1
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Yurina LV, Vasilyeva AD, Gavrilina ES, Ivanov VS, Obydennyi SI, Chabin IA, Indeykina MI, Kononikhin AS, Nikolaev EN, Rosenfeld MA. A role of methionines in the functioning of oxidatively modified fibrinogen. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141013. [PMID: 38582358 DOI: 10.1016/j.bbapap.2024.141013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/05/2024] [Accepted: 04/02/2024] [Indexed: 04/08/2024]
Abstract
Posttranslational modifications in fibrinogen resulting from induced oxidation or oxidative stress in the organism can have deleterious influence on optimal functioning of fibrinogen, causing a disturbance in assembly and properties of fibrin. The protective mechanism supporting the ability of fibrinogen to function in ROS-generating environment remains completely unexplored. The effects of very low and moderately low HOCl/-OCl concentrations on fibrinogen oxidative modifications, the fibrin network structure as well as the kinetics of both fibrinogen-to-fibrin conversion and fibrin hydrolysis have been explored in the current study. As opposed to 25 Μm, HOCl/-OCl, 10 μM HOCl/-OCl did not affect the functional activity of fibrinogen. It is shown for the first time that a number of Met residues, AαMet476, AαMet517, AαMet584, BβMet367, γMet264, and γMet94, identified in 10 μM HOCl/-OCl fibrinogen by the HPLC-MS/MS method, operate as ROS scavengers, performing an important antioxidant function. In turn, this indicates that the fibrinogen structure is adapted to the detrimental action of ROS. The results obtained in our study provide evidence for a protective mechanism responsible for maintaining the structure and functioning of fibrinogen molecules in the bloodstream under conditions of mild and moderate oxidative stress.
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Affiliation(s)
- L V Yurina
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Russia.
| | - A D Vasilyeva
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Russia
| | - E S Gavrilina
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Russia
| | - V S Ivanov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Russia
| | - S I Obydennyi
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology of Ministry of Healthcare of the Russian Federation, Russia; Centre for Theoretical Problems of Physicochemical Pharmacology, Russia
| | - I A Chabin
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology of Ministry of Healthcare of the Russian Federation, Russia; Sechenov First Moscow State Medical University (Sechenov University), Russia
| | - M I Indeykina
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Russia; Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - A S Kononikhin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - E N Nikolaev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia.
| | - M A Rosenfeld
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Russia
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2
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van Wijk KJ, Leppert T, Sun Z, Kearly A, Li M, Mendoza L, Guzchenko I, Debley E, Sauermann G, Routray P, Malhotra S, Nelson A, Sun Q, Deutsch EW. Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas. J Proteome Res 2024; 23:185-214. [PMID: 38104260 DOI: 10.1021/acs.jproteome.3c00536] [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] [Indexed: 12/19/2023]
Abstract
This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource (build 2023-10) providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected post-translational modifications (PTMs), and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18,267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins, and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome: the "dark" proteome. This dark proteome is highly enriched for E3 ligases, transcription factors, and for certain (e.g., CLE, IDA, PSY) but not other (e.g., THIONIN, CAP) signaling peptides families. A machine learning model trained on RNA expression data and protein properties predicts the probability that proteins will be detected. The model aids in discovery of proteins with short half-life (e.g., SIG1,3 and ERF-VII TFs) and for developing strategies to identify the missing proteins. PeptideAtlas is linked to TAIR, tracks in JBrowse, and several other community proteomics resources.
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Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Tami Leppert
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Alyssa Kearly
- Boyce Thompson Institute, Ithaca, New York 14853, United States
| | - Margaret Li
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Luis Mendoza
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Isabell Guzchenko
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Erica Debley
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Georgia Sauermann
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Pratyush Routray
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Sagunya Malhotra
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
| | - Andrew Nelson
- Boyce Thompson Institute, Ithaca, New York 14853, United States
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853, United States
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington 98109, United States
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3
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Louati K, Maalej A, Kolsi F, Kallel R, Gdoura Y, Borni M, Hakim LS, Zribi R, Choura S, Sayadi S, Chamkha M, Mnif B, Khemakhem Z, Boudawara TS, Boudawara MZ, Safta F. Shotgun Proteomic-Based Approach with a Q-Exactive Hybrid Quadrupole-Orbitrap High-Resolution Mass Spectrometer for Protein Adductomics on a 3D Human Brain Tumor Neurospheroid Culture Model: The Identification of Adduct Formation in Calmodulin-Dependent Protein Kinase-2 and Annexin-A1 Induced by Pesticide Mixture. J Proteome Res 2023; 22:3811-3832. [PMID: 37906427 PMCID: PMC10696604 DOI: 10.1021/acs.jproteome.3c00484] [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: 08/03/2023] [Revised: 09/27/2023] [Accepted: 10/16/2023] [Indexed: 11/02/2023]
Abstract
Pesticides are increasingly used in combinations in crop protection, resulting in enhanced toxicities for various organisms. Although protein adductomics is challenging, it remains a powerful bioanalytical tool to check environmental exposure and characterize xenobiotic adducts as putative toxicity biomarkers with high accuracy, facilitated by recent advances in proteomic methodologies and a mass spectrometry high-throughput technique. The present study aims to predict the potential neurotoxicity effect of imidacloprid and λ-cyhalothrin insecticides on human neural cells. Our protocol consisted first of 3D in vitro developing neurospheroids derived from human brain tumors and then treatment by pesticide mixture. Furthermore, we adopted a bottom-up proteomic-based approach using nanoflow ultraperformance liquid chromatography coupled with a high-resolution mass spectrometer for protein-adduct analysis with prediction of altered sites. Two proteins were selected, namely, calcium-calmodulin-dependent protein kinase-II (CaMK2) and annexin-A1 (ANXA1), as key targets endowed with primordial roles. De novo sequencing revealed several adduct formations in the active site of 82-ANXA1 and 228-CaMK2 as a result of neurotoxicity, predicted by the added mass shifts for the structure of electrophilic precursors. To the best of our knowledge, our study is the first to adopt a proteomic-based approach to investigate in depth pesticide molecular interactions and their potential to adduct proteins which play a crucial role in the neurotoxicity mechanism.
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Affiliation(s)
- Kaouthar Louati
- Faculty
of Pharmacy, Laboratory of Pharmacology, Analytics & Galenic Drug
Development-LR12ES09, University of Monastir, Road Avicenne, Monastir 5000, Tunisia
| | - Amina Maalej
- Laboratory
of Environmental Bioprocesses, Centre of
Biotechnology of Sfax, Road of Sidi-Mansour, P.O. Box 1177, Sfax 3018, Tunisia
| | - Fatma Kolsi
- Department
of Neurosurgery, Habib Bourguiba University
Hospital, Road El Ain
km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Rim Kallel
- Laboratory
of Pathological Anatomy and Cytology, Habib
Bourguiba University Hospital, Road El Ain km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Yassine Gdoura
- Department
of Neurosurgery, Habib Bourguiba University
Hospital, Road El Ain
km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Mahdi Borni
- Department
of Neurosurgery, Habib Bourguiba University
Hospital, Road El Ain
km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Leila Sellami Hakim
- Laboratory
of Pathological Anatomy and Cytology, Habib
Bourguiba University Hospital, Road El Ain km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
| | - Rania Zribi
- Higher
Institute of Applied Studies to Humanities of Tunis (ISEAHT), University of Tunis, 11 Road of Jebel Lakdhar, Tunis 1005, Tunisia
| | - Sirine Choura
- Laboratory
of Environmental Bioprocesses, Centre of
Biotechnology of Sfax, Road of Sidi-Mansour, P.O. Box 1177, Sfax 3018, Tunisia
| | - Sami Sayadi
- Biotechnology
Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha 2713, Qatar
| | - Mohamed Chamkha
- Laboratory
of Environmental Bioprocesses, Centre of
Biotechnology of Sfax, Road of Sidi-Mansour, P.O. Box 1177, Sfax 3018, Tunisia
| | - Basma Mnif
- Department
of Bacteriology, Habib Bourguiba University
Hospital, Road El Ain
km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Zouheir Khemakhem
- Legal Medicine
Department, Habib Bourguiba University Hospital, Road El Ain km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Tahya Sellami Boudawara
- Laboratory
of Pathological Anatomy and Cytology, Habib
Bourguiba University Hospital, Road El Ain km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Mohamed Zaher Boudawara
- Department
of Neurosurgery, Habib Bourguiba University
Hospital, Road El Ain
km 1.5, Avenue of Ferdaous, Sfax 3089, Tunisia
- Faculty
of Medicine, Avenue of Majida Boulila, University
of sfax, Sfax 3029, Tunisia
| | - Fathi Safta
- Faculty
of Pharmacy, Laboratory of Pharmacology, Analytics & Galenic Drug
Development-LR12ES09, University of Monastir, Road Avicenne, Monastir 5000, Tunisia
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4
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Maurer J, Grouzmann E, Eugster PJ. Tutorial review for peptide assays: An ounce of pre-analytics is worth a pound of cure. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1229:123904. [PMID: 37832388 DOI: 10.1016/j.jchromb.2023.123904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
The recent increase in peptidomimetic-based medications and the growing interest in peptide hormones has brought new attention to the quantification of peptides for diagnostic purposes. Indeed, the circulating concentrations of peptide hormones in the blood provide a snapshot of the state of the body and could eventually lead to detecting a particular health condition. Although extremely useful, the quantification of such molecules, preferably by liquid chromatography coupled to mass spectrometry, might be quite tricky. First, peptides are subjected to hydrolysis, oxidation, and other post-translational modifications, and, most importantly, they are substrates of specific and nonspecific proteases in biological matrixes. All these events might continue after sampling, changing the peptide hormone concentrations. Second, because they include positively and negatively charged groups and hydrophilic and hydrophobic residues, they interact with their environment; these interactions might lead to a local change in the measured concentrations. A phenomenon such as nonspecific adsorption to lab glassware or materials has often a tremendous effect on the concentration and needs to be controlled with particular care. Finally, the circulating levels of peptides might be low (pico- or femtomolar range), increasing the impact of the aforementioned effects and inducing the need for highly sensitive instruments and well-optimized methods. Thus, despite the extreme diversity of these peptides and their matrixes, there is a common challenge for all the assays: the need to keep concentrations unchanged from sampling to analysis. While significant efforts are often placed on optimizing the analysis, few studies consider in depth the impact of pre-analytical steps on the results. By working through practical examples, this solution-oriented tutorial review addresses typical pre-analytical challenges encountered during the development of a peptide assay from the standpoint of a clinical laboratory. We provide tips and tricks to avoid pitfalls as well as strategies to guide all new developments. Our ultimate goal is to increase pre-analytical awareness to ensure that newly developed peptide assays produce robust and accurate results.
