1
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Akhmadi A, Yeskendir A, Dey N, Mussakhmetov A, Shatkenova Z, Kulyyassov A, Andreeva A, Utepbergenov D. DJ-1 protects proteins from acylation by catalyzing the hydrolysis of highly reactive cyclic 3-phosphoglyceric anhydride. Nat Commun 2024; 15:2004. [PMID: 38443379 PMCID: PMC10915168 DOI: 10.1038/s41467-024-46391-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
Mutations in the human PARK7 gene that encodes protein DJ-1 lead to familial Parkinsonism due to loss of dopaminergic neurons. However, the molecular function of DJ-1 underpinning its cytoprotective effects are unclear. Recently, DJ-1 has been shown to prevent acylation of amino groups of proteins and metabolites by 1,3-bisphosphoglycerate. This acylation is indirect and thought to proceed via the formation of an unstable intermediate, presumably a cyclic 3-phosphoglyceric anhydride (cPGA). Several lines of evidence indicate that DJ-1 destroys cPGA, however this enzymatic activity has not been directly demonstrated. Here, we report simple and effective procedures for synthesis and quantitation of cPGA and present a comprehensive characterization of this highly reactive acylating electrophile. We demonstrate that DJ-1 is an efficient cPGA hydrolase with kcat/Km = 5.9 × 106 M-1s-1. Experiments with DJ-1-null cells reveal that DJ-1 protects against accumulation of 3-phosphoglyceroyl-lysine residues in proteins. Our results establish a definitive cytoprotective function for DJ-1 that uses catalytic hydrolysis of cPGA to mitigate the damage from this glycolytic byproduct.
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Affiliation(s)
- Aizhan Akhmadi
- Ph.D. Program in Life Sciences, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Adilkhan Yeskendir
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan
- Master Program, School of Medicine, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Nelly Dey
- Master Program, School of Medicine, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Arman Mussakhmetov
- National Center for Biotechnology, Astana, 010000, Kazakhstan
- Ph.D. Program in Biology, L.N. Gumilyov Eurasian National University, Astana, 010000, Kazakhstan
| | - Zariat Shatkenova
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan
| | | | - Anna Andreeva
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Darkhan Utepbergenov
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan.
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2
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Pérez-Sala D, Quinlan RA. The redox-responsive roles of intermediate filaments in cellular stress detection, integration and mitigation. Curr Opin Cell Biol 2024; 86:102283. [PMID: 37989035 DOI: 10.1016/j.ceb.2023.102283] [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: 05/31/2023] [Revised: 10/18/2023] [Accepted: 10/29/2023] [Indexed: 11/23/2023]
Abstract
Intermediate filaments are critical for cell and tissue homeostasis and for stress responses. Cytoplasmic intermediate filaments form versatile and dynamic assemblies that interconnect cellular organelles, participate in signaling and protect cells and tissues against stress. Here we have focused on their involvement in redox signaling and oxidative stress, which arises in numerous pathophysiological situations. We pay special attention to type III intermediate filaments, mainly vimentin, because it provides a physical interface for redox signaling, stress responses and mechanosensing. Vimentin possesses a single cysteine residue that is a target for multiple oxidants and electrophiles. This conserved residue fine tunes vimentin assembly, response to oxidative stress and crosstalk with other cellular structures. Here we integrate evidence from the intermediate filament and redox biology fields to propose intermediate filaments as redox sentinel networks of the cell. To support this, we appraise how vimentin detects and orchestrates cellular responses to oxidative and electrophilic stress.
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Affiliation(s)
- Dolores Pérez-Sala
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, C.S.I.C., 28040 Madrid, Spain.
| | - Roy A Quinlan
- Department of Biosciences, University of Durham, Upper Mountjoy Science Site, Durham, United Kingdom; Biophysical Sciences Institute, University of Durham, Durham, United Kingdom; Department of Biological Structure, University of Washington, Seattle, WA, United States.
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3
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Saroha P, Rathore AS. Production of bioactive recombinant monoclonal antibody fragment in periplasm of Escherichia coli expression system. Prep Biochem Biotechnol 2023; 53:1288-1296. [PMID: 37040146 DOI: 10.1080/10826068.2023.2195482] [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] [Indexed: 04/12/2023]
Abstract
The microbial expression system (Escherichia coli) is the most widely studied host for the production of biotherapeutic products, such as antibody fragments, single chain variable fragments and nanobodies. However, recombinant biotherapeutic proteins are often expressed as insoluble proteins, thereby limiting the utility of E. coli as expression system. To overcome this limitation, various strategies have been developed, such as changes at DNA level (codon optimization), fusion with soluble tags and variations in process parameters (temperature), and inducer concentration. However, there is no "one size fits all" strategy. The most commonly used approach involves induction at low temperature, as reducing the temperature during cultivation has been reported to increase bioactive protein production in E. coli. In this study, we examine the impact of various process parameters, such as temperature and inducer concentration, as well as, high plasmid copy number vector for achieving enhanced soluble expression of TNFα inhibitor Fab. An interaction amongst these parameters has been observed and their optimization has been demonstrated to result in expression of 30 ± 3 mg/L antibody fragment using E. coli. This case study illustrates how process optimization can contribute toward making biotherapeutics affordable.
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Affiliation(s)
- Preeti Saroha
- Department of Chemical Engineering, Indian Institute of Technology, Delhi, New Delhi, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology, Delhi, New Delhi, India
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4
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Yang H, Wang L, Xie Z, Shao S, Wu Y, Xu W, Gu B, Wang B. An improved sulfur-nitroso-proteome strategy for global profiling of sulfur-nitrosylated proteins and sulfur-nitrosylation sites in mice. J Chromatogr A 2023; 1705:464162. [PMID: 37336129 DOI: 10.1016/j.chroma.2023.464162] [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: 04/18/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
Comprehensive sulfur-nitrosylation (SNO) proteome coverage in complex biological systems remains challenging as a result of the low level of endogenous S-nitrosylation and its chemical instability. Herein, we optimized the synthesis route of SNOTRAP (SNO trapping by triaryl phosphine) probe and the proteomics pipeline (including preventing over-alkylation, sample washing, trypsin digestion). Preventing overalkylation was found to be the key factor resulting in a higher number of identified SNO proteins by evaluating various experimental conditions. With the improved SNOTRAP-based proteomic pipeline, we achieved an improvement of ∼10-fold on identification efficiency, and identified 1181 SNO proteins (1714 SNO sites) in mouse brain, representing the largest repository of endogenous S-nitrosylation. Moreover, we identified the consensus motif of SNO sites, suggesting the correlation with local hydrophobicity, acid-base catalysis, and the surrounding secondary structures for modification of specific cysteines by NO. Collectively, we provide a universal pipeline for the high-coverage identification of low-abundance SNO proteins with high enrichment efficiency, high specificity (98%), good reproducibility, and easy implementation, contributing to the elucidation of the mechanism(s) of nitrosative stress in multiple diseases.
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Affiliation(s)
- Hongmei Yang
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130017, China.
| | - Linxu Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Zhaoyang Xie
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130017, China
| | - Simeng Shao
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130017, China
| | - Yi Wu
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130017, China
| | - Weiyin Xu
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130017, China
| | - Bin Gu
- Department of Stomatology, the first medical center, General Hospital of the Chinese people's Liberation Army, Beijing 100036, China.
| | - Bo Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
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5
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Nehmeh B, Haydous F, Akoury E. Mass calibrants for positive chemical ionization-high resolution mass spectrometry (CI-HRMS) for the identification of unknown compounds using accurate mass measurements. RSC Adv 2023; 13:14001-14009. [PMID: 37181506 PMCID: PMC10167574 DOI: 10.1039/d3ra01977b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/01/2023] [Indexed: 05/16/2023] Open
Abstract
Gas Chromatography-Electron Ionization-Mass Spectrometry (GC-EI-MS) is still the most routinely performed method for metabolite profiling as compared to other hyphenated techniques. But when it comes to identification of unknown compounds, information on the molecular weight is not readily available because the molecular ion is not always found with electron ionization (EI). Thus, the use of chemical ionization (CI) is envisaged that commonly produces the molecular ion; in combination with accurate mass measurement, this technique would further allow for calculation of sum formulas of those compounds. However, for proper accuracy of analysis, a mass calibrant is needed. We set out to find a commercially available reference material with mass peaks that would qualify the substance as mass calibrant under CI conditions. Six commercially available mass calibrants, FC 43, PFK, Ultramark 1621, Ultramark 3200F, Triton X-100, and PEG 1000, were tested under CI conditions to understand their fragmentation behavior. Our findings indicate that Ultramark 1621 and PFK best fit the expectations of a mass calibrant for HRMS analysis whereby PFK provided a fragmentation pattern similar to EI outcomes thus enabling the use of mass reference tables commonly provided within commercial mass spectrometers. On the other hand, Ultramark 1621 is a mixture of fluorinated phosphazines that shows stable fragment intensities.
