1
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Saei AA, Lundin A, Lyu H, Gharibi H, Luo H, Teppo J, Zhang X, Gaetani M, Végvári Á, Holmdahl R, Gygi SP, Zubarev RA. Multifaceted Proteome Analysis at Solubility, Redox, and Expression Dimensions for Target Identification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401502. [PMID: 39120068 DOI: 10.1002/advs.202401502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 07/24/2024] [Indexed: 08/10/2024]
Abstract
Multifaceted interrogation of the proteome deepens the system-wide understanding of biological systems; however, mapping the redox changes in the proteome has so far been significantly more challenging than expression and solubility/stability analyses. Here, the first high-throughput redox proteomics approach integrated with expression analysis (REX) is devised and combined with the Proteome Integral Solubility Alteration (PISA) assay. The whole PISA-REX experiment with up to four biological replicates can be multiplexed into a single tandem mass tag TMTpro set. For benchmarking this compact tool, HCT116 cells treated with auranofin are analyzed, showing great improvement compared with previous studies. PISA-REX is then applied to study proteome remodeling upon stimulation of human monocytes by interferon α (IFN-α). Applying this tool to study the proteome changes in plasmacytoid dendritic cells (pDCs) isolated from wild-type versus Ncf1-mutant mice treated with interferon α, shows that NCF1 deficiency enhances the STAT1 pathway and modulates the expression, solubility, and redox state of interferon-induced proteins. Providing comprehensive multifaceted information on the proteome, the compact PISA-REX has the potential to become an industry standard in proteomics and to open new windows into the biology of health and disease.
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Affiliation(s)
- Amir A Saei
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Albin Lundin
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
| | - Hezheng Lyu
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
| | - Hassan Gharibi
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
| | - Huqiao Luo
- Division of Immunology, Medical Inflammation Research Group, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, SE-17 177, Sweden
| | - Jaakko Teppo
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, FI-00014, Finland
| | - Xuepei Zhang
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
| | - Massimiliano Gaetani
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
- SciLifeLab, Stockholm, SE-17 177, Sweden
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
| | - Rikard Holmdahl
- Division of Immunology, Medical Inflammation Research Group, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, SE-17 177, Sweden
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Roman A Zubarev
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
- SciLifeLab, Stockholm, SE-17 177, Sweden
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2
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Anjo SI, He Z, Hussain Z, Farooq A, McIntyre A, Laughton CA, Carvalho AN, Finelli MJ. Protein Oxidative Modifications in Neurodegenerative Diseases: From Advances in Detection and Modelling to Their Use as Disease Biomarkers. Antioxidants (Basel) 2024; 13:681. [PMID: 38929122 PMCID: PMC11200609 DOI: 10.3390/antiox13060681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Oxidation-reduction post-translational modifications (redox-PTMs) are chemical alterations to amino acids of proteins. Redox-PTMs participate in the regulation of protein conformation, localization and function, acting as signalling effectors that impact many essential biochemical processes in the cells. Crucially, the dysregulation of redox-PTMs of proteins has been implicated in the pathophysiology of numerous human diseases, including neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. This review aims to highlight the current gaps in knowledge in the field of redox-PTMs biology and to explore new methodological advances in proteomics and computational modelling that will pave the way for a better understanding of the role and therapeutic potential of redox-PTMs of proteins in neurodegenerative diseases. Here, we summarize the main types of redox-PTMs of proteins while providing examples of their occurrence in neurodegenerative diseases and an overview of the state-of-the-art methods used for their detection. We explore the potential of novel computational modelling approaches as essential tools to obtain insights into the precise role of redox-PTMs in regulating protein structure and function. We also discuss the complex crosstalk between various PTMs that occur in living cells. Finally, we argue that redox-PTMs of proteins could be used in the future as diagnosis and prognosis biomarkers for neurodegenerative diseases.
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Affiliation(s)
- Sandra I. Anjo
- CNC-Center for Neurosciences and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-517 Coimbra, Portugal
- Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal
| | - Zhicheng He
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Zohaib Hussain
- Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
| | - Aruba Farooq
- Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
| | - Alan McIntyre
- Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
| | - Charles A. Laughton
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Andreia Neves Carvalho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Mattéa J. Finelli
- Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
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3
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Chen Y, Wang C, Qi M, Wei Y, Jiang H, Du Z. Molecular targets of cisplatin in HeLa cells explored through competitive activity-based protein profiling strategy. J Inorg Biochem 2024; 254:112518. [PMID: 38460483 DOI: 10.1016/j.jinorgbio.2024.112518] [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: 01/30/2024] [Revised: 02/23/2024] [Accepted: 03/04/2024] [Indexed: 03/11/2024]
Abstract
Cisplatin is widely used as anticancer drugs, and DNA is considered as the main target. Considering its high affinity towards cysteines and the important role of cystine containing proteins, we applied a competitive activity-based protein profiling strategy to identify protein cysteines that bind with cisplatin in HeLa cells. Living cells were treated with cisplatin at cytotoxic concentrations, then the protein was extracted. After labeling with desthiobiotin iodoacetamide (DBIA) probe, protein was precipitated, digested and isotopically labeled, subsequently the peptides were combined, and the biotinylated cysteine-containing peptides were enriched and quantified by LC-MS/MS. A total of 3571 peptides which originated from 1871 proteins were identified using the DBIA probe. Among them, 46 proteins were screened as targets, including proteins that have been identified as binding proteins by previous study. A novel cisplatin target, calpain-1 (CAPN1), was identified and validated as binding with cisplatin in vitro.
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Affiliation(s)
- Yi Chen
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chenxi Wang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Meiling Qi
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yinyu Wei
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hongliang Jiang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhifeng Du
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan 430030, China.
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4
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Pillay CS, Rohwer JM. Computational models as catalysts for investigating redoxin systems. Essays Biochem 2024; 68:27-39. [PMID: 38356400 DOI: 10.1042/ebc20230036] [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: 10/23/2023] [Revised: 01/11/2024] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Thioredoxin, glutaredoxin and peroxiredoxin systems play central roles in redox regulation, signaling and metabolism in cells. In these systems, reducing equivalents from NAD(P)H are transferred by coupled thiol-disulfide exchange reactions to redoxins which then reduce a wide array of targets. However, the characterization of redoxin activity has been unclear, with redoxins regarded as enzymes in some studies and redox metabolites in others. Consequently, redoxin activities have been quantified by enzyme kinetic parameters in vitro, and redox potentials or redox ratios within cells. By analyzing all the reactions within these systems, computational models showed that many kinetic properties attributed to redoxins were due to system-level effects. Models of cellular redoxin networks have also been used to estimate intracellular hydrogen peroxide levels, analyze redox signaling and couple omic and kinetic data to understand the regulation of these networks in disease. Computational modeling has emerged as a powerful complementary tool to traditional redoxin enzyme kinetic and cellular assays that integrates data from a number of sources into a single quantitative framework to accelerate the analysis of redoxin systems.
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Affiliation(s)
- Ché S Pillay
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, South Africa
| | - Johann M Rohwer
- Laboratory for Molecular Systems Biology, Department of Biochemistry, University of Stellenbosch, Stellenbosch, South Africa
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5
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Neves RPD, Chagoyen M, Martinez-Lorente A, Iñiguez C, Calatrava A, Calabuig J, Iborra FJ. Each Cellular Compartment Has a Characteristic Protein Reactive Cysteine Ratio Determining Its Sensitivity to Oxidation. Antioxidants (Basel) 2023; 12:1274. [PMID: 37372004 DOI: 10.3390/antiox12061274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Signaling and detoxification of Reactive Oxygen Species (ROS) are important patho-physiologcal processes. Despite this, we lack comprehensive information on individual cells and cellular structures and functions affected by ROS, which is essential to build quantitative models of the effects of ROS. The thiol groups from cysteines (Cys) in proteins play a major role in redox defense, signaling, and protein function. In this study, we show that the proteins in each subcellular compartment contain a characteristic Cys amount. Using a fluorescent assay for -SH in thiolate form and amino groups in proteins, we show that the thiolate content correlates with ROS sensitivity and signaling properties of each compartment. The highest absolute thiolate concentration was found in the nucleolus, followed by the nucleoplasm and cytoplasm whereas protein thiolate groups per protein showed an inverse pattern. In the nucleoplasm, protein reactive thiols concentrated in SC35 speckles, SMN, and the IBODY that accumulated oxidized RNA. Our findings have important functional consequences, and explain differential sensitivity to ROS.
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Affiliation(s)
- Ricardo Pires das Neves
- Center for Neuroscience and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal
- IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Mónica Chagoyen
- Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain
| | - Antonio Martinez-Lorente
- Unidad de Investigación, Innovación y Docencia Médica, Hospital Universitario Vinalopó, 03293 Elx, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), 46020 Valencia, Spain
- Department of Biotecnology, University of Alicante, 03690 Alicante, Spain
| | - Carlos Iñiguez
- Department of Biotecnology, University of Alicante, 03690 Alicante, Spain
| | - Ana Calatrava
- Department of Pathology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain
| | | | - Francisco J Iborra
- Instituto de Biomedicina de Valencia, CSIC, Jaime Roig 11, 46010 Valencia, Spain
- Centro de Investigación Príncipe Felipe (CIPF), Primo Yufera 3, 46012 Valencia, Spain
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6
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Koeberle SC, Kipp AP, Stuppner H, Koeberle A. Ferroptosis-modulating small molecules for targeting drug-resistant cancer: Challenges and opportunities in manipulating redox signaling. Med Res Rev 2023; 43:614-682. [PMID: 36658724 PMCID: PMC10947485 DOI: 10.1002/med.21933] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/07/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023]
Abstract
Ferroptosis is an iron-dependent cell death program that is characterized by excessive lipid peroxidation. Triggering ferroptosis has been proposed as a promising strategy to fight cancer and overcome drug resistance in antitumor therapy. Understanding the molecular interactions and structural features of ferroptosis-inducing compounds might therefore open the door to efficient pharmacological strategies against aggressive, metastatic, and therapy-resistant cancer. We here summarize the molecular mechanisms and structural requirements of ferroptosis-inducing small molecules that target central players in ferroptosis. Focus is placed on (i) glutathione peroxidase (GPX) 4, the only GPX isoenzyme that detoxifies complex membrane-bound lipid hydroperoxides, (ii) the cystine/glutamate antiporter system Xc - that is central for glutathione regeneration, (iii) the redox-protective transcription factor nuclear factor erythroid 2-related factor (NRF2), and (iv) GPX4 repression in combination with induced heme degradation via heme oxygenase-1. We deduce common features for efficient ferroptotic activity and highlight challenges in drug development. Moreover, we critically discuss the potential of natural products as ferroptosis-inducing lead structures and provide a comprehensive overview of structurally diverse biogenic and bioinspired small molecules that trigger ferroptosis via iron oxidation, inhibition of the thioredoxin/thioredoxin reductase system or less defined modes of action.
