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Nybo T, Davies MJ, Rogowska-Wrzesinska A. Analysis of protein chlorination by mass spectrometry. Redox Biol 2019; 26:101236. [PMID: 31181457 PMCID: PMC6557747 DOI: 10.1016/j.redox.2019.101236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 01/04/2023] Open
Abstract
Chlorination of tyrosine is a commonly known effect/consequence of myeloperoxidase activity at sites of inflammation, and detection of 3-chlorotyrosine has been used as biomarker for inflammatory diseases. However, few studies have addressed site specific chlorination in proteins, and no methods for large scale chloroproteomics studies have yet been published. In this study, we present an optimized mass spectrometry based protocol to identify and quantify chlorinated peptides from single proteins modified by HOCl (100 and 500 μM, within estimated pathophysiological levels), at a high level of sensitivity and accuracy. Particular emphasis was placed on 1) sensitive and precise detection of modification sites, 2) the avoidance of loss or artefactual creation of modifications, 3) accurate quantification of peptide abundance and reduction of missing values problem, 4) monitoring the dynamics of modification in samples exposed to different oxidant concentrations and 5) development of guidelines for verification of chlorination sites assignment. A combination of an optimised sample preparation protocol, and improved data analysis approaches have allowed identification of 33 and 15 chlorination sites in laminin and fibronectin, respectively, reported in previous manuscripts [1,2]. The method was subsequently tested on murine basement membrane extract, which contains high levels of laminin in a complex mixture. Here, 10 of the major chlorination sites in laminin were recapitulated, highlighting the utility of the method in detecting damage in complex samples. An optimized mass spectrometry method is presented to detect protein chlorination. Reduction and alkylation leads to loss of chlorinated residues. Identification of modification sites in fibronectin and laminin induced by HOCl. Quantification of relative site occupancy (RSO) of chlorinated residues. Largest chloroproteomics dataset to date.
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Affiliation(s)
- Tina Nybo
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen N, Denmark; Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen N, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.
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2
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Powell T, Bowra S, Cooper HJ. Subcritical Water Hydrolysis of Peptides: Amino Acid Side-Chain Modifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1775-1786. [PMID: 28516297 PMCID: PMC5556142 DOI: 10.1007/s13361-017-1676-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/02/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
Previously we have shown that subcritical water may be used as an alternative to enzymatic digestion in the proteolysis of proteins for bottom-up proteomics. Subcritical water hydrolysis of proteins was shown to result in protein sequence coverages greater than or equal to that obtained following digestion with trypsin; however, the percentage of peptide spectral matches for the samples treated with trypsin were consistently greater than for those treated with subcritical water. This observation suggests that in addition to cleavage of the peptide bond, subcritical water treatment results in other hydrolysis products, possibly due to modifications of amino acid side chains. Here, a model peptide comprising all common amino acid residues (VQSIKCADFLHYMENPTWGR) and two further model peptides (VCFQYMDRGDR and VQSIKADFLHYENPTWGR) were treated with subcritical water with the aim of probing any induced amino acid side-chain modifications. The hydrolysis products were analyzed by direct infusion electrospray tandem mass spectrometry, either collision-induced dissociation or electron transfer dissociation, and liquid chromatography collision-induced dissociation tandem mass spectrometry. The results show preferential oxidation of cysteine to sulfinic and sulfonic acid, and oxidation of methionine. In the absence of cysteine and methionine, oxidation of tryptophan was observed. In addition, water loss from aspartic acid and C-terminal amidation were observed in harsher subcritical water conditions. Graphical Abstract ᅟ.
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Affiliation(s)
- Thomas Powell
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Steve Bowra
- Phytatec (UK) Ltd., Plas Gogerddan, Aberystwyth, SY23 3EB, UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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LaVoie SP, Mapolelo DT, Cowart DM, Polacco BJ, Johnson MK, Scott RA, Miller SM, Summers AO. Organic and inorganic mercurials have distinct effects on cellular thiols, metal homeostasis, and Fe-binding proteins in Escherichia coli. J Biol Inorg Chem 2015; 20:1239-51. [PMID: 26498643 PMCID: PMC4749482 DOI: 10.1007/s00775-015-1303-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/08/2015] [Indexed: 02/07/2023]
Abstract
The protean chemical properties of the toxic metal mercury (Hg) have made it attractive in diverse applications since antiquity. However, growing public concern has led to an international agreement to decrease its impact on health and the environment. During a recent proteomics study of acute Hg exposure in E. coli, we also examined the effects of inorganic and organic Hg compounds on thiol and metal homeostases. On brief exposure, lower concentrations of divalent inorganic mercury Hg(II) blocked bulk cellular thiols and protein-associated thiols more completely than higher concentrations of monovalent organomercurials, phenylmercuric acetate (PMA) and merthiolate (MT). Cells bound Hg(II) and PMA in excess of their available thiol ligands; X-ray absorption spectroscopy indicated nitrogens as likely additional ligands. The mercurials released protein-bound iron (Fe) more effectively than common organic oxidants and all disturbed the Na(+)/K(+) electrolyte balance, but none provoked efflux of six essential transition metals including Fe. PMA and MT made stable cysteine monothiol adducts in many Fe-binding proteins, but stable Hg(II) adducts were only seen in CysXxx(n)Cys peptides. We conclude that on acute exposure: (a) the distinct effects of mercurials on thiol and Fe homeostases reflected their different uptake and valences; (b) their similar effects on essential metal and electrolyte homeostases reflected the energy dependence of these processes; and (c) peptide phenylmercury-adducts were more stable or detectable in mass spectrometry than Hg(II)-adducts. These first in vivo observations in a well-defined model organism reveal differences upon acute exposure to inorganic and organic mercurials that may underlie their distinct toxicology.
