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Elftmaoui Z, Bignon E. Robust AMBER Force Field Parameters for Glutathionylated Cysteines. Int J Mol Sci 2023; 24:15022. [PMID: 37834470 PMCID: PMC10573104 DOI: 10.3390/ijms241915022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/02/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
S-glutathionylation is an oxidative post-translational modification, which is involved in the regulation of many cell signaling pathways. Increasing amounts of studies show that it is crucial in cell homeostasis and deregulated in several pathologies. However, the effect of S-glutathionylation on proteins' structure and activity is poorly understood, and a drastic lack of structural information at the atomic scale remains. Studies based on the use of molecular dynamics simulations, which can provide important information about modification-induced modulation of proteins' structure and function, are also sparse, and there is no benchmarked force field parameters for this modified cysteine. In this contribution, we provide robust AMBER parameters for S-glutathionylation, which we tested extensively against experimental data through a total of 33 μs molecular dynamics simulations. We show that our parameter set efficiently describes the global and local structural properties of S-glutathionylated proteins. These data provide the community with an important tool to foster new investigations into the effect of S-glutathionylation on protein dynamics and function, in a common effort to unravel the structural mechanisms underlying its critical role in cellular processes.
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Affiliation(s)
| | - Emmanuelle Bignon
- UMR 7019 LPCT, Université de Lorraine and CNRS, F-54000 Nancy, France
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2
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Li X, Gluth A, Zhang T, Qian WJ. Thiol redox proteomics: Characterization of thiol-based post-translational modifications. Proteomics 2023; 23:e2200194. [PMID: 37248656 PMCID: PMC10764013 DOI: 10.1002/pmic.202200194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023]
Abstract
Redox post-translational modifications on cysteine thiols (redox PTMs) have profound effects on protein structure and function, thus enabling regulation of various biological processes. Redox proteomics approaches aim to characterize the landscape of redox PTMs at the systems level. These approaches facilitate studies of condition-specific, dynamic processes implicating redox PTMs and have furthered our understanding of redox signaling and regulation. Mass spectrometry (MS) is a powerful tool for such analyses which has been demonstrated by significant advances in redox proteomics during the last decade. A group of well-established approaches involves the initial blocking of free thiols followed by selective reduction of oxidized PTMs and subsequent enrichment for downstream detection. Alternatively, novel chemoselective probe-based approaches have been developed for various redox PTMs. Direct detection of redox PTMs without any enrichment has also been demonstrated given the sensitivity of contemporary MS instruments. This review discusses the general principles behind different analytical strategies and covers recent advances in redox proteomics. Several applications of redox proteomics are also highlighted to illustrate how large-scale redox proteomics data can lead to novel biological insights.
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Affiliation(s)
- Xiaolu Li
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Austin Gluth
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
- Department of Biological Systems Engineering, Washington State University, Richland, WA 99354
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354
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3
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Li X, Zhang T, Day NJ, Feng S, Gaffrey MJ, Qian WJ. Defining the S-Glutathionylation Proteome by Biochemical and Mass Spectrometric Approaches. Antioxidants (Basel) 2022; 11:2272. [PMID: 36421458 PMCID: PMC9687251 DOI: 10.3390/antiox11112272] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/14/2022] [Indexed: 08/27/2023] Open
Abstract
Protein S-glutathionylation (SSG) is a reversible post-translational modification (PTM) featuring the conjugation of glutathione to a protein cysteine thiol. SSG can alter protein structure, activity, subcellular localization, and interaction with small molecules and other proteins. Thus, it plays a critical role in redox signaling and regulation in various physiological activities and pathological events. In this review, we summarize current biochemical and analytical approaches for characterizing SSG at both the proteome level and at individual protein levels. To illustrate the mechanism underlying SSG-mediated redox regulation, we highlight recent examples of functional and structural consequences of SSG modifications. Finally, we discuss the analytical challenges in characterizing SSG and the thiol PTM landscape, future directions for understanding of the role of SSG in redox signaling and regulation and its interplay with other PTMs, and the potential role of computational approaches to accelerate functional discovery.