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Affiliation(s)
- Bilal Nehmeh
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Beirut 1102-2801 Lebanon
| | - Fatima Haydous
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Beirut 1102-2801 Lebanon
| | - Elias Akoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Beirut 1102-2801 Lebanon
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6
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Cheng R, Lv X, Bu H, Xu Q, Wu J, Xie K, Tang J, Wang L, Zhuang J, Zhang Y, Zhang Y, Yan C, Lai Y. Design, synthesis, and evaluation of 4(1H)-quinolinone and urea derivatives as KRASG12C inhibitors with potent antitumor activity against KRAS-mutant non-small cell lung cancer. Eur J Med Chem 2022; 244:114808. [DOI: 10.1016/j.ejmech.2022.114808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/17/2022] [Accepted: 09/27/2022] [Indexed: 11/04/2022]
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7
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Ning Q, Li J. DLF-Sul: a multi-module deep learning framework for prediction of S-sulfinylation sites in proteins. Brief Bioinform 2022; 23:6658856. [PMID: 35945138 DOI: 10.1093/bib/bbac323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 11/14/2022] Open
Abstract
Protein S-sulfinylation is an important posttranslational modification that regulates a variety of cell and protein functions. This modification has been linked to signal transduction, redox homeostasis and neuronal transmission in studies. Therefore, identification of S-sulfinylation sites is crucial to understanding its structure and function, which is critical in cell biology and human diseases. In this study, we propose a multi-module deep learning framework named DLF-Sul for identification of S-sulfinylation sites in proteins. First, three types of features are extracted including binary encoding, BLOSUM62 and amino acid index. Then, sequential features are further extracted based on these three types of features using bidirectional long short-term memory network. Next, multi-head self-attention mechanism is utilized to filter the effective attribute information, and residual connection helps to reduce information loss. Furthermore, convolutional neural network is employed to extract local deep features information. Finally, fully connected layers acts as classifier that map samples to corresponding label. Performance metrics on independent test set, including sensitivity, specificity, accuracy, Matthews correlation coefficient and area under curve, reach 91.80%, 92.36%, 92.08%, 0.8416 and 96.40%, respectively. The results show that DLF-Sul is an effective tool for predicting S-sulfinylation sites. The source code is available on the website https://github.com/ningq669/DLF-Sul.
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Affiliation(s)
- Qiao Ning
- Information Science and Technology College, Dalian Maritime University, Dalian 116026, China
| | - Jinmou Li
- Information Science and Technology College, Dalian Maritime University, Dalian 116026, China
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8
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Datola A, Melchiorre M, Baroni F, Iozzino L, Palmese A. Characterization of disulfide bridges pattern of recombinant human interleukin 12 fusion protein p40 subunit and identification and quantification of cysteinylated free cysteine 252. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9313. [PMID: 35411965 PMCID: PMC10078324 DOI: 10.1002/rcm.9313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/31/2022] [Accepted: 04/10/2022] [Indexed: 05/05/2023]
Abstract
RATIONALE We show evidence of cysteinylation on Cys252 of recombinant human p40 subunit of interleukin 12 (IL-12). This was reported in 1996. However, no paper detailing this concept has been published yet. Our paper reports the quantification of Cys252 cysteinylation as well as the full disulfide bridges assignment by nonreducing peptide mapping using mass spectrometry (MS) detection. METHODS Nonreducing peptide mapping was applied for disulfide bridges assignment. This study presents an ad hoc method in which applying a neutral pH in the presence of an alkylating agent allowed to mitigate the formation of artifacts such as reshuffled disulfide bridges and permitted the detection of free cysteine. Ultra-high-performance liquid chromatography-MS analysis was performed on a Waters quadrupole time-of-flight Xevo G2-XS mass spectrometer acquiring data in MSE mode. MS data were processed using Expressionist MS Refiner 13.5 (Genedata). RESULTS Scouting experiments were performed using two batches of drug substance. An in-depth study of the LC tandem mass spectrometry profiles revealed the presence of additional species related to "free" Cys252; this cysteine residue was also detected in its S-cysteinylated and S-homocysteinylated forms. This result is consistent with that reported in literature so far. The relative abundance of overall "cysteinylated" species resulted in the range between 46% and 36%, which has also been confirmed using orthogonal techniques such as Ellman's assay. CONCLUSIONS Our data clearly demonstrate that the free cysteine (Cys252) on the p40 subunit of recombinant IL-12 is also present in its cysteinylated and homocysteinylated forms at a considerable rate. Our observations, although based on results obtained on an IL-12-derived fusion protein, are consistent with the current literature.
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Affiliation(s)
- Antonio Datola
- Analytical Development Biotech, Characterization and Innovative Analytics UnitGlobal Healthcare Operations, A Business of Merck KGaADarmstadtGermany
- Merck Serono S.p.A. Via Luigi EinaudiRomeItaly
| | - Maura Melchiorre
- Analytical Development Biotech, Characterization and Innovative Analytics UnitGlobal Healthcare Operations, A Business of Merck KGaADarmstadtGermany
- Merck Serono S.p.A. Via Luigi EinaudiRomeItaly
| | - Fabio Baroni
- Analytical Development Biotech, Characterization and Innovative Analytics UnitGlobal Healthcare Operations, A Business of Merck KGaADarmstadtGermany
- Merck Serono S.p.A. Via Luigi EinaudiRomeItaly
| | - Luisa Iozzino
- Analytical Development Biotech, Characterization and Innovative Analytics UnitGlobal Healthcare Operations, A Business of Merck KGaADarmstadtGermany
- Merck Serono S.p.A. Via Luigi EinaudiRomeItaly
| | - Angelo Palmese
- Analytical Development Biotech, Characterization and Innovative Analytics UnitGlobal Healthcare Operations, A Business of Merck KGaADarmstadtGermany
- Merck Serono S.p.A. Via Luigi EinaudiRomeItaly
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9
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Das N, Chakraborty B, RoyChaudhuri C. A review on nanopores based protein sensing in complex analyte. Talanta 2022; 243:123368. [DOI: 10.1016/j.talanta.2022.123368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/30/2022] [Accepted: 03/03/2022] [Indexed: 11/26/2022]
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10
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Kowalska M, Bąchor R. Catch, Modify and Analyze: Methods of Chemoselective Modification of Cysteine-Containing Peptides. Molecules 2022; 27:molecules27051601. [PMID: 35268701 PMCID: PMC8911932 DOI: 10.3390/molecules27051601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022] Open
Abstract
One effective solution in the analysis of complex mixtures, including protein or cell hydrolysates, is based on chemoselective derivatization of a selected group of compounds by using selective tags to facilitate detection. Another method is based on the capture of the desired compounds by properly designed solid supports, resulting in sample enrichment. Cysteine is one of the rarest amino acids, but at least one cysteine residue is present in more than 91% of human proteins, which clearly confirms its important role in biological systems. Some cysteine-containing peptides may serve as significant molecular biomarkers, which may emerge as key indices in the management of patients with particular diseases. In the current review, we describe recent advances in the development of cysteine-containing peptide modification techniques based on solution and solid phase derivatization and enrichment strategies.
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11
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Kavoor A, Kelly P, Ibba M. Escherichia coli alanyl-tRNA synthetase maintains proofreading activity and translational accuracy under oxidative stress. J Biol Chem 2022; 298:101601. [PMID: 35065077 PMCID: PMC8857464 DOI: 10.1016/j.jbc.2022.101601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that synthesize aminoacyl-tRNAs to facilitate translation of the genetic code. Quality control by aaRS proofreading and other mechanisms maintains translational accuracy, which promotes cellular viability. Systematic disruption of proofreading, as recently demonstrated for alanyl-tRNA synthetase (AlaRS), leads to dysregulation of the proteome and reduced viability. Recent studies showed that environmental challenges such as exposure to reactive oxygen species can also alter aaRS synthetic and proofreading functions, prompting us to investigate if oxidation might positively or negatively affect AlaRS activity. We found that while oxidation leads to modification of several residues in Escherichia coli AlaRS, unlike in other aaRSs, this does not affect proofreading activity against the noncognate substrates serine and glycine and only results in a 1.6-fold decrease in efficiency of cognate Ala-tRNAAla formation. Mass spectrometry analysis of oxidized AlaRS revealed that the critical proofreading residue in the editing site, Cys666, and three methionine residues (M217 in the active site, M658 in the editing site, and M785 in the C-Ala domain) were modified to cysteine sulfenic acid and methionine sulfoxide, respectively. Alanine scanning mutagenesis showed that none of the identified residues were solely responsible for the change in cognate tRNAAla aminoacylation observed under oxidative stress, suggesting that these residues may act as reactive oxygen species “sinks” to protect catalytically critical sites from oxidative damage. Combined, our results indicate that E. coli AlaRS proofreading is resistant to oxidative damage, providing an important mechanism of stress resistance that helps to maintain proteome integrity and cellular viability.
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Affiliation(s)
- Arundhati Kavoor
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, USA
| | - Paul Kelly
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, USA
| | - Michael Ibba
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Microbiology, The Ohio State University, Columbus, Ohio, USA; Schmid College of Science and Technology, Chapman University, Orange, California, USA.
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12
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Ardean C, Davidescu CM, Nemeş NS, Negrea A, Ciopec M, Duteanu N, Negrea P, Duda-Seiman D, Muntean D. Antimicrobial Activities of Chitosan Derivatives. Pharmaceutics 2021; 13:pharmaceutics13101639. [PMID: 34683932 PMCID: PMC8541518 DOI: 10.3390/pharmaceutics13101639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/09/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Considering the challenge created by the development of bacterial and fungal strains resistant to multiple therapeutic variants, new molecules and materials with specific properties against these microorganisms can be synthesized, like those synthesized from biopolymers such as chitosan with improved antimicrobial activities. Antimicrobial activities of seven obtained materials were tested on four reference strains belonging to American Type Culture Collection. The best antimicrobial activity was obtained by functionalization by impregnation of chitosan with quaternary ammonium salts, followed by that obtained by functionalization of chitosan with phosphonium. The lowest antibacterial and antifungal effects were expressed by Ch-THIO and Ch-MBT, but new materials obtained with these extractants may be precursors with a significant role in the direct control of active molecules, such as cell growth factors or cell signaling molecules.
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Affiliation(s)
- Cristina Ardean
- Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University of Timişoara, 2 Piata Victoriei, 300006 Timisoara, Romania; (C.A.); (A.N.); (M.C.); (P.N.)
| | - Corneliu Mircea Davidescu
- Renewable Energy Research Institute-ICER, University Politehnica of Timisoara, 138 Gavril Musicescu Street, 300501 Timisoara, Romania;
| | - Nicoleta Sorina Nemeş
- Renewable Energy Research Institute-ICER, University Politehnica of Timisoara, 138 Gavril Musicescu Street, 300501 Timisoara, Romania;
- Correspondence: (N.S.N.); (N.D.); (D.D.-S.)
| | - Adina Negrea
- Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University of Timişoara, 2 Piata Victoriei, 300006 Timisoara, Romania; (C.A.); (A.N.); (M.C.); (P.N.)
| | - Mihaela Ciopec
- Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University of Timişoara, 2 Piata Victoriei, 300006 Timisoara, Romania; (C.A.); (A.N.); (M.C.); (P.N.)
| | - Narcis Duteanu
- Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University of Timişoara, 2 Piata Victoriei, 300006 Timisoara, Romania; (C.A.); (A.N.); (M.C.); (P.N.)
