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Davidsen K, Sullivan LB. A robust method for measuring aminoacylation through tRNA-Seq. eLife 2024; 12:RP91554. [PMID: 39076160 PMCID: PMC11288633 DOI: 10.7554/elife.91554] [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: 07/31/2024] Open
Abstract
Current methods to quantify the fraction of aminoacylated tRNAs, also known as the tRNA charge, are limited by issues with either low throughput, precision, and/or accuracy. Here, we present an optimized charge transfer RNA sequencing (tRNA-Seq) method that combines previous developments with newly described approaches to establish a protocol for precise and accurate tRNA charge measurements. We verify that this protocol provides robust quantification of tRNA aminoacylation and we provide an end-to-end method that scales to hundreds of samples including software for data processing. Additionally, we show that this method supports measurements of relative tRNA expression levels and can be used to infer tRNA modifications through reverse transcription misincorporations, thereby supporting multipurpose applications in tRNA biology.
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Affiliation(s)
- Kristian Davidsen
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Molecular and Cellular Biology Program, University of WashingtonSeattleUnited States
| | - Lucas B Sullivan
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
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2
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Davidsen K, Sullivan LB. A robust method for measuring aminoacylation through tRNA-Seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.31.551363. [PMID: 37577502 PMCID: PMC10418082 DOI: 10.1101/2023.07.31.551363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Current methods to quantify the fraction of aminoacylated tRNAs, also known as the tRNA charge, are limited by issues with either low throughput, precision, and/or accuracy. Here, we present an optimized charge tRNA-Seq method that combines previous developments with newly described approaches to establish a protocol for precise and accurate tRNA charge measurements. We verify that this protocol provides robust quantification of tRNA aminoacylation and we provide an end-to-end method that scales to hundreds of samples including software for data processing. Additionally, we show that this method supports measurements of relative tRNA expression levels and can be used to infer tRNA modifications through reverse transcription misincorporations, thereby supporting multipurpose applications in tRNA biology.
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Affiliation(s)
- Kristian Davidsen
- Human Biology Division, Fred Hutchinson Cancer Center, United States
- Molecular and Cellular Biology Program, University of Washington, United States
| | - Lucas B Sullivan
- Human Biology Division, Fred Hutchinson Cancer Center, United States
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3
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Zhong Y, Lu Y, Lv L. Theanine in Tea: An Effective Scavenger of Single or Multiple Reactive Carbonyl Species at the Same Time. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37906124 DOI: 10.1021/acs.jafc.3c05483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Reactive carbonyl species (RCS) are generated during thermal food processing, and their accumulation in the body increases the risk of various chronic diseases. Herein, the RCS-scavenging ability of theanine, a unique nonproteinogenic amino acid, was evaluated in terms of the scavenging rate, reaction kinetics, and reaction pathway using LC-MS/MS. Three major products of theanine conjugated with acrolein (ACR) and glyoxal (GO) were prepared and identified using nuclear magnetic resonance. Thereafter, the simultaneous reactions of four types of RCS (namely, ACR, crotonaldehyde, methylglyoxal, and GO) with theanine were discussed in RCS-theanine and RCS-tea models. Under different reaction ratios, theanine could nonspecifically scavenge the four coexisting RCS by forming adducts with them. The amount of theanine-RCS adducts in green and black tea was more than that of catechin (epigallocatechin gallate, epigallocatechin, epicatechin gallate, and epicatechin)-RCS adducts despite the lower content of theanine than catechins. Thus, theanine, as a food additive and dietary supplement, could demonstrate new bioactivity as a promising RCS scavenger in food processing.
