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Burton NR, Polasky DA, Shikwana F, Ofori S, Yan T, Geiszler DJ, Veiga Leprevost FD, Nesvizhskii AI, Backus KM. Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics. J Am Chem Soc 2023; 145:21303-21318. [PMID: 37738129 DOI: 10.1021/jacs.3c05797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Mass spectrometry-based chemoproteomics has emerged as an enabling technology for functional biology and drug discovery. To address limitations of established chemoproteomics workflows, including cumbersome reagent synthesis and low throughput sample preparation, here, we established the silane-based cleavable isotopically labeled proteomics (sCIP) method. The sCIP method is enabled by a high yielding and scalable route to dialkoxydiphenylsilane fluorenylmethyloxycarbonyl (DADPS-Fmoc)-protected amino acid building blocks, which enable the facile synthesis of customizable, isotopically labeled, and chemically cleavable biotin capture reagents. sCIP is compatible with both MS1- and MS2-based quantitation, and the sCIP-MS2 method is distinguished by its click-assembled isobaric tags in which the reporter group is encoded in the sCIP capture reagent and balancer in the pan cysteine-reactive probe. The sCIP-MS2 workflow streamlines sample preparation with early stage isobaric labeling and sample pooling, allowing for high coverage and increased sample throughput via customized low cost six-plex sample multiplexing. When paired with a custom FragPipe data analysis workflow and applied to cysteine-reactive fragment screens, sCIP proteomics revealed established and unprecedented cysteine-ligand pairs, including the discovery that mitochondrial uncoupling agent FCCP acts as a covalent-reversible cysteine-reactive electrophile.
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Affiliation(s)
- Nikolas R Burton
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Flowreen Shikwana
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Samuel Ofori
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Tianyang Yan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Keriann M Backus
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California 90095, United States
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2
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Milkovic L, Zarkovic N, Marusic Z, Zarkovic K, Jaganjac M. The 4-Hydroxynonenal–Protein Adducts and Their Biological Relevance: Are Some Proteins Preferred Targets? Antioxidants (Basel) 2023; 12:antiox12040856. [PMID: 37107229 PMCID: PMC10135105 DOI: 10.3390/antiox12040856] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
It is well known that oxidative stress and lipid peroxidation (LPO) play a role in physiology and pathology. The most studied LPO product with pleiotropic capabilities is 4-hydroxynonenal (4-HNE). It is considered as an important mediator of cellular signaling processes and a second messenger of reactive oxygen species. The effects of 4-HNE are mainly attributed to its adduction with proteins. Whereas the Michael adducts thus formed are preferred in an order of potency of cysteine > histidine > lysine over Schiff base formation, it is not known which proteins are the preferred targets for 4-HNE under what physiological or pathological conditions. In this review, we briefly discuss the methods used to identify 4-HNE–protein adducts, the progress of mass spectrometry in deciphering the specific protein targets, and their biological relevance, focusing on the role of 4-HNE protein adducts in the adaptive response through modulation of the NRF2/KEAP1 pathway and ferroptosis.
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Affiliation(s)
- Lidija Milkovic
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruder Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Neven Zarkovic
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruder Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Zlatko Marusic
- Division of Pathology, Clinical Hospital Centre Zagreb, Kispaticeva 12, 10000 Zagreb, Croatia
| | - Kamelija Zarkovic
- Division of Pathology, Clinical Hospital Centre Zagreb, Kispaticeva 12, 10000 Zagreb, Croatia
| | - Morana Jaganjac
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruder Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
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3
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Li Z, Liu K, Xu P, Yang J. Benchmarking Cleavable Biotin Tags for Peptide-Centric Chemoproteomics. J Proteome Res 2022; 21:1349-1358. [PMID: 35467356 DOI: 10.1021/acs.jproteome.2c00174] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Click chemistry─specifically the copper-catalyzed azide-alkyne cycloaddition─has enabled the development of a wide range of chemical probes to analyze subsets of the functional proteome. The "clickable" proteome can be selectively enriched by using diverse cleavable biotin tags, but the direct identification of probe/tag-modified peptides (or peptide-centric analysis) remains challenging. Here, we evaluated the performance of five commercially available cleavable biotin tags in three most common chemoproteomic workflows, resulting in a comparative analysis of 15 methods. An acid-cleavable biotin tag with a dialkoxydiphenylsilane moiety, in combination with the protein "click", peptide "capture" workflow, outperforms all other methods in terms of enrichment efficiency, identification yield, and reproducibility, although its performance may be slightly compromised by the formation of an unwanted formate product revealed by blind search. Despite being inferior, photocleavable, and reduction-cleavable, biotin tags can also find their applicable sceneries, especially when dealing with acid-sensitive probes or probe-derived modifications. Furthermore, the systematic comparison of LC-MS/MS characteristics of tag-modified peptides provides valuable information for the future development of cleavable biotin reagents. Taken together, our data provides a much-needed practical guidance for researchers interested in developing and/or applying an ideal cleavable biotin tag to peptide-centric chemoproteomics.