- Correspondence: (N.S.N.); (N.D.); (D.D.-S.)
| | - Petru Negrea
- Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University of Timişoara, 2 Piata Victoriei, 300006 Timisoara, Romania; (C.A.); (A.N.); (M.C.); (P.N.)
| | - Daniel Duda-Seiman
- Department of Cardiology, Victor Babes University of Medicine and Pharmacy Timişoara, 2 Piata Eftimie Murgu, 300041 Timisoara, Romania
- Correspondence: (N.S.N.); (N.D.); (D.D.-S.)
| | - Delia Muntean
- Multidisciplinary Research Center on Antimicrobial Resistance, Department of Microbiology, Victor Babes University of Medicine and Pharmacy Timişoara, 2 Eftimie Murgu Square, 300041 Timisoara, Romania;
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Akter S, Khan MS, Smith EN, Flashman E. Measuring ROS and redox markers in plant cells. RSC Chem Biol 2021; 2:1384-1401. [PMID: 34704044 PMCID: PMC8495998 DOI: 10.1039/d1cb00071c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/28/2021] [Indexed: 01/05/2023] Open
Abstract
Reactive oxygen species (ROS) are produced throughout plant cells as a by-product of electron transfer processes. While highly oxidative and potentially damaging to a range of biomolecules, there exists a suite of ROS-scavenging antioxidant strategies that maintain a redox equilibrium. This balance can be disrupted in the event of cellular stress leading to increased ROS levels, which can act as a useful stress signal but, in excess, can result in cell damage and death. As crop plants become exposed to greater degrees of multiple stresses due to climate change, efforts are ongoing to engineer plants with greater stress tolerance. It is therefore important to understand the pathways underpinning ROS-mediated signalling and damage, both through measuring ROS themselves and other indicators of redox imbalance. The highly reactive and transient nature of ROS makes this challenging to achieve, particularly in a way that is specific to individual ROS species. In this review, we describe the range of chemical and biological tools and techniques currently available for ROS and redox marker measurement in plant cells and tissues. We discuss the limitations inherent in current methodology and opportunities for advancement.
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Affiliation(s)
- Salma Akter
- Department of Chemistry, University of Oxford Oxford UK
- Faculty of Biological Sciences, University of Dhaka Dhaka 1000 Bangladesh
| | - Mohammad Shahneawz Khan
- Department of Chemistry, University of Oxford Oxford UK
- Faculty of Biological Sciences, University of Dhaka Dhaka 1000 Bangladesh
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14
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Barbosa ED, Neto JXL, Teixeira DG, Bezerra KS, do Amaral VS, Oliveira JIN, Lima JPMS, Machado LD, Fulco UL. Exploring human porphobilinogen synthase metalloprotein by quantum biochemistry and evolutionary methods. Metallomics 2021; 13:6206860. [PMID: 33791795 DOI: 10.1093/mtomcs/mfab017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/16/2021] [Accepted: 03/21/2021] [Indexed: 12/16/2022]
Abstract
Previous studies have shown the porphobilinogen synthase (PBGS) zinc-binding mechanism and its conservation among the living cells. However, the precise molecular interaction of zinc with the active center of the enzyme is unknown. In particular, quantum chemistry techniques within the density functional theory (DFT) framework have been the key methodology to describe metalloproteins, when one is looking for a compromise between accuracy and computational feasibility. Considering this, we used DFT-based models within the molecular fractionation with conjugate caps scheme to evaluate the binding energy features of zinc interacting with the human PBGS. Besides, phylogenetic and clustering analyses were successfully employed in extracting useful information from protein sequences to identify groups of conserved residues that build the ions-binding site. Our results also report a conservative assessment of the relevant amino acids, as well as the benchmark analysis of the calculation models used. The most relevant intermolecular interactions in Zn2+-PBGS are due to the amino acids CYS0122, CYS0124, CYS0132, ASP0169, SER0168, ARG0221, HIS0131, ASP0120, GLY0133, VAL0121, ARG0209, and ARG0174. Among these residues, we highlighted ASP0120, GLY0133, HIS0131, SER0168, and ARG0209 by co-occurring in all clusters generated by unsupervised clustering analysis. On the other hand, the triple cysteines at 2.5 Å from zinc (CYS0122, CYS0124, and CYS0132) have the highest energy attraction and are absent in the taxa Viridiplantae, Sar, Rhodophyta, and some Bacteria. Additionally, the performance of the DFT-based models shows that the processing time-dependence is more associated with the choice of the basis set than the exchange-correlation functional.
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Affiliation(s)
- E D Barbosa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - J X Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - D G Teixeira
- Institute of Tropical Medicine, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - K S Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - V S do Amaral
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - J I N Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - J P M Santos Lima
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - L D Machado
- Departamento de Física Teórica e Experimental, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - U L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
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Banerjee I, Ghosh KC, Oheix E, Jean M, Naubron JV, Réglier M, Iranzo O, Sinha S. Synthesis of Protected 3,4- and 2,3-Dimercaptophenylalanines as Building Blocks for Fmoc-Peptide Synthesis and Incorporation of the 3,4-Analogue in a Decapeptide Using Solid-Phase Synthesis. J Org Chem 2021; 86:2210-2223. [PMID: 33491451 DOI: 10.1021/acs.joc.0c02359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
3,4-Dimercaptophenylalanines and 2,3-dimercaptophenylalanines have been synthesized for the first time by nucleophilic substitution of a protected aminomalonate on 3,4- and 2,3-dimercaptobenzyl bromide derivatives. The dithiol functions were protected as thioketals, and the key precursors, diphenylthioketal-protected dimercaptobenzyl bromides, were synthesized via two distinct routes from either dihydroxy benzoates or toluene-3,4-dithiol. Racemic mixtures of the fully protected amino acids were separated by chiral HPLC into the corresponding enantiomers. The absolute configuration of both 3,4- and 2,3-analogues could be assigned based on X-ray crystallography and VCD/DFT measurements. Thioketal groups were deprotected upon reaction with mercury oxide and aqueous tetrafluoroboric acid followed by treatment with H2S gas under an argon atmosphere to obtain the corresponding dimercapto amino acids. The optically pure l-Fmoc-protected 3,4-analogue (S- enantiomer) was successfully incorporated into a decapeptide using standard solid-phase peptide synthesis. Therefore, dithiolene-functionalized peptides are now accessible from a simple synthetic procedure, and this should afford new molecular tools for research into the catalysis, diagnostic, and nanotechnology fields.
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Affiliation(s)
- Isita Banerjee
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Keshab Ch Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Emmanuel Oheix
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13397 Marseille, France
| | - Marion Jean
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13397 Marseille, France
| | - Jean-Valère Naubron
- Aix Marseille Univ, CNRS, Centrale Marseille, FSCM-Spectropole,, 13397 Marseille, France
| | - Marius Réglier
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13397 Marseille, France
| | - Olga Iranzo
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, 13397 Marseille, France
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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16
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Yang CT, Devarie-Baez NO, Hamsath A, Fu XD, Xian M. S-Persulfidation: Chemistry, Chemical Biology, and Significance in Health and Disease. Antioxid Redox Signal 2020; 33:1092-1114. [PMID: 31547682 PMCID: PMC7583347 DOI: 10.1089/ars.2019.7889] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Significance: S-Persulfidation generates persulfide adducts (RSSH) on both small molecules and proteins. This process is believed to be critical in the regulation of biological functions of reactive sulfur species such as H2S, as well as in signal transduction. S-Persulfidation also plays regulatory roles in human health and diseases. Recent Advances: Some mechanisms underlying the generation of low-molecular-weight persulfides and protein S-persulfidation in living organisms have been uncovered. Some methods for the specific delivery of persulfides and the detection of persulfides in biological systems have been developed. These advances help to pave the road to better understand the functions of S-persulfidation. Critical Issues: Persulfides are highly reactive and unstable. Currently, their identification relies on trapping them by S-alkylation, but this is not always reliable due to rapid sulfur exchange reactions. Therefore, the presence, identity, and fates of persulfides in biological environments are sometimes difficult to track. Future Directions: Further understanding the fundamental chemistry/biochemistry of persulfides and development of more reliable detection methods are needed. S-Persulfidation in specific protein targets is essential in organismal physiological health and human disease states. Besides cardiovascular and neuronal systems, the roles of persulfidation in other systems need to be further explored. Contradictory results of persulfidation in biology, especially in cancer, need to be clarified.