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Affiliation(s)
- Yuqing Zhong
- Department of Food Science and Technology, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Nanjing 210023, P. R. China
| | - Yongling Lu
- Department of Food Science and Technology, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Nanjing 210023, P. R. China
| | - Lishuang Lv
- Department of Food Science and Technology, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2# Xuelin Road, Nanjing 210023, P. R. China
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Ebert B, Ebert D, Koebsch K, Maser E, Kisiela M. Carbonyl reductases from Daphnia are regulated by redox cycling compounds. FEBS J 2018; 285:2869-2887. [PMID: 29893480 DOI: 10.1111/febs.14578] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 05/20/2018] [Accepted: 06/11/2018] [Indexed: 01/22/2023]
Abstract
Oxidative stress is a major source of reactive carbonyl compounds that can damage cellular macromolecules, leading to so-called carbonyl stress. Aside from endogenously formed carbonyls, including highly reactive short-chain aldehydes and diketones, air pollutants derived from diesel exhaust like 9,10-phenanthrenequinone (PQ) can amplify oxidative stress by redox cycling, causing tissue damage. Carbonyl reductases (CRs), which are inducible in response to ROS, represent a fundamental enzymatic defense mechanism against oxidative stress. While commonly two carbonyl reductases (CBR1 and CBR3) are found in mammalian genomes, invertebrate model organisms like Drosophila melanogaster express no CR but a functional homolog to human CBR1, termed sniffer. The microcrustacean Daphnia is an ideal model organism to investigate the function of CRs because of its unique equipment with even four copies of the CR gene (CR1, CR2, CR3, CR4) in addition to one sniffer gene. Cloning and catalytic characterization of two carbonyl reductases CR1 and CR3 from D. magna and D. pulex arenata revealed that both proteins reductively metabolize aromatic dicarbonyls (e.g., menadione, PQ) and aliphatic α-diketones (e.g., 2,3-hexanedione), while sugar-derived aldehydes (methylglyoxal, glyoxal) and lipid peroxidation products such as acrolein and butanal were poor substrates, indicating no physiological function in the metabolism of short-chain aldehydes. Treatment of D. magna with redox cyclers like menadione and the pesticide paraquat led to an upregulation of CR1 and CR3 mRNA, suggesting a role in oxidative stress defense. Further studies are needed to investigate their potential to serve as novel biomarkers for oxidative stress in Daphnia.
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Affiliation(s)
- Bettina Ebert
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School Schleswig-Holstein, Kiel, Germany
| | - Dieter Ebert
- Departement Environmental Sciences, Zoology, Basel University, Switzerland
| | - Katrin Koebsch
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School Schleswig-Holstein, Kiel, Germany
| | - Edmund Maser
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School Schleswig-Holstein, Kiel, Germany
| | - Michael Kisiela
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School Schleswig-Holstein, Kiel, Germany.,Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Germany
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Schwarzenbolz U, Förster A, Henle T. Influence of high hydrostatic pressure on the reaction between glyoxal and lysine residues. Eur Food Res Technol 2017. [DOI: 10.1007/s00217-017-2846-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Diacetyl and related flavorant α-Diketones: Biotransformation, cellular interactions, and respiratory-tract toxicity. Toxicology 2017; 388:21-29. [PMID: 28179188 DOI: 10.1016/j.tox.2017.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/30/2017] [Accepted: 02/01/2017] [Indexed: 01/26/2023]
Abstract
Exposure to diacetyl and related α-diketones causes respiratory-tract damage in humans and experimental animals. Chemical toxicity is often associated with covalent modification of cellular nucleophiles by electrophilic chemicals. Electrophilic α-diketones may covalently modify nucleophilic arginine residues in critical proteins and, thereby, produce the observed respiratory-tract pathology. The major pathway for the biotransformation of α-diketones is reduction to α-hydroxyketones (acyloins), which is catalyzed by NAD(P)H-dependent enzymes of the short-chain dehydrogenase/reductase (SDR) and the aldo-keto reductase (AKR) superfamilies. Reduction of α-diketones to the less electrophilic acyloins is a detoxication pathway for α-diketones. The pyruvate dehydrogenase complex may play a significant role in the biotransformation of diacetyl to CO2. The interaction of toxic electrophilic chemicals with cellular nucleophiles can be predicted by the hard and soft, acids and bases (HSAB) principle. Application of the HSAB principle to the interactions of electrophilic α-diketones with cellular nucleophiles shows that α-diketones react preferentially with arginine residues. Furthermore, the respiratory-tract toxicity and the quantum-chemical reactivity parameters of diacetyl and replacement flavorant α-diketones are similar. Hence, the identified replacement flavorant α-diketones may pose a risk of flavorant-induced respiratory-tract toxicity. The calculated indices for the reaction of α-diketones with arginine support the hypothesis that modification of protein-bound arginine residues is a critical event in α-diketone-induced respiratory-tract toxicity.