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Affiliation(s)
- Jonathan Maurer
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Eric Grouzmann
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Philippe J Eugster
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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5
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Kartsonakis IA, Vardakas P, Goulis P, Perkas N, Kyriazis ID, Skaperda Z, Tekos F, Charitidis CA, Kouretas D. Toxicity assessment of core-shell and superabsorbent polymers in cell-based systems. ENVIRONMENTAL RESEARCH 2023; 228:115772. [PMID: 36967000 DOI: 10.1016/j.envres.2023.115772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 05/16/2023]
Abstract
The identification of health risks arising from occupational exposure to submicron/nanoscale materials is of particular interest and toxicological investigations designed to assess their hazardous properties can provide valuable insights. The core-shell polymers poly (methyl methacrylate)@poly (methacrylic acid-co-ethylene glycol dimethacrylate) [PMMA@P (MAA-co-EGDMA)] and poly (n-butyl methacrylate-co-ethylene glycol dimethacrylate)@poly (methyl methacrylate) [P (nBMA-co-EGDMA)@PMMA] could be utilized for the debonding of coatings and for the encapsulation and targeted delivery of various compounds. The hybrid superabsorbent core-shell polymers poly (methacrylic acid-co-ethylene glycol dimethacrylate)@silicon dioxide [P (MAA-co-EGDMA)@SiO2] could be utilized as internal curing agents in cementitious materials. Therefore, the characterization of their toxicological profile is essential to ensure their safety throughout manufacturing and the life cycle of the final products. Based on the above, the purpose of the present study was to assess the acute toxic effects of the above mentioned polymers on cell viability and on cellular redox state in EA. hy926 human endothelial cells and in RAW264.7 mouse macrophages. According to our results, the examined polymers did not cause any acute toxic effects on cell viability after any administration. However, the thorough evaluation of a panel of redox biomarkers revealed that they affected cellular redox state in a cell-specific manner. As regards EA. hy926 cells, the polymers disrupted redox homeostasis and promoted protein carbonylation. Concerning RAW264.7 cells, P (nBMA-co-EGDMA)@PMMA caused disturbances in redox equilibrium and special emphasis was placed on the triphasic dose-response effect detected in lipid peroxidation. Finally, P (MAA-co-EGDMA)@SiO2 activated cellular adaptive mechanisms in order to prevent from oxidative damage.
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Affiliation(s)
- Ioannis A Kartsonakis
- Research Lab of Advanced, Composite, Nano-Materials and Nanotechnology, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou St. Zografos, 15780, Athens, Greece
| | - Periklis Vardakas
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500, Larissa, Greece
| | - Panagiotis Goulis
- Research Lab of Advanced, Composite, Nano-Materials and Nanotechnology, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou St. Zografos, 15780, Athens, Greece
| | - Nikolaos Perkas
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500, Larissa, Greece
| | - Ioannis D Kyriazis
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500, Larissa, Greece
| | - Zoi Skaperda
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500, Larissa, Greece
| | - Fotios Tekos
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500, Larissa, Greece
| | - Constantinos A Charitidis
- Research Lab of Advanced, Composite, Nano-Materials and Nanotechnology, School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou St. Zografos, 15780, Athens, Greece.
| | - Demetrios Kouretas
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500, Larissa, Greece.
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6
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van Wijk KJ, Leppert T, Sun Z, Kearly A, Li M, Mendoza L, Guzchenko I, Debley E, Sauermann G, Routray P, Malhotra S, Nelson A, Sun Q, Deutsch EW. Mapping the Arabidopsis thaliana proteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543322. [PMID: 37333403 PMCID: PMC10274743 DOI: 10.1101/2023.06.01.543322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected PTMs, and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for building the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome - the 'dark' proteome. This dark proteome is highly enriched for certain ( e.g. CLE, CEP, IDA, PSY) but not other ( e.g. THIONIN, CAP,) signaling peptides families, E3 ligases, TFs, and other proteins with unfavorable physicochemical properties. A machine learning model trained on RNA expression data and protein properties predicts the probability for proteins to be detected. The model aids in discovery of proteins with short-half life ( e.g. SIG1,3 and ERF-VII TFs) and completing the proteome. PeptideAtlas is linked to TAIR, JBrowse, PPDB, SUBA, UniProtKB and Plant PTM Viewer.
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7
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Schifano F, Dell'Acqua S, Nicolis S, Casella L, Monzani E. Interaction and Redox Chemistry between Iron, Dopamine, and Alpha-Synuclein C-Terminal Peptides. Antioxidants (Basel) 2023; 12:antiox12040791. [PMID: 37107166 PMCID: PMC10135331 DOI: 10.3390/antiox12040791] [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: 02/25/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
α-Synuclein (αS), dopamine (DA), and iron have a crucial role in the etiology of Parkinson's disease. The present study aims to investigate the interplay between these factors by analyzing the DA/iron interaction and how it is affected by the presence of the C-terminal fragment of αS (Ac-αS119-132) that represents the iron-binding domain. At high DA:Fe molar ratios, the formation of the [FeIII(DA)2]- complex prevents the interaction with αS peptides, whereas, at lower DA:Fe molar ratios, the peptide is able to compete with one of the two coordinated DA molecules. This interaction is also confirmed by HPLC-MS analysis of the post-translational modifications of the peptide, where oxidized αS is observed through an inner-sphere mechanism. Moreover, the presence of phosphate groups in Ser129 (Ac-αSpS119-132) and both Ser129 and Tyr125 (Ac-αSpYpS119-132) increases the affinity for iron(III) and decreases the DA oxidation rate, suggesting that this post-translational modification may assume a crucial role for the αS aggregation process. Finally, αS interaction with cellular membranes is another key aspect for αS physiology. Our data show that the presence of a membrane-like environment induced an enhanced peptide effect over both the DA oxidation and the [FeIII(DA)2]- complex formation and decomposition.
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Affiliation(s)
- Fabio Schifano
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
- IUSS School for Advanced Studies of Pavia, Palazzo del Broletto, Piazza della Vittoria 15, 27100 Pavia, Italy
| | - Simone Dell'Acqua
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Stefania Nicolis
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Luigi Casella
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Enrico Monzani
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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8
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Grill B, Pavkov-Keller T, Grininger C, Darnhofer B, Gruber K, Hall M, Schwab H, Steiner K. Engineering TM1459 for Stabilisation against Inactivation by Amino Acid Oxidation. CHEM-ING-TECH 2023. [DOI: 10.1002/cite.202200176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Birgit Grill
- Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Austria
| | - Tea Pavkov-Keller
- Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Austria
- University of Graz Institute of Molecular Biosciences Humboldtstraße 50 8010 Graz Austria
| | - Christoph Grininger
- University of Graz Institute of Molecular Biosciences Humboldtstraße 50 8010 Graz Austria
| | - Barbara Darnhofer
- Medical University of Graz Core Facility Mass Spectrometry Stiftingtalstraße 24 8010 Graz Austria
| | - Karl Gruber
- Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Austria
- University of Graz Institute of Molecular Biosciences Humboldtstraße 50 8010 Graz Austria
| | - Mélanie Hall
- University of Graz Institute of Chemistry Heinrichstraße 28 8010 Graz Austria
| | - Helmut Schwab
- Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Austria
- Graz University of Technology Institute of Molecular Biotechnology Petersgasse 14 8010 Graz Austria
| | - Kerstin Steiner
- Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz Austria
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9
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Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors. Nat Biotechnol 2023; 41:239-251. [PMID: 36203013 DOI: 10.1038/s41587-022-01464-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 08/09/2022] [Indexed: 11/08/2022]
Abstract
Post-translational modification (PTM) of antigens provides an additional source of specificities targeted by immune responses to tumors or pathogens, but identifying antigen PTMs and assessing their role in shaping the immunopeptidome is challenging. Here we describe the Protein Modification Integrated Search Engine (PROMISE), an antigen discovery pipeline that enables the analysis of 29 different PTM combinations from multiple clinical cohorts and cell lines. We expanded the antigen landscape, uncovering human leukocyte antigen class I binding motifs defined by specific PTMs with haplotype-specific binding preferences and revealing disease-specific modified targets, including thousands of new cancer-specific antigens that can be shared between patients and across cancer types. Furthermore, we uncovered a subset of modified peptides that are specific to cancer tissue and driven by post-translational changes that occurred in the tumor proteome. Our findings highlight principles of PTM-driven antigenicity, which may have broad implications for T cell-mediated therapies in cancer and beyond.
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10
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Clemen R, Arlt K, Miebach L, von Woedtke T, Bekeschus S. Oxidized Proteins Differentially Affect Maturation and Activation of Human Monocyte-Derived Cells. Cells 2022; 11:cells11223659. [PMID: 36429087 PMCID: PMC9688260 DOI: 10.3390/cells11223659] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
In cancer, antigen-presenting cells (APC), including dendritic cells (DCs), take up and process proteins to mount adaptive antitumor immune responses. This often happens in the context of inflamed cancer, where reactive oxygen species (ROS) are ubiquitous to modify proteins. However, the inflammatory consequences of oxidized protein uptake in DCs are understudied. To this end, we investigated human monocyte-derived cell surface marker expression and cytokine release profiles when exposed to oxidized and native proteins. Seventeen proteins were analyzed, including viral proteins (e.g., CMV and HBV), inflammation-related proteins (e.g., HO1 and HMGB1), matrix proteins (e.g., Vim and Coll), and vastly in the laboratory used proteins (e.g., BSA and Ova). The multifaceted nature of inflammation-associated ROS was mimicked using gas plasma technology, generating reactive species cocktails for protein oxidation. Fourteen oxidized proteins led to elevated surface marker expression levels of CD25, CD40, CD80, CD86, and MHC-II as well as strongly modified release of IL6, IL8, IL10, IL12, IL23, MCP-1, and TNFα compared to their native counterparts. Especially IL8, heme oxygenase 2, and vimentin oxidation gave pronounced effects. Furthermore, protein kinase phospho-array studies in monocyte-derived cells pulsed with native vs. oxidized IL8 and insulin showed enhanced AKT and RSK2 phosphorylation. In summary, our data provide for the first time an overview of the functional consequences of oxidized protein uptake by human monocyte-derived cells and could therefore be a starting point for exploiting such principle in anticancer therapy in the future.
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Affiliation(s)
- Ramona Clemen
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Kevin Arlt
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Lea Miebach
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
- Department of General, Thoracic, Vascular, and Visceral Surgery, Greifswald University Medical Center, Ferdinand-Sauerbruch-Str., 17475 Greifswald, Germany
| | - Thomas von Woedtke
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
- Institute for Hygiene and Environmental Medicine, Greifswald University Medical Center, Ferdinand-Sauerbruch-Str., 17475 Greifswald, Germany
| | - Sander Bekeschus
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
- Correspondence:
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11
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Garrido Ruiz D, Sandoval-Perez A, Rangarajan AV, Gunderson EL, Jacobson MP. Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation. Biochemistry 2022; 61:2165-2176. [PMID: 36161872 PMCID: PMC9583617 DOI: 10.1021/acs.biochem.2c00349] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cysteine side chains
can exist in distinct oxidation
states depending
on the pH and redox potential of the environment, and cysteine oxidation
plays important yet complex regulatory roles. Compared with the effects
of post-translational modifications such as phosphorylation, the effects
of oxidation of cysteine to sulfenic, sulfinic, and sulfonic acid
on protein structure and function remain relatively poorly characterized.
We present an analysis of the role of cysteine reactivity as a regulatory
factor in proteins, emphasizing the interplay between electrostatics
and redox potential as key determinants of the resulting oxidation
state. A review of current computational approaches suggests underdeveloped
areas of research for studying cysteine reactivity through molecular
simulations.
