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Pineda-Alemán R, Cabarcas-Herrera C, Alviz-Amador A, Galindo-Murillo R, Pérez-Gonzalez H, Rodríguez-Cavallo E, Méndez-Cuadro D. Molecular dynamics of structural effects of reactive carbonyl species derivate of lipid peroxidation on bovine serum albumin. Biochim Biophys Acta Gen Subj 2024; 1868:130613. [PMID: 38593934 DOI: 10.1016/j.bbagen.2024.130613] [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: 07/03/2023] [Revised: 03/09/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Serum albumin is the most abundant protein in the Mammalia blood plasma at where plays a decisive role in the transport wide variety of hydrophobic ligands. BSA undergoes oxidative modifications like the carbonylation by the reactive carbonyl species (RCSs) 4-hydroxy-2-nonenal (HNE), 4 hydroxy-2-hexenal (HHE), malondialdehyde (MDA) and 4-oxo-2-nonenal (ONE), among others. The structural and functional changes induced by protein carbonylation have been associated with the advancement of neurodegenerative, cardiovascular, metabolic and cancer diseases. METHODS To elucidate structural effects of protein carbonylation with RCSs on BSA, parameters for six new non-standard amino acids were designated and molecular dynamics simulations of its mono‑carbonylated-BSA systems were conducted in the AMBER force field. Trajectories were evaluated by RMSD, RMSF, PCA, RoG and SASA analysis. RESULTS An increase in the conformational instability for all proteins modified with local changes were observed, without significant changes on the BSA global three-dimensional folding. A more relaxed compaction level and major solvent accessible surface area for modified systems was found. Four regions of high molecular fluctuation were identified in all modified systems, being the subdomains IA and IIIB those with the most remarkable local conformational changes. Regarding essential modes of domain movements, it was evidenced that the most representatives were those related to IA subdomain, while IIIB subdomain presented discrete changes. CONCLUSIONS RCSs induces local structural changes on mono‑carbonylated BSA. Also, this study extends our knowledge on how carbonylation by RCSs induce structural effects on proteins.
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Affiliation(s)
- Rafael Pineda-Alemán
- Analytical Chemistry and Biomedicine Group, Medicine Faculty, University of Cartagena, Cartagena, Colombia
| | - Camila Cabarcas-Herrera
- Analytical Chemistry and Biomedicine Group, Exact and Natural Sciences Faculty, University of Cartagena, Cartagena, Colombia
| | - Antistio Alviz-Amador
- Analytical Chemistry and Biomedicine Group, Pharmaceutical Sciences Faculty, University of Cartagena, Cartagena, Colombia
| | | | - Humberto Pérez-Gonzalez
- Department of Mathematics, Exact and Natural Sciences Faculty, University of Cartagena, Cartagena, Colombia
| | - Erika Rodríguez-Cavallo
- Analytical Chemistry and Biomedicine Group, Pharmaceutical Sciences Faculty, University of Cartagena, Cartagena, Colombia
| | - Darío Méndez-Cuadro
- Analytical Chemistry and Biomedicine Group, Exact and Natural Sciences Faculty, University of Cartagena, Cartagena, Colombia.
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2
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Protein Susceptibility to Peroxidation by 4-Hydroxynonenal in Hereditary Hemochromatosis. Int J Mol Sci 2023; 24:ijms24032922. [PMID: 36769239 PMCID: PMC9917916 DOI: 10.3390/ijms24032922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Iron overload caused by hereditary hemochromatosis (HH) increases free reactive oxygen species that, in turn, induce lipid peroxidation. Its 4-hydroxynonenal (HNE) by-product is a well-established marker of lipid peroxidation since it reacts with accessible proteins with deleterious consequences. Indeed, elevated levels of HNE are often detected in a wide variety of human diseases related to oxidative stress. Here, we evaluated HNE-modified proteins in the membrane of erythrocytes from HH patients and in organs of Hfe-/- male and female mice, a mouse model of HH. For this purpose, we used one- and two-dimensional gel electrophoresis, immunoblotting and MALDI-TOF/TOF analysis. We identified cytoskeletal membrane proteins and membrane receptors of erythrocytes bound to HNE exclusively in HH patients. Furthermore, kidney and brain of Hfe-/- mice contained more HNE-adducted protein than healthy controls. Our results identified main HNE-modified proteins suggesting that HH favours preferred protein targets for oxidation by HNE.