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Affiliation(s)
- Chun-Tao Yang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Protein Modification and Degradation Key Lab of Guangzhou and Guangdong, Key Laboratory of Molecular Clinical Pharmacology in School of Pharmaceutics Science, Guangzhou Medical University, Guangzhou, China.,Department of Chemistry, Washington State University, Pullman, Washington, USA
| | - Nelmi O Devarie-Baez
- Department of Chemistry, Washington State University-Tri Cities, Richland, Washington, USA
| | - Akil Hamsath
- Department of Chemistry, Washington State University, Pullman, Washington, USA
| | - Xiao-Dong Fu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Protein Modification and Degradation Key Lab of Guangzhou and Guangdong, Key Laboratory of Molecular Clinical Pharmacology in School of Pharmaceutics Science, Guangzhou Medical University, Guangzhou, China
| | - Ming Xian
- Department of Chemistry, Washington State University, Pullman, Washington, USA
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17
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Type III intermediate filaments as targets and effectors of electrophiles and oxidants. Redox Biol 2020; 36:101582. [PMID: 32711378 PMCID: PMC7381704 DOI: 10.1016/j.redox.2020.101582] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/05/2020] [Accepted: 05/13/2020] [Indexed: 12/20/2022] Open
Abstract
Intermediate filaments (IFs) play key roles in cell mechanics, signaling and homeostasis. Their assembly and dynamics are finely regulated by posttranslational modifications. The type III IFs, vimentin, desmin, peripherin and glial fibrillary acidic protein (GFAP), are targets for diverse modifications by oxidants and electrophiles, for which their conserved cysteine residue emerges as a hot spot. Pathophysiological examples of these modifications include lipoxidation in cell senescence and rheumatoid arthritis, disulfide formation in cataracts and nitrosation in endothelial shear stress, although some oxidative modifications can also be detected under basal conditions. We previously proposed that cysteine residues of vimentin and GFAP act as sensors for oxidative and electrophilic stress, and as hinges influencing filament assembly. Accumulating evidence indicates that the structurally diverse cysteine modifications, either per se or in combination with other posttranslational modifications, elicit specific functional outcomes inducing distinct assemblies or network rearrangements, including filament stabilization, bundling or fragmentation. Cysteine-deficient mutants are protected from these alterations but show compromised cellular performance in network assembly and expansion, organelle positioning and aggresome formation, revealing the importance of this residue. Therefore, the high susceptibility to modification of the conserved cysteine of type III IFs and its cornerstone position in filament architecture sustains their role in redox sensing and integration of cellular responses. This has deep pathophysiological implications and supports the potential of this residue as a drug target. Type III intermediate filaments can be modified by many oxidants and electrophiles. Oxidative modifications of type III IFs occur in normal and pathological conditions. The conserved cysteine residue acts as a hub for redox/electrophilic modifications. Cysteine modifications elicit structure-dependent type III IF rearrangements. Type III intermediate filaments act as sensors for oxidative and electrophilic stress.
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Poole LB, Furdui CM, King SB. Introduction to approaches and tools for the evaluation of protein cysteine oxidation. Essays Biochem 2020; 64:1-17. [PMID: 32031597 PMCID: PMC7477960 DOI: 10.1042/ebc20190050] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 12/15/2022]
Abstract
Oxidative modifications of cysteine thiols in cellular proteins are pivotal to the way signal-stimulated reactive oxygen species are sensed and elicit appropriate or sometimes pathological responses, but the dynamic and often transitory nature of these modifications offer a challenge to the investigator trying to identify such sites and the responses they elicit. A number of reagents and workflows have been developed to identify proteins undergoing oxidation and to query the timing, extent and location of such modifications, as described in this minireview. While no approach is perfect to capture all the redox information in a functioning cell, best practices described herein can enable considerable insights into the "redox world" of cells and organisms.
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Affiliation(s)
- Leslie B. Poole
- Department of Biochemistry, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, U.S.A
- Center for Redox Biology and Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, U.S.A
| | - Cristina M. Furdui
- Center for Redox Biology and Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, U.S.A
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, U.S.A
| | - S. Bruce King
- Center for Redox Biology and Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, U.S.A
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109, U.S.A
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19
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Gaillot C, Delolme F, Fabre L, Charreyre MT, Ladavière C, Favier A. Taking Advantage of Oxidation to Characterize Thiol-Containing Polymer Chains by MALDI-TOF Mass Spectrometry. Anal Chem 2020; 92:3804-3809. [PMID: 31990181 DOI: 10.1021/acs.analchem.9b05207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MALDI-TOF mass spectrometry analyses revealed the oxidation of thiol-containing polymer chain-ends during sample preparation using THF as solvent. In these conditions, the extent of oxidation was hardly reproducible, and led to various types of oxidized compounds. Preparing the samples at the last minute using commercial THF stabilized with an antioxidant led to more reproducible results, with the least oxidation. However, it is demonstrated herein that thiol oxidation can be advantageously taken into profit to further ascertain the presence of the thiol at the polymer chain-end. To force thiol oxidation we used THF without any antioxidant stabilizer, thus more prone to form peroxides. Thiol-containing polymer chains can thereby be indirectly evidenced by the formation of oxidation products such as chain-chain disulfide bonds and sulfonic acid chains-ends. More importantly, in these oxidizing conditions and in the negative mode, sulfonic acid-terminated polymer chains can be more sensitively detected than thiol ones (the low pKa of sulfonic acids facilitating their anionization in MALDI source). In conclusion, performing MALDI-TOF mass spectrometry analyses in oxidizing conditions, as complement to regular analyses, was found to be very useful for the chain-end identification of different thiol-containing polymer chains.
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Affiliation(s)
- Cassandre Gaillot
- Univ Lyon, Université Lyon 1, INSA de Lyon, CNRS, Laboratoire Ingénierie des Matériaux Polymères, UMR5223, F-69621 Villeurbanne, France
| | - Frédéric Delolme
- Univ Lyon, SFR BioSciences, Université Lyon 1, ENS de Lyon, Protein Science Facility, CNRS UMS3444, INSERM US8, F-69007 Lyon, France
| | - Laura Fabre
- Univ Lyon, Université Lyon 1, INSA de Lyon, CNRS, Laboratoire Ingénierie des Matériaux Polymères, UMR5223, F-69621 Villeurbanne, France
| | - Marie-Thérèse Charreyre
- Univ Lyon, Université Lyon 1, INSA de Lyon, CNRS, Laboratoire Ingénierie des Matériaux Polymères, UMR5223, F-69621 Villeurbanne, France
| | - Catherine Ladavière
- Univ Lyon, Université Lyon 1, INSA de Lyon, CNRS, Laboratoire Ingénierie des Matériaux Polymères, UMR5223, F-69621 Villeurbanne, France
| | - Arnaud Favier
- Univ Lyon, Université Lyon 1, INSA de Lyon, CNRS, Laboratoire Ingénierie des Matériaux Polymères, UMR5223, F-69621 Villeurbanne, France
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20
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Oliveira CX, Mocellin A, Menezes de Souza Lima F, Jesus Chaves Neto AM, Lima Azevedo D. DFT Study of L‐Cysteine Fragmentation Route using a Novel Protocol. ChemistrySelect 2019. [DOI: 10.1002/slct.201903453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Carlos Xavier Oliveira
- Institute of Physics University of Brasília Campus Darcy Ribeiro, Asa Norte Brasília-DF Brazil 70919-970
| | - Alexandra Mocellin
- Institute of Physics University of Brasília Campus Darcy Ribeiro, Asa Norte Brasília-DF Brazil 70919-970
| | | | | | - David Lima Azevedo
- Institute of Physics University of Brasília Campus Darcy Ribeiro, Asa Norte Brasília-DF Brazil 70919-970
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21
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Hawkins CL, Davies MJ. Detection, identification, and quantification of oxidative protein modifications. J Biol Chem 2019; 294:19683-19708. [PMID: 31672919 PMCID: PMC6926449 DOI: 10.1074/jbc.rev119.006217] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Exposure of biological molecules to oxidants is inevitable and therefore commonplace. Oxidative stress in cells arises from both external agents and endogenous processes that generate reactive species, either purposely (e.g. during pathogen killing or enzymatic reactions) or accidentally (e.g. exposure to radiation, pollutants, drugs, or chemicals). As proteins are highly abundant and react rapidly with many oxidants, they are highly susceptible to, and major targets of, oxidative damage. This can result in changes to protein structure, function, and turnover and to loss or (occasional) gain of activity. Accumulation of oxidatively-modified proteins, due to either increased generation or decreased removal, has been associated with both aging and multiple diseases. Different oxidants generate a broad, and sometimes characteristic, spectrum of post-translational modifications. The kinetics (rates) of damage formation also vary dramatically. There is a pressing need for reliable and robust methods that can detect, identify, and quantify the products formed on amino acids, peptides, and proteins, especially in complex systems. This review summarizes several advances in our understanding of this complex chemistry and highlights methods that are available to detect oxidative modifications-at the amino acid, peptide, or protein level-and their nature, quantity, and position within a peptide sequence. Although considerable progress has been made in the development and application of new techniques, it is clear that further development is required to fully assess the relative importance of protein oxidation and to determine whether an oxidation is a cause, or merely a consequence, of injurious processes.
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Affiliation(s)
- Clare L Hawkins
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen 2200, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen 2200, Denmark
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22
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Ulrich K, Jakob U. The role of thiols in antioxidant systems. Free Radic Biol Med 2019; 140:14-27. [PMID: 31201851 PMCID: PMC7041647 DOI: 10.1016/j.freeradbiomed.2019.05.035] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/04/2019] [Accepted: 05/31/2019] [Indexed: 02/07/2023]
Abstract
The sulfur biochemistry of the thiol group endows cysteines with a number of highly specialized and unique features that enable them to serve a variety of different functions in the cell. Typically highly conserved in proteins, cysteines are predominantly found in functionally or structurally crucial regions, where they act as stabilizing, catalytic, metal-binding and/or redox-regulatory entities. As highly abundant low molecular weight thiols, cysteine thiols and their oxidized disulfide counterparts are carefully balanced to maintain redox homeostasis in various cellular compartments, protect organisms from oxidative and xenobiotic stressors and partake actively in redox-regulatory and signaling processes. In this review, we will discuss the role of protein thiols as scavengers of hydrogen peroxide in antioxidant enzymes, use thiol peroxidases to exemplify how protein thiols contribute to redox signaling, provide an overview over the diverse set of low molecular weight thiol-based redox systems found in biology, and illustrate how thiol-based redox systems have evolved not only to protect against but to take full advantage of a world full of molecular oxygen.