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Affiliation(s)
| | | | | | | | | | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
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4
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Zhou Q, Yao S, Yang M, Guo Q, Li Y, Li L, Lei B. Superoxide dismutase 2 ameliorates mitochondrial dysfunction in skin fibroblasts of Leber’s hereditary optic neuropathy patients. Front Neurosci 2022; 16:917348. [PMID: 36017189 PMCID: PMC9398213 DOI: 10.3389/fnins.2022.917348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/22/2022] [Indexed: 11/20/2022] Open
Abstract
Background In Leber’s hereditary optic neuropathy (LHON), mtDNA mutations mediate mitochondrial dysfunction and apoptosis of retinal ganglion cells. Mitochondrial superoxide dismutase 2 (SOD2) is a crucial antioxidase against reactive oxygen species (ROS). This study aims to investigate whether SOD2 could ameliorate mtDNA mutation mediated mitochondrial dysfunction in skin fibroblasts of LHON patients and explore the underlying mechanisms. Methods The skin of normal healthy subjects and severe LHON patients harboring m.11778G > A mutation was taken to prepare immortalized skin fibroblast cell lines (control-iFB and LHON-iFB). LHON-iFB cells were transfected with SOD2 plasmid or negative control plasmid, respectively. In addition, human neuroblastoma SH-SY5Y cells and human primary retinal pigmental epithelium (hRPE) cells were stimulated by H2O2 after gene transfection. The oxygen consumption rate (OCR) was measured with a Seahorse extracellular flux analyzer. The level of ATP production, mitochondrial membrane potential, ROS and malondialdehyde (MDA) were measured separately with the corresponding assay kits. The expression level of SOD2, inflammatory cytokines and p-IκBα/IκBα was evaluated by western-blot. Assessment of apoptosis was performed by TUNEL assay. Results LHON-iFB exhibited lower OCR, ATP production, mitochondrial membrane potential but higher level of ROS and MDA than control-iFB. Western-blot revealed a significantly increased expression of IL-6 and p-IκBα/IκBα in LHON-iFB. Compared with the negative control, SOD2 overexpression increased OCR, ATP production and elevated mitochondrial membrane potential, but impaired ROS and MDA production. Besides, western-blot demonstrated exogenous SOD2 reduced the protein level of IL-6 and p-IκBα/IκBα. TUNEL assays suggested SOD2 inhibited cells apoptosis. Analogously, in SH-SY5Y and hRPE cells, SOD2 overexpression increased ATP production and mitochondrial membrane potential, but decreased ROS, MDA levels and suppressed apoptosis. Conclusion SOD2 upregulation inhibited cells apoptosis through ameliorating mitochondrial dysfunction and reducing NF-κB associated inflammatory response. This study further support exogenous SOD2 may be a promising therapy for the treatment of LHON.