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Affiliation(s)
- Stephen P LaVoie
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Daphne T Mapolelo
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
- Department of Chemistry, University of Botswana, P.O. Box 00704, Gaborone, Botswana
| | - Darin M Cowart
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Benjamin J Polacco
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Michael K Johnson
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Robert A Scott
- Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
| | - Susan M Miller
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Anne O Summers
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
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Profiling thiol metabolites and quantification of cellular glutathione using FT-ICR-MS spectrometry. Anal Bioanal Chem 2014; 406:4371-9. [PMID: 24858467 DOI: 10.1007/s00216-014-7810-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/31/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
We describe preparation and use of the quaternary ammonium-based α-iodoacetamide QDE and its isotopologue *QDE as reagents for chemoselective derivatization of cellular thiols. Direct addition of the reagents to live cells followed by adduct extraction into n-butanol and analysis by FT-ICR-MS provided a registry of matched isotope peaks from which molecular formulae of thiol metabolites were derived. Acidification to pH 4 during cell lysis and adduct formation further improves the chemoselectivity for thiol derivatization. Examination of A549 human lung adenocarcinoma cells using this approach revealed cysteine, cysteinylglycine, glutathione, and homocysteine as principal thiol metabolites as well as the sulfinic acid hypotaurine. The method is also readily applied to quantify the thiol metabolites, as demonstrated here by the quantification of both glutathione and glutathione disulfide in A549 cells at concentrations of 34.4 ± 11.5 and 10.1 ± 4.0 nmol/mg protein, respectively.
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Cong F, Diehl BG, Hill JL, Brown NR, Tien M. Covalent bond formation between amino acids and lignin: cross-coupling between proteins and lignin. PHYTOCHEMISTRY 2013; 96:449-56. [PMID: 24099658 DOI: 10.1016/j.phytochem.2013.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 08/27/2013] [Accepted: 09/11/2013] [Indexed: 05/10/2023]
Abstract
The present study characterized the products formed from the reaction of amino acids and in turn, proteins, with lignin resulting in cross-coupling. When added to reaction mixtures containing coniferyl alcohol, horseradish peroxidase and H2O2, three amino acids (Cys, Tyr, and Thr) are able to form adducts. The low molecular weight products were analyzed by HPLC and from each reaction mixture, one product was isolated and analyzed by LC/MS. LC/MS results are consistent with bond formation between the polar side-chain of these amino acids with Cα. These results are consistent with the cross-coupling of Cys, Tyr and Thr through a quinone methide intermediate. In addition to the free amino acids, it was found that the cross-coupling of proteins with protolignin through Cys or Tyr residues. The findings provide a mechanism by which proteins and lignin can cross-couple in the plant cell wall.
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Affiliation(s)
- Fang Cong
- Intercollege Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Development of a neuromedin U-human serum albumin conjugate as a long-acting candidate for the treatment of obesity and diabetes. Comparison with the PEGylated peptide. J Pept Sci 2013; 20:7-19. [DOI: 10.1002/psc.2582] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/11/2013] [Accepted: 10/11/2013] [Indexed: 12/12/2022]
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Paulech J, Solis N, Edwards AV, Puckeridge M, White MY, Cordwell SJ. Large-Scale Capture of Peptides Containing Reversibly Oxidized Cysteines by Thiol-Disulfide Exchange Applied to the Myocardial Redox Proteome. Anal Chem 2013; 85:3774-80. [DOI: 10.1021/ac400166e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jana Paulech
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Nestor Solis
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Alistair V.G. Edwards
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Max Puckeridge
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Melanie Y. White
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
| | - Stuart J. Cordwell
- School
of Molecular Bioscience and ‡Discipline of Pathology, School of Medical
Sciences, The University of Sydney, Australia
2006
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Characterization of reaction conditions providing rapid and specific cysteine alkylation for peptide-based mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:372-9. [DOI: 10.1016/j.bbapap.2012.08.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 07/22/2012] [Accepted: 08/03/2012] [Indexed: 01/07/2023]
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9
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Hansen RE, Winther JR. An introduction to methods for analyzing thiols and disulfides: Reactions, reagents, and practical considerations. Anal Biochem 2009; 394:147-58. [DOI: 10.1016/j.ab.2009.07.051] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 07/31/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
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10
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Yang Z, Attygalle AB. LC/MS characterization of undesired products formed during iodoacetamide derivatization of sulfhydryl groups of peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:233-43. [PMID: 17206739 DOI: 10.1002/jms.1157] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Many undesired by-products have been noticed during alkylation with iodoacetamide, a widely used derivatization reaction in proteomics for the determination of sulfhydryl groups in peptides and proteins. We report here that iodoacetamide reacts with the N-terminal NH2 and the C-terminal carboxylic acid groups, in addition to the peripheral residues bearing protic functional groups. If sufficient reaction time is given, the N-terminal NH2 group is readily dialkylated by iodoacetamide. In fact, the N-terminal NH2 group reacts even faster than the reactive sites present in residues, such as tyrosine or histidine. LC/MS investigations with certain reactive peptides show that by-products are formed in a relatively short reaction time, even at room temperature. Interestingly, derivatives formed in this way are useful for sequence determination of peptides by MS since the intensities of y'' ions are highly suppressed in the spectra of N-terminus mono- and dialkylated peptides, whereas those of b-ions are significantly enhanced. For example, in the spectrum of N,N-dicarboxamidomethyl derivative of Val-Ala-Ala-Phe (VAAF), the y-series ions are virtually absent. On the other hand, when the derivatization takes place at the carboxylic group, the y-series ions are markedly observed in the spectra of these undesired O-carboxamidomethyl derivatives.