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Mass spectrometric studies of the reaction of a blocked arginine with diketonic α-dicarbonyls. Amino Acids 2015; 48:873-885. [PMID: 26592498 DOI: 10.1007/s00726-015-2135-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/05/2015] [Indexed: 10/22/2022]
Abstract
The modification of arginine residues by diketonic α-dicarbonyls, in structural proteins and enzymes studies, is a process known for decades. The chemistry of these reaction processes is, however, not fully understood. Moreover, modification of arginine residues by reaction with α-dicarbonyls in glycation has also not been completely elucidated. Aspects related to the early stages of the condensation of arginine with one dicarbonyl molecule, leading to the formation of dihydroxyimidazolidines and their dehydrated forms, in particular, are here approached in more detail. Taking into consideration the usually rapid kinetics involved in the formation of the early reaction product species, we decided to use fast, sensitive and selective analytical techniques, such as electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (ESI-MS(n)) to monitor the reactions of a blocked arginine (acetyl-arginine) with several selected diketonic α-dicarbonyls, to identify and characterize the mentioned transient species and to probe the reaction mechanism involved. Compounds grouped into two different classes according to their structural similarity were identified, namely acetyl-dihydroxyimidazolidines and acetyl-bis(dihydroxyimidazolidines), together with their dehydrated species. The former compounds are known to exist in solution. The reactivity of acetyl-bis(dihydroxyimidazolidines) seems to be different from that of acetyl-dihydroxyimidazolidines. To note that dehydration appears to be reinforced in acetyl-bis(dihydroxyimidazolidines) chemistry with respect to acetyl-dihydroxyimidazolidine chemistry, while both structurally related compounds involve mostly dihemiaminals reactivity. Two different ion structures are proposed for single dehydrated acetyl-bis(dihydroxyimidazolidines), concerning the two more symmetrical and two more asymmetrical dicarbonyls reacted. In acetyl-bis(dihydroxyimidazolidines) formation, we concluded that the importance of single dehydration relies on the rapid minimization of sterics and energetics of the reaction moieties formed. These reactions occur also in a selective way, regarding the two compound structures proposed for single dehydrated acetyl-bis(dihydroxyimidazolidines). Further considerations are also established for the formation of single dehydrated acetyl-bis(dihydroxyimidazolidines). An explanation for the reversible nature of the reaction of arginine with diketonic dicarbonyls is also provided. This study reinforces the potential of the fast, sensitive and selective electrospray ionization mass spectrometry techniques for the investigation of transient species and their mechanistics, that might otherwise not be feasible by means of the most commonly used spectroscopic techniques.