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3
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Chemistry and Biochemistry Aspects of the 4-Hydroxy-2,3-trans-nonenal. Biomolecules 2022; 12:biom12010145. [PMID: 35053293 PMCID: PMC8773729 DOI: 10.3390/biom12010145] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
4-hydroxy-2,3-trans-nonenal (C9H16O2), also known as 4-hydroxy-2E-nonenal (C9H16O2; HNE) is an α,β-unsaturated hydroxyalkenal. HNE is a major aldehyde, formed in the peroxidation process of ω-6 polyunsaturated fatty acids (ω-6 PUFAs), such as linoleic and arachidonic acid. HNE is not only harmful but also beneficial. In the 1980s, the HNE was regarded as a “toxic product of lipid peroxidation” and the “second toxic messenger of free radicals”. However, already at the beginning of the 21st century, HNE was perceived as a reliable marker of oxidative stress, growth modulating factor and signaling molecule. Many literature data also indicate that an elevated level of HNE in blood plasma and cells of the animal and human body is observed in the course of many diseases, including cancer. On the other hand, it is currently proven that cancer cells divert to apoptosis if they are exposed to supraphysiological levels of HNE in the cancer microenvironment. In this review, we briefly summarize the current knowledge about the biological properties of HNE.
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Can Medicinal Plants and Bioactive Compounds Combat Lipid Peroxidation Product 4-HNE-Induced Deleterious Effects? Biomolecules 2020; 10:biom10010146. [PMID: 31963301 PMCID: PMC7022924 DOI: 10.3390/biom10010146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/27/2022] Open
Abstract
The toxic reactive aldehyde 4-hydroxynonenal (4-HNE) belongs to the advanced lipid peroxidation end products. Accumulation of 4-HNE and formation of 4-HNE adducts induced by redox imbalance participate in several cytotoxic processes, which contribute to the pathogenesis and progression of oxidative stress-related human disorders. Medicinal plants and bioactive natural compounds are suggested to be attractive sources of potential agents to mitigate oxidative stress, but little is known about the therapeutic potentials especially on combating 4-HNE-induced deleterious effects. Of note, some investigations clarify the attenuation of medicinal plants and bioactive compounds on 4-HNE-induced disturbances, but strong evidence is needed that these plants and compounds serve as potent agents in the prevention and treatment of disorders driven by 4-HNE. Therefore, this review highlights the pharmacological basis of these medicinal plants and bioactive compounds to combat 4-HNE-induced deleterious effects in oxidative stress-related disorders, such as neurotoxicity and neurological disorder, eye damage, cardiovascular injury, liver injury, and energy metabolism disorder. In addition, this review briefly discusses with special attention to the strategies for developing potential therapies by future applications of these medicinal plants and bioactive compounds, which will help biological and pharmacological scientists to explore the new vistas of medicinal plants in combating 4-HNE-induced deleterious effects.
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Alviz-Amador A, Galindo-Murillo R, Pérez-González H, Rodríguez-Cavallo E, Vivas-Reyes R, Méndez-Cuadro D. Effect of 4-HNE Modification on ZU5-ANK Domain and the Formation of Their Complex with β-Spectrin: A Molecular Dynamics Simulation Study. J Chem Inf Model 2019; 60:805-820. [DOI: 10.1021/acs.jcim.9b00772] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Antistio Alviz-Amador
- Analytical Chemistry and Biomedicine Group, Faculty of Exact and Natural Sciences, Campus of San Pablo, First floor Lab. 109, University of Cartagena, Cra. 50 #24-120, PA 130015, Cartagena, Colombia
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, Skaggs Pharmacy Research Building, University of Utah, 257 1400 E, Salt Lake City, Utah 84112, United States
| | - Humberto Pérez-González
- Analytical Chemistry and Biomedicine Group, Faculty of Exact and Natural Sciences, Campus of San Pablo, First floor Lab. 109, University of Cartagena, Cra. 50 #24-120, PA 130015, Cartagena, Colombia
| | - Erika Rodríguez-Cavallo
- Analytical Chemistry and Biomedicine Group, Faculty of Exact and Natural Sciences, Campus of San Pablo, First floor Lab. 109, University of Cartagena, Cra. 50 #24-120, PA 130015, Cartagena, Colombia
| | - Ricardo Vivas-Reyes
- Grupo de Química Cuántica y Teórica, Faculty of Exact and Natural Sciences, Campus of San Pablo, Second floor # 202, University of Cartagena, Cra. 50 #24-120, PA 130015, Cartagena, Colombia
| | - Darío Méndez-Cuadro
- Analytical Chemistry and Biomedicine Group, Faculty of Exact and Natural Sciences, Campus of San Pablo, First floor Lab. 109, University of Cartagena, Cra. 50 #24-120, PA 130015, Cartagena, Colombia
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Martín-Sierra C, Laranjeira P, Domingues MR, Paiva A. Lipoxidation and cancer immunity. Redox Biol 2019; 23:101103. [PMID: 30658904 PMCID: PMC6859558 DOI: 10.1016/j.redox.2019.101103] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/14/2018] [Accepted: 01/08/2019] [Indexed: 12/11/2022] Open
Abstract