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Affiliation(s)
- Solveigh C. Koeberle
- Michael Popp Institute, Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckTirolInnsbruckAustria
- Department of Molecular Nutritional Physiology, Institute of Nutritional SciencesFriedrich Schiller University JenaThüringenJenaGermany
| | - Anna P. Kipp
- Department of Molecular Nutritional Physiology, Institute of Nutritional SciencesFriedrich Schiller University JenaThüringenJenaGermany
| | - Hermann Stuppner
- Unit of Pharmacognosy, Institute of Pharmacy, Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckTirolInnsbruckAustria
| | - Andreas Koeberle
- Michael Popp Institute, Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckTirolInnsbruckAustria
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7
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Janciauskiene S, Tumpara S, Schebb NH, Buettner FFR, Mainka M, Sivaraman K, Immenschuh S, Grau V, Welte T, Olejnicka B. Indirect effect of alpha-1-antitrypsin on endotoxin-induced IL-1β secretion from human PBMCs. Front Pharmacol 2022; 13:995869. [PMID: 36249781 PMCID: PMC9564231 DOI: 10.3389/fphar.2022.995869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Human alpha-1-antitrypsin (AAT) encoded by the SERPINA1 gene, is an acute phase glycoprotein that regulates inflammatory responses via both protease inhibitory and non-inhibitory activities. We previously reported that AAT controls ATP-induced IL-1β release from human mononuclear cells by stimulating the release of small bioactive molecules. In the current study, we aimed to elucidate the identity of these putative effectors released from human PBMCs in response to AAT, which may inhibit the LPS-induced release of IL-1β. We pre-incubated human PBMCs alone or with different preparations of AAT (4 mg/ml) for 30 min at 37°C, 5% CO2, and collected cell supernatants filtered through centrifugal filters (cutoff 3 kDa) to eliminate AAT and other high molecular weight substances. Supernatants passed through the filters were used to culture PBMCs isolated from the autologous or a heterologous donors with or without adding LPS (1 μg/ml) for 6 h. Unexpectedly, supernatants from PBMCs pre-incubated with AAT (Zemaira®), but not with other AAT preparations tested or with oxidized AAT (Zemaira®), lowered the LPS-induced release of IL-1β by about 25%–60% without affecting IL1B mRNA. The reversed-phase liquid chromatography coupled with mass spectrometry did not confirm the hypothesis that small pro-resolving lipid mediators released from PBMCs after exposure to AAT (Zemaira®) are responsible for lowering the LPS-induced IL-1β release. Distinctively from other AAT preparations, AAT (Zemaira®) and supernatants from PBMCs pre-treated with this protein contained high levels of total thiols. In line, mass spectrometry analysis revealed that AAT (Zemaira®) protein contains freer Cys232 than AAT (Prolastin®). Our data show that a free Cys232 in AAT is required for controlling LPS-induced IL-1β release from human PBMCs. Further studies characterizing AAT preparations used to treat patients with inherited AAT deficiency remains of clinical importance.
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Affiliation(s)
- Sabina Janciauskiene
- Department of Respiratory Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany
- Department of Experimental Medicine, Lund University, Lund, Sweden
- *Correspondence: Sabina Janciauskiene,
| | - Srinu Tumpara
- Department of Respiratory Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Nils Helge Schebb
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Wuppertal, Germany
| | - Falk F. R. Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Malwina Mainka
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Wuppertal, Germany
| | - Kokilavani Sivaraman
- Department of Respiratory Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Stephan Immenschuh
- Institute for Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Veronika Grau
- Laboratory of Experimental Surgery, Department of General and Thoracic Surgery, Justus-Liebig-University Giessen, German Center for Lung Research, Giessen, Germany
| | - Tobias Welte
- Department of Respiratory Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany
| | - Beata Olejnicka
- Department of Respiratory Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany
- Department of Experimental Medicine, Lund University, Lund, Sweden
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8
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Montasell MC, Monge P, Carmali S, Dias Loiola LM, Andersen DG, Løvschall KB, Søgaard AB, Kristensen MM, Pütz JM, Zelikin AN. Chemical zymogens for the protein cysteinome. Nat Commun 2022; 13:4861. [PMID: 35982075 PMCID: PMC9388531 DOI: 10.1038/s41467-022-32609-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/08/2022] [Indexed: 12/18/2022] Open
Abstract
We present three classes of chemical zymogens established around the protein cysteinome. In each case, the cysteine thiol group was converted into a mixed disulfide: with a small molecule, a non-degradable polymer, or with a fast-depolymerizing fuse polymer (ZLA). The latter was a polydisulfide based on naturally occurring molecule, lipoic acid. Zymogen designs were applied to cysteine proteases and a kinase. In each case, enzymatic activity was successfully masked in full and reactivated by small molecule reducing agents. However, only ZLA could be reactivated by protein activators, demonstrating that the macromolecular fuse escapes the steric bulk created by the protein globule, collects activation signal in solution, and relays it to the active site of the enzyme. This afforded first-in-class chemical zymogens that are activated via protein-protein interactions. We also document zymogen exchange reactions whereby the polydisulfide is transferred between the interacting proteins via the "chain transfer" bioconjugation mechanism.
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Affiliation(s)
| | - Pere Monge
- Department of Chemistry, Aarhus University, 8000, Aarhus, Denmark
| | - Sheiliza Carmali
- Department of Chemistry, Aarhus University, 8000, Aarhus, Denmark.,School of Pharmacy, Queen's University Belfast, Belfast, UK
| | | | - Dante Guldbrandsen Andersen
- Department of Chemistry, Aarhus University, 8000, Aarhus, Denmark.,iNano Interdisciplinary Nanoscience Centre, Aarhus University, 8000, Aarhus, Denmark
| | | | - Ane Bretschneider Søgaard
- Department of Chemistry, Aarhus University, 8000, Aarhus, Denmark.,iNano Interdisciplinary Nanoscience Centre, Aarhus University, 8000, Aarhus, Denmark
| | | | | | - Alexander N Zelikin
- Department of Chemistry, Aarhus University, 8000, Aarhus, Denmark. .,iNano Interdisciplinary Nanoscience Centre, Aarhus University, 8000, Aarhus, Denmark.
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9
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Dai X, Shen L. Advances and Trends in Omics Technology Development. Front Med (Lausanne) 2022; 9:911861. [PMID: 35860739 PMCID: PMC9289742 DOI: 10.3389/fmed.2022.911861] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.
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10
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Pillay CS, John N. Can thiol-based redox systems be utilized as parts for synthetic biology applications? Redox Rep 2021; 26:147-159. [PMID: 34378494 PMCID: PMC8366655 DOI: 10.1080/13510002.2021.1966183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES Synthetic biology has emerged from molecular biology and engineering approaches and aims to develop novel, biologically-inspired systems for industrial and basic research applications ranging from biocomputing to drug production. Surprisingly, redoxin (thioredoxin, glutaredoxin, peroxiredoxin) and other thiol-based redox systems have not been widely utilized in many of these synthetic biology applications. METHODS We reviewed thiol-based redox systems and the development of synthetic biology applications that have used thiol-dependent parts. RESULTS The development of circuits to facilitate cytoplasmic disulfide bonding, biocomputing and the treatment of intestinal bowel disease are amongst the applications that have used thiol-based parts. We propose that genetically encoded redox sensors, thiol-based biomaterials and intracellular hydrogen peroxide generators may also be valuable components for synthetic biology applications. DISCUSSION Thiol-based systems play multiple roles in cellular redox metabolism, antioxidant defense and signaling and could therefore offer a vast and diverse portfolio of components, parts and devices for synthetic biology applications. However, factors limiting the adoption of redoxin systems for synthetic biology applications include the orthogonality of thiol-based components, limitations in the methods to characterize thiol-based systems and an incomplete understanding of the design principles of these systems.
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Affiliation(s)
- Ché S. Pillay
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Nolyn John
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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11
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Bull Sperm Capacitation Is Accompanied by Redox Modifications of Proteins. Int J Mol Sci 2021; 22:ijms22157903. [PMID: 34360666 PMCID: PMC8347624 DOI: 10.3390/ijms22157903] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 12/19/2022] Open
Abstract
The ability to fertilise an egg is acquired by the mammalian sperm during the complex biochemical process called capacitation. Capacitation is accompanied by the production of reactive oxygen species (ROS), but the mechanism of redox regulation during capacitation has not been elucidated. This study aimed to verify whether capacitation coincides with reversible oxidative post-translational modifications of proteins (oxPTMs). Flow cytometry, fluorescence microscopy and Western blot analyses were used to verify the sperm capacitation process. A fluorescent gel-based redox proteomic approach allowed us to observe changes in the level of reversible oxPTMs manifested by the reduction or oxidation of susceptible cysteines in sperm proteins. Sperm capacitation was accompanied with redox modifications of 48 protein spots corresponding to 22 proteins involved in the production of ROS (SOD, DLD), playing a role in downstream redox signal transfer (GAPDHS and GST) related to the cAMP/PKA pathway (ROPN1L, SPA17), acrosome exocytosis (ACRB, sperm acrosome associated protein 9, IZUMO4), actin polymerisation (CAPZB) and hyperactivation (TUBB4B, TUB1A). The results demonstrated that sperm capacitation is accompanied by altered levels of oxPTMs of a group of redox responsive proteins, filling gaps in our knowledge concerning sperm capacitation.
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12
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Majewska AM, Mostek A. Gel-based fluorescent proteomic tools for investigating cell redox signaling. A mini-review. Electrophoresis 2021; 42:1378-1387. [PMID: 33783010 DOI: 10.1002/elps.202000389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/26/2021] [Accepted: 03/08/2021] [Indexed: 11/07/2022]
Abstract
The specific chemical reactivity of thiol groups makes protein cysteines susceptible to reactions with reactive oxygen species (ROS) and reactive nitrogen species (RNS) resulting in the formation of various reversible and irreversible oxidative post-translational modifications (oxPTMs). This review highlights a number of gel-based redox proteomic approaches to detect protein oxPTMs, with particular emphasis on S-nitrosylation, which we believe are currently one of the most accurate way to analyze changes in the redox status of proteins. The information collected in this review relates to the recent progress regarding methods for the enrichment and identification of redox-modified proteins, with an emphasis on fluorescent gel proteomics. Gel-based fluorescent proteomic strategies are low-cost and easy-to-use tools for investigating the thiol proteome and can provide substantial information on redox signaling.