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Affiliation(s)
- Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Angelica Sandoval-Perez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Amith Vikram Rangarajan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Emma L Gunderson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
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12
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Chaiyarit S, Thongboonkerd V. Oxidized forms of uromodulin promote calcium oxalate crystallization and growth, but not aggregation. Int J Biol Macromol 2022; 214:542-553. [PMID: 35752338 DOI: 10.1016/j.ijbiomac.2022.06.132] [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: 03/26/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 11/19/2022]
Abstract
Roles of an abundant human urinary protein, uromodulin (UMOD), in kidney stone disease were previously controversial. Recently, we have demonstrated that oxidative modification reverses overall modulatory activity of whole urinary proteins, from inhibition to promotion of calcium oxalate (CaOx) stone-forming processes. We thus hypothesized that oxidation is one of the factors causing those previously controversial UMOD data on stone modulation. Herein, we addressed effects of performic-induced oxidation on CaOx crystal modulatory activity of UMOD. Sequence analyses revealed two EGF-like calcium-binding domains (65th-107th and 108th-149th), two other calcium-binding motifs (65th-92nd and 108th-135th), and three oxalate-binding motifs (199th-207th, 361st-368th and 601st-609th) in UMOD molecule. Analysis of tandem mass spectrometric dataset of whole urinary proteins confirmed marked increases in oxidation, dioxidation and trioxidation of UMOD in the performic-modified urine samples. UMOD was then purified from the normal urine and underwent performic-induced oxidative modification, which was confirmed by Oxyblotting. The oxidized UMOD significantly promoted CaOx crystallization and crystal growth, whereas the unmodified native UMOD inhibited CaOx crystal growth. However, the oxidized UMOD did not affect CaOx crystal aggregation. Therefore, our data indicate that oxidized forms of UMOD promote CaOx crystallization and crystal growth, which are the important processes for CaOx kidney stone formation.
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Affiliation(s)
- Sakdithep Chaiyarit
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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13
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The effect of hypochlorite- and peroxide-induced oxidation of plasminogen on damage to the structure and biological activity. Int J Biol Macromol 2022; 206:64-73. [DOI: 10.1016/j.ijbiomac.2022.02.128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 11/18/2022]
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14
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Attia MS, Youssef AO, Abdel-Sattar NA, Amin MA, Alharthi S, Mohamed EH, Mahmoud SA, Abou-Omar MN. A highly selective and sensitive spectrofluorimetric method for the assessment of 3-nitrotyrosine in serum using (Eu(TTA) 3Phen) photo probe. RSC Adv 2022; 12:4536-4542. [PMID: 35425515 PMCID: PMC8981050 DOI: 10.1039/d1ra07351f] [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: 10/02/2021] [Accepted: 01/22/2022] [Indexed: 11/21/2022] Open
Abstract
A simple, accurate and fast method was developed for the assessment of 3-nitrotyrosine as a biomarker for the early diagnosis of liver cirrhosis with minimal hepatic encephalopathy (MHE) using a (Eu(TTA)3Phen) photo probe. 3-Nitrotyrosine can remarkably quench the luminescence intensity of the (Eu(TTA)3Phen) complex in DMSO at pH = 9 and λem = 617 nm. The quenching of the luminescence intensity of (Eu(TTA)3Phen) complex particularly the electrical emission band at λem = 617 nm is used for the assessment of 3-nitrotyrosine in different serum samples of patients with liver cirrhosis. A simple, accurate and fast method was developed for the assessment of 3-nitrotyrosine as a biomarker for the early diagnosis of liver cirrhosis with minimal hepatic encephalopathy (MHE) using a (Eu(TTA)3Phen) photo probe.![]()
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Affiliation(s)
- Mohmed S Attia
- Chemistry Department, Faculty of Science, Ain Shams University Cairo 11566 Egypt
| | - Ahmed O Youssef
- Chemistry Department, Faculty of Science, Ain Shams University Cairo 11566 Egypt
| | - Nour A Abdel-Sattar
- Chemistry Department, Faculty of Science, Ain Shams University Cairo 11566 Egypt
| | - Mohammed A Amin
- Department of Chemistry, College of Science, Taif University P.O. Box 11099 Taif 21944 Saudi Arabia
| | - Sarah Alharthi
- Department of Chemistry, College of Science, Taif University P.O. Box 11099 Taif 21944 Saudi Arabia
| | - Ekram H Mohamed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, The British University in Egypt El Sherouk City Cairo Egypt
| | - Safwat A Mahmoud
- Physics Department, Faculty of Science, Northern Border University Arar Saudi Arabia
| | - Mona N Abou-Omar
- Department of Chemistry, Faculty of Women for Arts, Science and Education, Ain Shams University Cairo Egypt
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15
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Kavoor A, Kelly P, Ibba M. Escherichia coli alanyl-tRNA synthetase maintains proofreading activity and translational accuracy under oxidative stress. J Biol Chem 2022; 298:101601. [PMID: 35065077 PMCID: PMC8857464 DOI: 10.1016/j.jbc.2022.101601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that synthesize aminoacyl-tRNAs to facilitate translation of the genetic code. Quality control by aaRS proofreading and other mechanisms maintains translational accuracy, which promotes cellular viability. Systematic disruption of proofreading, as recently demonstrated for alanyl-tRNA synthetase (AlaRS), leads to dysregulation of the proteome and reduced viability. Recent studies showed that environmental challenges such as exposure to reactive oxygen species can also alter aaRS synthetic and proofreading functions, prompting us to investigate if oxidation might positively or negatively affect AlaRS activity. We found that while oxidation leads to modification of several residues in Escherichia coli AlaRS, unlike in other aaRSs, this does not affect proofreading activity against the noncognate substrates serine and glycine and only results in a 1.6-fold decrease in efficiency of cognate Ala-tRNAAla formation. Mass spectrometry analysis of oxidized AlaRS revealed that the critical proofreading residue in the editing site, Cys666, and three methionine residues (M217 in the active site, M658 in the editing site, and M785 in the C-Ala domain) were modified to cysteine sulfenic acid and methionine sulfoxide, respectively. Alanine scanning mutagenesis showed that none of the identified residues were solely responsible for the change in cognate tRNAAla aminoacylation observed under oxidative stress, suggesting that these residues may act as reactive oxygen species “sinks” to protect catalytically critical sites from oxidative damage. Combined, our results indicate that E. coli AlaRS proofreading is resistant to oxidative damage, providing an important mechanism of stress resistance that helps to maintain proteome integrity and cellular viability.
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Affiliation(s)
- Arundhati Kavoor
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, USA
| | - Paul Kelly
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, USA
| | - Michael Ibba
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Microbiology, The Ohio State University, Columbus, Ohio, USA; Schmid College of Science and Technology, Chapman University, Orange, California, USA.
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16
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Laroussi M, Bekeschus S, Keidar M, Bogaerts A, Fridman A, Lu XP, Ostrikov KK, Hori M, Stapelmann K, Miller V, Reuter S, Laux C, Mesbah A, Walsh J, Jiang C, Thagard SM, Tanaka H, Liu DW, Yan D, Yusupov M. Low Temperature Plasma for Biology, Hygiene, and Medicine: Perspective and Roadmap. IEEE TRANSACTIONS ON RADIATION AND PLASMA MEDICAL SCIENCES 2022. [DOI: 10.1109/trpms.2021.3135118] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Hipper E, Blech M, Hinderberger D, Garidel P, Kaiser W. Photo-Oxidation of Therapeutic Protein Formulations: From Radical Formation to Analytical Techniques. Pharmaceutics 2021; 14:72. [PMID: 35056968 PMCID: PMC8779573 DOI: 10.3390/pharmaceutics14010072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/25/2022] Open
Abstract
UV and ambient light-induced modifications and related degradation of therapeutic proteins are observed during manufacturing and storage. Therefore, to ensure product quality, protein formulations need to be analyzed with respect to photo-degradation processes and eventually protected from light exposure. This task usually demands the application and combination of various analytical methods. This review addresses analytical aspects of investigating photo-oxidation products and related mediators such as reactive oxygen species generated via UV and ambient light with well-established and novel techniques.
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Affiliation(s)
- Elena Hipper
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; (E.H.); (D.H.)
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany;
| | - Dariush Hinderberger
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; (E.H.); (D.H.)
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany;
| | - Wolfgang Kaiser
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany;
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18
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Proteomic and Bioinformatic Analysis of Decellularized Pancreatic Extracellular Matrices. Molecules 2021; 26:molecules26216740. [PMID: 34771149 PMCID: PMC8588251 DOI: 10.3390/molecules26216740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 01/15/2023] Open
Abstract
Tissue microenvironments are rich in signaling molecules. However, factors in the tissue matrix that can serve as tissue-specific cues for engineering pancreatic tissues have not been thoroughly identified. In this study, we performed a comprehensive proteomic analysis of porcine decellularized pancreatic extracellular matrix (dpECM). By profiling dpECM collected from subjects of different ages and genders, we showed that the detergent-free decellularization method developed in this study permits the preservation of approximately 62.4% more proteins than a detergent-based method. In addition, we demonstrated that dpECM prepared from young pigs contained approximately 68.5% more extracellular matrix proteins than those prepared from adult pigs. Furthermore, we categorized dpECM proteins by biological process, molecular function, and cellular component through gene ontology analysis. Our study results also suggested that the protein composition of dpECM is significantly different between male and female animals while a KEGG enrichment pathway analysis revealed that dpECM protein profiling varies significantly depending on age. This study provides the proteome of pancreatic decellularized ECM in different animal ages and genders, which will help identify the bioactive molecules that are pivotal in creating tissue-specific cues for engineering tissues in vitro.
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19
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van Wijk KJ, Leppert T, Sun Q, Boguraev SS, Sun Z, Mendoza L, Deutsch EW. The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. THE PLANT CELL 2021; 33:3421-3453. [PMID: 34411258 PMCID: PMC8566204 DOI: 10.1093/plcell/koab211] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/13/2021] [Indexed: 05/02/2023]
Abstract
We developed a resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis thaliana proteome, such as the significance of protein splice forms and post-translational modifications (PTMs), or simply to obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) data collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical, and biological metadata. Nearly 40 million out of ∼143 million MS/MS (tandem MS) spectra were matched to the reference genome Araport11, identifying ∼0.5 million unique peptides and 17,858 uniquely identified proteins (only isoform per gene) at the highest confidence level (false discovery rate 0.0004; 2 non-nested peptides ≥9 amino acid each), assigned canonical proteins, and 3,543 lower-confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified that were generated from pseudogenes, alternative start, stops, and/or splice variants, and small Open Reading Frames; these features should be considered when updating the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB, and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS/MS data.
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Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, USA
- Authors for correspondence: (K.J.V.W.), (E.W.D.)
| | - Tami Leppert
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853, USA
| | - Sascha S Boguraev
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, USA
| | - Zhi Sun
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Luis Mendoza
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
| | - Eric W Deutsch
- Institute for Systems Biology (ISB), Seattle, Washington 98109, USA
- Authors for correspondence: (K.J.V.W.), (E.W.D.)
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20
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Abstract
Protein oxidation is a topic of indisputable scientific interest given the impact of oxidized proteins on food quality and safety. Carbonylation is regarded as one of the most notable post-translational modifications in proteins and yet, this reaction and its consequences are poorly understood. From a mechanistic perspective, primary protein carbonyls (i.e. α-aminoadipic and γ-glutamic semialdehydes) have been linked to radical-mediated oxidative stress, but recent studies emphasize the role alternative carbonylation pathways linked to the Maillard reaction. Secondary protein carbonyls are introduced in proteins via covalent linkage of lipid carbonyls (i.e. protein-bound malondialdehyde). The high reactivity of protein carbonyls in foods and other biological systems indicates the intricate chemistry of these species and urges further research to provide insight into these molecular mechanisms and pathways. In particular, protein carbonyls are involved in the formation of aberrant and dysfunctional protein aggregates, undergo further oxidation to yield carboxylic acids of biological relevance and establish interactions with other biomolecules such as oxidizing lipids and phytochemicals. From a methodological perspective, the routine dinitrophenylhydrazine (DNPH) method is criticized not only for the lack of accuracy and consistency but also authors typically perform a poor interpretation of DNPH results, which leads to misleading conclusions. From a practical perspective, the biological relevance of protein carbonyls in the field of food science and nutrition is still a topic of debate. Though the implication of carbonylation on impaired protein functionality and poor protein digestibility is generally recognized, the underlying mechanism of such connections requires further clarification. From a medical perspective, protein carbonyls are highlighted as markers of protein oxidation, oxidative stress and disease. Yet, the specific role of specific protein carbonyls in the onset of particular biological impairments needs further investigations. Recent studies indicates that regardless of the origin (in vivo or dietary) protein carbonyls may act as signalling molecules which activate not only the endogenous antioxidant defences but also implicate the immune system. The present paper concisely reviews the most recent advances in this topic to identify, when applicable, potential fields of interest for future studies.