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Affiliation(s)
- Kathrin Ulrich
- Department of Molecular, Cellular, and Developmental Biology, University of Michgan, Ann Arbor, MI, 48109, USA
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology, University of Michgan, Ann Arbor, MI, 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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23
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Bruno G, Heusler T, Lackmann JW, von Woedtke T, Weltmann KD, Wende K. Cold physical plasma-induced oxidation of cysteine yields reactive sulfur species (RSS). CLINICAL PLASMA MEDICINE 2019. [DOI: 10.1016/j.cpme.2019.100083] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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24
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Lackmann JW, Bruno G, Jablonowski H, Kogelheide F, Offerhaus B, Held J, Schulz-von der Gathen V, Stapelmann K, von Woedtke T, Wende K. Nitrosylation vs. oxidation - How to modulate cold physical plasmas for biological applications. PLoS One 2019; 14:e0216606. [PMID: 31067274 PMCID: PMC6505927 DOI: 10.1371/journal.pone.0216606] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/24/2019] [Indexed: 02/07/2023] Open
Abstract
Thiol moieties are major targets for cold plasma-derived nitrogen and oxygen species, making CAPs convenient tools to modulate redox-signaling pathways in cells and tissues. The underlying biochemical pathways are currently under investigation but especially the role of CAP derived RNS is barely understood. Their potential role in protein thiol nitrosylation would be relevant in inflammatory processes such as wound healing and improving their specific production by CAP would allow for enhanced treatment options beyond the current application. The impact of a modified kINPen 09 argon plasma jet with nitrogen shielding on cysteine as a thiol-carrying model substance was investigated by FTIR spectroscopy and high-resolution mass spectrometry. The deposition of short-lived radical species was measured by electron paramagnetic resonance spectroscopy, long-lived species were quantified by ion chromatography (NO2-, NO3-) and xylenol orange assay (H2O2). Product profiles were compared to samples treated with the so-called COST jet, being introduced by a European COST initiative as a reference device, using both reference conditions as well as conditions adjusted to kINPen gas mixtures. While thiol oxidation was dominant under all tested conditions, an Ar + N2/O2 gas compositions combined with a nitrogen curtain fostered nitric oxide deposition and the desired generation of S-nitrosocysteine. Interestingly, the COST-jet revealed significant differences in its chemical properties in comparison to the kINPen by showing a more stable production of RNS with different gas admixtures, indicating a different •NO production pathway. Taken together, results indicate various chemical properties of kINPen and COST-jet as well as highlight the potential of plasma tuning not only by gas admixtures alone but by adjusting the surrounding atmosphere as well.
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Affiliation(s)
- Jan-Wilm Lackmann
- ZIK plasmatis at Leibniz Institute for Plasma Science and Technology (INP Greifswald e.V.), Greifswald, Germany
- * E-mail: (JWL); (KW)
| | - Giuliana Bruno
- ZIK plasmatis at Leibniz Institute for Plasma Science and Technology (INP Greifswald e.V.), Greifswald, Germany
| | - Helena Jablonowski
- ZIK plasmatis at Leibniz Institute for Plasma Science and Technology (INP Greifswald e.V.), Greifswald, Germany
| | - Friederike Kogelheide
- Institute for Electrical Engineering and Plasma Technology, Ruhr University Bochum, Bochum, Germany
| | - Björn Offerhaus
- Institute for Electrical Engineering and Plasma Technology, Ruhr University Bochum, Bochum, Germany
| | - Julian Held
- Experimental Physics II, Ruhr University Bochum, Bochum, Germany
| | | | - Katharina Stapelmann
- Institute for Electrical Engineering and Plasma Technology, Ruhr University Bochum, Bochum, Germany
- Plasma for Life Sciences, Department of Nuclear Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Thomas von Woedtke
- ZIK plasmatis at Leibniz Institute for Plasma Science and Technology (INP Greifswald e.V.), Greifswald, Germany
| | - Kristian Wende
- ZIK plasmatis at Leibniz Institute for Plasma Science and Technology (INP Greifswald e.V.), Greifswald, Germany
- * E-mail: (JWL); (KW)
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25
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Dyer RR, Ford KI, Robinson RAS. The roles of S-nitrosylation and S-glutathionylation in Alzheimer's disease. Methods Enzymol 2019; 626:499-538. [PMID: 31606089 PMCID: PMC6908309 DOI: 10.1016/bs.mie.2019.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alzheimer's disease (AD) is a debilitating dementia with complex pathophysiological alterations including modifications to endogenous cysteine. S-nitrosylation (SNO) is a well-studied posttranslational modification (PTM) in the context of AD while S-glutathionylation (PSSG) remains less studied. Excess reactive oxygen and reactive nitrogen species (ROS/RNS) directly or indirectly generate SNO and PSSG. SNO is dysregulated in AD and plays a pervasive role in processes such as protein function, cell signaling, metabolism, and apoptosis. Despite some studies into the role of SNO in AD, multiple identified SNO proteins lack deep investigation and SNO modifications outside of brain tissues are limited, leaving the full role of SNO in AD to be elucidated. PSSG homeostasis is perturbed in AD and may affect a myriad of cellular processes. Here we overview the role of nitric oxide (NO) in AD, discuss proteomic methodologies to investigate SNO and PSSG, and review SNO and PSSG in AD. A more thorough understanding of SNO, PSSG, and other cysteinyl PTMs in AD will be helpful for the development of novel therapeutics against neurodegenerative diseases.
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Affiliation(s)
- Ryan R Dyer
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
| | - Katarena I Ford
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, United States; Vanderbilt Memory & Alzheimer's Center, Nashville, TN, United States; Vanderbilt Institute of Chemical Biology, Nashville, TN, United States; Vanderbilt Brain Institute, Nashville, TN, United States.
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26
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Pratesi A, Cirri D, Ciofi L, Messori L. Reactions of Auranofin and Its Pseudohalide Derivatives with Serum Albumin Investigated through ESI-Q-TOF MS. Inorg Chem 2018; 57:10507-10510. [PMID: 30109928 DOI: 10.1021/acs.inorgchem.8b02177] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The reactions of auranofin and three pseudohalide derivatives with bovine serum albumin were explored by ESI-Q-TOF mass spectrometry; a detailed molecular description of the resulting adducts is achieved revealing even subtle differences in reactivity within this series of gold(I) complexes. Our study shows that this kind of investigative approach, formerly applied to the interactions of metal-based drugs with small model proteins of MW 10-15 kDa, e.g., cytochrome c and lysozyme, may now be extended with success to far larger proteins such as serum albumin (MW 66 kDa).
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Affiliation(s)
- Alessandro Pratesi
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff" , University of Florence , Via della Lastruccia 3 , Postal Code 50019 Sesto Fiorentino , Italy
| | - Damiano Cirri
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff" , University of Florence , Via della Lastruccia 3 , Postal Code 50019 Sesto Fiorentino , Italy
| | - Lorenzo Ciofi
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff" , University of Florence , Via della Lastruccia 3 , Postal Code 50019 Sesto Fiorentino , Italy
| | - Luigi Messori
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff" , University of Florence , Via della Lastruccia 3 , Postal Code 50019 Sesto Fiorentino , Italy
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27
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Holmila RJ, Vance SA, Chen X, Wu H, Shukla K, Bharadwaj MS, Mims J, Wary Z, Marrs G, Singh R, Molina AJ, Poole LB, King SB, Furdui CM. Mitochondria-targeted Probes for Imaging Protein Sulfenylation. Sci Rep 2018; 8:6635. [PMID: 29703899 PMCID: PMC5923234 DOI: 10.1038/s41598-018-24493-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/27/2018] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial reactive oxygen species (ROS) are essential regulators of cellular signaling, metabolism and epigenetics underlying the pathophysiology of numerous diseases. Despite the critical function of redox regulation in mitochondria, currently there are limited methods available to monitor protein oxidation in this key subcellular organelle. Here, we describe compounds for imaging sulfenylated proteins in mitochondria: DCP-NEt2-Coumarin (DCP-NEt2C) and rhodamine-based DCP-Rho1. Side-by-side comparison studies are presented on the reactivity of DCP-NEt2C and DCP-Rho1 with a model protein sulfenic acid (AhpC-SOH) and mitochondrial localization to identify optimized experimental conditions for labeling and visualization of protein sulfenylation that would be independent of mitochondria membrane potential and would not impact mitochondrial function. These probes are applied to image mitochondrial protein sulfenylation under conditions of serum starvation and in a cell culture model of lung cancer exposed to ionizing radiation and silver nanoparticles, agents serving dual functions as environmental stressors and cancer therapeutics.
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Affiliation(s)
- Reetta J Holmila
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, 27157, USA
| | - Stephen A Vance
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, 27109, USA
| | - Xiaofei Chen
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, 27157, USA
| | - Hanzhi Wu
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, 27157, USA
| | - Kirtikar Shukla
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, 27157, USA
| | - Manish S Bharadwaj
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, 27157, USA
| | - Jade Mims
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, 27157, USA
| | - Zack Wary
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, 27109, USA
| | - Glen Marrs
- Department of Biology, Wake Forest University, Winston-Salem, NC, 27109, USA
| | - Ravi Singh
- Department of Cancer Biology, Wake Forest University Health Sciences, Winston-Salem, NC, 27157, USA
| | - Anthony J Molina
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, 27157, USA
| | - Leslie B Poole
- Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC, 27157, USA
| | - S Bruce King
- Department of Chemistry, Wake Forest University, Winston-Salem, NC, 27109, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, 27157, USA.
