1
|
Luo S, Kong C, Ye D, Liu X, Wang Y, Meng G, Han Y, Xie L, Ji Y. Protein Persulfidation: Recent Progress and Future Directions. Antioxid Redox Signal 2023; 39:829-852. [PMID: 36943282 DOI: 10.1089/ars.2022.0064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Significance: Hydrogen sulfide (H2S) is considered to be a gasotransmitter along with carbon monoxide (CO) and nitric oxide (NO), and is known as a key regulator of physiological and pathological activities. S-sulfhydration (also known as persulfidation), a mechanism involving the formation of protein persulfides by modification of cysteine residues, is proposed here to explain the multiple biological functions of H2S. Investigating the properties of protein persulfides can provide a foundation for further understanding of the potential functions of H2S. Recent Advances: Multiple methods have been developed to determine the level of protein persulfides. It has been demonstrated that protein persulfidation is involved in many biological processes through various mechanisms including the regulation of ion channels, enzymes, and transcription factors, as well as influencing protein-protein interactions. Critical Issues: Some technical and theoretical questions remain to be solved. These include how to improve the specificity of the detection methods for protein persulfidation, why persulfidation typically occurs on one or a few thiols within a protein, how this modification alters protein functions, and whether protein persulfidation has organ-specific patterns. Future Directions: Optimizing the detection methods and elucidating the properties and molecular functions of protein persulfidation would be beneficial for current therapeutics. In this review, we introduce the detailed mechanism of the persulfidation process and discuss persulfidation detection methods. In addition, this review summarizes recent discoveries of the selectivity of protein persulfidation and the regulation of protein functions and cell signaling pathways by persulfidation. Antioxid. Redox Signal. 39, 829-852.
Collapse
Affiliation(s)
- Shanshan Luo
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, China
| | - Chuiyu Kong
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, China
| | - Danyu Ye
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, China
| | - Xingeng Liu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Yu Wang
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, China
| | - Guoliang Meng
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong, China
| | - Yi Han
- Department of Geriatrics, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liping Xie
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Yong Ji
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, China
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD), Harbin Medical University, Harbin, China
| |
Collapse
|
2
|
Bischoff E, Lang L, Zimmermann J, Luczak M, Kiefer AM, Niedner-Schatteburg G, Manolikakes G, Morgan B, Deponte M. Glutathione kinetically outcompetes reactions between dimedone and a cyclic sulfenamide or physiological sulfenic acids. Free Radic Biol Med 2023; 208:165-177. [PMID: 37541455 DOI: 10.1016/j.freeradbiomed.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
Dimedone and its derivates are used as selective probes for the nucleophilic detection of sulfenic acids in biological samples. Qualitative analyses suggested that dimedone also reacts with cyclic sulfenamides. Furthermore, under physiological conditions, dimedone must compete with the highly concentrated nucleophile glutathione. We therefore quantified the reaction kinetics for a cyclic sulfenamide model peptide and the sulfenic acids of glutathione and a model peroxiredoxin in the presence or absence of dimedone and glutathione. We show that the cyclic sulfenamide is stabilized at lower pH and that it reacts with dimedone. While reactions between dimedone and sulfenic acids or the cyclic sulfenamide have similar rate constants, glutathione kinetically outcompetes dimedone as a nucleophile by several orders of magnitude. Our comparative in vitro and intracellular analyses challenge the selectivity of dimedone. Consequently, the dimedone labeling of cysteinyl residues inside living cells points towards unidentified reaction pathways or unknown, kinetically competitive redox species.
Collapse
Affiliation(s)
- Eileen Bischoff
- Fachbereich Chemie & Landesforschungszentrum OPTIMAS, RPTU Kaiserslautern, Erwin-Schrödinger Straße 54, D-67663, Kaiserslautern, Germany
| | - Lukas Lang
- Fachbereich Chemie & Landesforschungszentrum OPTIMAS, RPTU Kaiserslautern, Erwin-Schrödinger Straße 54, D-67663, Kaiserslautern, Germany
| | - Jannik Zimmermann
- Zentrum für Human- und Molekularbiologie (ZHMB), Universität des Saarlandes, Biochemie Campus, Geb. B2.2, D-66123, Saarbrücken, Germany
| | - Maximilian Luczak
- Fachbereich Chemie & Landesforschungszentrum OPTIMAS, RPTU Kaiserslautern, Erwin-Schrödinger Straße 54, D-67663, Kaiserslautern, Germany
| | - Anna Maria Kiefer
- Fachbereich Biologie, RPTU Kaiserslautern, Paul-Ehrlich Straße 23, D-67663, Kaiserslautern, Germany
| | - Gereon Niedner-Schatteburg
- Fachbereich Chemie & Landesforschungszentrum OPTIMAS, RPTU Kaiserslautern, Erwin-Schrödinger Straße 54, D-67663, Kaiserslautern, Germany
| | - Georg Manolikakes
- Fachbereich Chemie & Landesforschungszentrum OPTIMAS, RPTU Kaiserslautern, Erwin-Schrödinger Straße 54, D-67663, Kaiserslautern, Germany
| | - Bruce Morgan
- Zentrum für Human- und Molekularbiologie (ZHMB), Universität des Saarlandes, Biochemie Campus, Geb. B2.2, D-66123, Saarbrücken, Germany
| | - Marcel Deponte
- Fachbereich Chemie & Landesforschungszentrum OPTIMAS, RPTU Kaiserslautern, Erwin-Schrödinger Straße 54, D-67663, Kaiserslautern, Germany.
| |
Collapse
|
3
|
Niu Y, Chen Z, Jiang Z, Yang Y, Liu G, Cheng X, Jiang Z, Zhang G, Tong L, Tang B. Detection of Cysteine Sulfenic Acid on E. coli Proteins with a Biotin-Benzoboroxole Probe. ACS Chem Biol 2023; 18:1351-1359. [PMID: 37260364 DOI: 10.1021/acschembio.3c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
S-sulfenylation of cysteine residues on proteins can effectively change protein structures and accordingly regulate their functions in vivo. Investigation of S-sulfenylation in different biological environments is thus vital for a systematic understanding of cellular redox regulation. In this work, a functional probe, biotin-benzoboroxole (Bio-ben), was designed for the detection of cysteine sulfenic acid (Cys-SOH). The performance of Bio-ben was characterized by small-molecule sulfenic acid, protein models, and proteome tests via mass spectra and western blotting. The results showed that Bio-ben was validated for cysteine sulfenic acid on proteins with good capture efficiency even at low concentrations. Compared with commonly used probes such as dimedone, the current probe has significantly shortened labeling time and exhibited comparable sensitivity. The proposed method provides a new approach for exploring S-sulfenylation in the oxidative modification of proteins and is helpful for related biological and clinical applications.
Collapse
Affiliation(s)
- Yaxin Niu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Zhongyao Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Guangzhao Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Xiufen Cheng
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Zhenhao Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Guanglu Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Lili Tong
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| |
Collapse
|
4
|
Cadiz Diaz A, Schmidt NA, Yamazaki M, Hsieh CJ, Lisse TS, Rieger S. Coordinated NADPH oxidase/hydrogen peroxide functions regulate cutaneous sensory axon de- and regeneration. Proc Natl Acad Sci U S A 2022; 119:e2115009119. [PMID: 35858442 PMCID: PMC9340058 DOI: 10.1073/pnas.2115009119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/30/2022] [Indexed: 01/21/2023] Open
Abstract
Tissue wounding induces cutaneous sensory axon regeneration via hydrogen peroxide (H2O2) that is produced by the epithelial NADPH oxidase, Duox1. Sciatic nerve injury instead induces axon regeneration through neuronal uptake of the NADPH oxidase, Nox2, from macrophages. We therefore reasoned that the tissue environment in which axons are damaged stimulates distinct regenerative mechanisms. Here, we show that cutaneous axon regeneration induced by tissue wounding depends on both neuronal and keratinocyte-specific mechanisms involving H2O2 signaling. Genetic depletion of H2O2 in sensory neurons abolishes axon regeneration, whereas keratinocyte-specific H2O2 depletion promotes axonal repulsion, a phenotype mirrored in duox1 mutants. Intriguingly, cyba mutants, deficient in the essential Nox subunit, p22Phox, retain limited axon regenerative capacity but display delayed Wallerian degeneration and axonal fusion, observed so far only in invertebrates. We further show that keratinocyte-specific oxidation of the epidermal growth factor receptor (EGFR) at a conserved cysteine thiol (C797) serves as an attractive cue for regenerating axons, leading to EGFR-dependent localized epidermal matrix remodeling via the matrix-metalloproteinase, MMP-13. Therefore, wound-induced cutaneous axon de- and regeneration depend on the coordinated functions of NADPH oxidases mediating distinct processes following injury.
Collapse
Affiliation(s)
| | | | - Mamiko Yamazaki
- Department of Regenerative Biology and Medicine, MDI Biological Laboratory, Bar Harbor, ME 04672
| | - Chia-Jung Hsieh
- Department of Biology, University of Miami, Coral Gables, FL 33146
| | - Thomas S. Lisse
- Department of Biology, University of Miami, Coral Gables, FL 33146
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Miami, FL 33136
| | - Sandra Rieger
- Department of Biology, University of Miami, Coral Gables, FL 33146
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Miami, FL 33136
| |
Collapse
|
5
|
Guillaubez JV, Pitrat D, Bretonnière Y, Lemoine J, Girod M. Relative quantification of sulfenic acids in plasma proteins using differential labelling and mass spectrometry coupled with 473 nm photo-dissociation analysis: A multiplexed approach applied to an Alzheimer's disease cohort. Talanta 2022; 250:123745. [PMID: 35870285 DOI: 10.1016/j.talanta.2022.123745] [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: 05/19/2022] [Revised: 07/11/2022] [Accepted: 07/15/2022] [Indexed: 10/17/2022]
Abstract
Cysteine (Cys) is subject to a variety of reversible post-translational modifications such as formation of sulfenic acid (Cys-SOH). If this modification is often involved in normal biological activities, it can also be the result of oxidative damage. Indeed, oxidative stress yields abnormal cysteine oxidations that affect protein function and structure and can lead to neurodegenerative diseases. In a context of population ageing, validation of novel biomarkers for detection of neurodegenerative diseases is important. However, Cys-SOH proteins investigation in large human cohorts is challenging due to their low abundance and lability under endogenous conditions. To improve the detection specificity towards the oxidized protein subpopulation, we developed a method that makes use of a mass spectrometer coupled with visible laser induced dissociation (LID) to add a stringent optical specificity to the mass selectivity. Since peptides do not naturally absorb in the visible range, this approach relies on the proper chemical derivatization of Cys-SOH with a chromophore functionalized with a cyclohexanedione. To compensate for the significant variability in total protein expression within the samples and any experimental bias, a normalizing strategy using free thiol (Cys-SH) cysteine peptides derivatized with a maleimide chromophore as internal references was used. Thanks to the differential tagging, oxidative ratios were then obtained for 69 Cys-containing peptides from 19 proteins tracked by parallel reaction monitoring (PRM) LID, in a cohort of 49 human plasma samples from Alzheimer disease (AD) patients. A statistical analysis indicated that, for the proteins monitored, the Cys oxidative ratio does not correlate with the diagnosis of AD. Nevertheless, the PRM-LID method allows the unbiased, sensitive and robust relative quantification of Cys oxidation within cohorts of samples.