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21
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Chaiyarit S, Thongboonkerd V. Oxidative Modifications Switch Modulatory Activities of Urinary Proteins From Inhibiting to Promoting Calcium Oxalate Crystallization, Growth, and Aggregation. Mol Cell Proteomics 2021; 20:100151. [PMID: 34562649 PMCID: PMC8551538 DOI: 10.1016/j.mcpro.2021.100151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 11/26/2022] Open
Abstract
The incidence/prevalence of kidney stone disease has been increasing around the globe, but its pathogenic mechanisms remained unclear. We evaluated effects of oxidative modifications of urinary proteins on calcium oxalate (CaOx) stone formation processes. Urinary proteins derived from 20 healthy individuals were modified by performic oxidation, and the presence of oxidatively modified urinary proteins was verified, quantified, and characterized by Oxyblot assay and tandem MS (nanoLC-electrospray ionization-linear trap quadrupole-Orbitrap-MS/MS). Subsequently, activities of oxidatively modified urinary proteins on CaOx stone formation processes were examined. Oxyblot assay confirmed the marked increase in protein oxidation level in the modified urine. NanoLC-electrospray ionization-linear trap quadrupole-Orbitrap-MS/MS identified a total of 193 and 220 urinary proteins in nonmodified and modified urine samples, respectively. Among these, there were 1121 and 5297 unambiguous oxidatively modified peptides representing 42 and 136 oxidatively modified proteins in the nonmodified and modified urine samples, respectively. Crystal assays revealed that oxidatively modified urinary proteins significantly promoted CaOx crystallization, crystal growth, and aggregation. By contrast, the nonmodified urinary proteins had inhibitory activities. This is the first direct evidence demonstrating that oxidative modifications of urinary proteins increase the risk of kidney stone disease by switching their modulatory activities from inhibiting to promoting CaOx crystallization, crystal growth, and aggregation.
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Affiliation(s)
- Sakdithep Chaiyarit
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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22
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Coremans C, Delporte C, Cotton F, Van De Borne P, Boudjeltia KZ, Van Antwerpen P. Mass Spectrometry for the Monitoring of Lipoprotein Oxidations by Myeloperoxidase in Cardiovascular Diseases. Molecules 2021; 26:molecules26175264. [PMID: 34500696 PMCID: PMC8434463 DOI: 10.3390/molecules26175264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 01/14/2023] Open
Abstract
Oxidative modifications of HDLs and LDLs by myeloperoxidase (MPO) are regularly mentioned in the context of atherosclerosis. The enzyme adsorbs on protein moieties and locally produces oxidizing agents to modify specific residues on apolipoproteins A-1 and B-100. Oxidation of lipoproteins by MPO (Mox) leads to dysfunctional Mox-HDLs associated with cholesterol-efflux deficiency, and Mox-LDLs that are no more recognized by the LDL receptor and become proinflammatory. Several modification sites on apoA-1 and B-100 that are specific to MPO activity are described in the literature, which seem relevant in patients with cardiovascular risk. The most appropriate analytical method to assess these modifications is based on liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). It enables the oxidized forms of apoA-1and apoB-100 to be quantified in serum, in parallel to a quantification of these apolipoproteins. Current standard methods to quantify apolipoproteins are based on immunoassays that are well standardized with good analytical performances despite the cost and the heterogeneity of the commercialized kits. Mass spectrometry can provide simultaneous measurements of quantity and quality of apolipoproteins, while being antibody-independent and directly detecting peptides carrying modifications for Mox-HDLs and Mox-LDLs. Therefore, mass spectrometry is a potential and reliable alternative for apolipoprotein quantitation.
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Affiliation(s)
- Catherine Coremans
- RD3-Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université Libre de Bruxelles, 1050 Brussels, Belgium; (C.D.); (P.V.A.)
- Correspondence: ; Tel.: +32-2-650-5331
| | - Cédric Delporte
- RD3-Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université Libre de Bruxelles, 1050 Brussels, Belgium; (C.D.); (P.V.A.)
| | - Frédéric Cotton
- Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Department of Clinical Chemistry, Université Libre de Bruxelles (ULB), 1000 Brussels, Belgium;
| | - Phillipe Van De Borne
- Department of Cardiology Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium;
| | - Karim Zouaoui Boudjeltia
- Laboratory of Experimental Medicine (ULB 222 Unit), CHU-Charleroi, ISPPC Hôpital Vésale, Université Libre de Bruxelles, 6110 Montigny-Le-Tilleul, Belgium;
| | - Pierre Van Antwerpen
- RD3-Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université Libre de Bruxelles, 1050 Brussels, Belgium; (C.D.); (P.V.A.)
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23
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Joyner PM. Protein Adducts and Protein Oxidation as Molecular Mechanisms of Flavonoid Bioactivity. Molecules 2021; 26:molecules26165102. [PMID: 34443698 PMCID: PMC8401221 DOI: 10.3390/molecules26165102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 02/05/2023] Open
Abstract
There are tens of thousands of scientific papers about flavonoids and their impacts on human health. However, despite the vast amount of energy that has been put toward studying these compounds, a unified molecular mechanism that explains their bioactivity remains elusive. One contributing factor to the absence of a general mechanistic explanation of their bioactivity is the complexity of flavonoid chemistry in aqueous solutions at neutral pH. Flavonoids have acidic protons, are redox active, and frequently auto-oxidize to produce an array of degradation products including electrophilic quinones. Flavonoids are also known to interact with specificity and high affinity with a variety of proteins, and there is evidence that some of these interactions may be covalent. This review summarizes the mechanisms of flavonoid oxidation in aqueous solutions at neutral pH and proposes the formation of protein-flavonoid adducts or flavonoid-induced protein oxidation as putative mechanisms of flavonoid bioactivity in cells. Nucleophilic residues in proteins may be able to form covalent bonds with flavonoid quinones; alternatively, specific amino acid residues such as cysteine, methionine, or tyrosine in proteins could be oxidized by flavonoids. In either case, these protein-flavonoid interactions would likely occur at specific binding sites and the formation of these types of products could effectively explain how flavonoids modify proteins in cells to induce downstream biochemical and cellular changes.
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Affiliation(s)
- P Matthew Joyner
- Natural Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, CA 90263, USA
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24
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Baumans F, Hanozin E, Baiwir D, Decroo C, Wattiez R, De Pauw E, Eppe G, Mazzucchelli G. Liquid chromatography setup-dependent artefactual methionine oxidation of peptides: The importance of an adapted quality control process. J Chromatogr A 2021; 1654:462449. [PMID: 34399143 DOI: 10.1016/j.chroma.2021.462449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/26/2022]
Abstract
In both biologics quality control experiments and protein post-translational modification studies, the analytical system used is not supposed to bring any artefactual modifications which could impair the results. In this work, we investigated oxidation of methionine-containing peptides during reversed-phase (RP) chromatographic separation. We first used a synthetic methionine-containing peptide to evaluate this artefactual phenomenon and then considered more complex samples (i.e., plasma and HeLa protein digests). The methionine oxidation levels of the peptides were systematically assessed and compared for the long-term use of the analytical column, the sample trapping time, the gradient length, the sample load and the nature of the stationary phase (HSS T3 from Waters, YMC Triart C18 from YMC Europe GmbH and BEH130 C18 from Waters). In addition to the oxidation of methionine in solution, we observed on the HSS T3 and the BEH130 stationary phases an additional broad peak corresponding to an on-column oxidized species. Considering the HSS T3 phase, our results highlight that the on-column oxidation level significantly increases with the age of the analytical column and the gradient length and reaches 56 % when a 1-year-old column set is used with a 180 min-long LC method. These levels go to 0 % and 18 % for the YMC Triart C18 and the BEH130 C18 phases respectively. Interestingly, the on-column oxidation proportion decreases as the injected sample load increases suggesting the presence of a discrete number of oxidation sites within the stationary phase of the analytical column. Those findings observed in different laboratories using distinct set of columns, albeit to varying degrees, strengthen the need for a standard of methionine-containing peptide that could be used as a quality control to appraise the status of the liquid chromatographic columns.
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Affiliation(s)
- France Baumans
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Emeline Hanozin
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Dominique Baiwir
- GIGA Proteomics Facility, University of Liege, Liege 4000, Belgium
| | - Corentin Decroo
- Proteomics and Microbiology Laboratory, University of Mons, Mons 7000, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, University of Mons, Mons 7000, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liege, Liege 4000, Belgium.
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Parenteral Nutrition and Oxidant Load in Neonates. Nutrients 2021; 13:nu13082631. [PMID: 34444799 PMCID: PMC8401055 DOI: 10.3390/nu13082631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/19/2021] [Accepted: 07/27/2021] [Indexed: 01/05/2023] Open
Abstract
Neonates with preterm, gastrointestinal dysfunction and very low birth weights are often intolerant to oral feeding. In such infants, the provision of nutrients via parenteral nutrition (PN) becomes necessary for short-term survival, as well as long-term health. However, the elemental nutrients in PN can be a major source of oxidants due to interactions between nutrients, imbalances of anti- and pro-oxidants, and environmental conditions. Moreover, neonates fed PN are at greater risk of oxidative stress, not only from dietary sources, but also because of immature antioxidant defences. Various interventions can lower the oxidant load in PN, including the supplementation of PN with antioxidant vitamins, glutathione, additional arginine and additional cysteine; reduced levels of pro-oxidant nutrients such as iron; protection from light and oxygen; and proper storage temperature. This narrative review of published data provides insight to oxidant molecules generated in PN, nutrient sources of oxidants, and measures to minimize oxidant levels.