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Chen HJC, Chen YC, Hsiao CF, Chen PF. Mass Spectrometric Analysis of Glyoxal and Methylglyoxal-Induced Modifications in Human Hemoglobin from Poorly Controlled Type 2 Diabetes Mellitus Patients. Chem Res Toxicol 2015; 28:2377-89. [DOI: 10.1021/acs.chemrestox.5b00380] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hauh-Jyun Candy Chen
- Department
of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
| | - Yu-Chin Chen
- Department
of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
| | - Chiung-Fong Hsiao
- Department
of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
| | - Pin-Fan Chen
- Buddhist Dalin Tzu Chi General Hospital, No.2, Minsheng Road, Dalin, Chia-Yi 622, Taiwan
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de Lorenzo V, Sekowska A, Danchin A. Chemical reactivity drives spatiotemporal organisation of bacterial metabolism. FEMS Microbiol Rev 2014; 39:96-119. [PMID: 25227915 DOI: 10.1111/1574-6976.12089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
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Cichocki JA, Smith GJ, Morris JB. Tissue sensitivity of the rat upper and lower extrapulmonary airways to the inhaled electrophilic air pollutants diacetyl and acrolein. Toxicol Sci 2014; 142:126-36. [PMID: 25145656 DOI: 10.1093/toxsci/kfu165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The target site for inhaled vapor-induced injury often differs in mouth-breathing humans compared with nose-breathing rats, thus complicating the use of rat inhalation toxicity data for assessment of human risk. We sought to examine sensitivity of respiratory/transitional nasal (RTM) and tracheobronchial (TBM) mucosa to two electrophilic irritant vapors: diacetyl and acrolein. Computational fluid dynamic physiologically based pharmacokinetic modeling was coupled with biomarker assessment to establish delivered dose-response relationships in RTM and TBM in male F344 rats following 6 h exposure to diacetyl or acrolein. Biomarkers included glutathione status, proinflammatory and antioxidant gene mRNA levels, and nuclear translocation of nuclear factor (erythroid-derived 2)-like 2 (Nrf2). Modeling revealed that 0.0094-0.1653 μg acrolein/min-cm(2) and 3.9-21.6 μg diacetyl/min-cm(2) were deposited into RTM/TBM. Results indicate RTM and TBM were generally of similar sensitivity to diacetyl and acrolein. For instance, both tissues displayed induction of antioxidant and proinflammatory genes, and nuclear accumulation of Nrf2 after electrophile exposure. Hierarchical cellular response patterns were similar in RTM and TBM but differed between vapors. Specifically, diacetyl exposure induced proinflammatory and antioxidant genes concomitantly at low exposure levels, whereas acrolein induced antioxidant genes at much lower exposure levels than that required to induce proinflammatory genes. Generally, diacetyl was less potent than acrolein, as measured by maximal induction of transcripts. In conclusion, the upper and lower extrapulmonary airways are of similar sensitivity to inhaled electrophilic vapors. Dosimetrically based extrapolation of nasal responses in nose-breathing rodents may provide an approach to predict risk to the lower airways of humans during mouth-breathing.
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Affiliation(s)
- Joseph A Cichocki
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269
| | - Gregory J Smith
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269
| | - John B Morris
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269
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Arena S, Salzano AM, Renzone G, D'Ambrosio C, Scaloni A. Non-enzymatic glycation and glycoxidation protein products in foods and diseases: an interconnected, complex scenario fully open to innovative proteomic studies. MASS SPECTROMETRY REVIEWS 2014; 33:49-77. [PMID: 24114996 DOI: 10.1002/mas.21378] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/09/2013] [Accepted: 03/09/2013] [Indexed: 06/02/2023]
Abstract
The Maillard reaction includes a complex network of processes affecting food and biopharmaceutical products; it also occurs in living organisms and has been strictly related to cell aging, to the pathogenesis of several (chronic) diseases, such as diabetes, uremia, cataract, liver cirrhosis and various neurodegenerative pathologies, as well as to peritoneal dialysis treatment. Dozens of compounds are involved in this process, among which a number of protein-adducted derivatives that have been simplistically defined as early, intermediate and advanced glycation end-products. In the last decade, various bottom-up proteomic approaches have been successfully used for the identification of glycation/glycoxidation protein targets as well as for the characterization of the corresponding adducts, including assignment of the modified amino acids. This article provides an updated overview of the mass spectrometry-based procedures developed to this purpose, emphasizing their partial limits with respect to current proteomic approaches for the analysis of other post-translational modifications. These limitations are mainly related to the concomitant sheer diversity, chemical complexity, and variable abundance of the various derivatives to be characterized. Some challenges to scientists are finally proposed for future proteomic investigations to solve main drawbacks in this research field.