Lipoxidation is a well-known reaction between electrophilic carbonyl species, formed during oxidation of lipids, and specific proteins that, in most cases, causes an alteration in proteins function. This can occur under physiological conditions but, in many cases, it has been associated to pathological process, including cancer. Lipoxidation may have an effect in cancer development through their effects in tumour cells, as well as through the alteration of immune components and the consequent modulation of the immune response. The formation of protein adducts affects different proteins in cancer, triggering different mechanism, such as proliferation, cell differentiation and apoptosis, among others, altering cancer progression. The divergent results obtained documented that the formation of lipoxidation adducts can have either anti-carcinogenic or pro-carcinogenic effects, depending on the cell type affected and the specific adduct formed. Moreover, lipoxidation adducts may alter the immune response, consequently causing either positive or negative alterations in cancer progression. Therefore, in this review, we summarize the effects of lipoxidation adducts in cancer cells and immune components and their consequences in the evolution of different types of cancer. Lipoxidation in tumour cells may lead to mechanism that interfere with cancer. Lipoxidation adducts can have either anti-carcinogenic or pro-carcinogenic effects. The triggered effects depend on the affected cell and the specific adduct formed. Lipoxidation affecting immune components may influence cancer progression. Lipoxidation may inhibit tumour progression through the inhibition of NFκB pathway.
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Affiliation(s)
- C Martín-Sierra
- Unidade de Gestão Operacional em Citometria, Centro Hospitalar e Universitário de Coimbra (CHUC), Portugal; Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - P Laranjeira
- Unidade de Gestão Operacional em Citometria, Centro Hospitalar e Universitário de Coimbra (CHUC), Portugal; Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - M R Domingues
- Mass Spectrometry Centre, Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal; Department of Chemistry & CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - A Paiva
- Unidade de Gestão Operacional em Citometria, Centro Hospitalar e Universitário de Coimbra (CHUC), Portugal; Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal; Instituto Politécnico de Coimbra, ESTESC-Coimbra Health School, Ciências Biomédicas Laboratoriais, Portugal.
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7
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Alviz-Amador A, Galindo-Murillo R, Pineda-Alemán R, Pérez-González H, Rodríguez-Cavallo E, Vivas-Reyes R, Méndez-Cuadro D. 4-HNE carbonylation induces local conformational changes on bovine serum albumin and thioredoxin. A molecular dynamics study. J Mol Graph Model 2019; 86:298-307. [DOI: 10.1016/j.jmgm.2018.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 10/22/2018] [Accepted: 11/01/2018] [Indexed: 01/09/2023]
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8
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Gesslbauer B, Kuerzl D, Valpatic N, Bochkov VN. Unbiased Identification of Proteins Covalently Modified by Complex Mixtures of Peroxidized Lipids Using a Combination of Electrophoretic Mobility Band Shift with Mass Spectrometry. Antioxidants (Basel) 2018; 7:antiox7090116. [PMID: 30200198 PMCID: PMC6162613 DOI: 10.3390/antiox7090116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 12/15/2022] Open
Abstract
Covalent modification of functionally important cell proteins by lipid oxidation products (LOPs) is a known mechanism initiating pathological consequences of oxidative stress. Identification of new proteins covalently modified by electrophilic lipids can be performed by a combination of chemical, immunological, and mass spectrometry-based methods, but requires prior knowledge either on the exact molecular structure of LOPs (e.g., 4-hydroxynonenal) or candidate protein targets. However, under the conditions of oxidative stress in vivo, a complex mixture of proteins (e.g., cytosolic proteome) reacts with a complex mixture of LOPs. Here we describe a method for detection of lipid-modified proteins that does not require an a priori knowledge on the chemical structure of LOPs or identity of target proteins. The method is based on the change of electrophoretic mobility of lipid-modified proteins, which is induced by conformational changes and cross-linking with other proteins. Abnormally migrating proteins are detected by mass spectrometry-based protein peptide sequencing. We applied this method to study effects of oxidized palmitoyl-arachidonoyl-phosphatidylcholine (OxPAPC) on endothelial cells. Several known, but also many new, OxPAPC-binding proteins were identified. We expect that this technically relatively simple method can be widely applied for label-free analysis of lipid-protein interactions in complex protein samples treated with different LOPs.
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Affiliation(s)
- Bernd Gesslbauer
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Humboldtstrasse 46, 8010 Graz, Austria.
| | - David Kuerzl
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Humboldtstrasse 46, 8010 Graz, Austria.
| | - Niko Valpatic
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Humboldtstrasse 46, 8010 Graz, Austria.
| | - Valery N Bochkov
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Humboldtstrasse 46, 8010 Graz, Austria.