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Affiliation(s)
- Qingru Zhou
- Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Shun Yao
- Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
- Henan Eye Hospital, Henan Provincial People’s Hospital, Henan Eye Institute, Zhengzhou, China
| | - Mingzhu Yang
- Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
- Henan Eye Hospital, Henan Provincial People’s Hospital, Henan Eye Institute, Zhengzhou, China
| | - Qingge Guo
- Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
- Henan Eye Hospital, Henan Provincial People’s Hospital, Henan Eye Institute, Zhengzhou, China
| | - Ya Li
- Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
- Henan Eye Hospital, Henan Provincial People’s Hospital, Henan Eye Institute, Zhengzhou, China
| | - Lei Li
- Xinxiang Medical University, Xinxiang, China
| | - Bo Lei
- Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, China
- Henan Eye Hospital, Henan Provincial People’s Hospital, Henan Eye Institute, Zhengzhou, China
- *Correspondence: Bo Lei,
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Sanz-Morello B, Ahmadi H, Vohra R, Saruhanian S, Freude KK, Hamann S, Kolko M. Oxidative Stress in Optic Neuropathies. Antioxidants (Basel) 2021; 10:1538. [PMID: 34679672 PMCID: PMC8532958 DOI: 10.3390/antiox10101538] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/07/2021] [Accepted: 09/12/2021] [Indexed: 01/23/2023] Open
Abstract
Increasing evidence indicates that changes in the redox system may contribute to the pathogenesis of multiple optic neuropathies. Optic neuropathies are characterized by the neurodegeneration of the inner-most retinal neurons, the retinal ganglion cells (RGCs), and their axons, which form the optic nerve. Often, optic neuropathies are asymptomatic until advanced stages, when visual impairment or blindness is unavoidable despite existing treatments. In this review, we describe systemic and, whenever possible, ocular redox dysregulations observed in patients with glaucoma, ischemic optic neuropathy, optic neuritis, hereditary optic neuropathies (i.e., Leber's hereditary optic neuropathy and autosomal dominant optic atrophy), nutritional and toxic optic neuropathies, and optic disc drusen. We discuss aspects related to anti/oxidative stress biomarkers that need further investigation and features related to study design that should be optimized to generate more valuable and comparable results. Understanding the role of oxidative stress in optic neuropathies can serve to develop therapeutic strategies directed at the redox system to arrest the neurodegenerative processes in the retina and RGCs and ultimately prevent vision loss.
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Affiliation(s)
- Berta Sanz-Morello
- Eye Translational Research Unit, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark; (B.S.-M.); (H.A.); (R.V.)
| | - Hamid Ahmadi
- Eye Translational Research Unit, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark; (B.S.-M.); (H.A.); (R.V.)
- Department of Ophthalmology, Rigshospitalet, 2600 Glostrup, Denmark;
| | - Rupali Vohra
- Eye Translational Research Unit, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark; (B.S.-M.); (H.A.); (R.V.)
- Group of Stem Cell Models for Studies of Neurodegenerative Diseases, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (S.S.); (K.K.F.)
| | - Sarkis Saruhanian
- Group of Stem Cell Models for Studies of Neurodegenerative Diseases, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (S.S.); (K.K.F.)
| | - Kristine Karla Freude
- Group of Stem Cell Models for Studies of Neurodegenerative Diseases, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (S.S.); (K.K.F.)
| | - Steffen Hamann
- Department of Ophthalmology, Rigshospitalet, 2600 Glostrup, Denmark;
| | - Miriam Kolko
- Eye Translational Research Unit, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark; (B.S.-M.); (H.A.); (R.V.)
- Department of Ophthalmology, Rigshospitalet, 2600 Glostrup, Denmark;
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6
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Bocca C, Le Paih V, Chao de la Barca JM, Kouassy Nzoughet J, Amati-Bonneau P, Blanchet O, Védie B, Géromin D, Simard G, Procaccio V, Bonneau D, Lenaers G, Orssaud C, Reynier P. A plasma metabolomic signature of Leber hereditary optic neuropathy showing taurine and nicotinamide deficiencies. Hum Mol Genet 2021; 30:21-29. [PMID: 33437983 PMCID: PMC8033144 DOI: 10.1093/hmg/ddab013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 01/02/2023] Open
Abstract
Leber's hereditary optic neuropathy (LHON) is the most common disorder due to mitochondrial DNA mutations and complex I deficiency. It is characterized by an acute vision loss, generally in young adults, with a higher penetrance in males. How complex I dysfunction induces the peculiar LHON clinical presentation remains an unanswered question. To gain an insight into this question, we carried out a non-targeted metabolomic investigation using the plasma of 18 LHON patients, during the chronic phase of the disease, comparing them to 18 healthy controls. A total of 500 metabolites were screened of which 156 were accurately detected. A supervised Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA) highlighted a robust model for disease prediction with a Q2 (cum) of 55.5%, with a reliable performance during the permutation test (cross-validation analysis of variance, P-value = 5.02284e-05) and a good prediction of a test set (P = 0.05). This model highlighted 10 metabolites with variable importance in the projection (VIP) > 0.8. Univariate analyses revealed nine discriminating metabolites, six of which were the same as those found in the Orthogonal Projections to Latent Structures Discriminant Analysis model. In total, the 13 discriminating metabolites identified underlining dietary metabolites (nicotinamide, taurine, choline, 1-methylhistidine and hippurate), mitochondrial energetic substrates (acetoacetate, glutamate and fumarate) and purine metabolism (inosine). The decreased concentration of taurine and nicotinamide (vitamin B3) suggest interesting therapeutic targets, given their neuroprotective roles that have already been demonstrated for retinal ganglion cells. Our results show a reliable predictive metabolomic signature in the plasma of LHON patients and highlighted taurine and nicotinamide deficiencies.
