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Gao Q, Hägglund P, Gamon LF, Davies MJ. Mapping of oxidative modifications on the alpha-keto glutarate dehydrogenase complex induced by singlet oxygen: effects on structure and activity. Free Radic Biol Med 2024:S0891-5849(24)00671-3. [PMID: 39299525 DOI: 10.1016/j.freeradbiomed.2024.09.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 09/06/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
The large multi-subunit mitochondrial alpha-keto glutarate dehydrogenase (KGDH) complex plays a key, rate-determining, role in the tricarboxylic acid (Krebs) cycle, catalyzing the conversion of alpha-keto glutarate to succinyl-CoA. This complex is both a source and target of oxidants, but the sites of modification and association with structural changes and activity loss are poorly understood. We report here oxidative modifications induced by Rose Bengal (RB) in the presence of O2, a source of singlet oxygen (1O2). A rapid loss of activity was detected, with this being dependent on light exposure, illumination time, and the presence of RB and O2. Activity loss was enhanced by D2O (consistent with 1O2 involvement), but diminished by both pre- and (to a lesser extent) post-illumination addition of lipoic acid and lipoamide. Aggregates containing all three KGDH subunits were detected on photooxidation. LC-MS experiments provided evidence for oxidation at 45 sites, including specific Met, His, Trp, Tyr residues and the lipoyllysine active-site cofactor. Products include mono- and di-oxygenated species, and kynurenine from Trp. Mapping of the modifications to the 3-D structure showed that these are localized to both the inner channel and the external surface, consistent with reactions of free 1O2, however the sites and extent of modification do not correlate with their solvent accessibility. These products are generated concurrently with loss of activity, indicative of strong links between these events. These data provide evidence for the impairment of KGDH activity by 1O2 via the oxidation of specific residues on the protein subunits of the complex.
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Affiliation(s)
- Qing Gao
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen 2200, Denmark
| | - Per Hägglund
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen 2200, Denmark
| | - Luke F Gamon
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen 2200, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen 2200, Denmark.
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2
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Zheng F, Yu C, Zhou X, Zou P. Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome. Nat Commun 2023; 14:2978. [PMID: 37221179 PMCID: PMC10205723 DOI: 10.1038/s41467-023-38565-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 05/05/2023] [Indexed: 05/25/2023] Open
Abstract
Mapping the subcellular organization of proteins is crucial for understanding their biological functions. Herein, we report a reactive oxygen species induced protein labeling and identification (RinID) method for profiling subcellular proteome in the context of living cells. Our method capitalizes on a genetically encoded photocatalyst, miniSOG, to locally generate singlet oxygen that reacts with proximal proteins. Labeled proteins are conjugated in situ with an exogenously supplied nucleophilic probe, which serves as a functional handle for subsequent affinity enrichment and mass spectrometry-based protein identification. From a panel of nucleophilic compounds, we identify biotin-conjugated aniline and propargyl amine as highly reactive probes. As a demonstration of the spatial specificity and depth of coverage in mammalian cells, we apply RinID in the mitochondrial matrix, capturing 477 mitochondrial proteins with 94% specificity. We further demonstrate the broad applicability of RinID in various subcellular compartments, including the nucleus and the endoplasmic reticulum (ER). The temporal control of RinID enables pulse-chase labeling of ER proteome in HeLa cells, which reveals substantially higher clearance rate for secreted proteins than ER resident proteins.
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Affiliation(s)
- Fu Zheng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Chenxin Yu
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Xinyue Zhou
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China.
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China.
- Chinese Institute for Brain Research (CIBR), Beijing, 102206, China.
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Aerssens D, Cadoni E, Tack L, Madder A. A Photosensitized Singlet Oxygen ( 1O 2) Toolbox for Bio-Organic Applications: Tailoring 1O 2 Generation for DNA and Protein Labelling, Targeting and Biosensing. Molecules 2022; 27:778. [PMID: 35164045 PMCID: PMC8838016 DOI: 10.3390/molecules27030778] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/17/2022] Open
Abstract
Singlet oxygen (1O2) is the excited state of ground, triplet state, molecular oxygen (O2). Photosensitized 1O2 has been extensively studied as one of the reactive oxygen species (ROS), responsible for damage of cellular components (protein, DNA, lipids). On the other hand, its generation has been exploited in organic synthesis, as well as in photodynamic therapy for the treatment of various forms of cancer. The aim of this review is to highlight the versatility of 1O2, discussing the main bioorganic applications reported over the past decades, which rely on its production. After a brief introduction on the photosensitized production of 1O2, we will describe the main aspects involving the biologically relevant damage that can accompany an uncontrolled, aspecific generation of this ROS. We then discuss in more detail a series of biological applications featuring 1O2 generation, including protein and DNA labelling, cross-linking and biosensing. Finally, we will highlight the methodologies available to tailor 1O2 generation, in order to accomplish the proposed bioorganic transformations while avoiding, at the same time, collateral damage related to an untamed production of this reactive species.