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28
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Cobley JN, Close GL, Bailey DM, Davison GW. Exercise redox biochemistry: Conceptual, methodological and technical recommendations. Redox Biol 2017; 12:540-548. [PMID: 28371751 PMCID: PMC5377294 DOI: 10.1016/j.redox.2017.03.022] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 12/16/2022] Open
Abstract
Exercise redox biochemistry is of considerable interest owing to its translational value in health and disease. However, unaddressed conceptual, methodological and technical issues complicate attempts to unravel how exercise alters redox homeostasis in health and disease. Conceptual issues relate to misunderstandings that arise when the chemical heterogeneity of redox biology is disregarded: which often complicates attempts to use redox-active compounds and assess redox signalling. Further, that oxidised macromolecule adduct levels reflect formation and repair is seldom considered. Methodological and technical issues relate to the use of out-dated assays and/or inappropriate sample preparation techniques that confound biochemical redox analysis. After considering each of the aforementioned issues, we outline how each issue can be resolved and provide a unifying set of recommendations. We specifically recommend that investigators: consider chemical heterogeneity, use redox-active compounds judiciously, abandon flawed assays, carefully prepare samples and assay buffers, consider repair/metabolism, use multiple biomarkers to assess oxidative damage and redox signalling.
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Affiliation(s)
- James N Cobley
- Department for Sport and Exercise Sciences, Abertay University, 40 Bell Street, Dundee, Scotland DD1 1HG, UK.
| | - Graeme L Close
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Tom Reilly Building, Liverpool, England L3 3AF, UK
| | - Damian M Bailey
- Neurovascular Research Laboratory, Faculty of Life Sciences and Education, University of South Wales, Wales, CF37 4AT, UK; Faculty of Medicine, Reichwald Health Sciences Centre, University of British Columbia-Okanagan, Kelowna, British Columbia, Canada
| | - Gareth W Davison
- Sport and Exercise Science Research Institute, Ulster University, Belfast, BT37 OQB, UK
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29
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Li Y. A ratiometric fluorescent chemosensor for the detection of cysteine in aqueous solution at neutral pH. LUMINESCENCE 2017; 32:1385-1390. [DOI: 10.1002/bio.3334] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 03/03/2017] [Accepted: 03/08/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Yuanyuan Li
- College of Chemistry, Chemical and Environmental Engineering; Henan University of Technology; Zhengzhou People's Republic of China
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30
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Heppner DE, Janssen-Heininger YMW, van der Vliet A. The role of sulfenic acids in cellular redox signaling: Reconciling chemical kinetics and molecular detection strategies. Arch Biochem Biophys 2017; 616:40-46. [PMID: 28126370 DOI: 10.1016/j.abb.2017.01.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/20/2017] [Accepted: 01/22/2017] [Indexed: 01/08/2023]
Abstract
The reversible oxidation of protein cysteine residues is well recognized as an important regulatory mechanism in redox-dependent cell signaling. Cysteine oxidation is diverse in nature and involves various post-translational modifications (sulfenic acids, disulfides, etc.) and the specific functional or structural impact of these specific oxidative events is still poorly understood. The proximal product of protein cysteine oxidation by biological reactive oxygen species (ROS) is sulfenic acid (Cys-SOH), and experimental evidence is accruing for the formation of Cys-SOH as intermediate in protein cysteine oxidation in various biological settings. However, the plausibility of protein Cys-SH oxidation by ROS has often been put in question because of slow reaction kinetics compared to more favorable reactions with abundant thiol-based reductants such as peroxiredoxins (Prx) or glutathione (GSH). This commentary aims to address this controversy by highlighting the unique physical properties in cells that may restrict ROS diffusion and allow otherwise less favorable cysteine oxidation of proteins. Some limitations of analytical tools to assess Cys-SOH are also discussed. We conclude that formation of Cys-SOH in biological systems cannot always be predicted based on kinetic analyses in homogenous solution, and may be facilitated by unique structural and physical properties of Cys-containing proteins within e.g. signaling complexes.
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Affiliation(s)
- David E Heppner
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT 05405, United States
| | | | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, VT 05405, United States.
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31
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Reisz JA, Chessler KM, Dzieciatkowska M, D'Alessandro A, Hansen KC. Blood and Plasma Proteomics: Targeted Quantitation and Posttranslational Redox Modifications. Methods Mol Biol 2017; 1619:353-371. [PMID: 28674896 DOI: 10.1007/978-1-4939-7057-5_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Proteome profiling using mass spectrometry is extensively utilized to understand the physiological characteristics of cells, tissues, fluids, and many other biological matrices. From the earliest days of the proteomics era, exploratory analyses of the blood protein complement have attracted a great deal of interest, owing to the pivotal importance of blood cells and biofluids (serum, plasma) for research and biomedical purposes. Once challenged by the high dynamic range of protein concentrations, low sensitivity of mass spectrometers, and poor annotation of proteomics databases, the techniques in this field have quickly evolved in recent years, particularly in the areas of absolute quantification of proteins and in mapping of posttranslational modifications. Here we describe (a) the design and production of heavy isotope-labeled peptides used as reporter internal standards for absolute protein quantification and (b) a redox proteomics approach to optimize sample preparation and database searching to elucidate oxidative modifications to protein amino acids. The two methods achieve complimentary goals in the field of blood research and pave the way for future translation of next-generation proteomics technologies into clinical practice.
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Affiliation(s)
- Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 E. 17th Ave., Aurora, CO, 80045, USA
| | - Katelyn M Chessler
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 E. 17th Ave., Aurora, CO, 80045, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 E. 17th Ave., Aurora, CO, 80045, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 E. 17th Ave., Aurora, CO, 80045, USA.
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 E. 17th Ave., Aurora, CO, 80045, USA
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32
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McGarry DJ, Shchepinova MM, Lilla S, Hartley RC, Olson MF. A Cell-Permeable Biscyclooctyne As a Novel Probe for the Identification of Protein Sulfenic Acids. ACS Chem Biol 2016; 11:3300-3304. [PMID: 27792307 DOI: 10.1021/acschembio.6b00742] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Reactive oxygen species act as important second messengers in cell signaling and homeostasis through the oxidation of protein thiols. However, the dynamic nature of protein oxidation and the lack of sensitivity of existing molecular probes have hindered our understanding of such reactions; therefore, new tools are required to address these challenges. We designed a bifunctional variant of the strained bicyclo[6.1.0]nonyne (BCN-E-BCN) that enables the tagging of intracellular protein sulfenic acids for biorthogonal copper-free click chemistry. In validation studies, BCN-E-BCN binds the sulfenylated form of the actin-severing protein cofilin, while mutation of the cognate cysteine residues abrogates its binding. BCN-E-BCN is cell permeable and reacts rapidly with cysteine sulfenic acids in cultured cells. Using different azide-tagged conjugates, we demonstrate that BCN-E-BCN can be used in various applications for the detection of sulfenylated proteins. Remarkably, cycloaddition of an azide-tagged fluorophore to BCN-E-BCN labeled proteins produced in vivo can be visualized by fluorescence microscopy to reveal their localization. These findings demonstrate a novel and multifaceted approach to the detection and trapping of sulfenic acids.
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Affiliation(s)
- David J McGarry
- Cancer Research UK Beatson Institute , Garscube Estate, Switchback Road, Glasgow G61 1BD, United Kingdom
| | - Maria M Shchepinova
- WestCHEM School of Chemistry, University of Glasgow , Glasgow G12 8QQ, United Kingdom
| | - Sergio Lilla
- Cancer Research UK Beatson Institute , Garscube Estate, Switchback Road, Glasgow G61 1BD, United Kingdom
| | - Richard C Hartley
- WestCHEM School of Chemistry, University of Glasgow , Glasgow G12 8QQ, United Kingdom
| | - Michael F Olson
- Cancer Research UK Beatson Institute , Garscube Estate, Switchback Road, Glasgow G61 1BD, United Kingdom
- Institute of Cancer Sciences, University of Glasgow , Glasgow G12 8QQ, United Kingdom
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33
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Allan KM, Loberg MA, Chepngeno J, Hurtig JE, Tripathi S, Kang MG, Allotey JK, Widdershins AH, Pilat JM, Sizek HJ, Murphy WJ, Naticchia MR, David JB, Morano KA, West JD. Trapping redox partnerships in oxidant-sensitive proteins with a small, thiol-reactive cross-linker. Free Radic Biol Med 2016; 101:356-366. [PMID: 27816612 PMCID: PMC5154803 DOI: 10.1016/j.freeradbiomed.2016.10.506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 10/14/2016] [Accepted: 10/27/2016] [Indexed: 12/15/2022]
Abstract
A broad range of redox-regulated proteins undergo reversible disulfide bond formation on oxidation-prone cysteine residues. Heightened reactivity of the thiol groups in these cysteines also increases susceptibility to modification by organic electrophiles, a property that can be exploited in the study of redox networks. Here, we explored whether divinyl sulfone (DVSF), a thiol-reactive bifunctional electrophile, cross-links oxidant-sensitive proteins to their putative redox partners in cells. To test this idea, previously identified oxidant targets involved in oxidant defense (namely, peroxiredoxins, methionine sulfoxide reductases, sulfiredoxin, and glutathione peroxidases), metabolism, and proteostasis were monitored for cross-link formation following treatment of Saccharomyces cerevisiae with DVSF. Several proteins screened, including multiple oxidant defense proteins, underwent intermolecular and/or intramolecular cross-linking in response to DVSF. Specific redox-active cysteines within a subset of DVSF targets were found to influence cross-linking; in addition, DVSF-mediated cross-linking of its targets was impaired in cells first exposed to oxidants. Since cross-linking appeared to involve redox-active cysteines in these proteins, we examined whether potential redox partners became cross-linked to them upon DVSF treatment. Specifically, we found that several substrates of thioredoxins were cross-linked to the cytosolic thioredoxin Trx2 in cells treated with DVSF. However, other DVSF targets, like the peroxiredoxin Ahp1, principally formed intra-protein cross-links upon DVSF treatment. Moreover, additional protein targets, including several known to undergo S-glutathionylation, were conjugated via DVSF to glutathione. Our results indicate that DVSF is of potential use as a chemical tool for irreversibly trapping and discovering thiol-based redox partnerships within cells.