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Affiliation(s)
- Simona Arena
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147, Naples, Italy
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Ruan ED, Wang H, Ruan Y, Juárez M. Study of fragmentation behavior of amadori rearrangement products in lysine-containing peptide model by tandem mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2013; 19:295-303. [PMID: 24575628 DOI: 10.1255/ejms.1237] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Protein and peptide glycation with reducing sugars through Maillard reaction is recognized as one of the most critical and fundamental reactions in food and in the human body. Amadori rearrangement products (ARPs) are formed at the initial stage of Maillard reaction and then may be converted into intermediate and advanced glycation products. We report here that using electrospray ionization-mass spectrometry (ESI-MS) to directly and rapidly characterize fragmentation behavior of ARPs in a Lysine-containing peptide-reducing sugars unambiguously model and identify the modification sites in glycated tri- and tetrapeptides. Tandem mass spectrometry (MS2) results showthat the sugar moiety was preferentially fragmented, whereby the neutral loss of small molecules, such as 18 Da (-H2O), 36 Da (-2 x H2O), 54 Da (-3 x H2O), 84 Da (-H2O-HCOH) and 162 Da from monosaccharide (glucose) moieties and 18 Da, 36 Da, 216 Da, 246 Da and 324 Da from disaccharide moieties. Among the fragmented ions, (M-84+H)+ of monosaccharides and (M-246+H)+ of disaccharides are relatively stable. Further multi-stage mass spectrometry (MS3) of (M-84+H)+ for tri- and longer peptides displays peptide sequence and glycation sites by providing modified y ions (y*), and/or modified b ions (b*) and even a modified a ion (a*). The study is useful to monitor and characterize PMTs of glycation in complex protein systems based on ESI-MS related techniques.
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Affiliation(s)
- Eric D Ruan
- Agriculture and Agri-Food Canada, Lacombe Research Centre, 6000C & E. TraiL, Lacombe, AB T4L 1W1, Canada.
| | - Hui Wang
- Agriculture and Agri-Food Canada, Lacombe Research Centre, 6000C & E. TraiL, Lacombe, AB T4L 1W1, Canada
| | - Yuanyuan Ruan
- Department of Bioengineering, Jilin AgricuLture Science and Technology CoLlege, Jilin 132101, China
| | - Manuel Juárez
- Agriculture and Agri-Food Canada, Lacombe Research Centre, 6000C & E. TraiL, Lacombe, AB T4L 1W1, Canada
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Saraiva MA, Borges CM, Florêncio MH. Reactions of aminoguanidine with α-dicarbonyl compounds studied by electrospray ionization mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2012; 18:385-397. [PMID: 22971697 DOI: 10.1255/ejms.1191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Aminoguanidine possesses extensive pharmacological properties. This drug is recognized as a powerful α-dicarbonyl scavenger. In order to better elucidate the reactivity of aminoguanidine with α-dicarbonyls, aminoguanidine was reacted with several aldehydic and diketonic α-dicarbonyls. Electrospray ionization mass spectrometry is a suitable technique to study chemical and biochemical processes, and was selected for the purpose. In aminoguanidine reactions, triazines were detected and, other compounds that have never been reported before were identified. Triazine precursor forms were detected, namely tetrahydrotriazines and singly dehydrated tetrahydrotriazines. Moreover, species with bicyclic ring structures, and dehydrated forms, were also identified in aminoguanidine reactions. These species appear to result from tetrahydrotriazines and triazines reactions with one dicarbonyl molecule. Experiments revealed that these bicyclic species, in particular the ones resulting from triazines reactivity, could exist in solution, since they were both identified in the reactions of aminoguanidine and of a selected triazine with the dicarbonyls studied. The results obtained, regarding aminoguanidine/triazines reactivities, appear to support the capability of triazines to condensate and form polycyclic ring structures, and also to support literature mechanistic data for dihydroimidazotriazines formation via dihydroxyimidazolidine-triazines. The data obtained in this study may prove to be valuable to complement solution information, concerning the reactivity of amines with α-dicarbonyls, in particular.
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Affiliation(s)
- Marco A Saraiva
- Centro de Química Estrutural, Instituto Superior Técnico, Campus Alameda, Av. Rovisco Pais, Torre Sul, 1049-001 Lisbon, Portugal.