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9
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Zuo Y, Jia CZ. CarSite: identifying carbonylated sites of human proteins based on a one-sided selection resampling method. MOLECULAR BIOSYSTEMS 2018; 13:2362-2369. [PMID: 28937156 DOI: 10.1039/c7mb00363c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Protein carbonylation is one of the most important biomarkers of oxidative protein damage and such protein damage is linked to various diseases and aging. It is thus vital that carbonylation sites are identified accurately. In this study, CarSite, a novel bioinformatics tool, was established to identify carbonylation sites in human proteins. The one-sided selection (OSS) resampling method was used to establish balanced training datasets and this resampling method is demonstrated to perform better than a Monte Carlo resampling method via 10-fold cross-validation tests on the Jia dataset. Moreover, the hybrid combination of position-specific amino acid propensity (PSAAP), composition of k-spaced amino acid pairs (CKSAAP), amino acid composition (AAC), and composition of hydrophobic and hydrophilic amino acids (CHHAA) was selected to optimize the performance of the predictor. On 10-fold cross-validation of the Jia dataset, CarSite obtained rates of sensitivity corresponding to K/P/R/T-type peptides of ∼21%, 22%, 19%, or 18% higher than those obtained by iCar-PseCp, respectively, which was previously considered as the best predictor for identifying carbonylation sites in human proteins. Furthermore, compared with other existing predictors, CarSite obtained much higher sensitivity and accuracy when tested on the same dataset.
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Affiliation(s)
- Yun Zuo
- Department of Mathematics, Dalian Maritime University, No. 1 Linghai Road, Dalian, 116026, China.
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10
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Guéraud F. 4-Hydroxynonenal metabolites and adducts in pre-carcinogenic conditions and cancer. Free Radic Biol Med 2017; 111:196-208. [PMID: 28065782 DOI: 10.1016/j.freeradbiomed.2016.12.025] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/14/2016] [Accepted: 12/17/2016] [Indexed: 12/22/2022]
Abstract
4-hydroxy-2-nonenal (HNE) is an amazing reactive compound, originating from lipid peroxidation within cells but also in food and considered as a "second messenger" of oxidative stress. Due to its chemical features, HNE is able to make covalent links with DNA, proteins and lipids. The aim of this review is to give a comprehensive summary of the chemical properties of HNE and of the consequences of its reactivity in relation to cancer development. The formation of exocyclic etheno-and propano-adducts and genotoxic effects are addressed. The adduction to cellular proteins and the repercussions on the regulation of cell signaling pathways involved in cancer development are reviewed, notably on the Nrf2/Keap1/ARE pathway. The metabolic pathways leading to the inactivation/elimination or, on the contrary, to the bioactivation of HNE are considered. A special focus is given on the link between HNE and colorectal cancer development, due to its occurrence in foodstuffs and in the digestive lumen, during digestion.
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Affiliation(s)
- Françoise Guéraud
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France.
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11
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Aslebagh R, Pfeffer BA, Fliesler SJ, Darie CC. Mass spectrometry-based proteomics of oxidative stress: Identification of 4-hydroxy-2-nonenal (HNE) adducts of amino acids using lysozyme and bovine serum albumin as model proteins. Electrophoresis 2016; 37:2615-2623. [PMID: 27184861 DOI: 10.1002/elps.201600134] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/29/2016] [Accepted: 05/09/2016] [Indexed: 12/25/2022]
Abstract
Modification of proteins by 4-hydroxy-2-nonenal (HNE), a reactive by-product of ω6 polyunsaturated fatty acid oxidation, on specific amino acid residues is considered a biomarker for oxidative stress, as occurs in many metabolic, hereditary, and age-related diseases. HNE modification of amino acids can occur either via Michael addition or by formation of Schiff-base adducts. These modifications typically occur on cysteine (Cys), histidine (His), and/or lysine (Lys) residues, resulting in an increase of 156 Da (Michael addition) or 138 Da (Schiff-base adducts), respectively, in the mass of the residue. Here, we employed biochemical and mass spectrometry (MS) approaches to determine the MS "signatures" of HNE-modified amino acids, using lysozyme and BSA as model proteins. Using direct infusion of unmodified and HNE-modified lysozyme into an electrospray quadrupole time-of-flight mass spectrometer, we were able to detect up to seven HNE modifications per molecule of lysozyme. Using nanoLC-MS/MS, we found that, in addition to N-terminal amino acids, Cys, His, and Lys residues, HNE modification of arginine (Arg), threonine (Thr), tryptophan (Trp), and histidine (His) residues can also occur. These sensitive and specific methods can be applied to the study of oxidative stress to evaluate HNE modification of proteins in complex mixtures from cells and tissues under diseased versus normal conditions.