Collapse
Affiliation(s)
- Jean-Valery Guillaubez
- Institut des Sciences Analytiques, UMR, 5280, Université Lyon 1, CNRS, Villeurbanne, France
| | - Delphine Pitrat
- Laboratoire de Chimie ENS Lyon, UMR, 5582, ENS Lyon CNRS et Université Lyon 1, France
| | - Yann Bretonnière
- Laboratoire de Chimie ENS Lyon, UMR, 5582, ENS Lyon CNRS et Université Lyon 1, France
| | - Jérôme Lemoine
- Institut des Sciences Analytiques, UMR, 5280, Université Lyon 1, CNRS, Villeurbanne, France
| | - Marion Girod
- Institut des Sciences Analytiques, UMR, 5280, Université Lyon 1, CNRS, Villeurbanne, France.
| |
Collapse
|
6
|
Lin S, He C. Development of Nonheme {FeNO} 7 Complexes Based on the Pyrococcus furiosus Rubredoxin for Red-Light-Controllable Nitric Oxide Release. Inorg Chem 2021; 60:14364-14370. [PMID: 34503329 DOI: 10.1021/acs.inorgchem.1c02089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nitric oxide (NO) is an essential biological messenger, contributing a significant role in a diverse range of physiological processes. The light-controllable NO releasers are of great interest because of their potential as agents for NO-related research and therapeutics. Herein, we developed a pair of red-light-controllable NO releasers, pfRd-C9A-{FeNO}7 and pfRd-C42A-{FeNO}7 (pfRd = Pyrococcus furiosus rubredoxin), by constructing a nonheme {FeNO}7 center within the redesigned iron-sulfur protein scaffolds. While shown to be both air and thermally stable, these complexes are highly sensitive to red-light irradiation with temporal precision, which was confirmed by electron paramagnetic resonance spin trapping and Griess assay. The temporally controlled NO release from these complexes was also demonstrated in DNA cleavage assay. Overall, this study demonstrates that such a protein-based nonheme iron nitrosyl system could be a viable chemical tool for precise NO administration.
Collapse
Affiliation(s)
- Shaomin Lin
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| |
Collapse
|
7
|
Guillaubez JV, Pitrat D, Bretonnière Y, Lemoine J, Girod M. Unbiased Detection of Cysteine Sulfenic Acid by 473 nm Photodissociation Mass Spectrometry: Toward Facile In Vivo Oxidative Status of Plasma Proteins. Anal Chem 2021; 93:2907-2915. [PMID: 33522244 DOI: 10.1021/acs.analchem.0c04484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cysteine (Cys) is prone to diverse post-translational modifications in proteins, including oxidation into sulfenic acid (Cys-SOH) by reactive oxygen species generated under oxidative stress. Detection of low-concentration and metastable Cys-SOH within complex biological matrices is challenging due to the dynamic concentration range of proteins in the samples. Herein, visible laser-induced dissociation (LID) implemented in a mass spectrometer was used for streamlining the detection of Cys oxidized proteins owing to proper derivatization of Cys-SOH with a chromophore tag functionalized with a cyclohexanedione group. Once grafted, peptides undergo a high fragmentation yield under LID, leading concomitantly to informative backbone ions and to a chromophore reporter ion. Seventy-nine percent of the Cys-containing tryptic peptides derived from human serum albumin and serotransferrin tracked by parallel reaction monitoring (PRM) were detected as targets subjected to oxidation. These candidates as well as Cys-containing peptides predicted by in silico trypsin digestion of five other human plasma proteins were then tracked in real plasma samples to pinpoint the endogenous Cys-SOH subpopulation. Most of the targeted peptides were detected in all plasma samples by LID-PRM, with significant differences in their relative amounts. By eliminating the signal of interfering co-eluted compounds, LID-PRM surpasses conventional HCD (higher-energy collisional dissociation)-PRM in detecting grafted Cys-SOH-containing peptides and allows now to foresee clinical applications in large human cohorts.
Collapse
Affiliation(s)
- Jean-Valery Guillaubez
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Delphine Pitrat
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Lyon I, Laboratoire de Chimie, F-69342 Lyon, France
| | - Yann Bretonnière
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Université Lyon I, Laboratoire de Chimie, F-69342 Lyon, France
| | - Jérôme Lemoine
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Marion Girod
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, Villeurbanne F-69100, France
| |
Collapse
|
8
|
A critical evaluation of probes for cysteine sulfenic acid. Curr Opin Chem Biol 2020; 60:55-65. [PMID: 32866852 DOI: 10.1016/j.cbpa.2020.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/18/2020] [Accepted: 07/24/2020] [Indexed: 12/31/2022]
Abstract
Cysteine oxidation is important in cellular redox regulation, signaling, and biocatalysis. To understand the biological relevance of cysteine oxidation, it is desirable to identify the proteins involved, the site of the oxidized cysteine, and the relevant oxidation states. Because the thiol of cysteine can be converted to a wide range of oxidation states, mapping these oxidative modifications is challenging. The dynamic and reversible nature of many cysteine oxidation states compounds the difficulty in such proteomic analyses. In this review, we examine methods to detect cysteine sulfenic acid - a particularly challenging functional group to analyze because of its reactive nature. We focus on the selectivity of recently reported probes and discuss some challenges and opportunities in this field.
Collapse
|
9
|
Amarnath Reddy KK, Moi S, Dolle A, Hosamani B, Krishnamurthy K, Prakash S, Raghothama S, Gowd KH. Synthesis of Peptide Cysteine Dimedone Using Fmoc‐Cys(Dmd)‐OH: Glutathione Cysteine Dimedone as a Probe in Investigating the Sulfenic Acid Mediated Oxidation of Glutathione. Helv Chim Acta 2020. [DOI: 10.1002/hlca.202000062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- K. Kasi Amarnath Reddy
- Department of ChemistrySchool of Chemical SciencesCentral University of Karnataka Kalaburagi 585367 Karnataka India
| | - Smriti Moi
- Department of ChemistrySchool of Chemical SciencesCentral University of Karnataka Kalaburagi 585367 Karnataka India
| | - Ashwini Dolle
- Department of ChemistrySchool of Chemical SciencesCentral University of Karnataka Kalaburagi 585367 Karnataka India
| | - Basavaprabhu Hosamani
- Department of ChemistrySchool of Chemical SciencesCentral University of Karnataka Kalaburagi 585367 Karnataka India
| | - Kiran Krishnamurthy
- NMR Research CentreIndian Institute of Science Bangalore 560012 Karnataka India
| | - Sunita Prakash
- Proteomic facilityMolecular Biophysics UnitIndian Institute of Science Bangalore 560012 Karnataka India
| | | | - Konkallu Hanumae Gowd
- Department of ChemistrySchool of Chemical SciencesCentral University of Karnataka Kalaburagi 585367 Karnataka India
| |
Collapse
|
10
|
Manuel AM, Walla MD, Dorn MT, Tanis RM, Piroli GG, Frizzell N. Fumarate and oxidative stress synergize to promote stability of C/EBP homologous protein in the adipocyte. Free Radic Biol Med 2020; 148:70-82. [PMID: 31883977 PMCID: PMC6961135 DOI: 10.1016/j.freeradbiomed.2019.12.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/22/2019] [Accepted: 12/24/2019] [Indexed: 12/13/2022]
Abstract
C/EBP homologous protein (CHOP) is a transcription factor that is elevated in adipose tissue across many models of diabetes and metabolic stress. Although increased CHOP levels are associated with the terminal response to endoplasmic reticulum stress and apoptosis, there is no evidence for CHOP mediated apoptosis in the adipose tissue during diabetes. CHOP protein levels increase in parallel with protein succination, a fumarate derived cysteine modification, in the adipocyte during metabolic stress. We investigated the factors contributing to sustained CHOP proteins levels in the adipocyte, with an emphasis on the regulation of CHOP protein turnover by metabolite-driven modification of Keap1 cysteines. CHOP protein stability was investigated in conditions of nutrient stress due to high glucose or elevated fumarate (fumarase knockdown model); where cysteine succination is specifically elevated. CHOP protein turnover is significantly reduced in models of elevated glucose and fumarate with a ~30% increase in CHOP stability (p > 0.01), in part due to decreased CHOP phosphorylation. Sustained CHOP levels occur in parallel with elevated heme-oxygenase-1, a production of increased Nrf2 transcriptional activity and Keap1 modification. While Keap1 is directly succinated in the presence of excess fumarate derived from genetic knockdown of fumarase (fumarate levels are elevated >20-fold), it is the oxidative modification of Keap1 that predominates in adipocytes matured in high glucose (fumarate increases 4-5 fold). Elevated fumarate indirectly regulates CHOP stability through the induction of oxidative stress. The antioxidant N-acetylcysteine (NAC) reduces fumarate levels, protein succination and CHOP levels in adipocytes matured in high glucose. Elevated CHOP does not contribute elevated apoptosis in adipocytes, but plays a redox-dependent role in decreasing the adipocyte secretion of interleukin-13, an anti-inflammatory chemokine. NAC treatment restores adipocyte IL-13 secretion, confirming the redox-dependent regulation of a potent anti-inflammatory eotaxin. This study demonstrates that physiological increases in the metabolite fumarate during high glucose exposure contributes to the presence of oxidative stress and sustained CHOP levels in the adipocyte during diabetes. The results reveal a novel metabolic link between mitochondrial metabolic stress and reduced anti-inflammatory adipocyte signaling as a consequence of reduced CHOP protein turnover.
