i>Deinococcus grandis</i> N-terminal tail extensions mini-ferritins biological small-angle X-ray scattering conformational changes |
| title | The Conformation of the N-Terminal Tails of <i>Deinococcus grandis</i> Dps Is Modulated by the Ionic Strength |
| title_full | The Conformation of the N-Terminal Tails of <i>Deinococcus grandis</i> Dps Is Modulated by the Ionic Strength |
| title_fullStr | The Conformation of the N-Terminal Tails of <i>Deinococcus grandis</i> Dps Is Modulated by the Ionic Strength |
| title_full_unstemmed | The Conformation of the N-Terminal Tails of <i>Deinococcus grandis</i> Dps Is Modulated by the Ionic Strength |
| title_short | The Conformation of the N-Terminal Tails of <i>Deinococcus grandis</i> Dps Is Modulated by the Ionic Strength |
| title_sort | conformation of the n terminal tails of i deinococcus grandis i dps is modulated by the ionic strength |
| topic | DNA-binding protein from starved cells (Dps) <i>Deinococcus grandis</i> N-terminal tail extensions mini-ferritins biological small-angle X-ray scattering conformational changes |
| url | https://www.mdpi.com/1422-0067/23/9/4871 |
| work_keys_str_mv | AT joaoplguerra theconformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT clementeblanchet theconformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT brunojcvieira theconformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT anavalmeida theconformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT joaocwaerenborgh theconformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT nykolacjones theconformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT sørenvhoffmann theconformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT pedrotavares theconformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT alicespereira theconformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT joaoplguerra conformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT clementeblanchet conformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT brunojcvieira conformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT anavalmeida conformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT joaocwaerenborgh conformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT nykolacjones conformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT sørenvhoffmann conformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT pedrotavares conformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength AT alicespereira conformationofthenterminaltailsofideinococcusgrandisidpsismodulatedbytheionicstrength |