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Affiliation(s)
| | | | | | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000 Gent, Belgium; (D.A.); (E.C.); (L.T.)
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Cossu M, Ledda L, Cossu A. Emerging trends in the photodynamic inactivation (PDI) applied to the food decontamination. Food Res Int 2021; 144:110358. [PMID: 34053551 DOI: 10.1016/j.foodres.2021.110358] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022]
Abstract
The food and drink manufacturing industry is constantly seeking for alternative sanitation and disinfection systems that may achieve the same antimicrobial efficiency of conventional chemical sanitisers and at the same time be convenient in terms of energy and water savings. A candidate technology for this purpose is the use of light in combination with photosensitisers (PS) to generate a bioactive effect against microbial agents in a process defined as photodynamic inactivation (PDI). This technology can be applied to the food processing of different food matrices to reduce the microbial load of foodborne pathogens such as bacteria, fungi, viruses and protozoa. Also, the PDI can be exploited to increase the shelf-life period of food by inactivation of spoiling microbes. This review analyses new developments in the last five years for PDI systems applied to the food decontamination from foodborne pathogens. The photosensitisation mechanisms and methods are reported to introduce the applied technology against microbial targets in food matrices. Recent blue light emitting diodes (LED) lamp systems for the PDI mediated by endogenous PS are discussed as well PDI technologies with the use of exogenous PS from plant sources such as curcumin and porphyrin-based molecules. The updated overview of the most recent developments in the PDI technology both in wavelengths and employed PS will provide further points of analysis for the advancement of the research on new competitive and effective disinfection systems in the food industry.
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Affiliation(s)
- Marco Cossu
- Department of Agriculture, University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Luigi Ledda
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche 10, 60131 Ancona, Italy
| | - Andrea Cossu
- Department of Natural Sciences, Faculty of Science and Technology, Middlesex University, The Burroughs, Hendon, London NW4 4BT, United Kingdom.
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Fuentes-Lemus E, Mariotti M, Hägglund P, Leinisch F, Fierro A, Silva E, Davies MJ, López-Alarcón C. Oxidation of lysozyme induced by peroxyl radicals involves amino acid modifications, loss of activity, and formation of specific crosslinks. Free Radic Biol Med 2021; 167:258-270. [PMID: 33731307 DOI: 10.1016/j.freeradbiomed.2021.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/21/2022]
Abstract
The present work examined the oxidation and crosslinking of the anti-bacterial enzyme lysozyme (Lyso), which is present in multiple biological fluids, and released from the cytoplasmic granules of macrophages and neutrophils at sites of infection and inflammation. It is therefore widely exposed to oxidants including peroxyl radicals (ROO•). We hypothesized that exposure to ROO• would generate specific modifications and inter- and intra-protein crosslinks via radical-radical reactions. Lyso was incubated with AAPH (2,2'-azobis(2-methylpropionamidine) dihydrochloride) as a ROO• source. Enzymatic activity was assessed, while oxidative modifications were detected and quantified using electrophoresis and liquid chromatography (UPLC) with fluorescence or mass detection (MS). Computational models of AAPH-Lyso interactions were developed. Exposure of Lyso to AAPH (10 and 100 mM for 3 h, and 20 mM for 1 h), at 37 °C, decreased enzymatic activity. 20 mM AAPH showed the highest efficiency of Lyso inactivation (1.78 mol of Lyso inactivated per ROO•). Conversion of Met to its sulfoxide, and to a lesser extent, Tyr oxidation to 3,4-dihydroxyphenylalanine and diTyr, were detected by UPLC-MS. Extensive transformation of Trp, involving short chain reactions, to kynurenine, oxindole, hydroxytryptophan, hydroperoxides or di-alcohols, and N-formyl-kynurenine was detected, with Trp62, Trp63 and Trp108 the most affected residues. Interactions of AAPH inside the negatively-charged catalytic pocket of Lyso, with Trp108, Asp52, and Glu35, suggest that Trp108 oxidation mediates, at least partly, Lyso inactivation. Crosslinks between Tyr20-Tyr23 (intra-molecular), and Trp62-Tyr23 (inter-molecular), were detected with both proximity (Tyr20-Tyr23), and chain flexibility (Trp62) appearing to favor the formation of covalent crosslinks.