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Affiliation(s)
- Zongmin Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Keke Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ping Xu
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing 102206, China
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4
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Protein Lipidation Types: Current Strategies for Enrichment and Characterization. Int J Mol Sci 2022; 23:ijms23042365. [PMID: 35216483 PMCID: PMC8880637 DOI: 10.3390/ijms23042365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
Post-translational modifications regulate diverse activities of a colossal number of proteins. For example, various types of lipids can be covalently linked to proteins enzymatically or non-enzymatically. Protein lipidation is perhaps not as extensively studied as protein phosphorylation, ubiquitination, or glycosylation although it is no less significant than these modifications. Evidence suggests that proteins can be attached by at least seven types of lipids, including fatty acids, lipoic acids, isoprenoids, sterols, phospholipids, glycosylphosphatidylinositol anchors, and lipid-derived electrophiles. In this review, we summarize types of protein lipidation and methods used for their detection, with an emphasis on the conjugation of proteins with polyunsaturated fatty acids (PUFAs). We discuss possible reasons for the scarcity of reports on PUFA-modified proteins, limitations in current methodology, and potential approaches in detecting PUFA modifications.
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5
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Chen Y, Wang C. Profiling of Protein Carbonylations in Ferroptosis by Chemical Proteomics. Methods Mol Biol 2022; 2543:141-153. [PMID: 36087265 DOI: 10.1007/978-1-0716-2553-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Ferroptosis is a new form of cell death with hallmark of lipid peroxidation and iron accumulation. It has been shown that lipid peroxidation can result in electrophilic metabolites which in turn induce protein carbonylations. Identification of specific carbonylated proteins and sites in ferroptotic cells will be of great significance for understanding the mechanism and discovering potential biomarkers for this new cell death. The protocol described herein is an optimized pipeline which combines the labeling of carbonylated proteins by a commercially available aniline-based probe with the tandem orthogonal proteolysis activity-based protein profiling (TOP-ABPP) strategy to portrait the landscape of carbonylations in ferroptotic cells.
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Affiliation(s)
- Ying Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
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6
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Perryman A, Speen AM, Kim HYH, Hoffman JR, Clapp PW, Rivera Martin W, Snouwaert JN, Koller BH, Porter NA, Jaspers I. Oxysterols Modify NLRP2 in Epithelial Cells, Identifying a Mediator of Ozone-induced Inflammation. Am J Respir Cell Mol Biol 2021; 65:500-512. [PMID: 34126877 DOI: 10.1165/rcmb.2021-0032oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Ozone (O3) is a prevalent air pollutant causing lung inflammation. Previous studies demonstrate that O3 oxidizes lipids, such as cholesterol, in the airway to produce oxysterols, such as secosterol-A (SecoA), which are electrophiles capable of forming covalent linkages preferentially with lysine residues and consequently modify protein function. The breadth of proteins modified by this oxysterol as well as the biological consequences in the lung are unknown. Using an alkynyl-tagged form of SecoA and shotgun proteomics, we identified 135 proteins to be modified bronchial epithelial cells. Among them was NLR Family Pyrin Domain Containing 2 (NLRP2) forming a SecoA-protein adduct at lysine (K1019) in the terminal leucine-rich-repeat, a known regulatory region for NLR proteins. NLRP2 expression in airway epithelial cells was characterized and CRISPR-Cas9 knockout and shRNA knockdown of NLRP2 was used to determine its function in O3-induced inflammation. No evidence for NLPR2 inflammasome formation or NLRP2-dependent increase in caspase-1 activity in response to O3 was observed. O3-induced pro-inflammatory gene expression for CXCL2 and CXCL8/IL8 was further enhanced in NLRP2 knockout cells, suggesting a negative regulatory role. Reconstitution of NLRP2 KO cells with K1019R mutant NLRP2 partially blocked SecoA adduction and enhanced O3-induced IL-8 release as compared to wild type NLRP2. Together, our findings uncover NLRP2 as a highly abundant, key component of pro-inflammatory signaling pathways in airway epithelial cells and as a novel mediator of O3-induced inflammation.