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Affiliation(s)
- Roshanak Aslebagh
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Bruce A Pfeffer
- Research Service, VA Western NY Healthcare System, Buffalo, NY, USA.,Departments of Ophthalmology and Biochemistry, SUNY- University at Buffalo, Buffalo, NY, USA.,SUNY Eye Institute, Buffalo, NY, USA
| | - Steven J Fliesler
- Research Service, VA Western NY Healthcare System, Buffalo, NY, USA.,Departments of Ophthalmology and Biochemistry, SUNY- University at Buffalo, Buffalo, NY, USA.,SUNY Eye Institute, Buffalo, NY, USA
| | - Costel C Darie
- Biochemistry and Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA.
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12
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Schaur RJ, Siems W, Bresgen N, Eckl PM. 4-Hydroxy-nonenal-A Bioactive Lipid Peroxidation Product. Biomolecules 2015; 5:2247-337. [PMID: 26437435 PMCID: PMC4693237 DOI: 10.3390/biom5042247] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 12/23/2022] Open
Abstract
This review on recent research advances of the lipid peroxidation product 4-hydroxy-nonenal (HNE) has four major topics: I. the formation of HNE in various organs and tissues, II. the diverse biochemical reactions with Michael adduct formation as the most prominent one, III. the endogenous targets of HNE, primarily peptides and proteins (here the mechanisms of covalent adduct formation are described and the (patho-) physiological consequences discussed), and IV. the metabolism of HNE leading to a great number of degradation products, some of which are excreted in urine and may serve as non-invasive biomarkers of oxidative stress.
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Affiliation(s)
- Rudolf J Schaur
- Institute of Molecular Biosciences, University of Graz, Heinrichstrasse 33a, 8010 Graz, Austria.
| | - Werner Siems
- Institute for Medical Education, KortexMed GmbH, Hindenburgring 12a, 38667 Bad Harzburg, Germany.
| | - Nikolaus Bresgen
- Division of Genetics, Department of Cell Biology, University of Salzburg, Hellbrunnerstasse 34, 5020 Salzburg, Austria.
| | - Peter M Eckl
- Division of Genetics, Department of Cell Biology, University of Salzburg, Hellbrunnerstasse 34, 5020 Salzburg, Austria.
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Takahashi R, Goto T, Oe T, Lee SH. Angiotensin II modification by decomposition products of linoleic acid-derived lipid hydroperoxide. Chem Biol Interact 2015; 239:87-99. [DOI: 10.1016/j.cbi.2015.06.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 05/27/2015] [Accepted: 06/20/2015] [Indexed: 12/20/2022]
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14
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Aldini G, Domingues MR, Spickett CM, Domingues P, Altomare A, Sánchez-Gómez FJ, Oeste CL, Pérez-Sala D. Protein lipoxidation: Detection strategies and challenges. Redox Biol 2015; 5:253-266. [PMID: 26072467 PMCID: PMC4477048 DOI: 10.1016/j.redox.2015.05.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/14/2015] [Accepted: 05/19/2015] [Indexed: 12/21/2022] Open
Abstract
Enzymatic and non-enzymatic lipid metabolism can give rise to reactive species that may covalently modify cellular or plasma proteins through a process known as lipoxidation. Under basal conditions, protein lipoxidation can contribute to normal cell homeostasis and participate in signaling or adaptive mechanisms, as exemplified by lipoxidation of Ras proteins or of the cytoskeletal protein vimentin, both of which behave as sensors of electrophilic species. Nevertheless, increased lipoxidation under pathological conditions may lead to deleterious effects on protein structure or aggregation. This can result in impaired degradation and accumulation of abnormally folded proteins contributing to pathophysiology, as may occur in neurodegenerative diseases. Identification of the protein targets of lipoxidation and its functional consequences under pathophysiological situations can unveil the modification patterns associated with the various outcomes, as well as preventive strategies or potential therapeutic targets. Given the wide structural variability of lipid moieties involved in lipoxidation, highly sensitive and specific methods for its detection are required. Derivatization of reactive carbonyl species is instrumental in the detection of adducts retaining carbonyl groups. In addition, use of tagged derivatives of electrophilic lipids enables enrichment of lipoxidized proteins or peptides. Ultimate confirmation of lipoxidation requires high resolution mass spectrometry approaches to unequivocally identify the adduct and the targeted residue. Moreover, rigorous validation of the targets identified and assessment of the functional consequences of these modifications are essential. Here we present an update on methods to approach the complex field of lipoxidation along with validation strategies and functional assays illustrated with well-studied lipoxidation targets.