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Affiliation(s)
- Cinzia Bocca
- Unité Mixte de Recherche (UMR) MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U1083, Université d'Angers, 49933 Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France
| | - Victor Le Paih
- Unité Mixte de Recherche (UMR) MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U1083, Université d'Angers, 49933 Angers, France
| | - Juan Manuel Chao de la Barca
- Unité Mixte de Recherche (UMR) MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U1083, Université d'Angers, 49933 Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France
| | | | - Patrizia Amati-Bonneau
- Unité Mixte de Recherche (UMR) MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U1083, Université d'Angers, 49933 Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France
| | - Odile Blanchet
- Centre de Ressources Biologiques, BB-0033-00038, Centre Hospitalier Universitaire, 49933 Angers, France
| | - Benoit Védie
- Plateformes Centre de Ressources Biologiques et Tumorothèque, BB-0033-00063, Hôpital Européen Georges Pompidou, Paris, France.,Hôpital Européen Georges Pompidou, Département de Biochimie, Assistance Publique - Hôpitaux de Paris (AP-HP), Université Paris Descartes, Paris, France
| | - Daniela Géromin
- Plateformes Centre de Ressources Biologiques et Tumorothèque, BB-0033-00063, Hôpital Européen Georges Pompidou, Paris, France
| | - Gilles Simard
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France
| | - Vincent Procaccio
- Unité Mixte de Recherche (UMR) MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U1083, Université d'Angers, 49933 Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France
| | - Dominique Bonneau
- Unité Mixte de Recherche (UMR) MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U1083, Université d'Angers, 49933 Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France
| | - Guy Lenaers
- Unité Mixte de Recherche (UMR) MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U1083, Université d'Angers, 49933 Angers, France
| | - Christophe Orssaud
- Unité Fonctionnelle d'Ophtalmologie, CRMR Ophtara, Hôpital Européen Georges Pompidou (HEGP), GH Paris Centre, Assistance Publique - Hôpitaux de Paris (AP-HP), 75015 Paris, France.,Service d'Ophtalmologie, Ophtara Hôpital Necker-Enfants Malades, GH Paris Centre, AP-HP, 149, rue de Sèvres, 75015 Paris, France
| | - Pascal Reynier
- Unité Mixte de Recherche (UMR) MITOVASC, Centre National de la Recherche Scientifique (CNRS) 6015, Institut National de la Santé et de la Recherche Médicale (INSERM) U1083, Université d'Angers, 49933 Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire, 49933 Angers, France
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Musaogullari A, Chai YC. Redox Regulation by Protein S-Glutathionylation: From Molecular Mechanisms to Implications in Health and Disease. Int J Mol Sci 2020; 21:ijms21218113. [PMID: 33143095 PMCID: PMC7663550 DOI: 10.3390/ijms21218113] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/19/2022] Open
Abstract
S-glutathionylation, the post-translational modification forming mixed disulfides between protein reactive thiols and glutathione, regulates redox-based signaling events in the cell and serves as a protective mechanism against oxidative damage. S-glutathionylation alters protein function, interactions, and localization across physiological processes, and its aberrant function is implicated in various human diseases. In this review, we discuss the current understanding of the molecular mechanisms of S-glutathionylation and describe the changing levels of expression of S-glutathionylation in the context of aging, cancer, cardiovascular, and liver diseases.
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