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Affiliation(s)
- Alexia Perryman
- University of North Carolina, Curriculum in Toxicology & Environmental Medicine, Chapel Hill, North Carolina, United States
| | - Adam M Speen
- US Environmental Protection Agency Office of Research and Development, 314974, Durham, North Carolina, United States
| | - Hye-Young H Kim
- Vanderbilt University, 5718, Nashville, Tennessee, United States
| | - Jessica R Hoffman
- University of North Carolina at Chapel Hill, Curriculum for the Environment and Ecology, Chapel Hill, North Carolina, United States
| | - Phillip W Clapp
- University of North Carolina at Chapel Hill School of Medicine, 6797, Pediatrics, Chapel Hill, North Carolina, United States
| | | | - John N Snouwaert
- University of North Carolina at Chapel Hill School of Medicine, 6797, Genetics, Chapel Hill, North Carolina, United States
| | | | - Ned A Porter
- Vanderbilt University, 5718, Nashville, Tennessee, United States
| | - Ilona Jaspers
- University of North Carolina, Pediatrics, Chapel Hill, North Carolina, United States;
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7
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Beard HA, Korovesis D, Chen S, Verhelst SHL. Cleavable linkers and their application in MS-based target identification. Mol Omics 2021; 17:197-209. [PMID: 33507200 DOI: 10.1039/d0mo00181c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covalent chemical probes are important tools in chemical biology. They range from post-translational modification (PTM)-derived metabolic probes, to activity-based probes and photoaffinity labels. Identification of the probe targets is often performed by tandem mass spectrometry-based proteomics methods. In the past fifteen years, cleavable linker technologies have been implemented in these workflows in order to identify probe targets with lower background and higher confidence. In addition, the linkers have enabled identification of modification sites. Overall, this has led to an increased knowledge of PTMs, enzyme function and drug action. This review gives an overview of the different types of cleavable linkers, and their benefits and limitations. Their applicability in target identification is also illustrated by several specific examples.
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Affiliation(s)
- Hester A Beard
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49 box 802, 3000 Leuven, Belgium.
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8
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Li Y, Tian C, Liu K, Zhou Y, Yang J, Zou P. A Clickable APEX Probe for Proximity-Dependent Proteomic Profiling in Yeast. Cell Chem Biol 2020; 27:858-865.e8. [DOI: 10.1016/j.chembiol.2020.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/24/2019] [Accepted: 05/08/2020] [Indexed: 10/24/2022]
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9
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Reactive Sterol Electrophiles: Mechanisms of Formation and Reactions with Proteins and Amino Acid Nucleophiles. CHEMISTRY (BASEL, SWITZERLAND) 2020; 2:390-417. [PMID: 35372835 PMCID: PMC8976181 DOI: 10.3390/chemistry2020025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Radical-mediated lipid oxidation and the formation of lipid hydroperoxides has been a focal point in the investigation of a number of human pathologies. Lipid peroxidation has long been linked to the inflammatory response and more recently, has been identified as the central tenet of the oxidative cell death mechanism known as ferroptosis. The formation of lipid electrophile-protein adducts has been associated with many of the disorders that involve perturbations of the cellular redox status, but the identities of adducted proteins and the effects of adduction on protein function are mostly unknown. Both cholesterol and 7-dehydrocholesterol (7-DHC), which is the immediate biosynthetic precursor to cholesterol, are oxidizable by species such as ozone and oxygen-centered free radicals. Product mixtures from radical chain processes are particularly complex, with recent studies having expanded the sets of electrophilic compounds formed. Here, we describe recent developments related to the formation of sterol-derived electrophiles and the adduction of these electrophiles to proteins. A framework for understanding sterol peroxidation mechanisms, which has significantly advanced in recent years, as well as the methods for the study of sterol electrophile-protein adduction, are presented in this review.
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10
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Non-enzymatic Lysine Lactoylation of Glycolytic Enzymes. Cell Chem Biol 2020; 27:206-213.e6. [PMID: 31767537 PMCID: PMC7395678 DOI: 10.1016/j.chembiol.2019.11.005] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/14/2019] [Accepted: 11/08/2019] [Indexed: 12/11/2022]
Abstract
Post-translational modifications (PTMs) regulate enzyme structure and function to expand the functional proteome. Many of these PTMs are derived from cellular metabolites and serve as feedback and feedforward mechanisms of regulation. We have identified a PTM that is derived from the glycolytic by-product, methylglyoxal. This reactive metabolite is rapidly conjugated to glutathione via glyoxalase 1, generating lactoylglutathione (LGSH). LGSH is hydrolyzed by glyoxalase 2 (GLO2), cycling glutathione and generating D-lactate. We have identified the non-enzymatic acyl transfer of the lactate moiety from LGSH to protein Lys residues, generating a "LactoylLys" modification on proteins. GLO2 knockout cells have elevated LGSH and a consequent marked increase in LactoylLys. Using an alkyne-tagged methylglyoxal analog, we show that these modifications are enriched on glycolytic enzymes and regulate glycolysis. Collectively, these data suggest a previously unexplored feedback mechanism that may serve to regulate glycolytic flux under hyperglycemic or Warburg-like conditions.