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Affiliation(s)
- Kristin M Allan
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Matthew A Loberg
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Juliet Chepngeno
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Jennifer E Hurtig
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Susmit Tripathi
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Min Goo Kang
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Jonathan K Allotey
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Afton H Widdershins
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Jennifer M Pilat
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Herbert J Sizek
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Wesley J Murphy
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Matthew R Naticchia
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Joseph B David
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States
| | - Kevin A Morano
- Department of Microbiology & Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - James D West
- Biochemistry & Molecular Biology Program, Departments of Biology and Chemistry, The College of Wooster, Wooster, OH, United States.
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34
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Gu L, Robinson RAS. Proteomic approaches to quantify cysteine reversible modifications in aging and neurodegenerative diseases. Proteomics Clin Appl 2016; 10:1159-1177. [PMID: 27666938 DOI: 10.1002/prca.201600015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/13/2016] [Accepted: 09/23/2016] [Indexed: 01/11/2023]
Abstract
Cysteine is a highly reactive amino acid and is subject to a variety of reversible post-translational modifications (PTMs), including nitrosylation, glutathionylation, palmitoylation, as well as formation of sulfenic acid and disulfides. These modifications are not only involved in normal biological activities, such as enzymatic catalysis, redox signaling, and cellular homeostasis, but can also be the result of oxidative damage. Especially in aging and neurodegenerative diseases, oxidative stress leads to aberrant cysteine oxidations that affect protein structure and function leading to neurodegeneration as well as other detrimental effects. Methods that can identify cysteine modifications by type, including the site of modification, as well as the relative stoichiometry of the modification can be very helpful for understanding the role of the thiol proteome and redox homeostasis in the context of disease. Cysteine reversible modifications however, are challenging to investigate as they are low abundant, diverse, and labile especially under endogenous conditions. Thanks to the development of redox proteomic approaches, large-scale quantification of cysteine reversible modifications is possible. These approaches cover a range of strategies to enrich, identify, and quantify cysteine reversible modifications from biological samples. This review will focus on nongel-based redox proteomics workflows that give quantitative information about cysteine PTMs and highlight how these strategies have been useful for investigating the redox thiol proteome in aging and neurodegenerative diseases.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
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35
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Wither MJ, Hansen KC, Reisz JA. Mass Spectrometry-Based Bottom-Up Proteomics: Sample Preparation, LC-MS/MS Analysis, and Database Query Strategies. ACTA ACUST UNITED AC 2016; 86:16.4.1-16.4.20. [PMID: 27801520 DOI: 10.1002/cpps.18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recent technological advances in mass spectrometry (MS) have made possible the investigation and quantification of complex mixtures of biomolecules. The exceptional sensitivity and resolving power of today's mass spectrometers allow for the detection of proteins and peptides at low femtomole quantities; however, these attributes demand high sample purity to minimize artifacts and achieve the highest degree of biomolecule identification. Tissue preparation for proteomic studies is particularly challenging due to their heterogeneity in cell type, presence of insoluble biomaterials, and wide diversity of biomolecules. The workflow described herein details sample preparation from tissues through protein extraction, proteolysis, and purification to generate peptides for MS analysis. Increased peptide resolution and a corresponding increase in protein identification is accomplished using polarity-based fractionation (C18 resin) at the peptide level. Additionally, approaches to instrument set up, including the use of nanoscale liquid chromatography and quadrupole Orbitrap MS, along with database searching, are described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Matthew J Wither
- Biological Mass Spectrometry Core, Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
| | - Kirk C Hansen
- Biological Mass Spectrometry Core, Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
| | - Julie A Reisz
- Biological Mass Spectrometry Core, Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
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36
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Matthews ML, He L, Horning BD, Olson EJ, Correia BE, Yates JR, Dawson PE, Cravatt BF. Chemoproteomic profiling and discovery of protein electrophiles in human cells. Nat Chem 2016; 9:234-243. [PMID: 28221344 PMCID: PMC5325178 DOI: 10.1038/nchem.2645] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022]
Abstract
Activity-based protein profiling (ABPP) serves as a chemical proteomic platform to discover and characterize functional amino acids in proteins on the basis of their enhanced reactivity towards small-molecule probes. This approach, to date, has mainly targeted nucleophilic functional groups, such as the side chains of serine and cysteine, using electrophilic probes. We show here that "reverse-polarity" (RP)-ABPP using clickable, nucleophilic hydrazine probes can capture and identify protein-bound electrophiles in cells, including the pyruvoyl cofactor of S-adenosyl-l-methionine decarboxylase (AMD1), which we find is dynamically controlled by intracellular methionine concentrations, and a heretofore unknown modification – an N-terminally bound glyoxylyl group – in the poorly characterized protein secernin-3. RP-ABPP thus provides a versatile method to monitor the metabolic regulation of electrophilic cofactors and discover novel types of electrophilic modifications on proteins in human cells. A chemical proteomic strategy is described for the discovery of protein-bound electrophilic groups in human cells and used to characterize dynamic regulation of the pyruvoyl catalytic cofactor in S-adenosyl-l-methionine decarboxylase and to discover an N-terminal glyoxylyl modification on Secernin proteins.
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Affiliation(s)
- Megan L Matthews
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Lin He
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA.,Bioinformatics Solutions Inc., Waterloo, Ontario N2L 6J2, Canada
| | - Benjamin D Horning
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Erika J Olson
- Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Bruno E Correia
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA.,École polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - John R Yates
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Philip E Dawson
- Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Benjamin F Cravatt
- Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
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37
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Gu L, Robinson RAS. High-throughput endogenous measurement of S-nitrosylation in Alzheimer's disease using oxidized cysteine-selective cPILOT. Analyst 2016; 141:3904-15. [PMID: 27152368 PMCID: PMC4904844 DOI: 10.1039/c6an00417b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reversible cysteine modifications play important physiological roles such as modulating enzymatic catalysis, maintaining redox homeostasis and conducting cellular signaling. These roles can be critical in the context of disease. Oxidative modifications such as S-nitrosylation (SNO) are signatures of neurodestruction in conditions of oxidative stress however are also indicators of neuroprotection and normal signaling in cellular environments with low concentrations of reactive oxygen and nitrogen species. SNO is a dynamic and low abundance modification and requires sensitive and selective analytical methods for its detection in biological tissues. Here we present an enhanced multiplexing strategy to study SNO in complex mixtures arising from tissues. This method, termed oxidized cysteine-selective cPILOT (OxcyscPILOT), allows simultaneous analysis of SNO-modified peptides in 12 samples. OxcyscPILOT has three primary steps: (1) blocking of free thiols by a cysteine-reactive reagent, (2) enrichment of peptides containing SNO on a solid phase resin, and (3) isotopic labeling and isobaric tagging of enriched peptides on the solid phase resin. This approach offers the advantage of allowing total protein abundance levels to be measured simultaneously with endogenous SNO levels and measurement of SNO levels across four biological replicates in a single analysis. Furthermore, the relative amount of SNO on a specific cysteine site can also be determined. A well-known model of Alzheimer's disease, the APP/PS-1 transgenic mouse model, was selected for demonstration of the method as several SNO-modified proteins have previously been reported in brain and synaptosomes from AD subjects. OxcyscPILOT analysis resulted in identification of 138 SNO-modified cysteines in brain homogenates that correspond to 135 proteins. Many of these SNO-modified proteins were only present in wild-type or AD mice, whereas 93 proteins had SNO signals in both WT and AD. Pathway analysis links SNO-modified proteins to various biological pathways especially metabolism and signal transduction, consistent with previous reports in the literature. The OxcyscPILOT strategy provides enhanced multiplexing capability to current redox proteomics methods to study oxidative modifications of cysteine.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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38
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Margaritelis NV, Cobley JN, Paschalis V, Veskoukis AS, Theodorou AA, Kyparos A, Nikolaidis MG. Principles for integrating reactive species into in vivo biological processes: Examples from exercise physiology. Cell Signal 2016; 28:256-71. [DOI: 10.1016/j.cellsig.2015.12.011] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/07/2015] [Accepted: 12/20/2015] [Indexed: 12/14/2022]
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39
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Gu L, Robinson RAS. A simple isotopic labeling method to study cysteine oxidation in Alzheimer's disease: oxidized cysteine-selective dimethylation (OxcysDML). Anal Bioanal Chem 2016; 408:2993-3004. [PMID: 26800981 DOI: 10.1007/s00216-016-9307-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/14/2015] [Accepted: 01/04/2016] [Indexed: 02/01/2023]
Abstract
Cysteine is widely involved in redox signaling pathways through a number of reversible and irreversible modifications. Reversible modifications (e.g., S-glutathionylation, S-nitrosylation, disulfide bonds, and sulfenic acid) are used to protect proteins from oxidative attack and maintain cellular homeostasis, while irreversible oxidations (e.g., sulfinic acid and sulfonic acid) serve as hallmarks of oxidative stress. Proteomic analysis of cysteine-enriched peptides coupled with reduction of oxidized thiols can be used to measure the oxidation states of cysteine, which is helpful for elucidating the role that oxidative stress plays in biology and disease. As an extension of our previously reported cysDML method, we have developed oxidized cysteine-selective dimethylation (OxcysDML), to investigate the site-specific total oxidation of cysteine residues in biologically relevant samples. OxcysDML employs (1) blocking of free thiols by a cysteine-reactive reagent, (2) enrichment of peptides containing reversibly oxidized cysteine by a solid phase resin, and (3) isotopic labeling of peptide amino groups to quantify cysteine modifications arising from different biological conditions. On-resin enrichment and labeling minimizes sample handing time and improves efficiency in comparison with other redox proteomic methods. OxcysDML is also inexpensive and flexible, as it can accommodate the exploration of various cysteine modifications. Here, we applied the method to liver tissues from a late-stage Alzheimer's disease (AD) mouse model and wild-type (WT) controls. Because we have previously characterized this proteome using the cysDML approach, we are able here to probe deeper into the redox status of cysteine in AD. OxcysDML identified 1129 cysteine sites (from 527 proteins), among which 828 cysteine sites underwent oxidative modifications. Nineteen oxidized cysteine sites had significant alteration levels in AD and represent proteins involved in metabolic processes. Overall, we have demonstrated OxcysDML as a simple, rapid, robust, and inexpensive redox proteomic approach that is useful for gaining deeper insight into the proteome of AD.