Collapse
Affiliation(s)
- Allison M Manuel
- Department of Pharmacology, Physiology & Neuroscience, School of Medicine, University of South Carolina, Columbia, SC, 29209, USA
| | - Michael D Walla
- Mass Spectrometry Center, Department of Chemistry & Biochemistry, University of South Carolina, Columbia, SC, 29205, USA
| | - Margaret T Dorn
- Department of Pharmacology, Physiology & Neuroscience, School of Medicine, University of South Carolina, Columbia, SC, 29209, USA
| | - Ross M Tanis
- Department of Pharmacology, Physiology & Neuroscience, School of Medicine, University of South Carolina, Columbia, SC, 29209, USA
| | - Gerardo G Piroli
- Department of Pharmacology, Physiology & Neuroscience, School of Medicine, University of South Carolina, Columbia, SC, 29209, USA
| | - Norma Frizzell
- Department of Pharmacology, Physiology & Neuroscience, School of Medicine, University of South Carolina, Columbia, SC, 29209, USA.
| |
Collapse
|
11
|
Rambacher KM, Moniri NH. Cysteine redox state regulates human β2-adrenergic receptor binding and function. Sci Rep 2020; 10:2934. [PMID: 32076070 PMCID: PMC7031529 DOI: 10.1038/s41598-020-59983-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/05/2020] [Indexed: 01/08/2023] Open
Abstract
Bronchoconstrictive airway disorders such as asthma are characterized by inflammation and increases in reactive oxygen species (ROS), which produce a highly oxidative environment. β2-adrenergic receptor (β2AR) agonists are a mainstay of clinical therapy for asthma and provide bronchorelaxation upon inhalation. We have previously shown that β2AR agonism generates intracellular ROS, an effect that is required for receptor function, and which post-translationally oxidizes β2AR cysteine thiols to Cys-S-sulfenic acids (Cys-S-OH). Furthermore, highly oxidative environments can irreversibly oxidize Cys-S-OH to Cys-S-sulfinic (Cys-SO2H) or S-sulfonic (Cys-SO3H) acids, which are incapable of further participating in homeostatic redox reactions (i.e., redox-deficient). The aim of this study was to examine the vitality of β2AR-ROS interplay and the resultant functional consequences of β2AR Cys-redox in the receptors native, oxidized, and redox-deficient states. Here, we show for the first time that β2AR can be oxidized to Cys-S-OH in situ, moreover, using both clonal cells and a human airway epithelial cell line endogenously expressing β2AR, we show that receptor redox state profoundly influences β2AR orthosteric ligand binding and downstream function. Specifically, homeostatic β2AR redox states are vital toward agonist-induced cAMP formation and subsequent CREB and G-protein-dependent ERK1/2 phosphorylation, in addition to β-arrestin-2 recruitment and downstream arrestin-dependent ERK1/2 phosphorylation and internalization. On the contrary, redox-deficient β2AR states exhibit decreased ability to signal via either Gαs or β-arrestin. Together, our results demonstrate a β2AR-ROS redox axis, which if disturbed, interferes with proper receptor function.
Collapse
Affiliation(s)
- Kalyn M Rambacher
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, GA30341, United States
| | - Nader H Moniri
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, GA30341, United States.
| |
Collapse
|
12
|
Shi Y, Carroll KS. Activity-Based Sensing for Site-Specific Proteomic Analysis of Cysteine Oxidation. Acc Chem Res 2020; 53:20-31. [PMID: 31869209 DOI: 10.1021/acs.accounts.9b00562] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Oxidative post-translational modifications (OxiPTMs) of cysteine residues are the molecular foundation of thiol-based redox regulation that modulates physiological events such as cell proliferation, differentiation, and migration and, when dysregulated, can lead to biomolecule damage and cell death. Common OxiPTMs of cysteine thiols (-SH) include reversible modifications such as S-sulfenylation (-SOH), S-glutathionylation (-SSG), disulfide formation (-SSR), S-nitrosylation (-SNO), and S-sulfhydration (-SSH) as well as more biologically stable modifications like S-sulfinylation (-SO2H) and S-sulfonylation (-SO3H). In the past decade, our laboratory has developed first-in-class chemistry-based tools and proteomic methods to advance the field of thiol-based redox biology and oxidative stress. In this Account, we take the reader through the historical aspects of probe development and application in our laboratory, highlighting key advances in our understanding of sulfur chemistry, in the test tube and in living systems. Offering superior resolution, throughput, accuracy, and reproducibility, mass spectrometry (MS)-based proteomics coupled to chemoselective "activity-based" small-molecule probes is the most rigorous technique for global mapping of cysteine OxiPTMs. Herein, we describe the evolution of this field from indirect detection to state-of-the-art site-centric quantitative chemoproteomic approaches that enable mapping of physiological and pathological changes in cysteine oxidation. These methods enable protein and site-level identification, mechanistic studies, mapping fold-changes, and modification stoichiometry. In particular, this Account focuses on activity-based methods for profiling S-sulfenylation, S-sulfinylation, and S-sulfhydration with an eye toward new reactions and methodologies developed in our group as well as their applications that have shed new light on fundamental processes of redox biology. Among several classes of sulfenic acid probes, dimedone-based C-nucleophiles possess superior chemical selectivity and compatibility with tandem MS. Cell-permeable dimedone derivatives with a bioconjugation handle are capable of detecting of S-sulfenylation in living cells. In-depth screening of a C-nucleophile library has yielded several entities with significantly enhanced reactivity over dimedone while maintaining selectivity, and reversible linear C-nucleophiles that enable controlled target release. C-Nucleophiles have also been implemented in tag-switch methods to detect S-sulfhydration. Most recently, activity-based detection of protein S-sulfinylation with electrophilic nitrogen species (ENS), such as C-nitroso compounds and electron deficient diazines, offers significant advantages in simplicity-of-use and target specificity compared to label-free methods. When feasible, the rich information provided by site-centric quantitative proteomics should not be tainted by oxidation artifacts from cell lysis. Therefore, chemoselective probes that function in a native environment with low cytotoxicity, good cell-permeability, and competitive kinetics are desired in modern redox chemoproteomics approaches. As our understanding of sulfur chemistry and redox signaling evolves, newly discovered cysteine OxiPTMs in microorganisms, plants, cells, tissues, and disease models should innovatively promote mechanistic and therapeutic research.
Collapse
Affiliation(s)
- Yunlong Shi
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Kate S. Carroll
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| |
Collapse
|
13
|
Abstract
Redox proteomics is a field of proteomics that is concerned with the characterization of the oxidation state of proteins to gain information about their modulated structure, function, activity, and involvement in different physiological pathways. Oxidative modifications of proteins have been shown to be implicated in normal physiological processes of cells as well as in pathomechanisms leading to the development of cancer, diabetes, neurodegenerative diseases, and some rare hereditary metabolic diseases, like classic galactosemia. Reactive oxygen species generate a variety of reversible and irreversible modifications in amino acid residue side chains and within the protein backbone. These oxidative post-translational modifications (Ox-PTMs) can participate in the activation of signal transduction pathways and mediate the toxicity of harmful oxidants. Thus the application of advanced redox proteomics technologies is important for gaining insights into molecular mechanisms of diseases. Mass-spectrometry-based proteomics is one of the most powerful methods that can be used to give detailed qualitative and quantitative information on protein modifications and allows us to characterize redox proteomes associated with diseases. This Review illustrates the role and biological consequences of Ox-PTMs under basal and oxidative stress conditions by focusing on protein carbonylation and S-glutathionylation, two abundant modifications with an impact on cellular pathways that have been intensively studied during the past decade.
Collapse
Affiliation(s)
- Atef Mannaa
- Borg AlArab Higher Institute of Engineering and Technology , New Borg AlArab City , Alexandria , Egypt
| | - Franz-Georg Hanisch
- Institute of Biochemistry II, Medical Faculty , University of Cologne , Joseph-Stelzmann-Str. 52 , 50931 Cologne , Germany
| |
Collapse
|
14
|
Characterization of Polysulfides, Polysulfanes, and Other Unique Species in the Reaction between GSNO and H 2S. Molecules 2019; 24:molecules24173090. [PMID: 31454893 PMCID: PMC6749520 DOI: 10.3390/molecules24173090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/17/2022] Open
Abstract
Glutathione-based products, GSnX, of the reaction of hydrogen sulfide, H2S, S-nitroso glutathione, and GSNO, at varied stoichiometries have been analyzed by liquid chromatography high-resolution mass spectrometry (LC-HRMS) and chemical trapping experiments. A wide variety of glutathione-based species with catenated sulfur chains have been identified including sulfanes (GSSnG), sulfides (GSSnH), and sulfenic acids (GSnOH); sulfinic (GSnO2H) and sulfonic (GSnO3H) acids are also seen in reactions exposed to air. The presence of each species of GSnX within the original reaction mixtures was confirmed using Single Ion Chromatograms (SICs), to demonstrate the separation on the LC column, and given approximate quantification by the peak area of the SIC. Further, confirmation for different GSnX families was obtained by trapping with species-specific reagents. Several unique GSnX families have been characterized, including bridging mixed di- and tetra-valent polysulfanes and internal trithionitrates (GSNHSnH) with polysulfane branches. Competitive trapping experiments suggest that the polysulfane chains are formed via the intermediacy of sulfenic acid species, GSSnOH. In the presence of radical trap vinylcyclopropane (VCP) the relative distributions of polysulfane speciation are relatively unaffected, suggesting that radical coupling is not a dominant pathway. Therefore, we suggest polysulfane catenation occurs via reaction of sulfides with sulfenic acids.