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11
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Gao D, Ashraf MZ, Zhang L, Kar N, Byzova TV, Podrez EA. Cross-linking modifications of HDL apoproteins by oxidized phospholipids: structural characterization, in vivo detection, and functional implications. J Biol Chem 2020; 295:1973-1984. [PMID: 31907281 DOI: 10.1074/jbc.ra119.008445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 12/16/2019] [Indexed: 01/05/2023] Open
Abstract
Apolipoprotein A-I (apoA-I) is cross-linked and dysfunctional in human atheroma. Although multiple mechanisms of apoA-I cross-linking have been demonstrated in vitro, the in vivo mechanisms of cross-linking are not well-established. We have recently demonstrated the highly selective and efficient modification of high-density lipoprotein (HDL) apoproteins by endogenous oxidized phospholipids (oxPLs), including γ-ketoalkenal phospholipids. In the current study, we report that γ-ketoalkenal phospholipids effectively cross-link apoproteins in HDL. We further demonstrate that cross-linking impairs the cholesterol efflux mediated by apoA-I or HDL3 in vitro and in vivo Using LC-MS/MS analysis, we analyzed the pattern of apoprotein cross-linking in isolated human HDL either by synthetic γ-ketoalkenal phospholipids or by oxPLs generated during HDL oxidation in plasma by the physiologically relevant MPO-H2O2-NO2 - system. We found that five histidine residues in helices 5-8 of apoA-I are preferably cross-linked by oxPLs, forming stable pyrrole adducts with lysine residues in the helices 3-4 of another apoA-I or in the central domain of apoA-II. We also identified cross-links of apoA-I and apoA-II with two minor HDL apoproteins, apoA-IV and apoE. We detected a similar pattern of apoprotein cross-linking in oxidized murine HDL. We further detected oxPL cross-link adducts of HDL apoproteins in plasma and aorta of hyperlipidemic LDLR-/- mice, including cross-link adducts of apoA-I His-165-apoA-I Lys-93, apoA-I His-154-apoA-I Lys-105, apoA-I His-154-apoA-IV Lys-149, and apoA-II Lys-30-apoE His-227. These findings suggest an important mechanism that contributes to the loss of HDL's atheroprotective function in vivo.
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Affiliation(s)
- Detao Gao
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Mohammad Z Ashraf
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Lifang Zhang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Niladri Kar
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Tatiana V Byzova
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Eugene A Podrez
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195.
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12
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Rabalski AJ, Bogdan AR, Baranczak A. Evaluation of Chemically-Cleavable Linkers for Quantitative Mapping of Small Molecule-Cysteinome Reactivity. ACS Chem Biol 2019; 14:1940-1950. [PMID: 31430117 DOI: 10.1021/acschembio.9b00424] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Numerous reagents have been developed to enable chemical proteomic analysis of small molecule-protein interactomes. However, the performance of these reagents has not been systematically evaluated and compared. Herein, we report our efforts to conduct a parallel assessment of two widely used chemically cleavable linkers equipped with dialkoxydiphenylsilane (DADPS linker) and azobenzene (AZO linker) moieties. Profiling a cellular cysteinome using the iodoacetamide alkyne probe demonstrated a significant discrepancy between the experimental results obtained through the application of each of the reagents. To better understand the source of observed discrepancy, we evaluated the key sample preparation steps. We also performed a mass tolerant database search strategy using MSFragger software. This resulted in identifying a previously unreported artifactual modification on the residual mass of the azobenzene linker. Furthermore, we conducted a comparative analysis of enrichment modes using both cleavable linkers. This effort determined that enrichment of proteolytic digests yielded a far greater number of identified cysteine residues than the enrichment conducted prior to protein digest. Inspired by recent studies where multiplexed quantitative labeling strategies were applied to cleavable biotin linkers, we combined this further optimized protocol using the DADPS cleavable linker with tandem mass tag (TMT) labeling to profile the FDA-approved covalent EGFR kinase inhibitor dacomitinib against the cysteinome of an epidermoid cancer cell line. Our analysis resulted in the detection and quantification of over 10,000 unique cysteine residues, a nearly 3-fold increase over previous studies that used cleavable biotin linkers for enrichment. Critically, cysteine residues corresponding to proteins directly as well as indirectly modulated by dacomitinib treatment were identified. Overall, our study suggests that the dialkoxydiphenylsilane linker could be broadly applied wherever chemically cleavable linkers are required for chemical proteomic characterization of cellular proteomes.