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Affiliation(s)
| | - Michele Mariotti
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen, Denmark
| | - Per Hägglund
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen, Denmark
| | - Fabian Leinisch
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen, Denmark
| | - Angélica Fierro
- Pontificia Universidad Católica de Chile(,) Facultad de Química y de Farmacia, Departamento de Química Orgánica, Santiago, Chile
| | - Eduardo Silva
- Pontificia Universidad Católica de Chile, Facultad de Química y de Farmacia, Departamento de Química Física, Santiago, Chile
| | - Michael J Davies
- University of Copenhagen, Department of Biomedical Sciences, Copenhagen, Denmark.
| | - Camilo López-Alarcón
- Pontificia Universidad Católica de Chile, Facultad de Química y de Farmacia, Departamento de Química Física, Santiago, Chile.
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Nagashima N, Ozawa S, Furuta M, Oi M, Hori Y, Tomita T, Sohma Y, Kanai M. Catalytic photooxygenation degrades brain Aβ in vivo. SCIENCE ADVANCES 2021; 7:7/13/eabc9750. [PMID: 33762329 PMCID: PMC7990327 DOI: 10.1126/sciadv.abc9750] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
Protein degradation induced by small molecules by recruiting endogenous protein degradation systems, such as ubiquitin-proteasome systems, to disease-related proteins is an emerging concept to inhibit the function of undruggable proteins. Protein targets without reliable ligands and/or existing outside the cells where ubiquitin-proteasome systems do not exist, however, are beyond the scope of currently available protein degradation strategies. Here, we disclose photooxygenation catalyst 7 that permeates the blood-brain barrier and selectively and directly degrades an extracellular Alzheimer's disease-related undruggable protein, amyloid-β protein (Aβ). Key was the identification of a compact but orange color visible light-activatable chemical catalyst whose activity can be switched on/off according to its molecular mobility, thereby ensuring high selectivity for aggregated Aβ. Chemical catalyst-promoted protein degradation can be applied universally for attenuating extracellular amyloids and various pathogenic proteins and is thus a new entry to induced protein degradation strategies.
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Affiliation(s)
- Nozomu Nagashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shuta Ozawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahiro Furuta
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Miku Oi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yukiko Hori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Taisuke Tomita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Youhei Sohma
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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7
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Zhao J, Zhu R, Zhang X, Zhang B, Liu Y, Li Y, Wang W, Phillips DL. A photoenhanced oxidation of amino acids and the cross-linking of lysozyme mediated by tetrazolium salts. Phys Chem Chem Phys 2021; 23:3761-3770. [PMID: 33538741 DOI: 10.1039/d0cp04887a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tetrazolium salts (TZs) are pervasively utilized as precursors in the dye industry, colorimetric probes in enzyme assays and for exploring nanomaterial toxicity, but its own toxicity is not investigated enough so far. Using femtosecond transient absorption spectroscopy, nanosecond pulse radiolysis (ns-PRL), western blotting and UV-vis absorption spectroscopy, here we characterized a neutral tetrazolinyl radical (with the same maximum absorption at 420 nm and different lifetimes of 5.0 and 9.0 μs for two selected TZs), the key intermediate of TZs reduction, and noticed TZs-formazan production under UV light irradiation accompanied by 41% increase in the cross-linking of lysozyme (Lyso, model protein) compared to TZs-free sample, which uncovered the photoenhanced oxidation of TZs towards Lyso. The ns-PRL in a reductive atmosphere simulated the electron/proton donors of amino acid residues in Lyso upon photoexcitation and revealed the reduction mechanism of TZs, as that first followed one-electron-transfer and then probably proton-coupled electron transfer. This is the first time to report on the photoenhanced oxidation mechanism of TZs, which would provide new insights into the applications of TZs in cell biology, "click" chemistry and nanotoxicology.
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Affiliation(s)
- Jianfeng Zhao
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong 11111, P. R. China
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