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Launay R, Chobert SC, Abby SS, Pierrel F, André I, Esque J. Structural Reconstruction of E. coli Ubi Metabolon Using an AlphaFold2-Based Computational Framework. J Chem Inf Model 2024. [PMID: 38710096 DOI: 10.1021/acs.jcim.4c00304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Ubiquinone (UQ) is a redox polyisoprenoid lipid found in the membranes of bacteria and eukaryotes that has important roles, notably one in respiratory metabolism, which sustains cellular bioenergetics. In Escherichia coli, several steps of the UQ biosynthesis take place in the cytosol. To perform these reactions, a supramolecular assembly called Ubi metabolon is involved. This latter is composed of seven proteins (UbiE, UbiG, UbiF, UbiH, UbiI, UbiJ, and UbiK), and its structural organization is unknown as well as its protein stoichiometry. In this study, a computational framework has been designed to predict the structure of this macromolecular assembly. In several successive steps, we explored the possible protein interactions as well as the protein stoichiometry, to finally obtain a structural organization of the complex. The use of AlphaFold2-based methods combined with evolutionary information enabled us to predict several models whose quality and confidence were further analyzed using different metrics and scores. Our work led to the identification of a "core assembly" that will guide functional and structural characterization of the Ubi metabolon.
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Affiliation(s)
- Romain Launay
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Sophie-Carole Chobert
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Sophie S Abby
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Isabelle André
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Jérémy Esque
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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Yusa M, Nagata T. Photoreduction of quinones by thiols sensitized by phthalocyanines. Photochem Photobiol Sci 2017; 16:1043-1048. [DOI: 10.1039/c7pp00115k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quinones were converted to hydroquinones by the action of red light (690 nm), with phthalocyanine as a photosensitizer and thiols as an electron donor.
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Affiliation(s)
- Masaaki Yusa
- Department of Structural Molecular Science
- The Graduate University for Advanced Studies
- Okazaki 444-8787
- Japan
| | - Toshi Nagata
- Department of Applied Chemistry
- Faculty of Science and Technology
- Meijo University
- Nagoya 468-8502
- Japan
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Fernández-Ariza J, Krick Calderón RM, Rodríguez-Morgade MS, Guldi DM, Torres T. Phthalocyanine–Perylenediimide Cart Wheels. J Am Chem Soc 2016; 138:12963-12974. [DOI: 10.1021/jacs.6b07432] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Javier Fernández-Ariza
- Departamento
de Química Orgánica, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Rafael M. Krick Calderón
- Department of Chemistry and Pharmacy & Interdisciplinary Center for Molecular Materials (ICMM), University of Erlangen−Nuremberg, Egerlandstraße 3, 91058 Erlangen, Germany
| | | | - Dirk M. Guldi
- Department of Chemistry and Pharmacy & Interdisciplinary Center for Molecular Materials (ICMM), University of Erlangen−Nuremberg, Egerlandstraße 3, 91058 Erlangen, Germany
| | - Tomás Torres
- Departamento
de Química Orgánica, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
- IMDEA-Nanociencia, c/ Faraday 9, Cantoblanco, 28049 Madrid, Spain
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Anstöter CS, Bull JN, Verlet JR. Ultrafast dynamics of temporary anions probed through the prism of photodetachment. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1203522] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Gamboa-Valero N, Astudillo PD, González-Fuentes MA, Leyva MA, Rosales-Hoz MDJ, González FJ. Hydrogen bonding complexes in the quinone-hydroquinone system and the transition to a reversible two-electron transfer mechanism. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2015.12.060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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