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Affiliation(s)
- Giancarlo Aldini
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - M Rosário Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, Aveiro 3810-193, Portugal
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston Triangle, Aston University, Birmingham B4 7ET, UK
| | - Pedro Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, Aveiro 3810-193, Portugal
| | - Alessandra Altomare
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Francisco J Sánchez-Gómez
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, Madrid 28040, Spain
| | - Clara L Oeste
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, Madrid 28040, Spain
| | - Dolores Pérez-Sala
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, Madrid 28040, Spain.
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15
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Kim HJ, Ha S, Lee HY, Lee KJ. ROSics: chemistry and proteomics of cysteine modifications in redox biology. MASS SPECTROMETRY REVIEWS 2015; 34:184-208. [PMID: 24916017 PMCID: PMC4340047 DOI: 10.1002/mas.21430] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 04/30/2013] [Accepted: 11/20/2013] [Indexed: 05/29/2023]
Abstract
Post-translational modifications (PTMs) occurring in proteins determine their functions and regulations. Proteomic tools are available to identify PTMs and have proved invaluable to expanding the inventory of these tools of nature that hold the keys to biological processes. Cysteine (Cys), the least abundant (1-2%) of amino acid residues, are unique in that they play key roles in maintaining stability of protein structure, participating in active sites of enzymes, regulating protein function and binding to metals, among others. Cys residues are major targets of reactive oxygen species (ROS), which are important mediators and modulators of various biological processes. It is therefore necessary to identify the Cys-containing ROS target proteins, as well as the sites and species of their PTMs. Cutting edge proteomic tools which have helped identify the PTMs at reactive Cys residues, have also revealed that Cys residues are modified in numerous ways. These modifications include formation of disulfide, thiosulfinate and thiosulfonate, oxidation to sulfenic, sulfinic, sulfonic acids and thiosulfonic acid, transformation to dehydroalanine (DHA) and serine, palmitoylation and farnesylation, formation of chemical adducts with glutathione, 4-hydroxynonenal and 15-deoxy PGJ2, and various other chemicals. We present here, a review of relevant ROS biology, possible chemical reactions of Cys residues and details of the proteomic strategies employed for rapid, efficient and sensitive identification of diverse and novel PTMs involving reactive Cys residues of redox-sensitive proteins. We propose a new name, "ROSics," for the science which describes the principles of mode of action of ROS at molecular levels.
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Affiliation(s)
- Hee-Jung Kim
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans UniversitySeoul, 120-750, Korea
| | - Sura Ha
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST)Daejeon, 305-701, Korea
| | - Hee Yoon Lee
- Department of Chemistry, Korea Advanced Institute of Science & Technology (KAIST)Daejeon, 305-701, Korea
| | - Kong-Joo Lee
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans UniversitySeoul, 120-750, Korea
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Lv H, Han J, Liu J, Zheng J, Liu R, Zhong D. CarSPred: a computational tool for predicting carbonylation sites of human proteins. PLoS One 2014; 9:e111478. [PMID: 25347395 PMCID: PMC4210226 DOI: 10.1371/journal.pone.0111478] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 09/26/2014] [Indexed: 12/15/2022] Open
Abstract
Protein carbonylation is one of the most pervasive oxidative stress-induced post-translational modifications (PTMs), which plays a significant role in the etiology and progression of several human diseases. It has been regarded as a biomarker of oxidative stress due to its relatively early formation and stability compared with other oxidative PTMs. Only a subset of proteins is prone to carbonylation and most carbonyl groups are formed from lysine (K), arginine (R), threonine (T) and proline (P) residues. Recent advancements in analysis of the PTM by mass spectrometry provided new insights into the mechanisms of protein carbonylation, such as protein susceptibility and exact modification sites. However, the experimental approaches to identifying carbonylation sites are costly, time-consuming and capable of processing a limited number of proteins, and there is no bioinformatics method or tool devoted to predicting carbonylation sites of human proteins so far. In the paper, a computational method is proposed to identify carbonylation sites of human proteins. The method extracted four kinds of features and combined the minimum Redundancy Maximum Relevance (mRMR) feature selection criterion with weighted support vector machine (WSVM) to achieve total accuracies of 85.72%, 85.95%, 83.92% and 85.72% for K, R, T and P carbonylation site predictions respectively using 10-fold cross-validation. The final optimal feature sets were analysed, the position-specific composition and hydrophobicity environment of flanking residues of modification sites were discussed. In addition, a software tool named CarSPred has been developed to facilitate the application of the method. Datasets and the software involved in the paper are available at https://sourceforge.net/projects/hqlstudio/files/CarSPred-1.0/.