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Affiliation(s)
- Zhihua Yang
- Center for Mass Spectrometry, Department of Chemistry and Chemical Biology, Stevens Institute of Technology, NJ 07030, USA
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11
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Russo A, Bump EA. Detection and quantitation of biological sulfhydryls. METHODS OF BIOCHEMICAL ANALYSIS 2006; 33:165-241. [PMID: 3282150 DOI: 10.1002/9780470110546.ch5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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12
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Yan JX, Kett WC, Herbert BR, Gooley AA, Packer NH, Williams KL. Identification and quantitation of cysteine in proteins separated by gel electrophoresis. J Chromatogr A 1998; 813:187-200. [PMID: 9697320 DOI: 10.1016/s0021-9673(98)00319-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A simple technique is introduced to identify and quantitate cysteine (Cys) after acid hydrolysis of protein. The technique involves using 9-fluorenylmethyl chloroformate (Fmoc)-based amino acid analysis that recovers all of the amino acids (asparagine and glutamine are recovered in their acidic forms) except tryptophan. Cys adducts with acrylamide and iodoacetamide have been observed in hydrolysates of gel-separated proteins. To enable quantitation of Cys by amino acid analysis, different conditions of reduction [dithiothreitol (DTT) and tributylphosphine] and alkylation [vinylpyridine, acrylamide and iodoacetamide] were compared. Optimal conditions for on-blot reduction (125 mM of DTT, pH 8.5, at 80 degrees C) and alkylation (0.25 M iodoacetamide, pH 8.5, at 37 degrees C) of proteins which have been separated by gel electrophoresis and blotted onto polyvinylidenedifluoride (PVDF) membrane were established to achieve complete recovery of alkylated Cys. Even with the optimal on-blot iodoacetamide alkylation, there may still be some acrylamide adducts present and these were able to be separated by HPLC along with the other 16 amino acids. The Cys content has been successfully determined by Fmoc-amino acid analysis of PVDF-blotted proteins separated by 1D or 2D gel electrophoresis. Lysine alkylation with iodoacetamide and acrylamide has also been characterised. Protein identification using amino acid composition including Cys has been introduced.
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Affiliation(s)
- J X Yan
- Macquarie University Centre for Analytical Biotechnology, School of Biological Sciences, Macquarie University, Sydney, NSW, Australia
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13
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Kozik A. Carbodiimide modification of carboxyl groups in egg white riboflavin-binding protein. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/0167-4838(82)90078-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ramanathan L, Guyer RB, Buss EG, Clagett CO. Chemical modifications of riboflavin-binding protein: effects on function and antigenicity. Mol Immunol 1980; 17:267-74. [PMID: 6156405 DOI: 10.1016/0161-5890(80)90079-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Westermann P, Heumann W, Bielka H. Changes in the reactivity of proteins of rat liver ribosomes against [14Ciodoacetamide depending on their organization in ribosomal subparticles, 80S ribosomes and on the attachment of poly-(U). Chem Biol Interact 1975; 10:429-39. [PMID: 1149173 DOI: 10.1016/0009-2797(75)90073-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
(1) The isolated mixtures of ribosomal proteins can be substituted by [14C]-iodoacetamide up to an average of about 2 equivalents per 20,000 dalton. The extent of substitution of single proteins measured after two-dimensional polyacrylamide gel electrophoresis shows that all proteins are reactive. (2) Also in the subunits, all proteins are accessible to substitution. Compared with isolated proteins, however, the reactivity is decreased and the amount of labelling for most proteins ranges as low as 5 to 20%. (3) Reassociation of ribosomal subunits decreases the reactivity of 12 proteins of the small subunit and that of 20 proteins of the large subunit. (4) The presence of messenger inhibits the substitution of 10 proteins of the small subunit and of 6 proteins of the large one. (5) Seven proteins of the small subunit and 3 proteins of the large one are influenced both by the other subunit and by messenger-RNA.
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