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Affiliation(s)
- Anna M Majewska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Agnieszka Mostek
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
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13
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Lorenzen I, Eble JA, Hanschmann EM. Thiol switches in membrane proteins - Extracellular redox regulation in cell biology. Biol Chem 2020; 402:253-269. [PMID: 33108336 DOI: 10.1515/hsz-2020-0266] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022]
Abstract
Redox-mediated signal transduction depends on the enzymatic production of second messengers such as hydrogen peroxide, nitric oxide and hydrogen sulfite, as well as specific, reversible redox modifications of cysteine-residues in proteins. So-called thiol switches induce for instance conformational changes in specific proteins that regulate cellular pathways e.g., cell metabolism, proliferation, migration, gene expression and inflammation. Reduction, oxidation and disulfide isomerization are controlled by oxidoreductases of the thioredoxin family, including thioredoxins, glutaredoxins, peroxiredoxins and protein dsisulfide isomerases. These proteins are located in different cellular compartments, interact with substrates and catalyze specific reactions. Interestingly, some of these proteins are released by cells. Their extracellular functions and generally extracellular redox control have been widely underestimated. Here, we give an insight into extracellular redox signaling, extracellular thiol switches and their regulation by secreted oxidoreductases and thiol-isomerases, a topic whose importance has been scarcely studied so far, likely due to methodological limitations. We focus on the secreted redox proteins and characterized thiol switches in the ectodomains of membrane proteins, such as integrins and the metalloprotease ADAM17, which are among the best-characterized proteins and discuss their underlying mechanisms and biological implications.
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Affiliation(s)
- Inken Lorenzen
- Centre of Biochemistry and Molecular Biology, Structural Biology, Christian-Albrecht University of Kiel, Am Botanischen Garten 1-9, D-24118Kiel, Germany
| | - Johannes A Eble
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, D-48149Münster, Germany
| | - Eva-Maria Hanschmann
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Life Science Center, Merowingerplatz 1a, D-40225Düsseldorf, Germany
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14
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A water-soluble and incubate-free fluorescent environment-sensitive probe for ultrafast visualization of protein thiols within living cells. Anal Chim Acta 2020; 1126:72-81. [DOI: 10.1016/j.aca.2020.06.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/22/2020] [Accepted: 06/09/2020] [Indexed: 12/19/2022]
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15
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Oliveira CS, Segatto ALA, Nogara PA, Piccoli BC, Loreto ÉLS, Aschner M, Rocha JBT. Transcriptomic and Proteomic Tools in the Study of Hg Toxicity: What Is Missing? Front Genet 2020; 11:425. [PMID: 32431728 PMCID: PMC7215068 DOI: 10.3389/fgene.2020.00425] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 04/06/2020] [Indexed: 01/08/2023] Open
Abstract
Mercury is a hazardous substance that has unique neurodevelopmental toxic effects in humans. However, the precise sequence of molecular events that culminate in Hg-induced neuropathology is still unknown. Though the omics studies have been generating an enormous amount of new data about Hg toxicity, our ability to interpret such a large quantity of information is still limited. In this opinion article, we will reinforce the necessity of new high throughput and accurate analytical proteomic methodologies, especially, thiol and selenol-proteome. Overall, we posit that improvements in thiol- and selenol-proteomic analyses will be pivotal in identifying the primary cellular targets of Hg. However, a better understanding of the complex cascades and molecular pathways involved in its toxicity will require extensive complementary studies in more complex systems.
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Affiliation(s)
- Cláudia S. Oliveira
- Programa Pós-Graduação Stricto Sensu em Biotecnologia Aplicada a Saúde da Criança e do Adolescente, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
- Faculdades Pequeno Príncipe, Curitiba, Brazil
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Ana L. A. Segatto
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Pablo A. Nogara
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Bruna C. Piccoli
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Élgion L. S. Loreto
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, NY, United States
| | - João B. T. Rocha
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil
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16
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Dennis KK, Go YM, Jones DP. Redox Systems Biology of Nutrition and Oxidative Stress. J Nutr 2019; 149:553-565. [PMID: 30949678 PMCID: PMC6461723 DOI: 10.1093/jn/nxy306] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 10/30/2018] [Accepted: 11/19/2018] [Indexed: 02/07/2023] Open
Abstract
Diet and nutrition contribute to both beneficial and harmful aspects of oxidative processes. The harmful processes, termed oxidative stress, occur with many human diseases. Major advances in understanding oxidative stress and nutrition have occurred with broad characterization of dietary oxidants and antioxidants, and with mechanistic studies showing antioxidant efficacy. However, randomized controlled trials in humans with free-radical-scavenging antioxidants and the glutathione precursor N-acetylcysteine have provided limited or inconsistent evidence for health benefits. This, combined with emerging redox theory, indicates that holistic models are needed to understand the interplay of nutrition and oxidative stress. The purpose of this article is to highlight how recent advances in redox theory and the development of new omics tools and data-driven approaches provide a framework for future nutrition and oxidative stress research. Here we describe why a holistic approach is needed to understand the impact of nutrition on oxidative stress and how recent advances in omics and data analysis methods are viable tools for systems nutrition approaches. Based on the extensive research on glutathione and related thiol antioxidant systems, we summarize the advancing framework for diet and oxidative stress in which antioxidant systems are a component of a larger redox network that serves as a responsive interface between the environment and an individual. The feasibility for redox network analysis has been established by experimental models in which dietary factors are systematically varied and oxidative stress markers are linked through integrated omics (metabolome, transcriptome, proteome). With this framework, integrated redox network models will support optimization of diet to protect against oxidative stress and disease.
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Affiliation(s)
| | - Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA
| | - Dean P Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA
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17
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Fobe TL, Kazakov A, Riccardi D. Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank. J Chem Inf Model 2019; 59:931-943. [PMID: 30694665 PMCID: PMC6999612 DOI: 10.1021/acs.jcim.8b00950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cysteine is a multifaceted amino acid that is central to the structure and function of many proteins. A disulfide bond formed between two cysteines restrains protein conformations through the strong covalent bond and torsions about the bond that prefer, energetically, ±90°. In this study, we transform over 30 000 Protein Databank files (PDBx/mmCIFs) into a single file, the SQLite database (Cys.sqlite). The database schema is designed to accommodate the structural information on both oxidized and reduced cysteines and to retain essential protein metadata to establish informational and biological provenance. Cys.sqlite contains over 95 000 peptide chains and 500 000 cysteines (700 000 structural conformers); there are over 265 000 cysteine disulfide bond conformations from structures solved with all available experimental methods. The structural information is analyzed with respect to sequence identity cutoff, the experimental method, and energetics of the disulfide. We find that as the experimental information becomes limiting and the influence of modeling becomes more pronounced, the observed average strain increases artificially. The database and analyses presented here can be used to improve the refinement of biological structures from experiments that are known to contain one or more disulfide bonds.
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Affiliation(s)
- Theodore L Fobe
- University of Maryland , Department of Chemical and Biomolecular Engineering , College Park , Maryland 20742 , United States
- Summer Undergraduate Research Fellowship , National Institute of Standards and Technology , Boulder , Colorado 80305 , United States
| | - Andrei Kazakov
- Applied Chemicals and Materials Division , National Institute of Standards and Technology , Boulder , Colorado 80305 , United States
| | - Demian Riccardi
- Applied Chemicals and Materials Division , National Institute of Standards and Technology , Boulder , Colorado 80305 , United States
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18
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Jakubowski H. Homocysteine Modification in Protein Structure/Function and Human Disease. Physiol Rev 2019; 99:555-604. [PMID: 30427275 DOI: 10.1152/physrev.00003.2018] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Epidemiological studies established that elevated homocysteine, an important intermediate in folate, vitamin B12, and one carbon metabolism, is associated with poor health, including heart and brain diseases. Earlier studies show that patients with severe hyperhomocysteinemia, first identified in the 1960s, exhibit neurological and cardiovascular abnormalities and premature death due to vascular complications. Although homocysteine is considered to be a nonprotein amino acid, studies over the past 2 decades have led to discoveries of protein-related homocysteine metabolism and mechanisms by which homocysteine can become a component of proteins. Homocysteine-containing proteins lose their biological function and acquire cytotoxic, proinflammatory, proatherothrombotic, and proneuropathic properties, which can account for the various disease phenotypes associated with hyperhomocysteinemia. This review describes mechanisms by which hyperhomocysteinemia affects cellular proteostasis, provides a comprehensive account of the biological chemistry of homocysteine-containing proteins, and discusses pathophysiological consequences and clinical implications of their formation.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, International Center for Public Health , Newark, New Jersey ; and Department of Biochemistry and Biotechnology, Poznań University of Life Sciences , Poznań , Poland
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19
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Aivazidis S, Anderson CC, Roede JR. Toxicant-mediated redox control of proteostasis in neurodegeneration. CURRENT OPINION IN TOXICOLOGY 2019; 13:22-34. [PMID: 31602419 PMCID: PMC6785977 DOI: 10.1016/j.cotox.2018.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Disruption in redox signaling and control of cellular processes has emerged as a key player in many pathologies including neurodegeneration. As protein aggregations are a common hallmark of several neuronal pathologies, a firm understanding of the interplay between redox signaling, oxidative and free radical stress, and proteinopathies is required to sort out the complex mechanisms in these diseases. Fortunately, models of toxicant-induced neurodegeneration can be utilized to evaluate and report mechanistic alterations in the proteostasis network (PN). The epidemiological links between environmental toxicants and neurological disease gives further credence into characterizing the toxicant-mediated PN disruptions observed in these conditions. Reviewed here are examples of mechanistic interaction between oxidative or free radical stress and PN alterations. Additionally, investigations into toxicant-mediated PN disruptions, specifically focusing on environmental metals and pesticides, are discussed. Finally, we emphasize the need to distinguish whether the presence of protein aggregations are contributory to phenotypes related to neurodegeneration, or if they are a byproduct of PN deficiencies.