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Affiliation(s)
- Liqing Gu
- Department of Chemistry, University of Pittsburgh, 111 Eberly Hall, 200 University Drive, Pittsburgh, PA, 15260, USA
| | - Renã A S Robinson
- Department of Chemistry, University of Pittsburgh, 111 Eberly Hall, 200 University Drive, Pittsburgh, PA, 15260, USA.
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Mock HP, Dietz KJ. Redox proteomics for the assessment of redox-related posttranslational regulation in plants. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:967-73. [PMID: 26784836 DOI: 10.1016/j.bbapap.2016.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/08/2016] [Indexed: 01/22/2023]
Abstract
The methodological developments of in vivo and in vitro protein labeling and subsequent detection enable sensitive and specific detection of redox modifications. Such methods are presently applied to diverse cells and tissues, subproteomes and developmental as well as environmental conditions. The chloroplast proteome is particularly suitable for such kind of studies, because redox regulation of chloroplast proteins is well established, many plastid proteins are abundant, redox network components have been inventoried in great depth, and functional consequences explored. Thus the repertoire of redox-related posttranslational modifications on the one hand side and their abundance on the other pose a challenge for the near future to understand their contribution to physiological regulation. The various posttranslational redox modifications are introduced, followed by a description of the available proteomics methods. The significance of the redox-related posttranslational modification is exemplarily worked out using established examples from photosynthesis. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Hans-Peter Mock
- Applied Biochemistry, Institute of Plant Genetics and Crop Plant Research, IPK, Corrensstrasse 3, 06466 Gatersleben, Germany.
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Faculty of Biology - W5-134, Bielefeld University, 33501 Bielefeld, Germany.
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Devarie-Baez NO, Silva Lopez EI, Furdui CM. Biological chemistry and functionality of protein sulfenic acids and related thiol modifications. Free Radic Res 2015; 50:172-94. [PMID: 26340608 DOI: 10.3109/10715762.2015.1090571] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Selective modification of proteins at cysteine residues by reactive oxygen, nitrogen or sulfur species formed under physiological and pathological states is emerging as a critical regulator of protein activity impacting cellular function. This review focuses primarily on protein sulfenylation (-SOH), a metastable reversible modification connecting reduced cysteine thiols to many products of cysteine oxidation. An overview is first provided on the chemistry principles underlining synthesis, stability and reactivity of sulfenic acids in model compounds and proteins, followed by a brief description of analytical methods currently employed to characterize these oxidative species. The following chapters present a selection of redox-regulated proteins for which the -SOH formation was experimentally confirmed and linked to protein function. These chapters are organized based on the participation of these proteins in the regulation of signaling, metabolism and epigenetics. The last chapter discusses the therapeutic implications of altered redox microenvironment and protein oxidation in disease.
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Affiliation(s)
- Nelmi O Devarie-Baez
- a Department of Internal Medicine, Section on Molecular Medicine , Wake Forest School of Medicine , Winston-Salem , NC , USA
| | - Elsa I Silva Lopez
- a Department of Internal Medicine, Section on Molecular Medicine , Wake Forest School of Medicine , Winston-Salem , NC , USA
| | - Cristina M Furdui
- a Department of Internal Medicine, Section on Molecular Medicine , Wake Forest School of Medicine , Winston-Salem , NC , USA
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Yang J, Carroll KS, Liebler DC. The Expanding Landscape of the Thiol Redox Proteome. Mol Cell Proteomics 2015; 15:1-11. [PMID: 26518762 DOI: 10.1074/mcp.o115.056051] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 12/18/2022] Open
Abstract
Cysteine occupies a unique place in protein chemistry. The nucleophilic thiol group allows cysteine to undergo a broad range of redox modifications beyond classical thiol-disulfide redox equilibria, including S-sulfenylation (-SOH), S-sulfinylation (-SO(2)H), S-sulfonylation (-SO(3)H), S-nitrosylation (-SNO), S-sulfhydration (-SSH), S-glutathionylation (-SSG), and others. Emerging evidence suggests that these post-translational modifications (PTM) are important in cellular redox regulation and protection against oxidative damage. Identification of protein targets of thiol redox modifications is crucial to understanding their roles in biology and disease. However, analysis of these highly labile and dynamic modifications poses challenges. Recent advances in the design of probes for thiol redox forms, together with innovative mass spectrometry based chemoproteomics methods make it possible to perform global, site-specific, and quantitative analyses of thiol redox modifications in complex proteomes. Here, we review chemical proteomic strategies used to expand the landscape of thiol redox modifications.
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Affiliation(s)
- Jing Yang
- From the ‡National Center for Protein Sciences · Beijing, Beijing, 102206, China; §State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, 102206, China;
| | - Kate S Carroll
- ¶Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458
| | - Daniel C Liebler
- ‖Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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Abstract
Protein S-sulfenylation is the reversible oxidative modification of cysteine thiol groups to form cysteine S-sulfenic acids. Mapping the specific sites of protein S-sulfenylation onto complex proteomes is crucial to understanding the molecular mechanisms controlling redox signaling and regulation. This protocol describes global, in situ, site-specific analysis of protein S-sulfenylation using sulfenic acid-specific chemical probes and mass spectrometry (MS)-based proteomics. The major steps in this protocol are as follows: (i) optimization of conditions for selective labeling of cysteine S-sulfenic acids in intact cells with the commercially available dimedone-based probe, DYn-2; (ii) tagging the modified cysteines with a functionalized biotin reagent containing a cleavable linker via Cu(I)-catalyzed azide-alkyne cycloaddition reaction; (iii) enrichment of the biotin-tagged tryptic peptides with streptavidin; (iv) liquid chromatography-tandem MS (LC-MS/MS)-based shotgun proteomics; and (v) computational data analysis. We also outline strategies for quantitative analysis of this modification in cells responding to redox perturbations and discuss special issues pertaining to experimental design of thiol redox studies. Our chemoproteomic platform should be broadly applicable to the investigation of other bio-orthogonal chemically engineered post-translational modifications. The entire analysis protocol takes ∼1 week to complete.
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Luebke JL, Giedroc DP. Cysteine sulfur chemistry in transcriptional regulators at the host-bacterial pathogen interface. Biochemistry 2015; 54:3235-49. [PMID: 25946648 DOI: 10.1021/acs.biochem.5b00085] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hosts employ myriad weapons to combat invading microorganisms as an integral feature of the host-bacterial pathogen interface. This interface is dominated by highly reactive small molecules that collectively induce oxidative stress. Successful pathogens employ transcriptional regulatory proteins that sense these small molecules directly or indirectly via a change in the ratio of reduced to oxidized low-molecular weight (LMW) thiols that collectively comprise the redox buffer in the cytoplasm. These transcriptional regulators employ either a prosthetic group or reactive cysteine residue(s) to effect changes in the transcription of genes that encode detoxification and repair systems that is driven by regulator conformational switching between high-affinity and low-affinity DNA-binding states. Cysteine harbors a highly polarizable sulfur atom that readily undergoes changes in oxidation state in response to oxidative stress to produce a range of regulatory post-translational modifications (PTMs), including sulfenylation (S-hydroxylation), mixed disulfide bond formation with LMW thiols (S-thiolation), di- and trisulfide bond formation, S-nitrosation, and S-alkylation. Here we discuss several examples of structurally characterized cysteine thiol-specific transcriptional regulators that sense changes in cellular redox balance, focusing on the nature of the cysteine PTM itself and the interplay of small molecule oxidative stressors in mediating a specific transcriptional response.
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Affiliation(s)
- Justin L Luebke
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
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Poole LB. The basics of thiols and cysteines in redox biology and chemistry. Free Radic Biol Med 2015; 80:148-57. [PMID: 25433365 PMCID: PMC4355186 DOI: 10.1016/j.freeradbiomed.2014.11.013] [Citation(s) in RCA: 596] [Impact Index Per Article: 66.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 10/20/2014] [Accepted: 11/17/2014] [Indexed: 02/06/2023]
Abstract
Cysteine is one of the least abundant amino acids, yet it is frequently found as a highly conserved residue within functional (regulatory, catalytic, or binding) sites in proteins. It is the unique chemistry of the thiol or thiolate group of cysteine that imparts to functional sites their specialized properties (e.g., nucleophilicity, high-affinity metal binding, and/or ability to form disulfide bonds). Highlighted in this review are some of the basic biophysical and biochemical properties of cysteine groups and the equations that apply to them, particularly with respect to pKa and redox potential. Also summarized are the types of low-molecular-weight thiols present in high concentrations in most cells, as well as the ways in which modifications of cysteinyl residues can impart or regulate molecular functions important to cellular processes, including signal transduction.
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Affiliation(s)
- Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
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Abstract
Due to their susceptibility towards redox modification, protein thiols represent primary targets for the modulation of protein activity, conformation and oligomerization. Until fairly recently, such modifications were considered "damage" as a result of oxidative stress, before researchers recognized their physiological importance for biologic signaling. This paradigm shift, and the associated necessity to accurately characterize and quantify the various pathways of thiol redox modifications not only for specific proteins, but also within the cellular environment, has enticed researchers to take a close look at the impact of environment and molecular (protein) structure on these reactions. This Special Issue on Redox Biology of Thiols in Signaling Pathways is the result of a workshop organized at the 2013 Annual Meeting of the Society for Free Radical Biology and Medicine in San Antonio, Texas, summarizing the contributions from many of the presenters. It will provide a stimulating synopsis on what is known, and what is not known, about the reaction mechanisms which underlie the role of thiols and oxidative processes in signaling pathways.
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Affiliation(s)
- Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157 USA
| | - Christian Schöneich
- Department of Pharmaceutical Chemistry, The University of Kansas, 2095 Constant Avenue, Lawrence, KS 66047, USA
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