Collapse
|
15
|
Abstract
SIGNIFICANCE Cellular reactive oxygen species (ROS) mediate redox signaling cascades that are critical to numerous physiological and pathological processes. Analytical methods to monitor cellular ROS levels and proteomic platforms to identify oxidative post-translational modifications (PTMs) of proteins are critical to understanding the triggers and consequences of redox signaling. Recent Advances: The prevalence and significance of redox signaling has recently been illuminated through the use of chemical probes that allow for sensitive detection of cellular ROS levels and proteomic dissection of oxidative PTMs directly in living cells. CRITICAL ISSUES In this review, we provide a comprehensive overview of chemical probes that are available for monitoring ROS and oxidative PTMs, and we highlight the advantages and limitations of these methods. FUTURE DIRECTIONS Despite significant advances in chemical probes, the low levels of cellular ROS and low stoichiometry of oxidative PTMs present challenges for accurately measuring the extent and dynamics of ROS generation and redox signaling. Further improvements in sensitivity and ability to spatially and temporally control readouts are essential to fully illuminate cellular redox signaling.
Collapse
Affiliation(s)
- Masahiro Abo
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts
| | | |
Collapse
|
16
|
Albertolle ME, Glass SM, Trefts E, Guengerich FP. Isotopic tagging of oxidized and reduced cysteines (iTORC) for detecting and quantifying sulfenic acids, disulfides, and free thiols in cells. J Biol Chem 2019; 294:6522-6530. [PMID: 30850396 DOI: 10.1074/jbc.ac118.007225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/07/2019] [Indexed: 12/22/2022] Open
Abstract
Oxidative modifications of cysteine residues are an important component in signaling pathways, enzymatic regulation, and redox homeostasis. Current direct and indirect methods detect specific modifications and a general binary population of "free" or "oxidized" cysteines, respectively. In an effort to combine both direct and indirect detection strategies, here we developed a method that we designate isotopic tagging of oxidized and reduced cysteines (iTORC). This method uses synthetic molecules for rapid isotopic coding of sulfenic acids, reduced cysteines, and disulfides in cells. Our approach utilizes isotopically distinct benzothiazine and halogenated benzothiazine probes to sequentially alkylate sulfenic acids and then free thiols and, finally, after a reduction step, cysteines oxidized to disulfides or other phosphine-reducible states. We ascertained that the iodinated benzothiazine probe has reduced cross-reactivity toward primary amines and is highly reactive with the cysteine of GSH, with a calculated rate constant of 2 × 105 m-1 s-1 (pH 8.0, 23 °C) (i.e. 10-20 times faster than N-ethylmaleimide). We applied iTORC to a mouse hepatocyte lysate to identify known sulfenylated and disulfide-bonded proteins, including elongation factor 1-α1 and mouse serum albumin, and found that iTORC reliably detected their expected oxidation status. This method can be easily employed to study the effects of oxidants on recombinant proteins and cell and tissue extracts, and the efficiencies of the alkylating agents enable completion of all three labeling steps within 2 h. In summary, we demonstrate here that halogenated benzothiazine-based alkylating agents can be utilized to rapidly measure the cellular thiol status in cells.
Collapse
Affiliation(s)
| | | | - Elijah Trefts
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | | |
Collapse
|
17
|
Linscheid MW. Molecules and elements for quantitative bioanalysis: The allure of using electrospray, MALDI, and ICP mass spectrometry side-by-side. MASS SPECTROMETRY REVIEWS 2019; 38:169-186. [PMID: 29603315 DOI: 10.1002/mas.21567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
To understand biological processes, not only reliable identification, but quantification of constituents in biological processes play a pivotal role. This is especially true for the proteome: protein quantification must follow protein identification, since sometimes minute changes in abundance tell the real tale. To obtain quantitative data, many sophisticated strategies using electrospray and MALDI mass spectrometry (MS) have been developed in recent years. All of them have advantages and limitations. Several years ago, we started to work on strategies, which are principally capable to overcome some of these limits. The fundamental idea is to use elemental signals as a measure for quantities. We began by replacing the radioactive 32 P with the "cold" natural 31 P to quantify modified nucleotides and phosphorylated peptides and proteins and later used tagging strategies for quantification of proteins more generally. To do this, we introduced Inductively Coupled Plasma Mass Spectrometry (ICP-MS) into the bioanalytical workflows, allowing not only reliable and sensitive detection but also quantification based on isotope dilution absolute measurements using poly-isotopic elements. The detection capability of ICP-MS becomes particularly attractive with heavy metals. The covalently bound proteins tags developed in our group are based on the well-known DOTA chelate complex (1,4,7,10-tetraazacyclododecane-N,N',N″,N‴-tetraacetic acid) carrying ions of lanthanoides as metal core. In this review, I will outline the development of this mutual assistance between molecular and elemental mass spectrometry and discuss the scope and limitations particularly of peptide and protein quantification. The lanthanoide tags provide low detection limits, but offer multiplexing capabilities due to the number of very similar lanthanoides and their isotopes. With isotope dilution comes previously unknown accuracy. Separation techniques such as electrophoresis and HPLC were used and just slightly adapted workflows, already in use for quantification in bioanalysis. Imaging mass spectrometry (MSI) with MALDI and laser ablation ICP-MS complemented the range of application in recent years.
Collapse
MESH Headings
- Animals
- Chelating Agents/chemistry
- Chromatography, High Pressure Liquid/instrumentation
- Chromatography, High Pressure Liquid/methods
- Heterocyclic Compounds, 1-Ring/chemistry
- Humans
- Lanthanoid Series Elements/chemistry
- Nucleotides/analysis
- Proteins/analysis
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- Workflow
Collapse
|
18
|
Dustin CM, Hristova M, Schiffers C, van der Vliet A. Proteomic Methods to Evaluate NOX-Mediated Redox Signaling. Methods Mol Biol 2019; 1982:497-515. [PMID: 31172492 DOI: 10.1007/978-1-4939-9424-3_30] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The NADPH oxidase (NOX) family of proteins is involved in regulating many diverse cellular processes, which is largely mediated by NOX-mediated reversible oxidation of target proteins in a process known as redox signaling. Protein cysteine residues are the most prominent targets in redox signaling, and to understand the mechanisms by which NOX affect cellular pathways, specific methodology is required to detect specific oxidative cysteine modifications and to identify targeted proteins. Among the many potential redox modifications involving cysteine residues, reversible modifications most relevant to NOX are sulfenylation (P-SOH) and S-glutathionylation (P-SSG), as both can induce structural or functional alterations. Various experimental approaches have been developed to detect these specific modifications, and this chapter will detail state-of-the-art methodology to selectively evaluate these modifications in specific target proteins in relation to NOX activation. We also discuss some of the limitations of these procedures and potential complementary approaches.
Collapse
Affiliation(s)
- Christopher M Dustin
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT, USA
| | - Milena Hristova
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT, USA
| | - Caspar Schiffers
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT, USA
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Vermont, Burlington, VT, USA.
| |
Collapse
|
19
|
Mass Spectrometry in Advancement of Redox Precision Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:327-358. [PMID: 31347057 DOI: 10.1007/978-3-030-15950-4_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Redox (portmanteau of reduction-oxidation) reactions involve the transfer of electrons between chemical species in biological processes fundamental to life. It is of outmost importance that cells maintain a healthy redox state by balancing the action of oxidants and antioxidants; failure to do so leads to a multitude of diseases including cancer, diabetes, fibrosis, autoimmune diseases, and cardiovascular and neurodegenerative diseases. From the perspective of precision medicine, it is therefore beneficial to interrogate the redox phenotype of the individual-similar to the use of genomic sequencing-in order to design tailored strategies for disease prevention and treatment. This chapter provides an overview of redox metabolism and focuses on how mass spectrometry (MS) can be applied to advance our knowledge in redox biology and precision medicine.
Collapse
|
20
|
Heppner DE, Dustin CM, Liao C, Hristova M, Veith C, Little AC, Ahlers BA, White SL, Deng B, Lam YW, Li J, van der Vliet A. Direct cysteine sulfenylation drives activation of the Src kinase. Nat Commun 2018; 9:4522. [PMID: 30375386 PMCID: PMC6207713 DOI: 10.1038/s41467-018-06790-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/19/2018] [Indexed: 01/17/2023] Open
Abstract
The Src kinase controls aspects of cell biology and its activity is regulated by intramolecular structural changes induced by protein interactions and tyrosine phosphorylation. Recent studies indicate that Src is additionally regulated by redox-dependent mechanisms, involving oxidative modification(s) of cysteines within the Src protein, although the nature and molecular-level impact of Src cysteine oxidation are unknown. Using a combination of biochemical and cell-based studies, we establish the critical importance of two Src cysteine residues, Cys-185 and Cys-277, as targets for H2O2-mediated sulfenylation (Cys-SOH) in redox-dependent kinase activation in response to NADPH oxidase-dependent signaling. Molecular dynamics and metadynamics simulations reveal the structural impact of sulfenylation of these cysteines, indicating that Cys-277-SOH enables solvent exposure of Tyr-416 to promote its (auto)phosphorylation, and that Cys-185-SOH destabilizes pTyr-527 binding to the SH2 domain. These redox-dependent Src activation mechanisms offer opportunities for development of Src-selective inhibitors in treatment of diseases where Src is aberrantly activated.
Collapse
Affiliation(s)
- David E Heppner
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA.
| | - Christopher M Dustin
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Chenyi Liao
- Department of Chemistry, College of Arts and Sciences, University of Vermont, 82 University Place, Burlington, VT, 05405, USA
| | - Milena Hristova
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Carmen Veith
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Andrew C Little
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Bethany A Ahlers
- Department of Biology, College of Arts and Sciences, University of Vermont, 109 Carrigan Drive, Burlington, VT, 05405, USA
| | - Sheryl L White
- Department of Neurological Sciences, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Bin Deng
- Department of Biology, College of Arts and Sciences, University of Vermont, 109 Carrigan Drive, Burlington, VT, 05405, USA
| | - Ying-Wai Lam
- Department of Biology, College of Arts and Sciences, University of Vermont, 109 Carrigan Drive, Burlington, VT, 05405, USA
| | - Jianing Li
- Department of Chemistry, College of Arts and Sciences, University of Vermont, 82 University Place, Burlington, VT, 05405, USA.