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Kim HJ, Kim SW, Lee JK, Yoon SH. A Simple and Sensitive High Performance Liquid Chromatography-Electrospray Ionization/Mass Spectrometry Method for the Quantification of Ethyl Pyruvate in Rat Plasma. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.4.1221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Gauthier MA, Klok HA. Arginine-Specific Modification of Proteins with Polyethylene Glycol. Biomacromolecules 2010; 12:482-93. [DOI: 10.1021/bm101272g] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Marc A. Gauthier
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
| | - Harm-Anton Klok
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
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16
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Saraiva M, Borges CM, Florêncio MH. Behaviour of 4-(-2-hydroxyethyl)-1-piperazineethanesulfonic acid under electrospray ionization mass spectrometry conditions. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:199-213. [PMID: 20212329 DOI: 10.1255/ejms.1061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Our previous experiments on ESI-MS analysis of reaction mixture solutions containing HEPES (4-(-2- hydroxyethyl)-1-piperazineethanesulfonic acid), a commonly used buffer, indicated that HEPES species did not significantly suppress analyte species, even in reaction mixture solutions with significant amounts of HEPES. With the purpose of investigating the behaviour of HEPES under ESI-MS conditions, HEPES aqueous solutions and HEPES aqueous solutions containing analyte with high and low polarity and with different acid/base chemistry, were therefore investigated. For electrosprayed aqueous solutions of HEPES with concentrations above 10(-5) M, an enhanced formation of HEPES multimer ions, regarding HEPES monomer ions formation, was observed. This enhanced formation of HEPES multimer ions is much higher than the one observed for other polar compounds, such as acetyl-arginine, acetyl-lysine and histidine. Information from solution behaviour such as, HEPES concentration, solution pH, and instrumental factors, namely the capillary temperature, was related with information from mass spectra. The results obtained led us to conclude that the formation of HEPES ions is related with the initial solution composition. The influence of analyte species on HEPES species formation, for electrosprayed HEPES solutions with analyte, was also investigated. The variations observed for HEPES monomer and multimer ions abundances, which were found to be consistent with those observed for analyte monomer ions abundances, were related with type of analyte, i.e. to their acid/base nature. Strikingly, the variations observed between HEPES monomer and multimer ions abundances, enable to discriminate among the different influence of analyte species on HEPES species formation. The results obtained also enabled to provide an explanation for the observation that HEPES species do not suppress significantly analyte species ion signals, when high concentrated HEPES solutions with analyte are electrosprayed. According to our results, the association behaviour between HEPES species seems to be preserved in the gas phase during electrospray ionization. This observation may provide some information that may be useful regarding the behaviours involved in the gas phase ion formation process from charged droplets during electrospray ionization or, at least, to differentiate among behaviours.
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Affiliation(s)
- Marco Saraiva
- Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal.
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Reisner HM, Lundblad RL. Identifying residues in antigenic determinants by chemical modification. Methods Mol Biol 2009; 524:103-117. [PMID: 19377940 DOI: 10.1007/978-1-59745-450-6_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Chemical modification of the side chains of amino acid residues was one of the first methods developed to investigate epitopes in protein antigens. The principle of the method is that alteration of the structure of a key residue of an epitope by a chemical modification will alter reactivity with antibody by affecting either specificity or avidity or both. Chemical modification has the advantage that it can be applied to discontinuous as well as continuous epitopes and may be of value in identifying cryptic epitopes. We consider here the several recent studies that have applied site-specific chemical modification to the identification of epitopes on antigens, including the use of formaldehyde, glutaraldehyde, and acid anhydrides, to produce allergoids where determinants important to reaction with IgE are modified but the ability to elicit an IgG response is retained. It is noteworthy that modification of amino groups with charge reversal appears to be the most useful approach. The approach to the use of site-specific chemical modification as a tool for the study of protein function is discussed, and emphasis is placed on the necessity to (1) validate the specificity of modification and (2) assess potential conformational change that may occur secondary to modification. Finally, a list of chemical reagents used for protein modification is presented, together with properties and references to use.