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Affiliation(s)
- Hongqiang Lv
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Jiuqiang Han
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
- * E-mail: (JQH); (JL)
| | - Jun Liu
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
- * E-mail: (JQH); (JL)
| | - Jiguang Zheng
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Ruiling Liu
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Dexing Zhong
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
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Lipoxidation adducts with peptides and proteins: deleterious modifications or signaling mechanisms? J Proteomics 2013; 92:110-31. [PMID: 23770299 DOI: 10.1016/j.jprot.2013.06.004] [Citation(s) in RCA: 289] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 05/20/2013] [Accepted: 06/03/2013] [Indexed: 11/23/2022]
Abstract
Protein lipoxidation refers to the modification by electrophilic lipid oxidation products to form covalent adducts, which for many years has been considered as a deleterious consequence of oxidative stress. Oxidized lipids or phospholipids containing carbonyl moieties react readily with lysine to form Schiff bases; alternatively, oxidation products containing α,β-unsaturated moieties are susceptible to nucleophilic attack by cysteine, histidine or lysine residues to yield Michael adducts, overall corresponding to a large number of possible protein adducts. The most common detection methods for lipoxidized proteins take advantage of the presence of reactive carbonyl groups to add labels, or use antibodies. These methods have limitations in terms of specificity and identification of the modification site. The latter question is satisfactorily addressed by mass spectrometry, which enables the characterization of the adduct structure. This has allowed the identification of lipoxidized proteins in physiological and pathological situations. While in many cases lipoxidation interferes with protein function, causing inhibition of enzymatic activity and increased immunogenicity, there are a small number of cases where lipoxidation results in gain of function or activity. For certain proteins lipoxidation may represent a form of redox signaling, although more work is required to confirm the physiological relevance and mechanisms of such processes. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Mulliner D, Schüürmann G. Model Suite for Predicting the Aquatic Toxicity of α,β-Unsaturated Esters Triggered by Their Chemoavailability. Mol Inform 2013; 32:98-107. [DOI: 10.1002/minf.201200101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 11/14/2012] [Indexed: 11/10/2022]
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Méndez D, Hernáez ML, Kamali AN, Diez A, Puyet A, Bautista JM. Differential carbonylation of cytoskeletal proteins in blood group O erythrocytes: Potential role in protection against severe malaria. INFECTION GENETICS AND EVOLUTION 2012; 12:1780-7. [DOI: 10.1016/j.meegid.2012.06.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 06/25/2012] [Accepted: 06/27/2012] [Indexed: 11/30/2022]
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Plasmodium yoelii blood-stage antigens newly identified by immunoaffinity using purified IgG antibodies from malaria-resistant mice. Immunobiology 2012; 217:823-30. [PMID: 22658767 DOI: 10.1016/j.imbio.2012.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/07/2012] [Indexed: 12/12/2022]
Abstract
As the search for an effective human malaria vaccine continues, understanding immune responses to Plasmodium in rodent models is perhaps the key to unlocking new vaccine strategies. The recruitment of parasite-specific antibodies is an important component of natural immunity against infection in blood-stage malaria. Here, we describe the use of sera from naturally surviving ICR mice after infection with lethal doses of Plasmodium yoelii yoelii 17XL to identify highly immunogenic blood-stage antigens. Immobilized protein A/G was used for the affinity-chromatography purification of the IgGs present in pooled sera from surviving mice. These protective IgGs, covalently immobilized on agarose columns, were then used to isolate reactive antigens from whole P. yoelii yoelii 17XL protein extracts obtained from the blood-stage malaria infection. Through proteomics analysis of the recovered parasite antigens, we were able to identify two endoplasmic reticulum lumen proteins: protein disulfide isomerase and a member of the heat shock protein 70 family. Also identified were the digestive protease plasmepsin and the 39 kDa-subunit of eukaryotic translation initiation factor 3, a ribosome associated protein. Of these four proteins, three have not been previously identified as antigenic during blood-stage malaria infection. This procedure of isolating and identifying parasite antigens using serum IgGs from malaria-protected individuals could be a novel strategy for the development of multi-antigen-based vaccine therapies.