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Kurhaluk N, Tkachenko H, Lukash O. Photoperiod-induced alterations in biomarkers of oxidative stress and biochemical pathways in rats of different ages: Focus on individual physiological reactivity. Chronobiol Int 2021; 38:1673-1691. [PMID: 34121553 DOI: 10.1080/07420528.2021.1939364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Effects of photoperiodicity caused by both the age and individual physiological reactivity estimated by resistance to hypobaric hypoxia on the levels of lipid peroxidation, protein oxidation (aldehydic and ketonic derivatives), total antioxidant capacity, activities of antioxidant enzymes (superoxide dismutase, catalase, glutathione peroxidase, and glutathione reductase), and biochemical parameters of aerobic and anaerobic pathways in hepatic tissue depending on the blood melatonin level were studied. The study was carried out on 96 6- and 21-month-old male rats divided into hypoxia resistance groups (LR, low resistance, HR, high resistance). The analyses were conducted at four photoperiods: winter (January), spring (March), summer (July), and autumn (October). Our results indicate a significant effect of melatonin, i.e. over 80%, revealed by the complete statistical model of the studied biomarkers of oxidative stress and oxygen-dependent parameters of metabolism. The effects of melatonin vary with age and between photoperiods, which in turn was determined by individual physiological reactivity. In terms of the photoperiods, the melatonin content in the group of the adult animals with low resistance to hypoxia decreased from winter to summer. In a group of old animals in comparison with adults, the melatonin content in all the studied photoperiods was much lower as well, regardless of their hypoxia resistance. In the group of old animals with low resistance to hypoxia, the melatonin content decreased throughout the photoperiods as follows: winter, autumn, summer, and spring. As can be concluded, spring is a critical period for old animals, particularly those with low hypoxia resistance. The important role of melatonin in these processes was also confirmed by our correlation analysis between oxidative stress biomarkers, energy-related metabolites, and antioxidant enzymes in the hepatic tissue of rats of different ages, with different resistance to hypoxia, and in different photoperiods. The melatonin concentration in the blood of highly resistant rats was higher than in those with low resistance to hypoxia. Melatonin determines the individual constitutional level of resistance to hypoxia and is responsible for individual enzymatic antioxidative responses, depending on the four photoperiods. Our studies have shown that melatonin levels are related to the redox characteristics of antioxidant defenses against lipid peroxidation and oxidative modification of proteins in old rats with low resistance to hypoxia, compared to a group of highly resistant adults. Finally, the melatonin-related mechanisms of antioxidative protection depend on metabolic processes in hepatic tissue and exhibit photoperiodical variability in adult and old rats.
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Affiliation(s)
- Natalia Kurhaluk
- Department of Zoology and Animal Physiology, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, Słupsk, Poland
| | - Halyna Tkachenko
- Department of Zoology and Animal Physiology, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, Słupsk, Poland
| | - Oleksandr Lukash
- Department of Ecology and Nature Protection, T.G. Shevchenko National University "Chernihiv Collegium", Chernihiv, Ukraine
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Kehm R, Baldensperger T, Raupbach J, Höhn A. Protein oxidation - Formation mechanisms, detection and relevance as biomarkers in human diseases. Redox Biol 2021; 42:101901. [PMID: 33744200 PMCID: PMC8113053 DOI: 10.1016/j.redox.2021.101901] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/06/2021] [Accepted: 02/12/2021] [Indexed: 12/16/2022] Open
Abstract
Generation of reactive oxygen species and related oxidants is an inevitable consequence of life. Proteins are major targets for oxidation reactions, because of their rapid reaction rates with oxidants and their high abundance in cells, extracellular tissues, and body fluids. Additionally, oxidative stress is able to degrade lipids and carbohydrates to highly reactive intermediates, which eventually attack proteins at various functional sites. Consequently, a wide variety of distinct posttranslational protein modifications is formed by protein oxidation, glycoxidation, and lipoxidation. Reversible modifications are relevant in physiological processes and constitute signaling mechanisms ("redox signaling"), while non-reversible modifications may contribute to pathological situations and several diseases. A rising number of publications provide evidence for their involvement in the onset and progression of diseases as well as aging processes. Certain protein oxidation products are chemically stable and formed in large quantity, which makes them promising candidates to become biomarkers of oxidative damage. Moreover, progress in the development of detection and quantification methods facilitates analysis time and effort and contributes to their future applicability in clinical routine. The present review outlines the most important classes and selected examples of oxidative protein modifications, elucidates the chemistry beyond their formation and discusses available methods for detection and analysis. Furthermore, the relevance and potential of protein modifications as biomarkers in the context of disease and aging is summarized.
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Affiliation(s)
- Richard Kehm
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558, Nuthetal, Germany.
| | - Tim Baldensperger
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558, Nuthetal, Germany.
| | - Jana Raupbach
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558, Nuthetal, Germany.
| | - Annika Höhn
- Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558, Nuthetal, Germany; German Center for Diabetes Research (DZD), 85764, Muenchen-Neuherberg, Germany.
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Clemen R, Freund E, Mrochen D, Miebach L, Schmidt A, Rauch BH, Lackmann J, Martens U, Wende K, Lalk M, Delcea M, Bröker BM, Bekeschus S. Gas Plasma Technology Augments Ovalbumin Immunogenicity and OT-II T Cell Activation Conferring Tumor Protection in Mice. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003395. [PMID: 34026437 PMCID: PMC8132054 DOI: 10.1002/advs.202003395] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/22/2021] [Indexed: 05/04/2023]
Abstract
Reactive oxygen species (ROS/RNS) are produced during inflammation and elicit protein modifications, but the immunological consequences are largely unknown. Gas plasma technology capable of generating an unmatched variety of ROS/RNS is deployed to mimic inflammation and study the significance of ROS/RNS modifications using the model protein chicken ovalbumin (Ova vs oxOva). Dynamic light scattering and circular dichroism spectroscopy reveal structural modifications in oxOva compared to Ova. T cells from Ova-specific OT-II but not from C57BL/6 or SKH-1 wild type mice presents enhanced activation after Ova addition. OxOva exacerbates this activation when administered ex vivo or in vivo, along with an increased interferon-gamma production, a known anti-melanoma agent. OxOva vaccination of wild type mice followed by inoculation of syngeneic B16F10 Ova-expressing melanoma cells shows enhanced T cell number and activation, decreased tumor burden, and elevated numbers of antigen-presenting cells when compared to their Ova-vaccinated counterparts. Analysis of oxOva using mass spectrometry identifies three hot spots regions rich in oxidative modifications that are associated with the increased T cell activation. Using Ova as a model protein, the findings suggest an immunomodulating role of multi-ROS/RNS modifications that may spur novel research lines in inflammation research and for vaccination strategies in oncology.
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Affiliation(s)
- Ramona Clemen
- ZIK plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix‐Hausdorff‐Str. 2Greifswald17489Germany
| | - Eric Freund
- ZIK plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix‐Hausdorff‐Str. 2Greifswald17489Germany
- Department of GeneralVisceralThoracicand Vascular SurgeryUniversity Medicine GreifswaldSauerbruchstr. DZ7Greifswald17475Germany
| | - Daniel Mrochen
- ZIK plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix‐Hausdorff‐Str. 2Greifswald17489Germany
- Department of ImmunologyUniversity Medicine GreifswaldSauerbruchstr. DZ7Greifswald17475Germany
| | - Lea Miebach
- ZIK plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix‐Hausdorff‐Str. 2Greifswald17489Germany
- Department of GeneralVisceralThoracicand Vascular SurgeryUniversity Medicine GreifswaldSauerbruchstr. DZ7Greifswald17475Germany
| | - Anke Schmidt
- ZIK plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix‐Hausdorff‐Str. 2Greifswald17489Germany
| | - Bernhard H. Rauch
- Institute of Pharmacology (C_Dat)University Medicine GreifswaldFelix‐Hausdorff‐Str. 1Greifswald17489Germany
| | - Jan‐Wilm Lackmann
- CECAD proteomics facilityUniversity of CologneJoseph‐Stelzmann‐Str. 26Cologne50931Germany
| | - Ulrike Martens
- ZIK HIKEUniversity of GreifswaldFleischmannstr. 42–44Greifswald17489Germany
- Institute of BiochemistryUniversity of GreifswaldFelix‐Hausdorff‐Str. 4Greifswald17489Germany
| | - Kristian Wende
- ZIK plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix‐Hausdorff‐Str. 2Greifswald17489Germany
| | - Michael Lalk
- Institute of BiochemistryUniversity of GreifswaldFelix‐Hausdorff‐Str. 4Greifswald17489Germany
| | - Mihaela Delcea
- ZIK HIKEUniversity of GreifswaldFleischmannstr. 42–44Greifswald17489Germany
- Institute of BiochemistryUniversity of GreifswaldFelix‐Hausdorff‐Str. 4Greifswald17489Germany
| | - Barbara M. Bröker
- Department of ImmunologyUniversity Medicine GreifswaldSauerbruchstr. DZ7Greifswald17475Germany
| | - Sander Bekeschus
- ZIK plasmatisLeibniz Institute for Plasma Science and Technology (INP)Felix‐Hausdorff‐Str. 2Greifswald17489Germany
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Cantrell LS, Schey KL. Proteomic characterization of the human lens and Cataractogenesis. Expert Rev Proteomics 2021; 18:119-135. [PMID: 33849365 DOI: 10.1080/14789450.2021.1913062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION The goal of this review is to highlight the triumphs and frontiers in measurement of the lens proteome as it relates to onset of age-related nuclear cataract. As global life expectancy increases, so too does the frequency of age-related nuclear cataracts. Molecular therapeutics do not exist for delay or relief of cataract onset in humans. Since lens fiber cells are incapable of protein synthesis after initial maturation, age-related changes in proteome composition and post-translational modification accumulation can be measured with various techniques. Several of these modifications have been associated with cataract onset. AREAS COVERED We discuss the impact of long-lived proteins on the lens proteome and lens homeostasis as well as proteomic techniques that may be used to measure proteomes at various levels of proteomic specificity and spatial resolution. EXPERT OPINION There is clear evidence that several proteome modifications are correlated with cataract formation. Past studies should be enhanced with cutting-edge, spatially resolved mass spectrometry techniques to enhance the specificity and sensitivity of modification detection as it relates to cataract formation.
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Affiliation(s)
- Lee S Cantrell
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
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Medeiros R, Sousa B, Rossi S, Afonso C, Bonino L, Pitt A, López E, Spickett C, Borthagaray G. Identification and relative quantification of 3-nitrotyrosine residues in fibrinogen nitrated in vitro and fibrinogen from ischemic stroke patient plasma using LC-MS/MS. Free Radic Biol Med 2021; 165:334-347. [PMID: 33548450 DOI: 10.1016/j.freeradbiomed.2021.01.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/29/2022]
Abstract
Ischemic stroke is one of the leading causes of death and disability worldwide. This acute vascular event interferes with blood supply to the brain and induces a burst of free radicals such as nitric oxide and superoxide, producing peroxynitrite, a precursor of strong nitrating agents. Fibrinogen is one of the most abundant plasma proteins; it plays a role in the hemostatic system, mediating clot formation, which can be affected by nitrotyrosine formation. We hypothesized that nitration of fibrinogen by ONOOH and ONOOCO2- radical products could be one of the early events of the ischemic stroke, and protein-bound 3-nitrotyrosine could be a potential biomarker for diagnosis and/or prognosis of this condition. A targeted mass spectrometry approach was developed to analyze the nitration of fibrinogen and its association with ischemic stroke. First, a comprehensive mapping of 3-nitrotyrosine locations and their relative quantification was performed by LC-MS/MS, using in vitro nitrated fibrinogen samples. Twenty different 3-nitrotyrosine residues were identified on fibrinogen nitrated in vitro, varying with the peroxynitrite tofibrinogen molar ratio used. Nine tyrosine residues that were consistently modified at different treatment ratios were chosen to perform a targeted LC-MS/MS analysis in clinical samples. Enriched fibrinogen fractions from clinical samples from 24 ischemic stroke and 12 patients with non-inflammatory conditions were analysed with this method. Three of the nine tyrosine residues analysed (βY452, βY475 and γY380) showed a significant difference between the ischemic stroke and non-inflammatory disease groups. ROC curve analysis suggested an association of these residues either individually or in combination with ischemic stroke. Different tyrosine nitration patterns were also observed in fibrinogen modified in vitro and in vivo, suggesting differences in the nitration process in these situations. This is the first study showing a putative association between the nitration profile of specific tyrosine residues in human fibrinogen and ischemic stroke.