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Affiliation(s)
- Howard M Reisner
- Department of Pathology and Laboratory Medicine, University of North Carolina, PO Box 16695, Chapel Hill, NC 27516, USA
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Mugo SM, Bottaro CS. Rapid analysis of alpha-dicarbonyl compounds by laser desorption/ionization mass spectrometry using 9-(3,4-diaminophenyl)acridine (DAA) as a reactive matrix. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:1087-1093. [PMID: 18335466 DOI: 10.1002/rcm.3450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A rapid, sensitive and selective method has been developed for the analysis of alpha-dicarbonyls using a readily ionizable compound, 9-(3,4-diaminophenyl)acridine (DAA), as a reactive matrix (derivatizing agent and ionization efficiency enhancer), by reactive matrix laser desorption/ionization time-of-flight mass spectrometry (RM-LDI-TOF MS). The reaction between the DAA and alpha-dicarbonyls resulted exclusively in formation of vacuum-stable dicarbonyl-quinoxaline acridine derivatives that were found to possess excellent ionization efficiency in positive ion mode, without the need to use an additional matrix. The alpha-dicarbonyls used as test compounds included methylglyoxal, dimethylglyoxal, and diphenylglyoxal. Both one-pot and rapid on-plate chemical modification approaches were employed with no extraction or purification necessary. The approach is particularly suitable for high-throughput analysis. The method was found to be selective and specific, with alpha-dicarbonyls unequivocally identified, even in complex matrices, e.g. beer. The figures of merit: relative standard deviation (RSD) 6.9-17%, (n = 4); limit of detection (LOD) < or =0.3 ng mL(-1) for the three standards tested using the one-pot derivatization method; and a good linear calibration curve using an internal standard derivatized in situ (R(2) > or = 0.979), demonstrate the applicability of the technique and its utility in improving the sensitivity and precision of the LDI analysis of small molecules.
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Affiliation(s)
- Samuel M Mugo
- Department of Chemistry, Memorial University of Newfoundland, St John's, NL, Canada
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O'Young J, Sukdeo N, Honek JF. Escherichia coli glyoxalase II is a binuclear zinc-dependent metalloenzyme. Arch Biochem Biophys 2007; 459:20-6. [PMID: 17196158 DOI: 10.1016/j.abb.2006.11.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Revised: 11/15/2006] [Accepted: 11/22/2006] [Indexed: 10/23/2022]
Abstract
Cytotoxic methylglyoxal is detoxified by the two-enzyme glyoxalase system. Glyoxalase I (GlxI) catalyzes conversion of non-enzymatically produced methylglyoxal-glutathione hemithioacetal into its corresponding thioester. Glyoxalase II (Glx II) hydrolyzes the thioester into d-lactate and free glutathione. Glyoxalase I and II are metalloenzymes, which possess mononuclear and binuclear active sites, respectively. There are two distinct classes of GlxI; the first class is Zn2+-dependent and is composed of GlxI from mainly eukaryotic organisms and the second class is composed of non-Zn2+-dependent (but Ni2+ or Co2+-dependent) GlxI enzymes (mainly prokaryotic and leishmanial species). GlxII is typically Zn2+-activated, containing Zn2+ and either Fe3+/Fe2+ or Mn2+ at the active site depending upon the biological source. To address whether two classes of GlxII might exist, glyoxalase II from Escherichia coli was cloned and overexpressed and characterized. Unlike E. coli GlxI, which is non-Zn2+-dependent, Zn2+ activates the E. coli GlxII enzyme, with no evidence for Ni2+ metal utilization.