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Affiliation(s)
- Adam J. Rabalski
- Drug Discovery Science & Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, United States
| | - Andrew R. Bogdan
- Drug Discovery Science & Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, United States
| | - Aleksandra Baranczak
- Drug Discovery Science & Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, United States
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13
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Nadendla K, Sarode BR, Friedman SH. Hydrophobic Tags for Highly Efficient Light-Activated Protein Release. Mol Pharm 2019; 16:2922-2928. [PMID: 31117739 DOI: 10.1021/acs.molpharmaceut.9b00140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We have previously described the photoactivated depot (PAD) approach for the light-stimulated release of therapeutic proteins such as insulin. The aim of this method is to release insulin from a shallow dermal depot in response to blood glucose information, using transcutaneous irradiation. Our first approach utilized a photocleavable group that linked insulin to an insoluble but injectable polymer bead. The bead conferred insolubility, ensuring that the injected material stayed at the site of injection, until light cleaved the link, and allowed insulin to be absorbed systemically. While this proved to be effective, the use of a polymer to ensure insolubility introduces two major design problems: (1) low concentration of insulin, as a majority of the material is composed of polymer, and (2) upon release of the insulin, the polymer has to be cleared from the system. To address these two problems, in this work, we have pursued "hydrophobic tags", photocleavable small nonpolar molecules that confer insolubility to the modified insulin prior to irradiation without the bulk or need for biodegradation required of polymers. We developed a combined solid- and solution-phase synthetic approach that allowed us to incorporate a range of small nonpolar moieties, including peptides, into the final depot materials. The resulting materials are >90% w/w insulin and have sharply decreased solubilities relative to unmodified insulin (≤1000 × lower). We demonstrated that they can be milled into low micron-sized particles that can be readily injected through a 31G needle. These suspensions can be prepared at an effective concentration of 20 mM insulin, a concentration at which 120 μL contains 7 days of insulin for a typical adult. Finally, upon photolysis, the insoluble particles release soluble, native insulin in a predictable fashion. These combined properties make these new modified insulins nearly ideal as candidates for PAD materials.
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Affiliation(s)
- Karthik Nadendla
- Division of Pharmaceutical Sciences , University of Missouri-Kansas City, School of Pharmacy , Kansas City , Missouri 64108 , United States
| | - Bhagyesh R Sarode
- Division of Pharmaceutical Sciences , University of Missouri-Kansas City, School of Pharmacy , Kansas City , Missouri 64108 , United States
| | - Simon H Friedman
- Division of Pharmaceutical Sciences , University of Missouri-Kansas City, School of Pharmacy , Kansas City , Missouri 64108 , United States
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14
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Nunes J, Charneira C, Morello J, Rodrigues J, Pereira SA, Antunes AMM. Mass Spectrometry-Based Methodologies for Targeted and Untargeted Identification of Protein Covalent Adducts (Adductomics): Current Status and Challenges. High Throughput 2019; 8:ht8020009. [PMID: 31018479 PMCID: PMC6631461 DOI: 10.3390/ht8020009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 12/12/2022] Open
Abstract
Protein covalent adducts formed upon exposure to reactive (mainly electrophilic) chemicals may lead to the development of a wide range of deleterious health outcomes. Therefore, the identification of protein covalent adducts constitutes a huge opportunity for a better understanding of events underlying diseases and for the development of biomarkers which may constitute effective tools for disease diagnosis/prognosis, for the application of personalized medicine approaches and for accurately assessing human exposure to chemical toxicants. The currently available mass spectrometry (MS)-based methodologies, are clearly the most suitable for the analysis of protein covalent modifications, providing accuracy, sensitivity, unbiased identification of the modified residue and conjugates along with quantitative information. However, despite the huge technological advances in MS instrumentation and bioinformatics tools, the identification of low abundant protein covalent adducts is still challenging. This review is aimed at summarizing the MS-based methodologies currently used for the identification of protein covalent adducts and the strategies developed to overcome the analytical challenges, involving not only sample pre-treatment procedures but also distinct MS and data analysis approaches.
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Affiliation(s)
- João Nunes
- Centro de Química Estrutural, Instituto Superior Técnico, ULisboa, 1049-001 Lisboa, Portugal.
| | - Catarina Charneira
- Centro de Química Estrutural, Instituto Superior Técnico, ULisboa, 1049-001 Lisboa, Portugal.
| | - Judit Morello
- Centro de Química Estrutural, Instituto Superior Técnico, ULisboa, 1049-001 Lisboa, Portugal.
| | - João Rodrigues
- Clarify Analytical, Rua dos Mercadores 128A, 7000-872 Évora, Portugal.
| | - Sofia A Pereira
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-006 Lisboa, Portugal.
| | - Alexandra M M Antunes
- Centro de Química Estrutural, Instituto Superior Técnico, ULisboa, 1049-001 Lisboa, Portugal.