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Affiliation(s)
- Romina Medeiros
- Facultad de Química, Universidad de La República, Montevideo, Uruguay.
| | - Bebiana Sousa
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Silvina Rossi
- Facultad de Química, Universidad de La República, Montevideo, Uruguay
| | - Catarina Afonso
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Luis Bonino
- Facultad de Química, Universidad de La República, Montevideo, Uruguay
| | - Andrew Pitt
- School of Life and Health Sciences, Aston University, Birmingham, UK; Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester. M1 7DN, UK
| | - Elizabeth López
- Facultad de Química, Universidad de La República, Montevideo, Uruguay
| | - Corinne Spickett
- School of Life and Health Sciences, Aston University, Birmingham, UK
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Moyer TB, Parsley NC, Sadecki PW, Schug WJ, Hicks LM. Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products. Nat Prod Rep 2021; 38:489-509. [PMID: 32929442 PMCID: PMC7956910 DOI: 10.1039/d0np00046a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: Up to July 2020Ribosomal antimicrobial peptide (AMP) natural products, also known as ribosomally synthesized and post-translationally modified peptides (RiPPs) or host defense peptides, demonstrate potent bioactivities and impressive complexity that complicate molecular and biological characterization. Tandem mass spectrometry (MS) has rapidly accelerated bioactive peptide sequencing efforts, yet standard workflows insufficiently address intrinsic AMP diversity. Herein, orthogonal approaches to accelerate comprehensive and accurate molecular characterization without the need for prior isolation are reviewed. Chemical derivatization, proteolysis (enzymatic and chemical cleavage), multistage MS fragmentation, and separation (liquid chromatography and ion mobility) strategies can provide complementary amino acid composition and post-translational modification data to constrain sequence solutions. Examination of two complex case studies, gomesin and styelin D, highlights the practical implementation of the proposed approaches. Finally, we emphasize the importance of heterogeneous AMP peptidoforms that confer varying biological function, an area that warrants significant further development.
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Affiliation(s)
- Tessa B Moyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Tomin T, Schittmayer M, Sedej S, Bugger H, Gollmer J, Honeder S, Darnhofer B, Liesinger L, Zuckermann A, Rainer PP, Birner-Gruenberger R. Mass Spectrometry-Based Redox and Protein Profiling of Failing Human Hearts. Int J Mol Sci 2021; 22:ijms22041787. [PMID: 33670142 PMCID: PMC7916846 DOI: 10.3390/ijms22041787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Oxidative stress contributes to detrimental functional decline of the myocardium, leading to the impairment of the antioxidative defense, dysregulation of redox signaling, and protein damage. In order to precisely dissect the changes of the myocardial redox state correlated with oxidative stress and heart failure, we subjected left-ventricular tissue specimens collected from control or failing human hearts to comprehensive mass spectrometry-based redox and quantitative proteomics, as well as glutathione status analyses. As a result, we report that failing hearts have lower glutathione to glutathione disulfide ratios and increased oxidation of a number of different proteins, including constituents of the contractile machinery as well as glycolytic enzymes. Furthermore, quantitative proteomics of failing hearts revealed a higher abundance of proteins responsible for extracellular matrix remodeling and reduced abundance of several ion transporters, corroborating contractile impairment. Similar effects were recapitulated by an in vitro cell culture model under a controlled oxygen atmosphere. Together, this study provides to our knowledge the most comprehensive report integrating analyses of protein abundance and global and peptide-level redox state in end-stage failing human hearts as well as oxygen-dependent redox and global proteome profiles of cultured human cardiomyocytes.
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Affiliation(s)
- Tamara Tomin
- Faculty of Technical Chemistry, Institute of Chemical Technologies and Analytics, Vienna University of Technology-TU Wien, Getreidemarkt 9/164, 1060 Vienna, Austria;
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
| | - Matthias Schittmayer
- Faculty of Technical Chemistry, Institute of Chemical Technologies and Analytics, Vienna University of Technology-TU Wien, Getreidemarkt 9/164, 1060 Vienna, Austria;
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
- Correspondence: (M.S.); (P.P.R.); (R.B.-G.)
| | - Simon Sedej
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
- Division of Cardiology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (H.B.); (J.G.)
- Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Heiko Bugger
- Division of Cardiology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (H.B.); (J.G.)
| | - Johannes Gollmer
- Division of Cardiology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (H.B.); (J.G.)
| | - Sophie Honeder
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
| | - Barbara Darnhofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
| | - Laura Liesinger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
| | - Andreas Zuckermann
- Cardiac Transplantation, Department of Cardiac Surgery, Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria;
| | - Peter P. Rainer
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
- Division of Cardiology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (H.B.); (J.G.)
- Correspondence: (M.S.); (P.P.R.); (R.B.-G.)
| | - Ruth Birner-Gruenberger
- Faculty of Technical Chemistry, Institute of Chemical Technologies and Analytics, Vienna University of Technology-TU Wien, Getreidemarkt 9/164, 1060 Vienna, Austria;
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010 Graz, Austria; (S.H.); (B.D.); (L.L.)
- BiotechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria;
- Correspondence: (M.S.); (P.P.R.); (R.B.-G.)
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Fedorowicz J, Wierzbicka M, Cebrat M, Wiśniewska P, Piątek R, Zalewska-Piątek B, Szewczuk Z, Sączewski J. Application of Safirinium N-Hydroxysuccinimide Esters to Derivatization of Peptides for High-Resolution Mass Spectrometry, Tandem Mass Spectrometry, and Fluorescent Labeling of Bacterial Cells. Int J Mol Sci 2020; 21:ijms21249643. [PMID: 33348897 PMCID: PMC7767236 DOI: 10.3390/ijms21249643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 12/16/2022] Open
Abstract
Mass spectrometry methods are commonly used in the identification of peptides and biomarkers. Due to a relatively low abundance of proteins in biological samples, there is a need for the development of novel derivatization methods that would improve MS detection limits. Hence, novel fluorescent N–hydroxysuccinimide esters of dihydro-[1,2,4]triazolo[4,3-a]pyridin-2-ium carboxylates (Safirinium P dyes) have been synthesized. The obtained compounds, which incorporate quaternary ammonium salt moieties, easily react with aliphatic amine groups of peptides, both in solution and on the solid support; thus, they can be applied for derivatization as ionization enhancers. Safirinium tagging experiments with ubiquitin hydrolysate revealed that the sequence coverage level was high (ca. 80%), and intensities of signals were enhanced up to 8-fold, which proves the applicability of the proposed tags in the bottom–up approach. The obtained results confirmed that the novel compounds enable the detection of trace amounts of peptides, and fixed positive charge within the tags results in high ionization efficiency. Moreover, Safirinium NHS esters have been utilized as imaging agents for fluorescent labeling and the microscopic visualization of living cells such as E. coli Top10 bacterial strain.
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Affiliation(s)
- Joanna Fedorowicz
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland
- Correspondence: ; Tel.: +48-58-349-1957
| | - Magdalena Wierzbicka
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (M.W.); (M.C.); (Z.S.)
| | - Marek Cebrat
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (M.W.); (M.C.); (Z.S.)
| | - Paulina Wiśniewska
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (P.W.); (J.S.)
| | - Rafał Piątek
- Department of Molecular Biotechnology and Microbiology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland; (R.P.); (B.Z.-P.)
| | - Beata Zalewska-Piątek
- Department of Molecular Biotechnology and Microbiology, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland; (R.P.); (B.Z.-P.)
| | - Zbigniew Szewczuk
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (M.W.); (M.C.); (Z.S.)
| | - Jarosław Sączewski
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416 Gdańsk, Poland; (P.W.); (J.S.)
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The challenge of detecting modifications on proteins. Essays Biochem 2020; 64:135-153. [PMID: 31957791 DOI: 10.1042/ebc20190055] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.
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Simultaneous LC-MS/MS-Based Quantification of Free 3-Nitro-l-tyrosine, 3-Chloro-l-tyrosine, and 3-Bromo-l-tyrosine in Plasma of Colorectal Cancer Patients during Early Postoperative Period. Molecules 2020; 25:molecules25215158. [PMID: 33167555 PMCID: PMC7663926 DOI: 10.3390/molecules25215158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/31/2020] [Accepted: 11/01/2020] [Indexed: 12/12/2022] Open
Abstract
Quantification with satisfactory specificity and sensitivity of free 3-Nitro-l-tyrosine (3-NT), 3-Chloro-l-tyrosine (3-CT), and 3-Bromo-l-tyrosine (3-BT) in biological samples as potential inflammation, oxidative stress, and cancer biomarkers is analytically challenging. We aimed at developing a liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based method for their simultaneous analysis without an extract purification step by solid-phase extraction. Validation of the developed method yielded the following limits of detection (LOD) and quantification (LOQ) for 3-NT, 3-BT, and 3-CT: 0.030, 0.026, 0.030 ng/mL (LODs) and 0.100, 0.096, 0.098 ng/mL (LOQs). Coefficients of variation for all metabolites and tested concentrations were <10% and accuracy was within 95-105%. Method applicability was tested on colorectal cancer patients during the perioperative period. All metabolites were significantly higher in cancer patients than healthy controls. The 3-NT was significantly lower in advanced cancer and 3-BT showed a similar tendency. Dynamics of 3-BT in the early postoperative period were affected by type of surgery and presence of surgical site infections. In conclusion, a sensitive and specific LC-MS/MS method for simultaneous quantification of free 3-NT, 3-BT, and 3-CT in human plasma has been developed.
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36
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Lama S, Merlin-Zhang O, Yang C. In Vitro and In Vivo Models for Evaluating the Oral Toxicity of Nanomedicines. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2177. [PMID: 33142878 PMCID: PMC7694082 DOI: 10.3390/nano10112177] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023]
Abstract
Toxicity studies for conventional oral drug formulations are standardized and well documented, as required by the guidelines of administrative agencies such as the US Food & Drug Administration (FDA), the European Medicines Agency (EMA) or European Medicines Evaluation Agency (EMEA), and the Japanese Pharmaceuticals and Medical Devices Agency (PMDA). Researchers tend to extrapolate these standardized protocols to evaluate nanoformulations (NFs) because standard nanotoxicity protocols are still lacking in nonclinical studies for testing orally delivered NFs. However, such strategies have generated many inconsistent results because they do not account for the specific physicochemical properties of nanomedicines. Due to their tiny size, accumulated surface charge and tension, sizeable surface-area-to-volume ratio, and high chemical/structural complexity, orally delivered NFs may generate severe topical toxicities to the gastrointestinal tract and metabolic organs, including the liver and kidney. Such toxicities involve immune responses that reflect different mechanisms than those triggered by conventional formulations. Herein, we briefly analyze the potential oral toxicity mechanisms of NFs and describe recently reported in vitro and in vivo models that attempt to address the specific oral toxicity of nanomedicines. We also discuss approaches that may be used to develop nontoxic NFs for oral drug delivery.
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Affiliation(s)
| | | | - Chunhua Yang
- Center for Diagnostics and Therapeutics, Digestive Disease Research Group, Institute for Biomedical Sciences, Petite Science Center, Suite 754, 100 Piedmont Ave SE, Georgia State University, Atlanta, GA 30303, USA; (S.L.); (O.M.-Z.)