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Affiliation(s)
- Jason O'Young
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ont., Canada N2L 3G1
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Saraiva MA, Borges CM, Florêncio MH. Towards the control and inhibition of glycation-the role of the guanidine reaction center with aldehydic and diketonic dicarbonyls. A mass spectrometry study. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:1346-68. [PMID: 17039581 DOI: 10.1002/jms.1109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Glycation of proteins by glucose and formation of end-stage adducts (AGEs, advanced glycation end products) has been implicated in pathological mechanisms associated with diabetic complications, macrovascular disease, chronic and renal insufficiency, Alzheimer's disease, and aging. Of the carbonyl containing compounds involved in this process, alpha-dicarbonyls have particular importance, being established as direct intermediates in the formation of well-known AGEs. The guanidino group, present in arginine residues, suffers direct modifications by sugars and its derivatives, and is considered to be an important chemical basis, targeting the control and inhibition of glycation. Seven dicarbonyl compounds, aldehydic and diketonic, were reacted with guanidine, in an attempt to establish structure/activity relationships. Electrospray mass spectrometry, together with tandem mass spectrometry, was used to identify and characterize the reaction products. The reactivity of guanidine was found to vary with the dicarbonyls used. For glyoxal, a high amount of dihydroxyimidazolidine was formed, whereas for methylglyoxal, dihydroxyimidazolidine was slowly converted into hydroimidazolone. Interestingly, aqueous guanidine was found to prevent argpyrimidine formation. The formation of several amine-dicarbonyl moieties was observed for the larger alkyl-diketonic dicarbonyls reaction systems, in particular. Molecular structures, bearing a polar chain, of an imidazole ring, and a nonpolar one, of alkyl groups, located at both sides of the imidazole rings, were attributed to these moieties. Gas-phase experiments suggested that the larger alkyl groups have a preference for being located at one of the sides of the imidazole rings. Moreover, the referred amine-dicarbonyl moieties are formed via (dihydroxyimidazolidine - 2H2O) moieties. The latter (dihydroxyimidazolidine - 2H2O) moieties are formed in high amounts in the larger alkyl-diketonic dicarbonyl reactions. Since these moieties react with dicarbonyl molecules, and react even faster with already modified amine functions, we can foresee that these species may be useful for controlling and inhibiting glycation of larger biomolecules, such as proteins.
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Affiliation(s)
- Marco A Saraiva
- Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Lisbon, Campo Grande, C8, 1749-016 Lisbon, Portugal
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Saraiva MA, Borges CM, Florêncio MH. Non-enzymatic model glycation reactions--a comprehensive study of the reactivity of a modified arginine with aldehydic and diketonic dicarbonyl compounds by electrospray mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:755-70. [PMID: 16646000 DOI: 10.1002/jms.1031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Non-enzymatic glycation (Maillard reaction) of long-lived proteins is a major contributor to the pathology of diabetes, and possibly aging and Alzheimer's disease. Among the amino residues in proteins arginine plays an important role, and its modification by sugar moieties generates the so-called advanced glycation end products (AGEs). Moreover, alpha-dicarbonyl compounds have been found as the main participants in those modifications. Four alpha-dicarbonyl compounds, aldehydic and ketonic, were reacted with the modified amino acid N(alpha)-acetyl-L-arginine (AcArg), in an attempt to establish structure/activity relationships for the reactivity of alpha-dicarbonyls with the amine compound. Electrospray ionization mass spectrometry (ESI-MS), combined with tandem mass spectrometry (MS/MS), was used to identify and characterize reagents, intermediates and reaction products. The fragmentation patterns of precursor ions showed similarities in all reaction systems studied, in which fragmentation of the amino acid residue prevails, especially for the dehydrated and/or multiple dehydrated precursor ions. For the non-hydrated ion species, fragmentation of the arginyl guanidino group was mainly observed. Specific information regarding the nature of the ions formed, in which the dicarbonyl electrophile character played an important role, was obtained. As an example, singly and doubly hydrated acetyl-argpyrimidine ions were detected for the methylglyoxal reaction only. For symmetrical dicarbonyls, glyoxal and diacetyl, the importance of steric contributions with respect to the energetic ones is discussed. Furthermore, the dehydrated acetyl-tetrahydropyrimidine ions for methylglyoxal and phenylglyoxal reactions revealed fragment ion compositions including the protonated molecules of acetyl-argpyrimidine, -hydroimidazolone and -5-methylimidazolone. An explanation for the acetyl-argpyrimidine formation from the acetyl-hydroimidazolone formation reaction is proposed. Aspects such as the amount of acetyl-hydroimidazolone formed, the response of the hydration equilibria of the dicarbonyl forms to the new unhydrated dicarbonyls introduced by the reversal of the acetyl-hydroimidazolone formation reaction and the stability of the dicarbonyl intermediate involved in the acetyl-argpyrimidine formation are proposed, as being responsible to control the formation of acetyl-argpyrimidine.
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Affiliation(s)
- Marco A Saraiva
- Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Lisbon, Campo Grande C8, 1749-016 Lisbon, Portugal
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