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15
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Chavas TEJ, Fuchter MJ, DiMaggio PA. Unbiased Mass Spectrometry Elucidation of the Targets and Mechanisms of Activity-Based Probes: A Case Study Involving Sulfonyl Fluorides. ACS Chem Biol 2018; 13:2897-2907. [PMID: 30192509 DOI: 10.1021/acschembio.8b00530] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The elucidation of protein/drug interactions remains a major challenge in drug discovery. Liquid chromatography-tandem mass spectrometry has emerged as a tremendously powerful technology for this endeavor, but its full potential has yet to be realized owing in part to unresolved challenges in data analysis. Herein, we demonstrate how tandem mass spectrometry can comprehensively map small molecule/peptide adducts when combined with unconstrained sequencing. Using a published sulfonyl fluoride activity-based probe as a model system, this method enabled the discovery of several unreported sites of interaction with its target proteins. Crucially, this probe was found to undergo quantitative displacement and hydrolysis from the target protein's active site. Isotopic labeling experiments provided a mechanistic rationale for the observed hydrolysis that involves neighboring-group participation. A chemical biology tagging strategy that leverages the probe's observed lability was developed and shown to be compatible with the original small molecule inhibitor in discovery profiling experiments.
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Affiliation(s)
- Thomas E. J. Chavas
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Matthew J. Fuchter
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Peter A. DiMaggio
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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16
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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.
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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
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17
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Xie Y, Dahlin JL, Oakley AJ, Casarotto MG, Board PG, Baell JB. Reviewing Hit Discovery Literature for Difficult Targets: Glutathione Transferase Omega-1 as an Example. J Med Chem 2018; 61:7448-7470. [PMID: 29652143 DOI: 10.1021/acs.jmedchem.8b00318] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Early stage drug discovery reporting on relatively new or difficult targets is often associated with insufficient hit triage. Literature reviews of such targets seldom delve into the detail required to critically analyze the associated screening hits reported. Here we take the enzyme glutathione transferase omega-1 (GSTO1-1) as an example of a relatively difficult target and review the associated literature involving small-molecule inhibitors. As part of this process we deliberately pay closer-than-usual attention to assay interference and hit quality aspects. We believe this Perspective will be a useful guide for future development of GSTO1-1 inhibitors, as well serving as a template for future review formats of new or difficult targets.
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Affiliation(s)
- Yiyue Xie
- Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , Victoria 3052 , Australia
| | - Jayme L Dahlin
- Department of Pathology , Brigham and Women's Hospital , Boston , Massachusetts 02135 , United States
| | - Aaron J Oakley
- School of Chemistry , University of Wollongong , Wollongong , NSW 2522 , Australia
| | - Marco G Casarotto
- John Curtin School of Medical Research , Australian National University , Canberra , ACT 2600 , Australia
| | - Philip G Board
- John Curtin School of Medical Research , Australian National University , Canberra , ACT 2600 , Australia
| | - Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , Victoria 3052 , Australia.,School of Pharmaceutical Sciences , Nanjing Tech University , Nanjing , 211816 , People's Republic of China
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18
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Chen Y, Liu Y, Lan T, Qin W, Zhu Y, Qin K, Gao J, Wang H, Hou X, Chen N, Friedmann Angeli JP, Conrad M, Wang C. Quantitative Profiling of Protein Carbonylations in Ferroptosis by an Aniline-Derived Probe. J Am Chem Soc 2018; 140:4712-4720. [PMID: 29569437 DOI: 10.1021/jacs.8b01462] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ferroptosis is a regulated form of necrotic cell death implicated in carcinogenesis and neurodegeneration that is driven by phospholipid peroxidation. Lipid-derived electrophiles (LDEs) generated during this process can covalently modify proteins ("carbonylation") and affect their functions. Here we report the development of a quantitative chemoproteomic method to profile carbonylations in ferroptosis by an aniline-derived probe. Using the method, we established a global portrait of protein carbonylations in ferroptosis with >400 endogenously modified proteins and for the first time, identified >20 residue sites with endogenous LDE modifications in ferroptotic cells. Specifically, we discovered and validated a novel cysteine site of modification on voltage-dependent anion-selective channel protein 2 (VDAC2) that might play an important role in sensitizing LDE signals and mediating ferroptosis. Our results will contribute to the understanding of ferroptotic signaling and pathogenesis and provide potential biomarkers for ferroptosis detection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Marcus Conrad