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA.
| |
Collapse
|
21
|
Abstract
The concept of cell signaling in the context of nonenzyme-assisted protein modifications by reactive electrophilic and oxidative species, broadly known as redox signaling, is a uniquely complex topic that has been approached from numerous different and multidisciplinary angles. Our Review reflects on five aspects critical for understanding how nature harnesses these noncanonical post-translational modifications to coordinate distinct cellular activities: (1) specific players and their generation, (2) physicochemical properties, (3) mechanisms of action, (4) methods of interrogation, and (5) functional roles in health and disease. Emphasis is primarily placed on the latest progress in the field, but several aspects of classical work likely forgotten/lost are also recollected. For researchers with interests in getting into the field, our Review is anticipated to function as a primer. For the expert, we aim to stimulate thought and discussion about fundamentals of redox signaling mechanisms and nuances of specificity/selectivity and timing in this sophisticated yet fascinating arena at the crossroads of chemistry and biology.
Collapse
Affiliation(s)
- Saba Parvez
- Department of Pharmacology and Toxicology, College of
Pharmacy, University of Utah, Salt Lake City, Utah, 84112, USA
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Marcus J. C. Long
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Jesse R. Poganik
- Ecole Polytechnique Fédérale de Lausanne,
Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Yimon Aye
- Ecole Polytechnique Fédérale de Lausanne,
Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
- Department of Biochemistry, Weill Cornell Medicine, New
York, New York, 10065, USA
| |
Collapse
|
22
|
Albertolle ME, Phan TTN, Pozzi A, Guengerich FP. Sulfenylation of Human Liver and Kidney Microsomal Cytochromes P450 and Other Drug-Metabolizing Enzymes as a Response to Redox Alteration. Mol Cell Proteomics 2018; 17:889-900. [PMID: 29374135 DOI: 10.1074/mcp.ra117.000382] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The lumen of the endoplasmic reticulum (ER) provides an oxidizing environment to aid in the formation of disulfide bonds, which is tightly regulated by both antioxidant proteins and small molecules. On the cytoplasmic side of the ER, cytochrome P450 (P450) proteins have been identified as a superfamily of enzymes that are important in the formation of endogenous chemicals as well as in the detoxication of xenobiotics. Our previous report described oxidative inhibition of P450 Family 4 enzymes via oxidation of the heme-thiolate cysteine to a sulfenic acid (-SOH) (Albertolle, M. E. et al. (2017) J. Biol. Chem. 292, 11230-11242). Further proteomic analyses of murine kidney and liver microsomes led to the finding that a number of other drug-metabolizing enzymes located in the ER are also redox-regulated in this manner. We expanded our analysis of sulfenylated enzymes to human liver and kidney microsomes. Evaluation of the sulfenylation, catalytic activity, and spectral properties of P450s 1A2, 2C8, 2D6, and 3A4 led to the identification of two classes of redox sensitivity in P450 enzymes: heme-thiolate-sensitive and thiol-insensitive. These findings provide evidence for a mammalian P450 regulatory mechanism, which may also be relevant to other drug-metabolizing enzymes. (Data are available via ProteomeXchange with identifier PXD007913.).
Collapse
Affiliation(s)
- Matthew E Albertolle
- From the ‡Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Thanh T N Phan
- From the ‡Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Ambra Pozzi
- §Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232-6602.,¶Veterans Affairs Medical Center, Nashville, Tennessee, 37232
| | - F Peter Guengerich
- From the ‡Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146;
| |
Collapse
|
23
|
Alcock LJ, Perkins MV, Chalker JM. Chemical methods for mapping cysteine oxidation. Chem Soc Rev 2018; 47:231-268. [DOI: 10.1039/c7cs00607a] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Methods to characterise oxidative modifications of cysteine help clarify their role in protein function in both healthy and diseased cells.
Collapse
Affiliation(s)
- Lisa J. Alcock
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
| | - Michael V. Perkins
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
| | - Justin M. Chalker
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
| |
Collapse
|
24
|
Kumagai Y, Abiko Y, Cong NL. Chemical toxicology of reactive species in the atmosphere: two decades of progress in an electron acceptor and an electrophile. J Toxicol Sci 2017; 41:SP37-SP47. [PMID: 28003638 DOI: 10.2131/jts.41.sp37] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Air pollutants such as diesel exhaust particles (DEP) are thought to cause pulmonary diseases such as asthma as a result of oxidative stress. While DEP contain a large number of polycyclic aromatic hydrocarbons, we have focused on 9,10-phenanthrenequinone (9,10-PQ) and 1,2-naphthoquinone (1,2-NQ) because of their chemical properties based on their oxidative and chemical modification capabilities. We have found that 9,10-PQ interacts with electron donors such as NADPH (in the presence of enzymes) and dithiols, resulting in generation of excess reactive oxygen species (ROS) through redox cycling. We have also shown that 1,2-NQ is able to modify protein thiols, leading to protein adducts associated with activation of redox signal transduction pathways at lower concentrations and toxicity at higher concentrations. In this review, we briefly introduce our findings from the last two decades.
Collapse
|
25
|
Garcia FJ, Carroll KS. An immunochemical approach to detect oxidized protein tyrosine phosphatases using a selective C-nucleophile tag. MOLECULAR BIOSYSTEMS 2017; 12:1790-8. [PMID: 26757830 DOI: 10.1039/c5mb00847f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein tyrosine phosphatases are crucial regulators of signal transduction and function as antagonists towards protein tyrosine kinases to control reversible tyrosine phosphorylation, thereby regulating fundamental physiological processes. Growing evidence has supported the notion that reversible oxidative inactivation of the catalytic cysteine residue in protein tyrosine phosphatases serves as an oxidative post-translational modification that regulates its activity to influence downstream signaling by promoting phosphorylation and induction of the signaling cascade. The oxidation of cysteine to the sulfenic acid is often transient and difficult to detect, thus making it problematic in understanding the role that this oxidative post-translational modification plays in redox-biology and pathogenesis. Several methods to detect cysteine oxidation in biological systems have been developed, though targeted approaches to directly detect oxidized phosphatases are still lacking. Herein we describe the development of a novel immunochemical approach to directly profile oxidized phosphatases. This immunochemical approach consists of an antibody designed to recognize the conserved sequence of the PTP active site (VHCDMDSAG) harboring the catalytic cysteine modified with dimedone (CDMD), a nucleophile that chemoselectively reacts with cysteine sulfenic acids to form a stable thioether adduct. Additionally, we provide biochemical and mass spectrometry workflows to be used in conjugation with this newly developed immunochemical approach to assist in the identification and quantification of basal and oxidized phosphatases.
Collapse
Affiliation(s)
- Francisco J Garcia
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Kate S Carroll
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| |
Collapse
|
26
|
Albertolle ME, Kim D, Nagy LD, Yun CH, Pozzi A, Savas Ü, Johnson EF, Guengerich FP. Heme-thiolate sulfenylation of human cytochrome P450 4A11 functions as a redox switch for catalytic inhibition. J Biol Chem 2017; 292:11230-11242. [PMID: 28533430 DOI: 10.1074/jbc.m117.792200] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/16/2017] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 (P450, CYP) 4A11 is a human fatty acid ω-hydroxylase that catalyzes the oxidation of arachidonic acid to the eicosanoid 20-hydroxyeicosatetraenoic acid (20-HETE), which plays important roles in regulating blood pressure regulation. Variants of P450 4A11 have been associated with high blood pressure and resistance to anti-hypertensive drugs, and 20-HETE has both pro- and antihypertensive properties relating to increased vasoconstriction and natriuresis, respectively. These physiological activities are likely influenced by the redox environment, but the mechanisms are unclear. Here, we found that reducing agents (e.g. dithiothreitol and tris(2-carboxyethyl)phosphine) strongly enhanced the catalytic activity of P450 4A11, but not of 10 other human P450s tested. Conversely, added H2O2 attenuated P450 4A11 catalytic activity. Catalytic roles of five of the potentially eight implicated Cys residues of P450 4A11 were eliminated by site-directed mutagenesis. Using an isotope-coded dimedone/iododimedone-labeling strategy and mass spectrometry of peptides, we demonstrated that the heme-thiolate cysteine (Cys-457) is selectively sulfenylated in an H2O2 concentration-dependent manner. This sulfenylation could be reversed by reducing agents, including dithiothreitol and dithionite. Of note, we observed heme ligand cysteine sulfenylation of P450 4A11 ex vivo in kidneys and livers derived from CYP4A11 transgenic mice. We also detected sulfenylation of murine P450 4a12 and 4b1 heme peptides in kidneys. To our knowledge, reversible oxidation of the heme thiolate has not previously been observed in P450s and may have relevance for 20-HETE-mediated functions.
Collapse
Affiliation(s)
- Matthew E Albertolle
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Donghak Kim
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.,the Department of Biological Sciences, Konkuk University, Seoul 05025, Korea
| | - Leslie D Nagy
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Chul-Ho Yun
- the School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Ambra Pozzi
- the Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232-6602.,the Veterans Affairs Medical Center, Nashville, Tennessee 37232, and
| | - Üzen Savas
- the Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037
| | - Eric F Johnson
- the Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146,
| |
Collapse
|
27
|
Duan J, Gaffrey MJ, Qian WJ. Quantitative proteomic characterization of redox-dependent post-translational modifications on protein cysteines. MOLECULAR BIOSYSTEMS 2017; 13:816-829. [PMID: 28357434 PMCID: PMC5493446 DOI: 10.1039/c6mb00861e] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein thiols play a crucial role in redox signaling, in the regulation of enzymatic activity and protein function, and in maintaining redox homeostasis in living systems. The unique chemical reactivity of the thiol group makes protein cysteines susceptible to reactions with reactive oxygen and nitrogen species that form various reversible and irreversible post-translational modifications (PTMs). The reversible PTMs in particular are major components of redox signaling and are involved in the regulation of various cellular processes under physiological and pathological conditions. The biological significance of these redox PTMs in both healthy and disease states has been increasingly recognized. Herein, we review recent advances in quantitative proteomic approaches for investigating redox PTMs in complex biological systems, including general considerations of sample processing, chemical or affinity enrichment strategies, and quantitative approaches. We also highlight a number of redox proteomic approaches that enable effective profiling of redox PTMs for specific biological applications. Although technical limitations remain, redox proteomics is paving the way to a better understanding of redox signaling and regulation in both healthy and disease states.