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37
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Díaz-Velasco S, González A, Peña FJ, Estévez M. Noxious effects of selected food-occurring oxidized amino acids on differentiated CACO-2 intestinal human cells. Food Chem Toxicol 2020; 144:111650. [PMID: 32745570 DOI: 10.1016/j.fct.2020.111650] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/27/2022]
Abstract
The harmful effects of food-occurring oxidized amino acids, namely, aminoadipic acid (AAA), dityrosine (DTYR), L-kynurenine (KN), kynurenic acid (KA) and 3-nitrotyrosine (3NT), were studied on differentiated CACO-2 cells by flow cytometry and quantification of glutathione (GSH), and allysine. Cells were exposed to food-relevant doses (200 μM) of each compound for 4 or 72h and compared to a control (no stimulated cells). All oxidized amino acids induced apoptosis and results indicated that underlying mechanisms depended on the chemical nature of the species. AAA, KN and KA caused ROS generation and severe oxidative stress in 96%, 98% and 89% of exposed cells (77% in control cells), leading to significant GSH depletion and allysine accretion (1.5, 1.5 and 1.6 nmol allysine/mg protein, respectively at 4h; control: 0.22 nmol/mg protein; p < 0.05). DTYR and 3NT induced significant apoptosis to 29% and 25% of cells (control: 16%; p < 0.05) and necrosis to 28% and 26% of cells (control: 23%) at 72h by ROS-independent mechanisms. KN and KA were found to induce a cycle arrest effect on CACO-2 cells. These findings emphasize the potential harmful effects of the intake of oxidized proteins and amino acids and urge the necessity of carrying out further molecular studies.
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Affiliation(s)
- S Díaz-Velasco
- IPROCAR Research Institute, TECAL Research Group, University of Extremadura, 10003, Cáceres, Spain
| | - A González
- Institute of Molecular Pathology Biomarkers, University of Extremadura, 10003, Cáceres, Spain
| | - F J Peña
- Spermatology Laboratory, University of Extremadura, 10003, Cáceres, Spain
| | - Mario Estévez
- IPROCAR Research Institute, TECAL Research Group, University of Extremadura, 10003, Cáceres, Spain.
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Jayathirtha M, Dupree EJ, Manzoor Z, Larose B, Sechrist Z, Neagu AN, Petre BA, Darie CC. Mass Spectrometric (MS) Analysis of Proteins and Peptides. Curr Protein Pept Sci 2020; 22:92-120. [PMID: 32713333 DOI: 10.2174/1389203721666200726223336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 01/09/2023]
Abstract
The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zaen Manzoor
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Brianna Larose
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zach Sechrist
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania
| | - Brindusa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, Al. I. Cuza University of Iasi, Iasi, Romania, Center for Fundamental Research and Experimental Development in Translation Medicine - TRANSCEND, Regional Institute of Oncology, Iasi, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
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Abstract
Aromatase CYP19A1 catalyzes the synthesis of estrogens in endocrine, reproductive and central nervous systems. Higher levels of 17β-estradiol (E2) are associated with malignancies and diseases of the breast, ovary and endometrium, while low E2 levels increase the risk for osteoporosis, cardiovascular diseases and cognitive disorders. E2, the transcriptional activator of the estrogen receptors, is also known to be involved in non-genomic signaling as a neurotransmitter/neuromodulator, with recent evidence for rapid estrogen synthesis (RES) within the synaptic terminal. Although regulation of brain aromatase activity by phosphorylation/dephosphorylation has been suggested, it remains obscure in the endocrine and reproductive systems. RES and overabundance of estrogens could stimulate the genomic and non-genomic signaling pathways, and genotoxic effects of estrogen metabolites. Here, by utilizing biochemical, cellular, mass spectrometric, and structural data we unequivocally demonstrate phosphorylation of human placental aromatase and regulation of its activity. We report that human aromatase has multiple phosphorylation sites, some of which are consistently detectable. Phosphorylation of the residue Y361 at the reductase-coupling interface significantly elevates aromatase activity. Other sites include the active site residue S478 and several at the membrane interface. We present the evidence that two histidine residues are phosphorylated. Furthermore, oxidation of two proline residues near the active site may have implications in regulation. Taken together, the results demonstrate that aromatase activity is regulated by phosphorylation and possibly other post-translational modifications. Protein level regulation of aromatase activity not only represents a paradigm shift in estrogen-mediated biology, it could also explain unresolved clinical questions such as aromatase inhibitor resistance.
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40
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Vasilyeva A, Yurina L, Shchegolikhin A, Indeykina M, Bugrova A, Kononikhin A, Nikolaev E, Rosenfeld M. The Structure of Blood Coagulation Factor XIII Is Adapted to Oxidation. Biomolecules 2020; 10:E914. [PMID: 32560304 PMCID: PMC7355775 DOI: 10.3390/biom10060914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/11/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022] Open
Abstract
The blood coagulation factor XIII (FXIII) plays a critical role in supporting coagulation and fibrinolysis due to both the covalent crosslinking of fibrin polymers, rendering them resistant to plasmin lysis, and the crosslinking of fibrin to proteins of the fibrinolytic system. The hypochlorite-mediated oxidation of the blood coagulation factor XIII (FXIII) at the different stages of its enzymatic activation is studied for the first time in this paper. The consolidated results obtained with the aid of MS/MS, electrophoresis, and colorimetry demonstrate that in the process of FXIII's conversion into FXIIIa, the vulnerability of FXIII to hypochlorite-induced oxidation increased as follows: native FXIII < FXIII + Ca2+ << FXIII + Ca2+/thrombin. The modification sites were detected among all the structural regions of the catalytic FXIII-A subunit, except for the activation peptide, and embraced several sushi domains of the FXIII-B subunit. Oxidized amino acid residues belonging to FXIII-A are surface-exposed residues and can perform an antioxidant role. The regulatory FXIII-B subunits additionally contribute to the antioxidant defense of the catalytic center of the FXIII-A subunits. Taken together, the present data along with the data from previous studies demonstrate that the FXIII proenzyme structure is adapted to oxidation.
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Affiliation(s)
- Alexandra Vasilyeva
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia; (L.Y.); (A.S.); (M.I.); (A.B.); (M.R.)
| | - Lyubov Yurina
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia; (L.Y.); (A.S.); (M.I.); (A.B.); (M.R.)
| | - Alexander Shchegolikhin
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia; (L.Y.); (A.S.); (M.I.); (A.B.); (M.R.)
| | - Maria Indeykina
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia; (L.Y.); (A.S.); (M.I.); (A.B.); (M.R.)
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Center of Chemical Physics, Russian Academy of Sciences, Chernogolovka, 142432 Moscow, Russia
| | - Anna Bugrova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia; (L.Y.); (A.S.); (M.I.); (A.B.); (M.R.)
| | - Alexey Kononikhin
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701 Moscow, Russia
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
| | - Eugene Nikolaev
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
| | - Mark Rosenfeld
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia; (L.Y.); (A.S.); (M.I.); (A.B.); (M.R.)
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41
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Gamon LF, Guo C, He J, Hägglund P, Hawkins CL, Davies MJ. Absolute quantitative analysis of intact and oxidized amino acids by LC-MS without prior derivatization. Redox Biol 2020; 36:101586. [PMID: 32505089 PMCID: PMC7276450 DOI: 10.1016/j.redox.2020.101586] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 01/15/2023] Open
Abstract
The precise characterization and quantification of oxidative protein damage is a significant challenge due to the low abundance, large variety, and heterogeneity of modifications. Mass spectrometry (MS)-based techniques at the peptide level (proteomics) provide a detailed but limited picture due to incomplete sequence coverage and imperfect enzymatic digestion. This is particularly problematic with oxidatively modified and cross-linked/aggregated proteins. There is a pressing need for methods that can quantify large numbers of modified amino acids, which are often present in low abundance compared to the high background of non-damaged amino acids, in a rapid and reliable fashion. We have developed a protocol using zwitterionic ion-exchange chromatography coupled with LC-MS to simultaneously quantify both parent amino acids and their respective oxidation products. Proteins are hydrolyzed with methanesulfonic acid in the presence of tryptamine and purified by strong cation exchange solid phase extraction. The method was validated for the common amino acids (excluding Gln, Asn, Cys) and the oxidation products 3-chlorotyrosine (3-ClTyr), 3-nitrotyrosine (3-NO2Tyr), di-tyrosine, Nε-(1-carboxymethyl)-l-lysine, o,o’-di-tyrosine, 3,4,-dihydroxyphenylalanine, hydroxy-tryptophan and kynurenine. Linear standard curves were observed over ~3 orders of magnitude dynamic range (2–1000 pmol for parent amino acids, 80 fmol–20 pmol for oxidation products) with limit-of-quantification values as low as 200 fmol (o,o’-di-tyrosine). The validated method was used to quantify Tyr and Trp loss, and formation of 3-NO2Tyr on the isolated protein anastellin treated with peroxynitrous acid, and for 3-ClTyr formation (over a 2 orders of magnitude range) in cell lysates and complex protein mixtures treated with hypochlorous acid. Identification and quantification of oxidative protein damage is a major challenge. A versatile LC-MS assay is reported that involves hydrolysis to free amino acids. Quantification is possible for both parent amino acids and products in single runs. A dynamic range of 2-3 orders of magnitude is available for most analytes. Example of use with pure proteins, extracellular matrix and cell lysates are given.
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Affiliation(s)
- Luke F Gamon
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Chaorui Guo
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jianfei He
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Per Hägglund
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Clare L Hawkins
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael J Davies
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
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42
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Bychkova AV, Lopukhova MV, Wasserman LA, Pronkin PG, Degtyarev YN, Shalupov AI, Vasilyeva AD, Yurina LV, Kovarski AL, Kononikhin AS, Nikolaev EN. Interaction between immunoglobulin G and peroxidase-like iron oxide nanoparticles: Physicochemical and structural features of the protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140300. [PMID: 31676449 DOI: 10.1016/j.bbapap.2019.140300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/26/2019] [Accepted: 09/28/2019] [Indexed: 10/25/2022]
Abstract
The study is devoted to the oxidative modification of immunoglobulin G (IgG) on the surface of peroxidase-like iron oxide magnetic nanoparticles (MNPs) under conditions of induced reactive oxygen species (ROS) generation and without them. A pronounced change of thermodynamic parameters of denaturation has been detected for IgG in solutions containing MNPs under hydrogen peroxide action during 24 h of incubation. Dynamic light scattering measurements and UV-Visible spectrophotometry have been used to show aggregation in these solutions. Ferromagnetic resonance (FMR) was used to compare IgG coating thickness on individual MNPs under conditions of induced ROS generation and without them. The similarity between IgG adsorption on MNPs under these conditions after 24 h of incubation has been confirmed by the fluorescence measurements. The sites of IgG oxidative modifications that take place on MNPs surface and some evidences of the influence of oxidative modification and adsorption on the chemical structure of IgG were revealed by HPLC MS/MS analysis.