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Affiliation(s)
- Stefanos Aivazidis
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Colin C Anderson
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - James R Roede
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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20
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Anjo SI, Melo MN, Loureiro LR, Sabala L, Castanheira P, Grãos M, Manadas B. oxSWATH: An integrative method for a comprehensive redox-centered analysis combined with a generic differential proteomics screening. Redox Biol 2019; 22:101130. [PMID: 30737169 PMCID: PMC6435957 DOI: 10.1016/j.redox.2019.101130] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/27/2019] [Accepted: 01/28/2019] [Indexed: 12/21/2022] Open
Abstract
Most of the redox proteomics strategies are focused on the identification and relative quantification of cysteine oxidation without considering the variation in the total levels of the proteins. However, protein synthesis and protein degradation also belong to the regulatory mechanisms of the cells, being therefore important to consider the changes in total protein levels in PTMs-focused analyses, such as cysteine redox characterization. Therefore, a novel integrative approach combining the SWATH-MS method with differential alkylation using a combination of commonly available alkylating reagents (oxSWATH) is presented, by which it is possible to integrate the information regarding relative cysteine oxidation with the analysis of the total protein levels in a cost-effective high-throughput approach. The proposed method was tested using a redox-regulated protein and further applied to a comparative analysis of secretomes obtained from cells cultured under control or oxidative stress conditions to strengthen the importance of considering the overall proteome changes. Using the OxSWATH method it was possible to determine both the relative proportion of reduced and reversible oxidized oxoforms, as well as the total levels of each oxoform by taking into consideration the total levels of the protein. Therefore, using OxSWATH the comparative analyses can be performed at two different levels by considering the relative proportion or the total levels at both peptide and protein level. Moreover, since samples are acquired in SWATH-MS mode, besides the redox centered analysis, a generic differential protein expression analysis can also be performed, allowing a truly comprehensive evaluation of proteomics changes upon the oxidative stimulus. Data are available via ProteomeXchange and SWATHAtlas with the identifiers PXD006802, PXD006802, and PASS01210. Determination of redox changes considering protein total levels. Integrative redoxomics and common differential proteomics in a single analysis. Differential alkylation strategy using commonly available alkylating agents. First untargeted label-free quantitative method to study cysteine oxidation.
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Affiliation(s)
- Sandra I Anjo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal; Faculty of Medicine, University of Coimbra, Coimbra, Portugal.
| | - Matilde N Melo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Liliana R Loureiro
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Lúcia Sabala
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | | | - Mário Grãos
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Biocant, Technology Transfer Association, Cantanhede, Portugal
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
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21
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Wiśniewski K, Jóźwik-Pruska J, Bieńkowski M, Bobeff EJ, Bryl M, Kałużna-Czaplińska J, Jaskólski DJ. Isoprostanes as potential cerebral vasospasm biomarkers. Neurol Neurochir Pol 2018; 52:643-651. [PMID: 30314904 DOI: 10.1016/j.pjnns.2018.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/01/2018] [Accepted: 09/25/2018] [Indexed: 11/29/2022]
Abstract
Despite enormous progress in medicine, symptomatic cerebral vasospasm (CVS), remains an unexplained clinical problem, which leaves both physicians and patients helpless and relying on chance, due to the lack of specific marker indicative of imminent danger as well as the lack of specific treatment. In our opinion CVS occurrence depends on dynamic disbalance between free radicals' formation (oxidative stress) and antioxidant activity. Isoprostanes are products of free-radical peroxidation of polyunsaturated fatty acids, and seem to mark a promising path for the research aiming to unravel its possible mechanism. Not only are they the biomarkers of oxidative stress in vivo and in vitro, but also have manifold biological effects (including vasoactive, inflammatory and mitogenic) via activation of the thromboxane A2 receptor (TBXA2R), both in physiological and pathophysiological processes. This review addresses the importance of isoprostanes in CVS in quest of appropriate biomarkers.
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Affiliation(s)
- Karol Wiśniewski
- Department of Neurosurgery and Neurooncology, Medical University of Lodz, Barlicki University Hospital, Kopcińskiego 22, 90-153 Lodz, Poland.
| | - Jagoda Jóźwik-Pruska
- Institute of General and Ecological Chemistry, Department of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Michał Bieńkowski
- Department of Molecular Pathology and Neuropathology, Chair of Oncology, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland
| | - Ernest J Bobeff
- Department of Neurosurgery and Neurooncology, Medical University of Lodz, Barlicki University Hospital, Kopcińskiego 22, 90-153 Lodz, Poland
| | - Maciej Bryl
- Department of Neurosurgery and Neurooncology, Medical University of Lodz, Barlicki University Hospital, Kopcińskiego 22, 90-153 Lodz, Poland
| | - Joanna Kałużna-Czaplińska
- Institute of General and Ecological Chemistry, Department of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Dariusz J Jaskólski
- Department of Neurosurgery and Neurooncology, Medical University of Lodz, Barlicki University Hospital, Kopcińskiego 22, 90-153 Lodz, Poland
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22
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Oliveira CS, Nogara PA, Ardisson-Araújo DMP, Aschner M, Rocha JBT, Dórea JG. Neurodevelopmental Effects of Mercury. ADVANCES IN NEUROTOXICOLOGY 2018; 2:27-86. [PMID: 32346667 PMCID: PMC7188190 DOI: 10.1016/bs.ant.2018.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The toxicology of mercury (Hg) is of concern since this metal is ubiquitously distributed in the environment, and living organisms are routinely exposed to Hg at low to high levels. The toxic effects of Hg are well studied and it is known that they may differ depending on the Hg chemical species. In this chapter, we emphasize the neurotoxic effects of Hg during brain development. The immature brain is more susceptible to Hg exposure, since all the Hg chemical forms, not only the organic ones, can harm it. The possible consequences of Hg exposure during the early stages of development, the additive effects with other co-occurring neurotoxicants, and the known mechanisms of action and targets will be addressed in this chapter.
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Affiliation(s)
- Cláudia S Oliveira
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Pablo A Nogara
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Daniel M P Ardisson-Araújo
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
- Laboratório de Virologia de Insetos, Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - João B T Rocha
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - José G Dórea
- Professor Emeritus, Faculdade de Ciências da Saúde, Universidade de Brasília, Brasília, DF, Brazil
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23
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Petkowski JJ, Bains W, Seager S. Natural Products Containing a Nitrogen-Sulfur Bond. JOURNAL OF NATURAL PRODUCTS 2018; 81:423-446. [PMID: 29364663 DOI: 10.1021/acs.jnatprod.7b00921] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Only about 100 natural products are known to contain a nitrogen-sulfur (N-S) bond. This review thoroughly categorizes N-S bond-containing compounds by structural class. Information on biological source, biological activity, and biosynthesis is included, if known. We also review the role of N-S bond functional groups as post-translational modifications of amino acids in proteins and peptides, emphasizing their role in the metabolism of the cell.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - William Bains
- Rufus Scientific , 37 The Moor, Melbourn, Royston, Herts SG8 6ED, U.K
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Department of Physics, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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24
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Lee J, Kang E, Kobayashi S, Homma T, Sato H, Seo H, Fujii J. The viability of primary hepatocytes is maintained under a low cysteine-glutathione redox state with a marked elevation in ophthalmic acid production. Exp Cell Res 2017; 361:178-191. [DOI: 10.1016/j.yexcr.2017.10.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 12/22/2022]
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25
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Borotto NB, McClory PJ, Martin BR, Håkansson K. Targeted Annotation of S-Sulfonylated Peptides by Selective Infrared Multiphoton Dissociation Mass Spectrometry. Anal Chem 2017; 89:8304-8310. [PMID: 28708386 DOI: 10.1021/acs.analchem.7b01461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein S-sulfinylation (R-SO2-) and S-sulfonylation (R-SO3-) are irreversible oxidative post-translational modifications of cysteine residues. Greater than 5% of cysteines are reported to occupy these higher oxidation states, which effectively inactivate the corresponding thiols and alter the electronic and physical properties of modified proteins. Such higher oxidation states are reached after excessive exposure to cellular oxidants, and accumulate across different disease states. Despite widespread and functionally relevant cysteine oxidation across the proteome, there are currently no robust methods to profile higher order cysteine oxidation. Traditional data-dependent liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods generally miss low-occupancy modifications in complex analyses. Here, we present a data-independent acquisition (DIA) LC/MS-based approach, leveraging the high IR absorbance of sulfoxides at 10.6 μm, for selective dissociation and discovery of S-sulfonated peptides. Across peptide standards and protein digests, we demonstrate selective infrared multiphoton dissociation (IRMPD) of S-sulfonated peptides in the background of unmodified peptides. This selective DIA IRMPD LC/MS-based approach allows identification and annotation of S-sulfonated peptides across complex mixtures while providing sufficient sequence information to localize the modification site.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Phillip J McClory
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Brent R Martin
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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26
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Gallego-Villar L, Hannibal L, Häberle J, Thöny B, Ben-Omran T, Nasrallah GK, Dewik AN, Kruger WD, Blom HJ. Cysteamine revisited: repair of arginine to cysteine mutations. J Inherit Metab Dis 2017; 40:555-567. [PMID: 28643139 PMCID: PMC5740875 DOI: 10.1007/s10545-017-0060-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/22/2017] [Accepted: 05/30/2017] [Indexed: 12/22/2022]
Abstract
Cysteamine is a small aminothiol endogenously derived from coenzyme A degradation. For some decades, synthetic cysteamine has been employed for the treatment of cystinosis, and new uses of the drug continue to emerge. In this review, we discuss the role of cysteamine in cellular and extracellular homeostasis and focus on the potential use of aminothiols to reconstitute the function of proteins harboring arginine (Arg) to cysteine (Cys) mutations, via repair of the Cys residue into a moiety that introduces an amino group, as seen in basic amino acid residues Lys and Arg. Cysteamine has been utilized in vitro and ex vivo in four different genetic disorders, and thus provides "proof of principle" that aminothiols can modify Cys residues. Other aminothiols such as mercaptoethylguanidine (MEG) with closer structural resemblance to the guanidinium moiety of Arg are under examination for their predicted enhanced capacity to reconstitute loss of function. Although the use of aminothiols holds clinical potential, more studies are required to refine specificity and treatment design. The efficacy of aminothiols to target proteins may vary substantially depending on their specific extracellular and intracellular locations. Redox potential, pH, and specific aminothiol abundance in each physiological compartment are expected to influence the reactivity and turnover of cysteamine and analogous drugs. Upcoming research will require the use of suitable cell and animal models featuring Arg to Cys mutations. Since, in general, Arg to Cys changes comprise about 8% of missense mutations, repair of this specific mutation may provide promising avenues for many genetic diseases.