Collapse
Affiliation(s)
- Jicheng Duan
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | | | | |
Collapse
|
28
|
Long MJC, Poganik JR, Ghosh S, Aye Y. Subcellular Redox Targeting: Bridging in Vitro and in Vivo Chemical Biology. ACS Chem Biol 2017; 12:586-600. [PMID: 28068059 DOI: 10.1021/acschembio.6b01148] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Networks of redox sensor proteins within discrete microdomains regulate the flow of redox signaling. Yet, the inherent reactivity of redox signals complicates the study of specific redox events and pathways by traditional methods. Herein, we review designer chemistries capable of measuring flux and/or mimicking subcellular redox signaling at the cellular and organismal level. Such efforts have begun to decipher the logic underlying organelle-, site-, and target-specific redox signaling in vitro and in vivo. These data highlight chemical biology as a perfect gateway to interrogate how nature choreographs subcellular redox chemistry to drive precision redox biology.
Collapse
Affiliation(s)
- Marcus J. C. Long
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Jesse R. Poganik
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Souradyuti Ghosh
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
| | - Yimon Aye
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14850, United States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
| |
Collapse
|
29
|
Wages PA. Detecting Protein Sulfenylation in Cells Exposed to a Toxicant. ACTA ACUST UNITED AC 2017; 71:17.18.1-17.18.12. [PMID: 28146279 DOI: 10.1002/cptx.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein sulfenylation is a post-translational modification that is linked to many cell signaling networks and specific protein functions, thus the detection of any sulfenylated protein after a toxicological exposure is of importance. Specifically, the detection of protein sulfenylation can provide multiple levels of mechanistic insight towards understanding the impact of a toxicological exposure. For instance, sulfenylation is caused by only a handful of reactive chemical species. Any altered sulfenylation suggests a change in cellular health, and the elucidation of the specific protein target that undergoes sulfenylation can help ascertain downstream targets and associated adverse outcomes. This document describes straightforward approaches to detect protein sulfenylation of total protein as well as individual proteins of interest with a focus on immunoblotting approaches. © 2017 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Phillip A Wages
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee
| |
Collapse
|
30
|
Lisse TS, Rieger S. IKKα regulates human keratinocyte migration through surveillance of the redox environment. J Cell Sci 2017; 130:975-988. [PMID: 28122935 PMCID: PMC5358334 DOI: 10.1242/jcs.197343] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/16/2017] [Indexed: 02/06/2023] Open
Abstract
Although the functions of H2O2 in epidermal wound repair are conserved throughout evolution, the underlying signaling mechanisms are largely unknown. In this study we used human keratinocytes (HEK001) to investigate H2O2-dependent wound repair mechanisms. Scratch wounding led to H2O2 production in two or three cell layers at the wound margin within ∼30 min and subsequent cysteine modification of proteins via sulfenylation. Intriguingly, exogenous H2O2 treatment resulted in preferential sulfenylation of keratinocytes that adopted a migratory phenotype and detached from neighboring cells, suggesting that one of the primary functions of H2O2 is to stimulate signaling factors involved in cell migration. Based on previous findings that revealed epidermal growth factor receptor (EGFR) involvement in H2O2-dependent cell migration, we analyzed oxidation of a candidate upstream target, the inhibitor of κB kinase α (IKKα; encoded by CHUK), as a mechanism of action. We show that IKKα is sulfenylated at a conserved cysteine residue in the kinase domain, which correlates with de-repression of EGF promoter activity and increased EGF expression. Thus, this indicates that IKKα promotes migration through dynamic interactions with the EGF promoter depending on the redox state within cells. Summary: This study provides a newly identified mechanism by which H2O2-dependent oxidation of the inhibitor of κB kinase α and de-repression of epidermal growth factor promoter activity stimulates keratinocyte migration.
Collapse
Affiliation(s)
- Thomas S Lisse
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, 159 Old Bar Harbor Road, Salisbury Cove, ME 04672, USA .,The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Sandra Rieger
- Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, 159 Old Bar Harbor Road, Salisbury Cove, ME 04672, USA
| |
Collapse
|
31
|
ZHANG XQ, CHEN C, FANG CY, LU HJ. Progress of Analytical Methods for Protein Cysteine Post-translational Modifications. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60974-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
32
|
Heppner DE, Hristova M, Dustin CM, Danyal K, Habibovic A, van der Vliet A. The NADPH Oxidases DUOX1 and NOX2 Play Distinct Roles in Redox Regulation of Epidermal Growth Factor Receptor Signaling. J Biol Chem 2016; 291:23282-23293. [PMID: 27650496 DOI: 10.1074/jbc.m116.749028] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Indexed: 12/31/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) plays a critical role in regulating airway epithelial homeostasis and responses to injury. Activation of EGFR is regulated by redox-dependent processes involving reversible cysteine oxidation by reactive oxygen species (ROS) and involves both ligand-dependent and -independent mechanisms, but the precise source(s) of ROS and the molecular mechanisms that control tyrosine kinase activity are incompletely understood. Here, we demonstrate that stimulation of EGFR activation by ATP in airway epithelial cells is closely associated with dynamic reversible oxidation of cysteine residues via sequential sulfenylation and S-glutathionylation within EGFR and the non-receptor-tyrosine kinase Src. Moreover, the intrinsic kinase activity of recombinant Src or EGFR was in both cases enhanced by H2O2 but not by GSSG, indicating that the intermediate sulfenylation is the activating modification. H2O2-induced increase in EGFR tyrosine kinase activity was not observed with the C797S variant, confirming Cys-797 as the redox-sensitive cysteine residue that regulates kinase activity. Redox-dependent regulation of EGFR activation in airway epithelial cells was found to strongly depend on activation of either the NADPH oxidase DUOX1 or the homolog NOX2, depending on the activation mechanism. Whereas DUOX1 and Src play a primary role in EGFR transactivation by wound-derived signals such as ATP, direct ligand-dependent EGFR activation primarily involves NOX2 with a secondary role for DUOX1 and Src. Collectively, our findings establish that redox-dependent EGFR kinase activation involves a dynamic and reversible cysteine oxidation mechanism and that this activation mechanism variably involves DUOX1 and NOX2.
Collapse
Affiliation(s)
- David E Heppner
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Milena Hristova
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Christopher M Dustin
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Karamatullah Danyal
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Aida Habibovic
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Albert van der Vliet
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| |
Collapse
|
33
|
Chen W, Pacheco A, Takano Y, Day JJ, Hanaoka K, Xian M. A Single Fluorescent Probe to Visualize Hydrogen Sulfide and Hydrogen Polysulfides with Different Fluorescence Signals. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604892] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Wei Chen
- Department of Chemistry; Washington State University; Pullman WA 99164 USA
| | - Armando Pacheco
- Department of Chemistry; Washington State University; Pullman WA 99164 USA
| | - Yoko Takano
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; Tokyo 113-0033 Japan
| | - Jacob J. Day
- Department of Chemistry; Washington State University; Pullman WA 99164 USA
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; Tokyo 113-0033 Japan
| | - Ming Xian
- Department of Chemistry; Washington State University; Pullman WA 99164 USA
| |
Collapse
|
34
|
Chen W, Pacheco A, Takano Y, Day JJ, Hanaoka K, Xian M. A Single Fluorescent Probe to Visualize Hydrogen Sulfide and Hydrogen Polysulfides with Different Fluorescence Signals. Angew Chem Int Ed Engl 2016; 55:9993-6. [PMID: 27410794 DOI: 10.1002/anie.201604892] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Indexed: 11/11/2022]
Abstract
Hydrogen sulfide (H2 S) and hydrogen polysulfides (H2 Sn , n>1) are endogenous regulators of many physiological processes. In order to better understand the symbiotic relationship and cellular cross-talk between H2 S and H2 Sn , it is highly desirable to develop single fluorescent probes which enable dual-channel discrimination between H2 S and H2 Sn . Herein, we report the rational design, synthesis, and evaluation of the first dual-detection fluorescent probe DDP-1 that can visualize H2 S and H2 Sn with different fluorescence signals. The probe showed high selectivity and sensitivity to H2 S and H2 Sn in aqueous media and in cells.
Collapse
Affiliation(s)
- Wei Chen
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Armando Pacheco
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Yoko Takano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Jacob J Day
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ming Xian
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA.
| |
Collapse
|
35
|
Pan J, Carroll KS. Chemical biology approaches to study protein cysteine sulfenylation. Biopolymers 2016; 101:165-72. [PMID: 23576224 DOI: 10.1002/bip.22255] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/01/2013] [Indexed: 01/08/2023]
Abstract
The oxidation of cysteine thiol side chains by hydrogen peroxide to afford protein sulfenyl modifications is an important mechanism in signal transduction. In addition, aberrant protein sulfenylation contributes to a range of human pathologies, including cancer. Efforts to elucidate the roles of protein sulfenylation in physiology and disease have been hampered by the lack of techniques to probe these modifications in native environments with molecular specificity. In this review, we trace the history of chemical and biological methods that have been developed to detect protein sulfenylation and illustrate how a recent cell-permeable chemical reporter, DYn-2, has been used to detect and identify intracellular targets of endogenous H2 O2 during growth factor signaling, including the epidermal growth factor receptor. The array of new tools and methods discussed herein enables the discovery of new biological roles for cysteine sulfenylation in human health and disease.