- Institute of Developmental Genetics , Helmholtz Zentrum Munchen , Munchen , Germany
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19
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Gao D, Podrez EA. Characterization of covalent modifications of HDL apoproteins by endogenous oxidized phospholipids. Free Radic Biol Med 2018; 115:57-67. [PMID: 29155052 PMCID: PMC5767518 DOI: 10.1016/j.freeradbiomed.2017.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/11/2017] [Accepted: 11/14/2017] [Indexed: 12/31/2022]
Abstract
High density lipoprotein (HDL) is cardioprotective, unless it is pathologically modified under oxidative stress. Covalent modifications of lipid-free apoA-I, the most abundant apoprotein in HDL, compromise its atheroprotective functions. HDL is enriched in oxidized phospholipids (oxPL) in vivo in oxidative stress. Furthermore, oxidized phospholipids can covalently modify HDL apoproteins. We have now carried out a systematic analysis of modifications of HDL apoproteins by endogenous oxPL. Human HDL or plasma were oxidized using a physiologically relevant MPO-H2O2-NO2- system or AIPH, or were exposed to synthetic oxPL. Protein adduction by oxPL was assessed using LC-MS/MS and MALDI-TOF MS. The pattern of HDL apoprotein modification by oxPL was independent of the oxidation systems used. ApoA-I and apoA-II were the major modification targets. OxPL with a γ-hydroxy (or oxo)-alkenal were mostly responsible for modifications, and the Michael adduct was the most abundant adduct. Histidines and lysines in helices 5-8 of apoA-I were highly susceptible to oxPL modifications, while lysines in helices 1, 2, 4 and 10 were resistant to modification by oxPL. In plasma exposed to oxidation or synthetic oxPL, oxPL modification was highly selective, and four histidines (H155, H162, H193 and H199) in helices 6-8 of apoA-I were the main modification target. H710 and H3613 in apoB-100 of LDL and K190 of human serum albumin were also modified by oxPL but to a lesser extent. Comparison of oxPL with short chain aldehyde HNE using MALDI-TOF MS demonstrated high selectivity and efficiency of oxPL in the modification of HDL apoproteins. These findings provide a novel insight into a potential mechanism of the loss of atheroprotective function of HDL in conditions of oxidative stress.
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Affiliation(s)
- Detao Gao
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, United States
| | - Eugene A Podrez
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, United States.
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20
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Madea D, Slanina T, Klán P. A 'photorelease, catch and photorelease' strategy for bioconjugation utilizing a p-hydroxyphenacyl group. Chem Commun (Camb) 2018; 52:12901-12904. [PMID: 27738680 DOI: 10.1039/c6cc07496k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A bioorthogonal 'catch and photorelease' strategy, which combines alkyne-azide cycloaddition between p-hydroxyphenacyl azide and alkyne derivatives to form a 1,2,3-triazole adduct and subsequent photochemical release of the triazole moiety via a photo-Favorskii rearrangement, is introduced. The first step can also involve photorelease of a strained alkyne and its Cu-free click reaction with azide.
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Affiliation(s)
- D Madea
- Department of Chemistry and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
| | - T Slanina
- Department of Chemistry and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
| | - P Klán
- Department of Chemistry and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
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21
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Sharifzadeh S, Shirley JD, Carlson EE. Activity-Based Protein Profiling Methods to Study Bacteria: The Power of Small-Molecule Electrophiles. Curr Top Microbiol Immunol 2018; 420:23-48. [PMID: 30232601 DOI: 10.1007/82_2018_135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
ABPP methods have been utilized for the last two decades as a means to investigate complex proteomes in all three domains of life. Extensive use in eukaryotes has provided a more fundamental understanding of the biological processes involved in numerous diseases and has driven drug discovery and treatment campaigns. However, the use of ABPP in prokaryotes has been less common, although it has gained more attention over the last decade. The urgent need for understanding bacteriophysiology and bacterial pathogenicity at a foundational level has never been more apparent, as the rise in antibiotic resistance has resulted in the inadequate and ineffective treatment of infections. This is not only a result of resistance to clinically used antibiotics, but also a lack of new drugs and equally as important, new drug targets. ABPP provides a means for which new, clinically relevant drug targets may be identified through gaining insight into biological processes. In this chapter, we place particular focus on the discussion of ABPP strategies that have been applied to study different classes of bacterial enzymes.
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Affiliation(s)
- Shabnam Sharifzadeh
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA.