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Affiliation(s)
- L Gallego-Villar
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, University Medical Centre Freiburg, Mathildenstrasse 1, 79106, Freiburg, Germany
| | - Luciana Hannibal
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, University Medical Centre Freiburg, Mathildenstrasse 1, 79106, Freiburg, Germany
| | - J Häberle
- University Children's Hospital and Children's Research Center, Zurich, Switzerland
| | - B Thöny
- University Children's Hospital and Children's Research Center, Zurich, Switzerland
| | - T Ben-Omran
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - G K Nasrallah
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Al-N Dewik
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - W D Kruger
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - H J Blom
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, University Medical Centre Freiburg, Mathildenstrasse 1, 79106, Freiburg, Germany.
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Smith MR, Fernandes J, Go YM, Jones DP. Redox dynamics of manganese as a mitochondrial life-death switch. Biochem Biophys Res Commun 2017; 482:388-398. [PMID: 28212723 PMCID: PMC5382988 DOI: 10.1016/j.bbrc.2016.10.126] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 12/16/2022]
Abstract
Sten Orrenius, M.D., Ph.D., pioneered many areas of cellular and molecular toxicology and made seminal contributions to our knowledge of oxidative stress and glutathione (GSH) metabolism, organellar functions and Ca+2-dependent mechanisms of cell death, and mechanisms of apoptosis. On the occasion of his 80th birthday, we summarize current knowledge on redox biology of manganese (Mn) and its role in mechanisms of cell death. Mn is found in all organisms and has critical roles in cell survival and death mechanisms by regulating Mn-containing enzymes such as manganese superoxide dismutase (SOD2) or affecting expression and activity of caspases. Occupational exposures to Mn cause "manganism", a Parkinson's disease-like condition of neurotoxicity, and experimental studies show that Mn exposure leads to accumulation of Mn in the brain, especially in mitochondria, and neuronal cell death occurs with features of an apoptotic mechanism. Interesting questions are why a ubiquitous metal that is essential for mitochondrial function would accumulate to excessive levels, cause increased H2O2 production and lead to cell death. Is this due to the interactions of Mn with other essential metals, such as iron, or with toxic metals, such as cadmium? Why is the Mn loading in the human brain so variable, and why is there such a narrow window between dietary adequacy and toxicity? Are non-neuronal tissues similarly vulnerable to insufficiency and excess, yet not characterized? We conclude that Mn is an important component of the redox interface between an organism and its environment and warrants detailed studies to understand the role of Mn as a mitochondrial life-death switch.
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Affiliation(s)
- Matthew Ryan Smith
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jolyn Fernandes
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Dean P Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA.
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Jones DP. Hydrogen peroxide and central redox theory for aerobic life: A tribute to Helmut Sies: Scout, trailblazer, and redox pioneer. Arch Biochem Biophys 2016; 595:13-8. [PMID: 27095208 PMCID: PMC4838774 DOI: 10.1016/j.abb.2015.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 09/05/2015] [Accepted: 09/05/2015] [Indexed: 02/07/2023]
Abstract
When Rafael Radi and I wrote about Helmut Sies for the Redox Pioneer series, I was disappointed that the Editor restricted us to the use of "Pioneer" in the title. My view is that Helmut was always ahead of the pioneers: He was a scout discovering paths for exploration and a trailblazer developing strategies and methods for discovery. I have known him for nearly 40 years and greatly enjoyed his collegiality as well as brilliance in scientific scholarship. He made monumental contributions to 20th century physiological chemistry beginning with his first measurement of H2O2 in rat liver. While continuous H2O2 production is dogma today, the concept of H2O2 production in mammalian tissues was largely buried for half a century. He continued this leadership in research on oxidative stress, GSH, selenium, and singlet oxygen, during the timeframe when physiological chemistry and biochemistry transitioned to contemporary 21st century systems biology. His impact has been extensive in medical and health sciences, especially in nutrition, aging, toxicology and cancer. I briefly summarize my interactions with Helmut, stressing our work together on the redox code, a set of principles to link mitochondrial respiration, bioenergetics, H2O2 metabolism, redox signaling and redox proteomics into central redox theory.
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Affiliation(s)
- Dean P Jones
- Department of Medicine, Emory University, Atlanta, GA 30322, USA.
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Padayachee L, Pillay CS. The thioredoxin system and not the Michaelis-Menten equation should be fitted to substrate saturation datasets from the thioredoxin insulin assay. Redox Rep 2016; 21:170-179. [PMID: 26102065 PMCID: PMC8900709 DOI: 10.1179/1351000215y.0000000024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Abstract
INTRODUCTION The thioredoxin system, consisting of thioredoxin reductase, thioredoxin and NADPH, is present in most living organisms and reduces a large array of target protein disulfides. OBJECTIVE The insulin reduction assay is commonly used to characterise thioredoxin activity in vitro, but it is not clear whether substrate saturation datasets from this assay should be fitted and modeled with the Michaelis-Menten equation (thioredoxin enzyme model), or fitted to the thioredoxin system with insulin reduction described by mass-action kinetics (redox couple model). METHODS We utilized computational modeling and in vitro assays to determine which of these approaches yield consistent and accurate kinetic parameter sets for insulin reduction. RESULTS Using computational modeling, we found that fitting to the redox couple model, rather than to the thioredoxin enzyme model, resulted in consistent parameter sets over a range of thioredoxin reductase concentrations. Furthermore, we established that substrate saturation in this assay was due to the progressive redistribution of the thioredoxin moiety into its oxidised form. We then confirmed these results in vitro using the yeast thioredoxin system. DISCUSSION This study shows how consistent parameter sets for thioredoxin activity can be obtained regardless of the thioredoxin reductase concentration used in the insulin reduction assay, and validates computational systems biology modeling studies that have described the thioredoxin system with the redox couple modeling approach.
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Affiliation(s)
- Letrisha Padayachee
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road Campus, Pietermaritzburg3201, South Africa
| | - Ché S. Pillay
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road Campus, Pietermaritzburg3201, South Africa
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Pillay CS, Eagling BD, Driscoll SRE, Rohwer JM. Quantitative measures for redox signaling. Free Radic Biol Med 2016; 96:290-303. [PMID: 27151506 DOI: 10.1016/j.freeradbiomed.2016.04.199] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/25/2016] [Accepted: 04/29/2016] [Indexed: 12/17/2022]
Abstract
Redox signaling is now recognized as an important regulatory mechanism for a number of cellular processes including the antioxidant response, phosphokinase signal transduction and redox metabolism. While there has been considerable progress in identifying the cellular machinery involved in redox signaling, quantitative measures of redox signals have been lacking, limiting efforts aimed at understanding and comparing redox signaling under normoxic and pathogenic conditions. Here we have outlined some of the accepted principles for redox signaling, including the description of hydrogen peroxide as a signaling molecule and the role of kinetics in conferring specificity to these signaling events. Based on these principles, we then develop a working definition for redox signaling and review a number of quantitative methods that have been employed to describe signaling in other systems. Using computational modeling and published data, we show how time- and concentration- dependent analyses, in particular, could be used to quantitatively describe redox signaling and therefore provide important insights into the functional organization of redox networks. Finally, we consider some of the key challenges with implementing these methods.
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Affiliation(s)
- Ché S Pillay
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road, Pietermaritzburg 3201, South Africa.
| | - Beatrice D Eagling
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road, Pietermaritzburg 3201, South Africa
| | - Scott R E Driscoll
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road, Pietermaritzburg 3201, South Africa
| | - Johann M Rohwer
- Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, 7602 Stellenbosch, South Africa
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To V, Dzananovic E, McKenna SA, O’Neil J. The Dynamic Landscape of the Full-Length HIV-1 Transactivator of Transcription. Biochemistry 2016; 55:1314-25. [DOI: 10.1021/acs.biochem.5b01178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vu To
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Edis Dzananovic
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A. McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Joe O’Neil
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Abstract
Oxidative stress is now a well-researched area with thousands of new articles appearing every year. We want to give the reader here an overview of the topics in biomedical and basic oxidative stress research which are covered by the authors of this thematic issue. We also want to give the newcomer a short introduction into some of the basic concepts, definitions and analytical procedures used in this field.
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Lennicke C, Rahn J, Heimer N, Lichtenfels R, Wessjohann LA, Seliger B. Redox proteomics: Methods for the identification and enrichment of redox-modified proteins and their applications. Proteomics 2015; 16:197-213. [PMID: 26508685 DOI: 10.1002/pmic.201500268] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/14/2015] [Accepted: 10/15/2015] [Indexed: 01/24/2023]
Abstract
PTMs are defined as covalent additions to functional groups of amino acid residues in proteins like phosphorylation, glycosylation, S-nitrosylation, acetylation, methylation, lipidation, SUMOylation as well as oxidation. Oxidation of proteins has been characterized as a double-edged sword. While oxidative modifications, in particular of cysteine residues, are widely involved in the regulation of cellular homeostasis, oxidative stress resulting in the oxidation of biomolecules along with the disruption of their biological functions can be associated with the development of diseases, such as cancer, diabetes, and neurodegenerative diseases, respectively. This is also the case for advanced glycation end products, which result from chemical reactions of keto compounds such as oxidized sugars with proteins. The role of oxidative modifications under physiological and pathophysiological conditions remains largely unknown. Recently, novel technologies have been established that allow the enrichment, identification, and characterization of specific oxidative PTMs (oxPTMs). This is essential to develop strategies to prevent and treat diseases that are associated with oxidative stress. Therefore this review will focus on (i) the methods and technologies, which are currently applied for the detection, identification, and quantification of oxPTMs including the design of high throughput approaches and (ii) the analyses of oxPTMs related to physiological and pathological conditions.