Collapse
Affiliation(s)
- Jia Pan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, 33456
| | | |
Collapse
|
36
|
Gupta V, Paritala H, Carroll KS. Reactivity, Selectivity, and Stability in Sulfenic Acid Detection: A Comparative Study of Nucleophilic and Electrophilic Probes. Bioconjug Chem 2016; 27:1411-8. [PMID: 27123991 DOI: 10.1021/acs.bioconjchem.6b00181] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The comparative reaction efficiencies of currently used nucleophilic and electrophilic probes toward cysteine sulfenic acid have been thoroughly evaluated in two different settings-(i) a small molecule dipeptide based model and (ii) a recombinant protein model. We further evaluated the stability of corresponding thioether and sulfoxide adducts under reducing conditions which are commonly encountered during proteomic protocols and in cell analysis. Powered by the development of new cyclic and linear C-nucleophiles, the unsurpassed efficiency in the capture of sulfenic acid under competitive conditions is achieved and thus holds great promise as highly potent tools for activity-based sulfenome profiling.
Collapse
Affiliation(s)
- Vinayak Gupta
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Hanumantharao Paritala
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| | - Kate S Carroll
- Department of Chemistry, The Scripps Research Institute , Jupiter, Florida 33458, United States
| |
Collapse
|
37
|
Zhou P, Yao J, Hu G, Fang J. Naphthalimide Scaffold Provides Versatile Platform for Selective Thiol Sensing and Protein Labeling. ACS Chem Biol 2016; 11:1098-105. [PMID: 26813105 DOI: 10.1021/acschembio.5b00856] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reversible thiol modifications are fundamental of cellular redox regulation. Specific thiol detection, including thiol sensing and protein thiols labeling, is critical to study such modifications. We reported the discovery of 4-methylsulfonyl-N-n-butyl-1,8-naphthalimide (MSBN), a highly selective fluorogenic probe for thiols based on the 1,8-naphthalimide scaffold. Thiols react with MSBN nearly quantitatively via nucleophilic aromatic substitution to replace the methylsulfonyl group and restore the quenched fluorescence (>100-fold increase). MSBN was employed to selectively image thiols in live cells and specifically label protein thiols with a turn-on signal to determine diverse reversible protein thiol modifications. In addition, we introduced a bulky group into the MSBN as a mass tag to create a probe MSBN-TPP, which readily discriminates the reduced thioredoxin from the oxidized one. The specific reaction of MSBN with thiols and the easy manipulation of the naphthalimide unit enable MSBN a versatile scaffold in developing novel probes for thiol-based protein bioconjugation and studying various thiol modifications.
Collapse
Affiliation(s)
- Pengcheng Zhou
- State Key Laboratory of Applied
Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Juan Yao
- State Key Laboratory of Applied
Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Guodong Hu
- State Key Laboratory of Applied
Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Jianguo Fang
- State Key Laboratory of Applied
Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| |
Collapse
|
38
|
Gupta V, Carroll KS. Profiling the Reactivity of Cyclic C-Nucleophiles towards Electrophilic Sulfur in Cysteine Sulfenic Acid. Chem Sci 2016; 7:400-415. [PMID: 26819701 PMCID: PMC4724439 DOI: 10.1039/c5sc02569a] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022] Open
Abstract
Oxidation of a protein cysteine thiol to sulfenic acid, termed S-sulfenylation, is a reversible post-translational modification that plays a crucial role in regulating protein function and is correlated with disease states. The majority of reaction-based small molecule and immunochemical probes used for detecting sulfenic acids are based on the 5,5-dimethyl-1,3-cyclohexanedione (dimedone) scaffold, which is selective, but suffers from low reactivity. In addition, mechanistic details and features that diminish or enhance nucleophile reactivity remain largely unknown. A significant hurdle to resolving the aforementioned issues has been the chemically unstable nature of small-molecule sulfenic acid models. Herein, we report a facile mass spectrometry-based assay and repurposed dipeptide-based model to screen a library of cyclic C-nucleophiles for reactivity with sulfenic acid under aqueous conditions. Observed rate constants for ~100 cyclic C-nucleophiles were obtained and, from this collection, we have identified novel compounds with more than 200-fold enhanced reactivity, as compared to dimedone. The increase in reactivity and retention of selectivity of these C-nucleophiles were validated in secondary assays, including a protein model for sulfenic acid. Together, this work represents a significant step toward developing new chemical reporters for detecting protein S-sulfenylation with superior kinetic resolution. The enhanced rates and varied composition of the C-nucleophiles should enable more comprehensive analyses of the sulfenome and serve as the foundation for reversible or irreversible nucleophilic covalent inhibitors that target oxidized cysteine residues in therapeutically important proteins.
Collapse
Affiliation(s)
- Vinayak Gupta
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , USA .
| | - Kate S. Carroll
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , USA .
| |
Collapse
|
39
|
Lennicke C, Rahn J, Heimer N, Lichtenfels R, Wessjohann LA, Seliger B. Redox proteomics: Methods for the identification and enrichment of redox-modified proteins and their applications. Proteomics 2015; 16:197-213. [PMID: 26508685 DOI: 10.1002/pmic.201500268] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/14/2015] [Accepted: 10/15/2015] [Indexed: 01/24/2023]
Abstract
PTMs are defined as covalent additions to functional groups of amino acid residues in proteins like phosphorylation, glycosylation, S-nitrosylation, acetylation, methylation, lipidation, SUMOylation as well as oxidation. Oxidation of proteins has been characterized as a double-edged sword. While oxidative modifications, in particular of cysteine residues, are widely involved in the regulation of cellular homeostasis, oxidative stress resulting in the oxidation of biomolecules along with the disruption of their biological functions can be associated with the development of diseases, such as cancer, diabetes, and neurodegenerative diseases, respectively. This is also the case for advanced glycation end products, which result from chemical reactions of keto compounds such as oxidized sugars with proteins. The role of oxidative modifications under physiological and pathophysiological conditions remains largely unknown. Recently, novel technologies have been established that allow the enrichment, identification, and characterization of specific oxidative PTMs (oxPTMs). This is essential to develop strategies to prevent and treat diseases that are associated with oxidative stress. Therefore this review will focus on (i) the methods and technologies, which are currently applied for the detection, identification, and quantification of oxPTMs including the design of high throughput approaches and (ii) the analyses of oxPTMs related to physiological and pathological conditions.
Collapse
Affiliation(s)
- Claudia Lennicke
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Jette Rahn
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Nadine Heimer
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Rudolf Lichtenfels
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | | | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| |
Collapse
|
40
|
Brewer TF, Garcia FJ, Onak CS, Carroll KS, Chang CJ. Chemical approaches to discovery and study of sources and targets of hydrogen peroxide redox signaling through NADPH oxidase proteins. Annu Rev Biochem 2015; 84:765-90. [PMID: 26034893 DOI: 10.1146/annurev-biochem-060614-034018] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hydrogen peroxide (H2O2) is a prime member of the reactive oxygen species (ROS) family of molecules produced during normal cell function and in response to various stimuli, but if left unchecked, it can inflict oxidative damage on all types of biological macromolecules and lead to cell death. In this context, a major source of H2O2 for redox signaling purposes is the NADPH oxidase (Nox) family of enzymes, which were classically studied for their roles in phagocytic immune response but have now been found to exist in virtually all mammalian cell types in various isoforms with distinct tissue and subcellular localizations. Downstream of this tightly regulated ROS generation, site-specific, reversible covalent modification of proteins, particularly oxidation of cysteine thiols to sulfenic acids, represents a prominent posttranslational modification akin to phosphorylation as an emerging molecular mechanism for transforming an oxidant signal into a dynamic biological response. We review two complementary types of chemical tools that enable (a) specific detection of H2O2 generated at its sources and (b) mapping of sulfenic acid posttranslational modification targets that mediate its signaling functions, which can be used to study this important chemical signal in biological systems.
Collapse
|
41
|
Wages PA, Lavrich KS, Zhang Z, Cheng WY, Corteselli E, Gold A, Bromberg P, Simmons SO, Samet JM. Protein Sulfenylation: A Novel Readout of Environmental Oxidant Stress. Chem Res Toxicol 2015; 28:2411-8. [PMID: 26605980 DOI: 10.1021/acs.chemrestox.5b00424] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oxidative stress is a commonly cited mechanism of toxicity of environmental agents. Ubiquitous environmental chemicals such as the diesel exhaust component 1,2-naphthoquinone (1,2-NQ) induce oxidative stress by redox cycling, which generates hydrogen peroxide (H2O2). Cysteinyl thiolate residues on regulatory proteins are subjected to oxidative modification by H2O2 in physiological contexts and are also toxicological targets of oxidant stress induced by environmental contaminants. We investigated whether exposure to environmentally relevant concentrations of 1,2-NQ can induce H2O2-dependent oxidation of cysteinyl thiols in regulatory proteins as a readout of oxidant stress in human airway epithelial cells. BEAS-2B cells were exposed to 0-1000 μM 1,2-NQ for 0-30 min, and levels of H2O2 were measured by ratiometric spectrofluorometry of HyPer. H2O2-dependent protein sulfenylation was measured using immunohistochemistry, immunoblotting, and isotopic mass spectrometry. Catalase overexpression was used to investigate the relationship between H2O2 generation and protein sulfenylation in cells exposed to 1,2-NQ. Multiple experimental approaches showed that exposure to 1,2-NQ at concentrations as low as 3 μM induces H2O2-dependent protein sulfenylation in BEAS-2B cells. Moreover, the time of onset and duration of 1,2-NQ-induced sulfenylation of the regulatory proteins GAPDH and PTP1B showed significant differences. Oxidative modification of regulatory cysteinyl thiols in human lung cells exposed to relevant concentrations of an ambient air contaminant represents a novel marker of oxidative environmental stress.