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Affiliation(s)
- Anna V Bychkova
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia.
| | - Mariia V Lopukhova
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Luybov A Wasserman
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Pavel G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Yevgeniy N Degtyarev
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexander I Shalupov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Alexandra D Vasilyeva
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Lyubov' V Yurina
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Alexander L Kovarski
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina str., 4, 119334 Moscow, Russia
| | - Alexey S Kononikhin
- Talrose Institute for Energy Problems of Chemical Physics, Semenov Federal Center of Chemical Physic, Russian Academy of Sciences, Moscow, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Evgene N Nikolaev
- Talrose Institute for Energy Problems of Chemical Physics, Semenov Federal Center of Chemical Physic, Russian Academy of Sciences, Moscow, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Russia
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43
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Fernández-d'Arlas B. Tough and Functional Cross-linked Bioplastics from Sheep Wool Keratin. Sci Rep 2019; 9:14810. [PMID: 31616010 PMCID: PMC6794297 DOI: 10.1038/s41598-019-51393-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/20/2019] [Indexed: 11/21/2022] Open
Abstract
Novel bioplastic films derived from wool keratins were prepared by protein solution in an alkaline mild oxidative method that splits disulphide (-S-S-) bonds. The native structure of the keratin macromolecules was partially modified upon extraction as revealed by the decrease of the β-sheet to α-helices/coils ratio but high molecular weight fractions (31, 22 and 13 KDa) was retained permitting film formation and plastic behaviour of films. Keratin films were plasticised with glycerol and sodium dodecyl sulphonic acid (SDS), which provided different hydrophobic character to bioplastics. Water content in the films depend on the relative humidity (RH), being able to absorb up to 35 wt% H2O at an ambient of 80% RH. Films were mechanically, thermally and optically analysed. The spectroscopic analyses revelled that these bioplastic films absorb UV light, what is interesting for packaging applications. Thermogravimetric and thermomechanical analysis revealed high stability of keratin macromolecules up to 200 °C with no inherent thermal transitions. Tough bioplastics (19 ± 4 MJ∙ m-3) were obtained after thermal cross-linking with glycerol and formaldehyde outperforming mechanical properties previously reported for protein films.
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Affiliation(s)
- Borja Fernández-d'Arlas
- Institute for Advanced Materials (INAMAT), Universidad Pública de Navarra (UPNA), Centro Jerónimo de Ayanz, Pamplona, España, Spain.
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44
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Tailor A, Waddington JC, Hamlett J, Maggs J, Kafu L, Farrell J, Dear GJ, Whitaker P, Naisbitt DJ, Park K, Meng X. Definition of Haptens Derived from Sulfamethoxazole: In Vitro and in Vivo. Chem Res Toxicol 2019; 32:2095-2106. [DOI: 10.1021/acs.chemrestox.9b00282] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arun Tailor
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, U.K
| | - James C. Waddington
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, U.K
| | - Jane Hamlett
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, U.K
| | - James Maggs
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, U.K
| | - Laila Kafu
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, U.K
| | - John Farrell
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, U.K
| | - Gordon J. Dear
- GlaxoSmithKline, Park Road, Ware, Hertfordshire SG12 0DP, U.K
| | - Paul Whitaker
- Regional Adult Cystic Fibrosis Unit, St. James’s University Hospital, Leeds LS9 7TF, U.K
| | - Dean J. Naisbitt
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, U.K
| | - Kevin Park
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, U.K
| | - Xiaoli Meng
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, U.K
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45
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Tomin T, Schittmayer M, Honeder S, Heininger C, Birner-Gruenberger R. Irreversible oxidative post-translational modifications in heart disease. Expert Rev Proteomics 2019; 16:681-693. [PMID: 31361162 PMCID: PMC6816499 DOI: 10.1080/14789450.2019.1645602] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Development of specific biomarkers aiding early diagnosis of heart failure is an ongoing challenge. Biomarkers commonly used in clinical routine usually act as readouts of an already existing acute condition rather than disease initiation. Functional decline of cardiac muscle is greatly aggravated by increased oxidative stress and damage of proteins. Oxidative post-translational modifications occur already at early stages of tissue damage and are thus regarded as potential up-coming disease markers. Areas covered: Clinical practice regarding commonly used biomarkers for heart disease is briefly summarized. The types of oxidative post-translational modification in cardiac pathologies are discussed with a special focus on available quantitative techniques and characteristics of individual modifications with regard to their stability and analytical accessibility. As irreversible oxidative modifications trigger protein degradation pathways or cause protein aggregation, both influencing biomarker abundance, a chapter is dedicated to their regulation in the heart.
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Affiliation(s)
- Tamara Tomin
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria.,Institute of Chemical Technologies and Analytics, Vienna University of Technology , Vienna , Austria
| | - Matthias Schittmayer
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria.,Institute of Chemical Technologies and Analytics, Vienna University of Technology , Vienna , Austria
| | - Sophie Honeder
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria
| | - Christoph Heininger
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria
| | - Ruth Birner-Gruenberger
- Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz , Graz , Austria.,Omics Center Graz, BioTechMed-Graz , Graz , Austria.,Institute of Chemical Technologies and Analytics, Vienna University of Technology , Vienna , Austria
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46
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Yurina L, Vasilyeva A, Indeykina M, Bugrova A, Biryukova M, Kononikhin A, Nikolaev E, Rosenfeld M. Ozone-induced damage of fibrinogen molecules: identification of oxidation sites by high-resolution mass spectrometry. Free Radic Res 2019; 53:430-455. [DOI: 10.1080/10715762.2019.1600686] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lyubov Yurina
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexandra Vasilyeva
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria Indeykina
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Anna Bugrova
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Marina Biryukova
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey Kononikhin
- Moskovskij Fiziko-Tehniceskij Institut, Dolgoprudnyi, Russian Federation
| | - Evgene Nikolaev
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Moscow, Russian Federation
| | - Mark Rosenfeld
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
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47
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Enache TA, Matei E, Diculescu VC. Electrochemical Sensor for Carbonyl Groups in Oxidized Proteins. Anal Chem 2019; 91:1920-1927. [PMID: 30574784 DOI: 10.1021/acs.analchem.8b03969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interaction of proteins with free radicals leads, among other types of damages, to the production of stable carbonyl groups, which can be used as a quantification of oxidative stress at proteins level. The aim of this study was the development of an electrochemical sensor for the detection of carbonyl groups in proteins oxidized by reactive oxygen species. Its working principle is based on the redox properties of dinitrophenylhydrazine (DNPH). BSA was used as a model protein and its oxidation achieved through Fenton reactions. Using differential pulse voltammetry at glassy carbon electrode, the electrochemical behavior of DNPH and of the native and oxidized BSA was investigated in solution. It has been shown that the hydrazine moiety of the DNPH is the electroactive center and is responsible for carbonyl complexation. Special attention was paid to the immobilization of the DNPH in order to retain its redox properties, and this was achieved on a mixed 4-styrenesulfonic acid-nafion matrix. The sensor's surface characterization and the detection of carbonyl groups in oxidized protein were performed by voltammetry, Fourier-transformed infrared spectroscopy and scanning electron microscopy while the voltammetric results were confirmed by surface plasmon resonance measurements. It has been shown that upon interaction with carbonyl groups of the oxidized protein, the oxidation peak of the hydrazine moiety of DNPH decreases as a function of incubation time and protein concentration. The sensor sensitivity was 0.015 nmol carbonyl per mg of oxidized protein and detection limits of 50 μg oxidized BSA and 0.75 pmol carbonyls.
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Affiliation(s)
- Teodor Adrian Enache
- National Institute of Materials Physics , Atomistilor 405A , 077125 , Magurele , Romania
| | - Elena Matei
- National Institute of Materials Physics , Atomistilor 405A , 077125 , Magurele , Romania
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Mass Spectrometry in Advancement of Redox Precision Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:327-358. [PMID: 31347057 DOI: 10.1007/978-3-030-15950-4_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Redox (portmanteau of reduction-oxidation) reactions involve the transfer of electrons between chemical species in biological processes fundamental to life. It is of outmost importance that cells maintain a healthy redox state by balancing the action of oxidants and antioxidants; failure to do so leads to a multitude of diseases including cancer, diabetes, fibrosis, autoimmune diseases, and cardiovascular and neurodegenerative diseases. From the perspective of precision medicine, it is therefore beneficial to interrogate the redox phenotype of the individual-similar to the use of genomic sequencing-in order to design tailored strategies for disease prevention and treatment. This chapter provides an overview of redox metabolism and focuses on how mass spectrometry (MS) can be applied to advance our knowledge in redox biology and precision medicine.
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Afonso CB, Spickett CM. Lipoproteins as targets and markers of lipoxidation. Redox Biol 2018; 23:101066. [PMID: 30579928 PMCID: PMC6859580 DOI: 10.1016/j.redox.2018.101066] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/28/2018] [Accepted: 12/05/2018] [Indexed: 12/24/2022] Open
Abstract
Lipoproteins are essential systemic lipid transport particles, composed of apolipoproteins embedded in a phospholipid and cholesterol monolayer surrounding a cargo of diverse lipid species. Many of the lipids present are susceptible to oxidative damage by lipid peroxidation, giving rise to the formation of reactive lipid peroxidation products (rLPPs). In view of the close proximity of the protein and lipid moieties within lipoproteins, the probability of adduct formation between rLPPs and amino acid residues of the proteins, a process called lipoxidation, is high. There has been interest for many years in the biological effects of such modifications, but the field has been limited to some extent by the availability of methods to determine the sites and exact nature of such modification. More recently, the availability of a wide range of antibodies to lipoxidation products, as well as advances in analytical techniques such as liquid chromatography tandem mass spectrometry (LC-MSMS), have increased our knowledge substantially. While most work has focused on LDL, oxidation of which has long been associated with pro-inflammatory responses and atherosclerosis, some studies on HDL, VLDL and Lipoprotein(a) have also been reported. As the broader topic of LDL oxidation has been reviewed previously, this review focuses on lipoxidative modifications of lipoproteins, from the historical background through to recent advances in the field. We consider the main methods of analysis for detecting rLPP adducts on apolipoproteins, including their advantages and disadvantages, as well as the biological effects of lipoxidized lipoproteins and their potential roles in diseases. Lipoproteins can be modified by reactive Lipid Peroxidation Products (rLPPs). Lipoprotein lipoxidation is known to occur in several inflammatory diseases. Biochemical, immunochemical and mass spectrometry methods can detect rLPP adducts. Due to higher information output, MS can facilitate localization of modifications. Antibodies against some rLPPs have been used to identify lipoxidation in vivo.
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Affiliation(s)
- Catarina B Afonso
- School of Life and Health Sciences, Aston University, Aston Triangle, Aston University, Birmingham B4 7ET, UK
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Aston University, Birmingham B4 7ET, UK.
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Abstract
The concept of cell signaling in the context of nonenzyme-assisted protein modifications by reactive electrophilic and oxidative species, broadly known as redox signaling, is a uniquely complex topic that has been approached from numerous different and multidisciplinary angles. Our Review reflects on five aspects critical for understanding how nature harnesses these noncanonical post-translational modifications to coordinate distinct cellular activities: (1) specific players and their generation, (2) physicochemical properties, (3) mechanisms of action, (4) methods of interrogation, and (5) functional roles in health and disease. Emphasis is primarily placed on the latest progress in the field, but several aspects of classical work likely forgotten/lost are also recollected. For researchers with interests in getting into the field, our Review is anticipated to function as a primer. For the expert, we aim to stimulate thought and discussion about fundamentals of redox signaling mechanisms and nuances of specificity/selectivity and timing in this sophisticated yet fascinating arena at the crossroads of chemistry and biology.
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Affiliation(s)
- Saba Parvez
- Department of Pharmacology and Toxicology, College of
Pharmacy, University of Utah, Salt Lake City, Utah, 84112, USA
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Marcus J. C. Long
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Jesse R. Poganik
- Ecole Polytechnique Fédérale de Lausanne,
Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Yimon Aye
- Ecole Polytechnique Fédérale de Lausanne,
Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
- Department of Biochemistry, Weill Cornell Medicine, New
York, New York, 10065, USA
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