Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen
Interaction of molecular oxygen <sup>3</sup>O<sub>2</sub> with the flavin-dependent protein miniSOG after light illumination results in creation of singlet oxygen <sup>1</sup>O<sub>2</sub> and superoxide O<sub>2</sub><sup>●−</sup&g...
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| Format: | Article |
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MDPI AG
2023-04-01
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| Series: | Biophysica |
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| Online Access: | https://www.mdpi.com/2673-4125/3/2/16 |
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| author | Igor Polyakov Anna Kulakova Alexander Nemukhin |
| author_facet | Igor Polyakov Anna Kulakova Alexander Nemukhin |
| author_sort | Igor Polyakov |
| collection | DOAJ |
| description | Interaction of molecular oxygen <sup>3</sup>O<sub>2</sub> with the flavin-dependent protein miniSOG after light illumination results in creation of singlet oxygen <sup>1</sup>O<sub>2</sub> and superoxide O<sub>2</sub><sup>●−</sup>. Despite the recently resolved crystal structures of miniSOG variants, oxygen-binding sites near the flavin chromophore are poorly characterized. We report the results of computational studies of the protein−oxygen systems using molecular dynamics (MD) simulations with force-field interaction potentials and quantum mechanics/molecular mechanics (QM/MM) potentials for the original miniSOG and the mutated protein. We found several oxygen-binding pockets and pointed out possible tunnels bridging the bulk solvent and the isoalloxazine ring of the chromophore. These findings provide an essential step toward understanding photophysical properties of miniSOG—an important singlet oxygen photosensitizer. |
| first_indexed | 2024-03-11T02:42:14Z |
| format | Article |
| id | doaj.art-d644868447b342baa0735afb88f0e38c |
| institution | Directory Open Access Journal |
| issn | 2673-4125 |
| language | English |
| last_indexed | 2024-03-11T02:42:14Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biophysica |
| spelling | doaj.art-d644868447b342baa0735afb88f0e38c2023-11-18T09:32:00ZengMDPI AGBiophysica2673-41252023-04-013225226210.3390/biophysica3020016Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet OxygenIgor Polyakov0Anna Kulakova1Alexander Nemukhin2Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, RussiaDepartment of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, RussiaDepartment of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, RussiaInteraction of molecular oxygen <sup>3</sup>O<sub>2</sub> with the flavin-dependent protein miniSOG after light illumination results in creation of singlet oxygen <sup>1</sup>O<sub>2</sub> and superoxide O<sub>2</sub><sup>●−</sup>. Despite the recently resolved crystal structures of miniSOG variants, oxygen-binding sites near the flavin chromophore are poorly characterized. We report the results of computational studies of the protein−oxygen systems using molecular dynamics (MD) simulations with force-field interaction potentials and quantum mechanics/molecular mechanics (QM/MM) potentials for the original miniSOG and the mutated protein. We found several oxygen-binding pockets and pointed out possible tunnels bridging the bulk solvent and the isoalloxazine ring of the chromophore. These findings provide an essential step toward understanding photophysical properties of miniSOG—an important singlet oxygen photosensitizer.https://www.mdpi.com/2673-4125/3/2/16miniSOG proteinmolecular oxygensinglet oxygenmolecular dynamicsQM/MM |
| spellingShingle | Igor Polyakov Anna Kulakova Alexander Nemukhin Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen Biophysica miniSOG protein molecular oxygen singlet oxygen molecular dynamics QM/MM |
| title | Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen |
| title_full | Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen |
| title_fullStr | Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen |
| title_full_unstemmed | Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen |
| title_short | Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen |
| title_sort | computational modeling of the interaction of molecular oxygen with the minisog protein a light induced source of singlet oxygen |
| topic | miniSOG protein molecular oxygen singlet oxygen molecular dynamics QM/MM |
| url | https://www.mdpi.com/2673-4125/3/2/16 |
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