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Affiliation(s)
- Claudia Lennicke
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Jette Rahn
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Nadine Heimer
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Rudolf Lichtenfels
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | | | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
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Kramer PA, Duan J, Qian WJ, Marcinek DJ. The Measurement of Reversible Redox Dependent Post-translational Modifications and Their Regulation of Mitochondrial and Skeletal Muscle Function. Front Physiol 2015; 6:347. [PMID: 26635632 PMCID: PMC4658434 DOI: 10.3389/fphys.2015.00347] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/09/2015] [Indexed: 12/28/2022] Open
Abstract
Mitochondrial oxidative stress is a common feature of skeletal myopathies across multiple conditions; however, the mechanism by which it contributes to skeletal muscle dysfunction remains controversial. Oxidative damage to proteins, lipids, and DNA has received the most attention, yet an important role for reversible redox post-translational modifications (PTMs) in pathophysiology is emerging. The possibility that these PTMs can exert dynamic control of muscle function implicates them as a mechanism contributing to skeletal muscle dysfunction in chronic disease. Herein, we discuss the significance of thiol-based redox dependent modifications to mitochondrial, myofibrillar, and excitation-contraction (EC) coupling proteins with an emphasis on how these changes could alter skeletal muscle performance under chronically stressed conditions. A major barrier to a better mechanistic understanding of the role of reversible redox PTMs in muscle function is the technical challenges associated with accurately measuring the changes of site-specific redox PTMs. Here we will critically review current approaches with an emphasis on sample preparation artifacts, quantitation, and specificity. Despite these challenges, the ability to accurately quantify reversible redox PTMs is critical to understanding the mechanisms by which mitochondrial oxidative stress contributes to skeletal muscle dysfunction in chronic diseases.
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Affiliation(s)
- Philip A Kramer
- Department of Radiology, University of Washington Seattle, WA, USA
| | - Jicheng Duan
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - David J Marcinek
- Department of Radiology, University of Washington Seattle, WA, USA ; Department of Bioengineering, University of Washington Seattle, WA, USA
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Abstract
This review is focused on formation and biological significance of hydropersulfides, i.e. S-sulfhydration process. Biogenesis and properties of reactive sulfur species and their role in redox signaling are presented. The effect of S-sulfhydration on protein function is discussed. For many years reactive oxygen and nitrogen species (ROS and RNS) have been recognized as key messengers in the process of thiol-based redox regulation. Relatively recently, literature reports began to mention reactive sulfur species (RSS) and their role in thiol regulation. This review is focused on biogenesis and biological properties of RSS, including: hydropersulfides, polysulfides and hydrogen sulfide (H2S). Based on the most up-to-date literature data, the paper presents biological significance of S-sulfhydration process. In this reaction, sulfane sulfur is transferred to the–SH groups forming hydropersulfides. Protein cysteine residues, called ‘redox switches’ are susceptible to such reversible modifications. In line with the most recent reports, it was emphasized that sulfane sulfur-containing compounds (mainly hydrogen persulfides and polysulfides) are real and better mediators of S-sulfhydration-based signalling than H2S. We also overviewed proteins participating in the formation and transport of RSS and in mitochondrial H2S oxidation. In addition, we reviewed many reports about proteins unrelated to sulfur metabolism which are modified by S-sulfhydration that influences their catalytic activity. We also addressed the problem of the regulatory function of S-sulfhydration reaction in the activation of KATP channels (vasorelaxant) and transcription factors (e.g. NFκB) as well as in the mechanism of therapeutic action of garlic-derived sulfur compounds. Some aspects of comparison between RNS and RSS are also discussed in this review.
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Dwivedi G, Gran MA, Bagchi P, Kemp ML. Dynamic Redox Regulation of IL-4 Signaling. PLoS Comput Biol 2015; 11:e1004582. [PMID: 26562652 PMCID: PMC4642971 DOI: 10.1371/journal.pcbi.1004582] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/29/2015] [Indexed: 12/22/2022] Open
Abstract
Quantifying the magnitude and dynamics of protein oxidation during cell signaling is technically challenging. Computational modeling provides tractable, quantitative methods to test hypotheses of redox mechanisms that may be simultaneously operative during signal transduction. The interleukin-4 (IL-4) pathway, which has previously been reported to induce reactive oxygen species and oxidation of PTP1B, may be controlled by several other putative mechanisms of redox regulation; widespread proteomic thiol oxidation observed via 2D redox differential gel electrophoresis upon IL-4 treatment suggests more than one redox-sensitive protein implicated in this pathway. Through computational modeling and a model selection strategy that relied on characteristic STAT6 phosphorylation dynamics of IL-4 signaling, we identified reversible protein tyrosine phosphatase (PTP) oxidation as the primary redox regulatory mechanism in the pathway. A systems-level model of IL-4 signaling was developed that integrates synchronous pan-PTP oxidation with ROS-independent mechanisms. The model quantitatively predicts the dynamics of IL-4 signaling over a broad range of new redox conditions, offers novel hypotheses about regulation of JAK/STAT signaling, and provides a framework for interrogating putative mechanisms involving receptor-initiated oxidation. Incomplete reduction of oxygen during respiration results in the formation of highly reactive molecules known as reactive oxygen species (ROS) that react indiscriminately with cellular components and adversely affect cellular function. For a long time ROS were thought solely to be undesirable byproducts of respiration. Indeed, high levels of ROS are associated with a number of diseases. Despite these facts, antioxidants, agents that neutralize ROS, have not shown any clinical benefits when used as oral supplements. This paradox is partially explained by discoveries over the last two decades demonstrating that ROS are not always detrimental and may be essential for controlling physiological processes like cell signaling. However, the mechanisms by which ROS react with biomolecules are not well understood. In this work we have combined biological experiments with novel computational methods to identify the most important mechanisms of ROS-mediated regulation in the IL-4 signaling pathway of the immune system. We have also developed a detailed computer model of the IL-4 pathway and its regulation by ROS dependent and independent methods. Our work enhances the understanding of principles underlying regulation of cell signaling by ROS and has potential implications in advancing therapeutic methods targeting ROS and their adverse effects.
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Affiliation(s)
- Gaurav Dwivedi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - Margaret A. Gran
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - Pritha Bagchi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - Melissa L. Kemp
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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Frijhoff J, Winyard PG, Zarkovic N, Davies SS, Stocker R, Cheng D, Knight AR, Taylor EL, Oettrich J, Ruskovska T, Gasparovic AC, Cuadrado A, Weber D, Poulsen HE, Grune T, Schmidt HHHW, Ghezzi P. Clinical Relevance of Biomarkers of Oxidative Stress. Antioxid Redox Signal 2015; 23:1144-70. [PMID: 26415143 PMCID: PMC4657513 DOI: 10.1089/ars.2015.6317] [Citation(s) in RCA: 535] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
SIGNIFICANCE Oxidative stress is considered to be an important component of various diseases. A vast number of methods have been developed and used in virtually all diseases to measure the extent and nature of oxidative stress, ranging from oxidation of DNA to proteins, lipids, and free amino acids. RECENT ADVANCES An increased understanding of the biology behind diseases and redox biology has led to more specific and sensitive tools to measure oxidative stress markers, which are very diverse and sometimes very low in abundance. CRITICAL ISSUES The literature is very heterogeneous. It is often difficult to draw general conclusions on the significance of oxidative stress biomarkers, as only in a limited proportion of diseases have a range of different biomarkers been used, and different biomarkers have been used to study different diseases. In addition, biomarkers are often measured using nonspecific methods, while specific methodologies are often too sophisticated or laborious for routine clinical use. FUTURE DIRECTIONS Several markers of oxidative stress still represent a viable biomarker opportunity for clinical use. However, positive findings with currently used biomarkers still need to be validated in larger sample sizes and compared with current clinical standards to establish them as clinical diagnostics. It is important to realize that oxidative stress is a nuanced phenomenon that is difficult to characterize, and one biomarker is not necessarily better than others. The vast diversity in oxidative stress between diseases and conditions has to be taken into account when selecting the most appropriate biomarker.
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Affiliation(s)
- Jeroen Frijhoff
- 1 Faculty of Health, Medicine and Life Sciences, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University , Maastricht, the Netherlands
| | - Paul G Winyard
- 2 University of Exeter Medical School , Exeter, United Kingdom
| | | | - Sean S Davies
- 4 Department of Medicine, Vanderbilt University , Nashville, Tennessee.,5 Division of Clinical Pharmacology, Department of Pharmacology, Vanderbilt University , Nashville, Tennessee
| | - Roland Stocker
- 6 Vascular Biology Division, Victor Chang Cardiac Research Institute , Darlinghurst, New South Wales, Australia .,7 School of Medical Sciences, University of New South Wales , Sydney, New South Wales, Australia
| | - David Cheng
- 6 Vascular Biology Division, Victor Chang Cardiac Research Institute , Darlinghurst, New South Wales, Australia
| | - Annie R Knight
- 2 University of Exeter Medical School , Exeter, United Kingdom
| | | | - Jeannette Oettrich
- 1 Faculty of Health, Medicine and Life Sciences, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University , Maastricht, the Netherlands
| | - Tatjana Ruskovska
- 8 Faculty of Medical Sciences, Goce Delcev University , Stip, Macedonia
| | | | - Antonio Cuadrado
- 9 Centro de Investigación Biomedica en Red sobre Enfermedades Neurodegenerativas (CIBERNED) , ISCIII, Madrid, Spain .,10 Instituto de Investigaciones Biomedicas "Alberto Sols" UAM-CSIC , Madrid, Spain .,11 Instituto de Investigacion Sanitaria La Paz (IdiPaz) , Madrid, Spain .,12 Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid , Madrid, Spain
| | - Daniela Weber
- 13 Department of Molecular Toxicology, German Institute of Human Nutrition (DIfE) , Nuthetal, Germany
| | - Henrik Enghusen Poulsen
- 14 Faculty of Health Science, University of Copenhagen , Copenhagen, Denmark .,15 Bispebjerg-Frederiksberg Hospital , Copenhagen, Denmark
| | - Tilman Grune
- 13 Department of Molecular Toxicology, German Institute of Human Nutrition (DIfE) , Nuthetal, Germany
| | - Harald H H W Schmidt
- 1 Faculty of Health, Medicine and Life Sciences, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University , Maastricht, the Netherlands
| | - Pietro Ghezzi
- 16 Brighton and Sussex Medical School , Brighton, United Kingdom
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Womersley JS, Uys JD. S-Glutathionylation and Redox Protein Signaling in Drug Addiction. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 137:87-121. [PMID: 26809999 DOI: 10.1016/bs.pmbts.2015.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Drug addiction is a chronic relapsing disorder that comes at a high cost to individuals and society. Therefore understanding the mechanisms by which drugs exert their effects is of prime importance. Drugs of abuse increase the production of reactive oxygen and nitrogen species resulting in oxidative stress. This change in redox homeostasis increases the conjugation of glutathione to protein cysteine residues; a process called S-glutathionylation. Although traditionally regarded as a protective mechanism against irreversible protein oxidation, accumulated evidence suggests a more nuanced role for S-glutathionylation, namely as a mediator in redox-sensitive protein signaling. The reversible modification of protein thiols leading to alteration in function under different physiologic/pathologic conditions provides a mechanism whereby change in redox status can be translated into a functional response. As such, S-glutathionylation represents an understudied means of post-translational protein modification that may be important in the mechanisms underlying drug addiction. This review will discuss the evidence for S-glutathionylation as a redox-sensing mechanism and how this may be involved in the response to drug-induced oxidative stress. The function of S-glutathionylated proteins involved in neurotransmission, dendritic spine structure, and drug-induced behavioral outputs will be reviewed with specific reference to alcohol, cocaine, and heroin.