Collapse
Affiliation(s)
- Phillip A Wages
- Curriculum in Toxicology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7310, United States
| | - Katelyn S Lavrich
- Curriculum in Toxicology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7310, United States
| | - Zhenfa Zhang
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7400, United States
| | - Wan-Yun Cheng
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency , Research Triangle Park, North Carolina 27711, United States
| | - Elizabeth Corteselli
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7400, United States
| | - Avram Gold
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7400, United States
| | - Philip Bromberg
- Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7310, United States
| | - Steven O Simmons
- National Center for Computational Toxicology, U.S. Environmental Protection Agency , Research Triangle Park, North Carolina 27711, United States
| | - James M Samet
- Curriculum in Toxicology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7310, United States.,Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency , Chapel Hill, North Carolina 27711, United States
| |
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
Bui VM, Lu CT, Ho TT, Lee TY. MDD-SOH: exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs. Bioinformatics 2015; 32:165-72. [PMID: 26411868 DOI: 10.1093/bioinformatics/btv558] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 09/18/2015] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED S-sulfenylation (S-sulphenylation, or sulfenic acid), the covalent attachment of S-hydroxyl (-SOH) to cysteine thiol, plays a significant role in redox regulation of protein functions. Although sulfenic acid is transient and labile, most of its physiological activities occur under control of S-hydroxylation. Therefore, discriminating the substrate site of S-sulfenylated proteins is an essential task in computational biology for the furtherance of protein structures and functions. Research into S-sulfenylated protein is currently very limited, and no dedicated tools are available for the computational identification of SOH sites. Given a total of 1096 experimentally verified S-sulfenylated proteins from humans, this study carries out a bioinformatics investigation on SOH sites based on amino acid composition and solvent-accessible surface area. A TwoSampleLogo indicates that the positively and negatively charged amino acids flanking the SOH sites may impact the formulation of S-sulfenylation in closed three-dimensional environments. In addition, the substrate motifs of SOH sites are studied using the maximal dependence decomposition (MDD). Based on the concept of binary classification between SOH and non-SOH sites, Support vector machine (SVM) is applied to learn the predictive model from MDD-identified substrate motifs. According to the evaluation results of 5-fold cross-validation, the integrated SVM model learned from substrate motifs yields an average accuracy of 0.87, significantly improving the prediction of SOH sites. Furthermore, the integrated SVM model also effectively improves the predictive performance in an independent testing set. Finally, the integrated SVM model is applied to implement an effective web resource, named MDD-SOH, to identify SOH sites with their corresponding substrate motifs. AVAILABILITY AND IMPLEMENTATION The MDD-SOH is now freely available to all interested users at http://csb.cse.yzu.edu.tw/MDDSOH/. All of the data set used in this work is also available for download in the website. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT francis@saturn.yzu.edu.tw.
Collapse
Affiliation(s)
- Van-Minh Bui
- Department of Computer Science and Engineering and
| | | | - Thi-Trang Ho
- Department of Computer Science and Engineering and
| | - Tzong-Yi Lee
- Department of Computer Science and Engineering and Innovation Center for Big Data and Digital Convergence, Yuan Ze University, Taoyuan 320, Taiwan
| |
Collapse
|
44
|
Chen W, Rosser EW, Matsunaga T, Pacheco A, Akaike T, Xian M. The Development of Fluorescent Probes for Visualizing Intracellular Hydrogen Polysulfides. Angew Chem Int Ed Engl 2015; 54:13961-5. [PMID: 26381762 DOI: 10.1002/anie.201506887] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 01/02/2023]
Abstract
Endogenous hydrogen polysulfides (H2Sn; n>1) have been recognized as important regulators in sulfur-related redox biology. H2Sn can activate tumor suppressors, ion channels, and transcription factors with higher potency than H2S. Although H2Sn are drawing increasing attention, their exact mechanisms of action are still poorly understood. A major hurdle in this field is the lack of reliable and convenient methods for H2Sn detection. Herein we report a H2Sn-mediated benzodithiolone formation under mild conditions. This method takes advantage of the unique dual reactivity of H2Sn as both a nucleophile and an electrophile. Based on this reaction, three fluorescent probes (PSP-1, PSP-2, and PSP-3) were synthesized and evaluated. Among the probes prepared, PSP-3 showed a desirable off/on fluorescence response to H2Sn and high specificity. The probe was successfully applied in visualizing intracellular H2Sn.
Collapse
Affiliation(s)
- Wei Chen
- Department of Chemistry, Washington State University, Pullman, WA 99164 (USA)
| | - Ethan W Rosser
- Department of Chemistry, Washington State University, Pullman, WA 99164 (USA)
| | - Tetsuro Matsunaga
- Department of Environmental Health Sciences and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, 980-8575 (Japan)
| | - Armando Pacheco
- Department of Chemistry, Washington State University, Pullman, WA 99164 (USA)
| | - Takaaki Akaike
- Department of Environmental Health Sciences and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, 980-8575 (Japan)
| | - Ming Xian
- Department of Chemistry, Washington State University, Pullman, WA 99164 (USA).
| |
Collapse
|
45
|
Chen W, Rosser EW, Matsunaga T, Pacheco A, Akaike T, Xian M. The Development of Fluorescent Probes for Visualizing Intracellular Hydrogen Polysulfides. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506887] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Wei Chen
- Department of Chemistry, Washington State University, Pullman, WA 99164 (USA)
| | - Ethan W. Rosser
- Department of Chemistry, Washington State University, Pullman, WA 99164 (USA)
| | - Tetsuro Matsunaga
- Department of Environmental Health Sciences and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, 980‐8575 (Japan)
| | - Armando Pacheco
- Department of Chemistry, Washington State University, Pullman, WA 99164 (USA)
| | - Takaaki Akaike
- Department of Environmental Health Sciences and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, 980‐8575 (Japan)
| | - Ming Xian
- Department of Chemistry, Washington State University, Pullman, WA 99164 (USA)
| |
Collapse
|
46
|
Differential alkylation-based redox proteomics--Lessons learnt. Redox Biol 2015; 6:240-252. [PMID: 26282677 PMCID: PMC4543216 DOI: 10.1016/j.redox.2015.08.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 01/11/2023] Open
Abstract
Cysteine is one of the most reactive amino acids. This is due to the electronegativity of sulphur atom in the side chain of thiolate group. It results in cysteine being present in several distinct redox forms inside the cell. Amongst these, reversible oxidations, S-nitrosylation and S-sulfenylation are crucial mediators of intracellular redox signalling, with known associations to health and disease. Study of their functionalities has intensified thanks to the development of various analytical strategies, with particular contribution from differential alkylation-based proteomics methods. Presented here is a critical evaluation of differential alkylation-based strategies for the analysis of S-nitrosylation and S-sulfenylation. The aim is to assess the current status and to provide insights for future directions in the dynamically evolving field of redox proteomics. To achieve that we collected 35 original research articles published since 2010 and analysed them considering the following parameters, (i) resolution of modification site, (ii) quantitative information, including correction of modification levels by protein abundance changes and determination of modification site occupancy, (iii) throughput, including the amount of starting material required for analysis. The results of this meta-analysis are the core of this review, complemented by issues related to biological models and sample preparation in redox proteomics, including conditions for free thiol blocking and labelling of target cysteine oxoforms.
Collapse
|
47
|
Medina-Cleghorn D, Nomura DK. Exploring metabolic pathways and regulation through functional chemoproteomic and metabolomic platforms. ACTA ACUST UNITED AC 2015; 21:1171-84. [PMID: 25237861 DOI: 10.1016/j.chembiol.2014.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 07/15/2014] [Accepted: 07/21/2014] [Indexed: 02/07/2023]
Abstract
Genome sequencing efforts have revealed a strikingly large number of uncharacterized genes, including poorly or uncharacterized metabolic enzymes, metabolites, and metabolic networks that operate in normal physiology, and those enzymes and pathways that may be rewired under pathological conditions. Although deciphering the functions of the uncharacterized metabolic genome is a challenging prospect, it also presents an opportunity for identifying novel metabolic nodes that may be important in disease therapy. In this review, we will discuss the chemoproteomic and metabolomic platforms used in identifying, characterizing, and targeting nodal metabolic pathways important in physiology and disease, describing an integrated workflow for functional mapping of metabolic enzymes.
Collapse
Affiliation(s)
- Daniel Medina-Cleghorn
- Program in Metabolic Biology and Molecular Toxicology, Department of Nutritional Sciences and Toxicology, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Daniel K Nomura
- Program in Metabolic Biology and Molecular Toxicology, Department of Nutritional Sciences and Toxicology, 127 Morgan Hall, Berkeley, CA 94720, USA.
| |
Collapse
|
48
|
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.
Collapse
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
| |
Collapse
|
49
|
Baez NOD, Reisz JA, Furdui CM. Mass spectrometry in studies of protein thiol chemistry and signaling: opportunities and caveats. Free Radic Biol Med 2015; 80:191-211. [PMID: 25261734 PMCID: PMC4355329 DOI: 10.1016/j.freeradbiomed.2014.09.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/08/2014] [Accepted: 09/11/2014] [Indexed: 12/13/2022]
Abstract
Mass spectrometry (MS) has become a powerful and widely utilized tool in the investigation of protein thiol chemistry, biochemistry, and biology. Very early biochemical studies of metabolic enzymes have brought to light the broad spectrum of reactivity profiles that distinguish cysteine thiols with functions in catalysis and protein stability from other cysteine residues in proteins. The development of MS methods for the analysis of proteins using electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI) coupled with the emergence of high-resolution mass analyzers has been instrumental in advancing studies of thiol modifications, both in single proteins and within the cellular context. This article reviews MS instrumentation and methods of analysis employed in investigations of thiols and their reactivity toward a range of small biomolecules. A selected number of studies are detailed to highlight the advantages brought about by the MS technologies along with the caveats associated with these analyses.
Collapse
Affiliation(s)
- Nelmi O Devarie Baez
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Julie A Reisz
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| |
Collapse
|
50
|
Zhang Y, Zhang C, Jiang H, Yang P, Lu H. Fishing the PTM proteome with chemical approaches using functional solid phases. Chem Soc Rev 2015; 44:8260-87. [DOI: 10.1039/c4cs00529e] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Currently available chemical approaches for the enrichment and separation of a PTM proteome using functional solid phases were reviewed.
Collapse
Affiliation(s)
- Ying Zhang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
- Key Laboratory of Glycoconjugates Research Ministry of Public Health
| | - Cheng Zhang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
| | - Hucong Jiang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
| | - Haojie Lu
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
- Key Laboratory of Glycoconjugates Research Ministry of Public Health
| |
Collapse
|