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Guo J, Prokai L. To tag or not to tag: a comparative evaluation of immunoaffinity-labeling and tandem mass spectrometry for the identification and localization of posttranslational protein carbonylation by 4-hydroxy-2-nonenal, an end-product of lipid peroxidation. J Proteomics 2011; 74:2360-9. [PMID: 21835276 DOI: 10.1016/j.jprot.2011.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 06/02/2011] [Accepted: 07/13/2011] [Indexed: 01/26/2023]
Abstract
Posttranslational carbonylation of proteins by the covalent attachment of the lipid peroxidation product 4-hydroxy-2-nonenal (HNE) is a biomarker of oxidative stress. Tandem mass spectrometry (MS/MS) has become an essential tool for characterization of this modification. Chemical tagging methods have been used to facilitate the immunoaffinity-based enrichment or even quantification of HNE-modified peptides and proteins. With MS/MS spectra of the untagged modified peptides considered as references, a comparative evaluation is presented focusing on the impact of affinity-tagging with four carbonyl-specific reagents (2,4-dinitrophenyl hydrazine, biotin hydrazide, biotinamidohexanoic acid hydrazide and N'-aminooxymethylcarbonyl-hydrazino D-biotin) on collision-induced dissociation of the tagged HNE-carbonylated peptides. Our study has shown that chemical labeling may not be carried out successfully for all the peptides and with all the reagents. The attachment of a tag usually cannot circumvent the occurrence of strong neutral losses observed with untagged species and, in addition, fragmentation of the introduced tag may also happen. Chemical tagging of certain peptides may, nevertheless, afford more sequence ions upon MS/MS than the untagged carbonylated peptide, especially when Michael addition of the lipid peroxidation product occurs on cysteine residues. Therefore, tagging may increase the confidence of identifications of HNE-modified peptides by database searches.
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Affiliation(s)
- Jia Guo
- Department of Molecular Biology & Immunology, University of North Texas Health Science Center, Fort Worth, USA
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Protein targets for carbonylation by 4-hydroxy-2-nonenal in rat liver mitochondria. J Proteomics 2011; 74:2370-9. [PMID: 21801862 DOI: 10.1016/j.jprot.2011.07.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 06/27/2011] [Accepted: 07/12/2011] [Indexed: 02/03/2023]
Abstract
Protein carbonylation has been associated with various pathophysiological processes. A representative reactive carbonyl species (RCS), 4-hydroxy-2-nonenal (HNE), has been implicated specifically as a causative factor for the initiation and/or progression of various diseases. To date, however, little is known about the proteins and their modification sites susceptible to "carbonyl stress" by this RCS, especially in the liver. Using chemoprecipitation based on a solid-phase hydrazine chemistry coupled with LC-MS/MS bottom-up approach and database searching, we identified several protein-HNE adducts in isolated rat liver mitochondria upon HNE exposure. The identification of selected major protein targets, such as the ATP synthase β-subunit, was further confirmed by immunoblotting and a gel-based approach in combination with LC-MS/MS. A network was also created based on the identified protein targets, which showed that the main protein interactions were associated with cell death, tumor morphology and drug metabolism, implicating the toxic nature of HNE in the liver mitoproteome. The functional consequence of carbonylation was illustrated by its detrimental impact on the activity of ATP synthase, a representative major mitochondrial protein target for HNE modifications.
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Méndez D, Linares M, Diez A, Puyet A, Bautista JM. Stress response and cytoskeletal proteins involved in erythrocyte membrane remodeling upon Plasmodium falciparum invasion are differentially carbonylated in G6PD A- deficiency. Free Radic Biol Med 2011; 50:1305-13. [PMID: 21376116 DOI: 10.1016/j.freeradbiomed.2011.02.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 02/18/2011] [Accepted: 02/23/2011] [Indexed: 12/30/2022]
Abstract
Multiple glucose-6-phosphate dehydrogenase (G6PD)-deficient alleles have reached polymorphic frequencies because of the protection they confer against malaria infection. A protection mechanism based on enhanced phagocytosis of parasitized G6PD-deficient erythrocytes that are oxidatively damaged is well accepted. Although an association of this phenotype with the impairment of the antioxidant defense in G6PD deficiency has been demonstrated, the dysfunctional pathway leading to membrane damage and modified exposure of the malaria-infected red cell to the host is not known. Thus, in this study, erythrocytes from the common African variant G6PD A- were used to analyze by redox proteomics the major oxidative changes occurring in the host membrane proteins during the intraerythrocytic development of Plasmodium falciparum, the most lethal malaria parasite. Fifteen carbonylated membrane proteins exclusively identified in infected G6PD A- red blood cells revealed selective oxidation of host proteins upon malarial infection. As a result, three pathways in the host erythrocyte were oxidatively damaged in G6PD A-: (1) traffic/assembly of exported parasite proteins in red cell cytoskeleton and surface, (2) oxidative stress defense proteins, and (3) stress response proteins. Additional identification of hemichromes associated with membrane proteins also supports a role for specific oxidative modifications in protection against malaria by G6PD polymorphisms.
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Affiliation(s)
- Darío Méndez
- Departamento de Bioquímica y Biología Molecular IV, Universidad Complutense de Madrid, Ciudad Universitaria, 28040 Madrid, Spain
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Mulliner D, Wondrousch D, Schüürmann G. Predicting Michael-acceptor reactivity and toxicity through quantum chemical transition-state calculations. Org Biomol Chem 2011; 9:8400-12. [DOI: 10.1039/c1ob06065a] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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