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Affiliation(s)
- Jacqueline S Womersley
- Department of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Joachim D Uys
- Department of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA.
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Differential alkylation-based redox proteomics--Lessons learnt. Redox Biol 2015; 6:240-252. [PMID: 26282677 PMCID: PMC4543216 DOI: 10.1016/j.redox.2015.08.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 01/11/2023] Open
Abstract
Cysteine is one of the most reactive amino acids. This is due to the electronegativity of sulphur atom in the side chain of thiolate group. It results in cysteine being present in several distinct redox forms inside the cell. Amongst these, reversible oxidations, S-nitrosylation and S-sulfenylation are crucial mediators of intracellular redox signalling, with known associations to health and disease. Study of their functionalities has intensified thanks to the development of various analytical strategies, with particular contribution from differential alkylation-based proteomics methods. Presented here is a critical evaluation of differential alkylation-based strategies for the analysis of S-nitrosylation and S-sulfenylation. The aim is to assess the current status and to provide insights for future directions in the dynamically evolving field of redox proteomics. To achieve that we collected 35 original research articles published since 2010 and analysed them considering the following parameters, (i) resolution of modification site, (ii) quantitative information, including correction of modification levels by protein abundance changes and determination of modification site occupancy, (iii) throughput, including the amount of starting material required for analysis. The results of this meta-analysis are the core of this review, complemented by issues related to biological models and sample preparation in redox proteomics, including conditions for free thiol blocking and labelling of target cysteine oxoforms.
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Evolutionary volatile Cysteines and protein disorder in the fast evolving tunicate Oikopleura dioica. Mar Genomics 2015; 24 Pt 1:47-54. [PMID: 26228312 DOI: 10.1016/j.margen.2015.07.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/20/2015] [Accepted: 07/20/2015] [Indexed: 12/14/2022]
Abstract
Cysteine (Cys) is regarded as the most conservative amino acid in nature, something that does not occur in the tunicate Oikopleura dioica, where this amino acid is one of the fastest evolving. In this work we analyze some of the causes of this intriguing absence of conservation. Considering the well-known stabilizing role of Cys, it was first investigated whether the lack of conservation was accompanied by an increase in intrinsic protein disorder. In contrast to expectations, it was found that O. dioica is the chordate that has the lowest levels of intrinsic disorder, while vertebrates (represented by Bos taurus) contain the most disordered proteins. Oikopleura proteins are shorter than their homologs in other Chordates (Ciona and B. taurus proteins are respectively 11% and 18% longer). This process of protein shortening was more intense in intrinsic disordered regions. As a result proteins became not only shorter but also more compact. It is also reported here that the conservation/divergence behavior of Cys depends on whether they are located in ordered or disordered regions. In the four species analyzed, disordered Cys are majorly (> 75%) not conserved at all. Ordered Cys instead, are much more free to diverge in Oikopleura than in the other chordates. We hypothesize that the preferential deletion of disordered regions resulted in a decreased protein disorder and a direct elimination (by deletion) of many ancestral Cys. Besides, the alterations (shortening or complete elimination) of some disordered regions (loops/random coils) probably promoted further Cys evolutionary volatility, because some ancestral Cys (and other amino acids which play a role in stability like Trp) located outside deleted regions became redundant due to the loss of their stabilizing partners.
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41
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Pyruvate dehydrogenase complex and nicotinamide nucleotide transhydrogenase constitute an energy-consuming redox circuit. Biochem J 2015; 467:271-80. [PMID: 25643703 DOI: 10.1042/bj20141447] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cellular proteins rely on reversible redox reactions to establish and maintain biological structure and function. How redox catabolic (NAD+/NADH) and anabolic (NADP+/NADPH) processes integrate during metabolism to maintain cellular redox homoeostasis, however, is unknown. The present work identifies a continuously cycling mitochondrial membrane potential (ΔΨm)-dependent redox circuit between the pyruvate dehydrogenase complex (PDHC) and nicotinamide nucleotide transhydrogenase (NNT). PDHC is shown to produce H2O2 in relation to reducing pressure within the complex. The H2O2 produced, however, is effectively masked by a continuously cycling redox circuit that links, via glutathione/thioredoxin, to NNT, which catalyses the regeneration of NADPH from NADH at the expense of ΔΨm. The net effect is an automatic fine-tuning of NNT-mediated energy expenditure to metabolic balance at the level of PDHC. In mitochondria, genetic or pharmacological disruptions in the PDHC-NNT redox circuit negate counterbalance changes in energy expenditure. At the whole animal level, mice lacking functional NNT (C57BL/6J) are characterized by lower energy-expenditure rates, consistent with their well-known susceptibility to diet-induced obesity. These findings suggest the integration of redox sensing of metabolic balance with compensatory changes in energy expenditure provides a potential mechanism by which cellular redox homoeostasis is maintained and body weight is defended during periods of positive and negative energy balance.
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Abstract
Metazoan genomes encode exposure memory systems to enhance survival and reproductive potential by providing mechanisms for an individual to adjust during lifespan to environmental resources and challenges. These systems are inherently redox networks, arising during evolution of complex systems with O2 as a major determinant of bioenergetics, metabolic and structural organization, defense, and reproduction. The network structure decreases flexibility from conception onward due to differentiation and cumulative responses to environment (exposome). The redox theory of aging is that aging is a decline in plasticity of genome–exposome interaction that occurs as a consequence of execution of differentiation and exposure memory systems. This includes compromised mitochondrial and bioenergetic flexibility, impaired food utilization and metabolic homeostasis, decreased barrier and defense capabilities and loss of reproductive fidelity and fecundity. This theory accounts for hallmarks of aging, including failure to maintain oxidative or xenobiotic defenses, mitochondrial integrity, proteostasis, barrier structures, DNA repair, telomeres, immune function, metabolic regulation and regenerative capacity. A redox interface connects an organism and its environment. Genetically encoded exposure memory systems evolved along with multicellularity in an O2-rich environment. Exposure memory allows an individual to adapt to resources and threats during lifespan. Aging is an irreversible decline in adaptability due to execution of exposure memory systems.
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Affiliation(s)
- Dean P Jones
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, GA 30322, USA.
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Lee JJ, Ha S, Kim HJ, Ha HJ, Lee HY, Lee KJ. Sulfhydryl-specific probe for monitoring protein redox sensitivity. ACS Chem Biol 2014; 9:2883-94. [PMID: 25354229 DOI: 10.1021/cb500839j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Reactive oxygen species (ROS) regulate various biological processes by modifying reactive cysteine residues in the proteins participating in the relevant signaling pathways. Identification of ROS target proteins requires specific reagents that identify ROS-sensitive cysteine sulfhydryls that differ from the known alkylating agents, iodoacetamide and N-ethylmaleimide, which react nonspecifically with oxidized cysteines including sulfenic and sulfinic acid. We designed and synthesized a novel reagent, methyl-3-nitro-4-(piperidin-1-ylsulfonyl)benzoate (NPSB-1), that selectively and specifically reacts with the sulfhydryl of cysteines in model compounds. We validated the specificity of this reagent by allowing it to react with recombinant proteins followed by peptide sequencing with nanoUPLC-ESI-q-TOF tandem mass spectrometry (MS/MS), and mutant studies employed it to identify cellular proteins containing redox-sensitive cysteine residues. We also obtained proteins from cells treated with various concentrations of hydrogen peroxide, labeled them with biotinylated NPSB-1 (NPSB-B), pulled them down with streptavidin beads, and identified them with MS/MS. We grouped these proteins into four families: (1) those having reactive cysteine residues easily oxidized by hydrogen peroxide, (2) those with cysteines reactive only under mild oxidative stress, (3) those with cysteines reactive only after exposure to oxidative stress, and (4) those with cysteines that are reactive regardless of oxidative stress. These results confirm that NPSBs can serve as novel chemical probes for specifically capturing reactive cysteine residues and as powerful tools for measuring their oxidative sensitivity and can help to understand the function of cysteine modifications in ROS-mediated signaling pathways.
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Affiliation(s)
- Jae-Jin Lee
- Graduate
School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea 120-750
| | - Sura Ha
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST), Daejeon, Korea 305-701
| | - Hee-Jung Kim
- Graduate
School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea 120-750
| | - Hyun Joo Ha
- Graduate
School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea 120-750
| | - Hee-Yoon Lee
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST), Daejeon, Korea 305-701
| | - Kong-Joo Lee
- Graduate
School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea 120-750
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Pan X, Liang Z, Li J, Wang S, Kong F, Xu K, Tang B. Active-Site-Matched Fluorescent Probes for Rapid and Direct Detection of Vicinal-Sulfydryl-Containing Peptides/Proteins in Living Cells. Chemistry 2014; 21:2117-22. [DOI: 10.1002/chem.201405349] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Indexed: 11/10/2022]
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45
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van der Vliet A, Janssen-Heininger YMW. Hydrogen peroxide as a damage signal in tissue injury and inflammation: murderer, mediator, or messenger? J Cell Biochem 2014; 115:427-35. [PMID: 24122865 DOI: 10.1002/jcb.24683] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 09/24/2013] [Indexed: 12/17/2022]
Abstract
Tissue injury and inflammation are associated with increased production of reactive oxygen species (ROS), which have the ability to induce oxidative injury to various biomolecules resulting in protein dysfunction, genetic instability, or cell death. However, recent observations indicate that formation of hydrogen peroxide (H2 O2 ) during tissue injury is also an essential feature of the ensuing wound healing response, and functions as an early damage signal to control several critical aspects of the wound healing process. Because innate oxidative wound responses must be tightly coordinated to avoid chronic inflammation or tissue injury, a more complete understanding is needed regarding the origins and dynamics of ROS production, and their critical biological targets. This prospect highlights the current experimental evidence implicating H2 O2 in early epithelial wound responses, and summarizes technical advances and approaches that may help distinguish its beneficial actions from its more deleterious actions in conditions of chronic tissue injury or inflammation.
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Affiliation(s)
- Albert van der Vliet
- Department of Pathology, College of Medicine, University of Vermont, Burlington, Vermont, 05405
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46
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Groitl B, Jakob U. Thiol-based redox switches. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1844:1335-43. [PMID: 24657586 PMCID: PMC4059413 DOI: 10.1016/j.bbapap.2014.03.007] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 03/04/2014] [Accepted: 03/11/2014] [Indexed: 11/30/2022]
Abstract
Regulation of protein function through thiol-based redox switches plays an important role in the response and adaptation to local and global changes in the cellular levels of reactive oxygen species (ROS). Redox regulation is used by first responder proteins, such as ROS-specific transcriptional regulators, chaperones or metabolic enzymes to protect cells against mounting levels of oxidants, repair the damage and restore redox homeostasis. Redox regulation of phosphatases and kinases is used to control the activity of select eukaryotic signaling pathways, making reactive oxygen species important second messengers that regulate growth, development and differentiation. In this review we will compare different types of reversible protein thiol modifications, elaborate on their structural and functional consequences and discuss their role in oxidative stress response and ROS adaptation. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.
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Affiliation(s)
- Bastian Groitl
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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Abstract
Tunicates have been extensively studied because of their crucial phylogenetic location (the closest living relatives of vertebrates) and particular developmental plan. Recent genome efforts have disclosed that tunicates are also remarkable in their genome organization and molecular evolutionary patterns. Here, we review these latter aspects, comparing the similarities and specificities of two model species of the group: Oikopleura dioica and Ciona intestinalis. These species exhibit great genome plasticity and Oikopleura in particular has undergone a process of extreme genome reduction and compaction that can be explained in part by gene loss, but is mostly due to other mechanisms such as shortening of intergenic distances and introns, and scarcity of mobile elements. In Ciona, genome reorganization was less severe being more similar to the other chordates in several aspects. Rates and patterns of molecular evolution are also peculiar in tunicates, being Ciona about 50% faster than vertebrates and Oikopleura three times faster. In fact, the latter species is considered as the fastest evolving metazoan recorded so far. Two processes of increase in evolutionary rates have taken place in tunicates. One of them is more extreme, and basically restricted to genes encoding regulatory proteins (transcription regulators, chromatin remodeling proteins, and metabolic regulators), and the other one is less pronounced but affects the whole genome. Very likely adaptive evolution has played a very significant role in the first, whereas the functional and/or evolutionary causes of the second are less clear and the evidence is not conclusive. The evidences supporting the incidence of increased mutation and less efficient negative selection are presented and discussed.
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Affiliation(s)
- Luisa Berná
- Sección Biomatemática, Facultad de Ciencias, Universidad de la República, Montevideo, UruguayUnidad de Biología Molecular, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Fernando Alvarez-Valin
- Sección Biomatemática, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Moreno ML, Escobar J, Izquierdo-Álvarez A, Gil A, Pérez S, Pereda J, Zapico I, Vento M, Sabater L, Marina A, Martínez-Ruiz A, Sastre J. Disulfide stress: a novel type of oxidative stress in acute pancreatitis. Free Radic Biol Med 2014; 70:265-77. [PMID: 24456905 DOI: 10.1016/j.freeradbiomed.2014.01.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/26/2013] [Accepted: 01/07/2014] [Indexed: 11/25/2022]
Abstract
Glutathione oxidation and protein glutathionylation are considered hallmarks of oxidative stress in cells because they reflect thiol redox status in proteins. Our aims were to analyze the redox status of thiols and to identify mixed disulfides and targets of redox signaling in pancreas in experimental acute pancreatitis as a model of acute inflammation associated with glutathione depletion. Glutathione depletion in pancreas in acute pancreatitis is not associated with any increase in oxidized glutathione levels or protein glutathionylation. Cystine and homocystine levels as well as protein cysteinylation and γ-glutamyl cysteinylation markedly rose in pancreas after induction of pancreatitis. Protein cysteinylation was undetectable in pancreas under basal conditions. Targets of disulfide stress were identified by Western blotting, diagonal electrophoresis, and proteomic methods. Cysteinylated albumin was detected. Redox-sensitive PP2A and tyrosine protein phosphatase activities diminished in pancreatitis and this loss was abrogated by N-acetylcysteine. According to our findings, disulfide stress may be considered a specific type of oxidative stress in acute inflammation associated with protein cysteinylation and γ-glutamylcysteinylation and oxidation of the pair cysteine/cystine, but without glutathione oxidation or changes in protein glutathionylation. Two types of targets of disulfide stress were identified: redox buffers, such as ribonuclease inhibitor or albumin, and redox-signaling thiols, which include thioredoxin 1, APE1/Ref1, Keap1, tyrosine and serine/threonine phosphatases, and protein disulfide isomerase. These targets exhibit great relevance in DNA repair, cell proliferation, apoptosis, endoplasmic reticulum stress, and inflammatory response. Disulfide stress would be a specific mechanism of redox signaling independent of glutathione redox status involved in inflammation.
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Affiliation(s)
- Mari-Luz Moreno
- Department of Physiology, School of Pharmacy, University of Valencia, 46100 Burjasot (Valencia), Spain
| | - Javier Escobar
- Department of Physiology, School of Pharmacy, University of Valencia, 46100 Burjasot (Valencia), Spain; Division of Neonatology, University Hospital Materno-Infantil La Fe, 46026 Valencia, Spain
| | - Alicia Izquierdo-Álvarez
- Servicio de Inmunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain
| | - Anabel Gil
- Department of Physiology, School of Pharmacy, University of Valencia, 46100 Burjasot (Valencia), Spain
| | - Salvador Pérez
- Department of Physiology, School of Pharmacy, University of Valencia, 46100 Burjasot (Valencia), Spain
| | - Javier Pereda
- Department of Physiology, School of Pharmacy, University of Valencia, 46100 Burjasot (Valencia), Spain
| | - Inés Zapico
- Servicio de Inmunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain; Centro de Biología Molecular Severo Ochoa, CSIC-Universidad Autónoma de Madrid, Madrid, Spain
| | - Máximo Vento
- Division of Neonatology, University Hospital Materno-Infantil La Fe, 46026 Valencia, Spain
| | - Luis Sabater
- Department of Surgery, University Clinic Hospital, University of Valencia, 46010 Valencia, Spain
| | - Anabel Marina
- Centro de Biología Molecular Severo Ochoa, CSIC-Universidad Autónoma de Madrid, Madrid, Spain
| | - Antonio Martínez-Ruiz
- Servicio de Inmunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain
| | - Juan Sastre
- Department of Physiology, School of Pharmacy, University of Valencia, 46100 Burjasot (Valencia), Spain.
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Pan KT, Chen YY, Pu TH, Chao YS, Yang CY, Bomgarden RD, Rogers JC, Meng TC, Khoo KH. Mass spectrometry-based quantitative proteomics for dissecting multiplexed redox cysteine modifications in nitric oxide-protected cardiomyocyte under hypoxia. Antioxid Redox Signal 2014; 20:1365-81. [PMID: 24152285 PMCID: PMC3936484 DOI: 10.1089/ars.2013.5326] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 08/22/2013] [Accepted: 09/07/2013] [Indexed: 11/13/2022]
Abstract
AIMS Distinctive states of redox-dependent cysteine (Cys) modifications are known to regulate signaling homeostasis under various pathophysiological conditions, including myocardial injury or protection in response to ischemic stress. Recent evidence further implicates a dynamic interplay among these modified forms following changes in cellular redox environment. However, a precise delineation of multiplexed Cys modifications in a cellular context remains technically challenging. To this end, we have now developed a mass spectrometry (MS)-based quantitative approach using a set of novel iodoacetyl-based Cys-reactive isobaric tags (irreversible isobaric iodoacetyl Cys-reactive tandem mass tag [iodoTMT]) endowed with unique irreversible Cys-reactivities. RESULTS We have established a sequential iodoTMT-switch procedure coupled with efficient immunoenrichment and advanced shotgun liquid chromatography-MS/MS analysis. This workflow allows us to differentially quantify the multiple redox-modified forms of a Cys site in the original cellular context. In one single analysis, we have identified over 260 Cys sites showing quantitative differences in multiplexed redox modifications from the total lysates of H9c2 cardiomyocytes experiencing hypoxia in the absence and presence of S-nitrosoglutathione (GSNO), indicative of a distinct pattern of individual susceptibility to S-nitrosylation or S-glutathionylation. Among those most significantly affected are proteins functionally implicated in hypoxic damage from which we showed that GSNO would protect. INNOVATION We demonstrate for the first time how quantitative analysis of various Cys-redox modifications occurring in biological samples can be performed precisely and simultaneously at proteomic levels. CONCLUSION We have not only developed a new approach to map global Cys-redoxomic regulation in vivo, but also provided new evidences implicating Cys-redox modifications of key molecules in NO-mediated ischemic cardioprotection.
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Affiliation(s)
- Kuan-Ting Pan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Yi-Yun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Tsung-Hsien Pu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, Taiwan
| | - Yu-Shu Chao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chun-Yi Yang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | | | | | - Tzu-Ching Meng
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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Abstract
Sulfhydryl-dependent formation of interprotein disulfide bonds in response to physiological oxidative stimuli is emerging as an important mechanism in the regulation of various biological activities. Soluble guanylyl cyclase (sGC) and cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG) are key enzymes for actions caused by cGMP-elevating agents, including nitric oxide (NO). Both sGC and PKG are dimers. The dimerization of sGC is obligatory for its activity, whereas the dimerization of PKG improving its signaling efficacy. sGC dimerization is decreased by endogenous and exogenous thiol reductants, associated with reduced cGMP elevation and attenuated vasodilatation to NO. The dimerization of PKG Iα is increased by oxidative stress, coincident with improved PKG signaling and augmented vasodilatation to NO. In coronary arteries, the dimerizations and activities of sGC and PKG are increased by hypoxia, accompanied by enhanced relaxation induced by NO. In contrast, the dimerizations and activities of these enzymes and NO-induced relaxation of pulmonary arteries are reduced by hypoxia. These opposite effects may result from divergent changes in the redox status of cytoplasmic reduced nicotinamide adenine dinucleotide phosphate between coronary and pulmonary arteries in response to hypoxia.
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