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22
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Beavers WN, Rose KL, Galligan JJ, Mitchener MM, Rouzer CA, Tallman KA, Lamberson CR, Wang X, Hill S, Ivanova PT, Alex Brown H, Zhang B, Porter NA, Marnett LJ. Protein Modification by Endogenously Generated Lipid Electrophiles: Mitochondria as the Source and Target. ACS Chem Biol 2017; 12:2062-2069. [PMID: 28613820 PMCID: PMC6174696 DOI: 10.1021/acschembio.7b00480] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Determining the impact of lipid electrophile-mediated protein damage that occurs during oxidative stress requires a comprehensive analysis of electrophile targets adducted under pathophysiological conditions. Incorporation of ω-alkynyl linoleic acid into the phospholipids of macrophages prior to activation by Kdo2-lipid A, followed by protein extraction, click chemistry, and streptavidin affinity capture, enabled a systems-level survey of proteins adducted by lipid electrophiles generated endogenously during the inflammatory response. Results revealed a dramatic enrichment for membrane and mitochondrial proteins as targets for adduction. A marked decrease in adduction in the presence of MitoTEMPO demonstrated a primary role for mitochondrial superoxide in electrophile generation and indicated an important role for mitochondria as both a source and target of lipid electrophiles, a finding that has not been revealed by prior studies using exogenously provided electrophiles.
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Affiliation(s)
- William N. Beavers
- Departments of Chemistry, AB. Hancock Memorial Laboratory for Cancer Research, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Kristie L. Rose
- Departments of Biochemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Departments of Vanderbilt Mass Spectrometry Research Center, Vanderbilt Institute for Chemical Biology, Vanderbilt Center in Molecular Toxicology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - James J. Galligan
- Departments of Biochemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Michelle M. Mitchener
- Departments of Chemistry, AB. Hancock Memorial Laboratory for Cancer Research, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Carol A. Rouzer
- Departments of Biochemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Keri A. Tallman
- Departments of Chemistry, AB. Hancock Memorial Laboratory for Cancer Research, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Connor R. Lamberson
- Departments of Chemistry, AB. Hancock Memorial Laboratory for Cancer Research, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Xiaojing Wang
- Departments of Biomedical Informatics, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Salisha Hill
- Departments of Vanderbilt Mass Spectrometry Research Center, Vanderbilt Institute for Chemical Biology, Vanderbilt Center in Molecular Toxicology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Pavlina T. Ivanova
- Departments of Pharmacology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - H. Alex Brown
- Departments of Biochemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Departments of Pharmacology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Bing Zhang
- Departments of Biomedical Informatics, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Ned A. Porter
- Departments of Chemistry, AB. Hancock Memorial Laboratory for Cancer Research, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Lawrence J. Marnett
- Departments of Chemistry, AB. Hancock Memorial Laboratory for Cancer Research, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Departments of Biochemistry, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
- Departments of Pharmacology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, United States
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23
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Chemoproteomic profiling of targets of lipid-derived electrophiles by bioorthogonal aminooxy probe. Redox Biol 2017; 12:712-718. [PMID: 28411555 PMCID: PMC5390668 DOI: 10.1016/j.redox.2017.04.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 04/01/2017] [Indexed: 01/28/2023] Open
Abstract
Redox imbalance in cells induces lipid peroxidation and generates a class of highly reactive metabolites known as lipid-derived electrophiles (LDEs) that can modify proteins and affects their functions. Identifying targets of LDEs is critical to understand how such modifications are functionally implicated in oxidative-stress associated diseases. Here we report a quantitative chemoproteomic method to globally profile protein targets and sites modified by LDEs. In this strategy, we designed and synthesized an alkyne-functionalized aminooxy probe to react with LDE-modified proteins for imaging and proteomic profiling. Using this probe, we successfully quantified >4000 proteins modified by 4-hydroxy-2-nonenal (HNE) of high confidence in mammalian cell lysate and combined with a tandem-orthogonal proteolysis activity-based protein profiling (TOP-ABPP) strategy, we identified ~400 residue sites targeted by HNE including reactive cysteines in peroxiredoxins, an important family of enzymes with anti-oxidant roles. Our method expands the toolbox to quantitatively profile protein targets of endogenous electrophiles and the enlarged inventory of LDE-modified proteins and sites will contribute to functional elucidation of cellular pathways affected by oxidative stress.
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24
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Tallman KA, Kim HYH, Korade Z, Genaro-Mattos TC, Wages PA, Liu W, Porter NA. Probes for protein adduction in cholesterol biosynthesis disorders: Alkynyl lanosterol as a viable sterol precursor. Redox Biol 2017; 12:182-190. [PMID: 28258022 PMCID: PMC5333532 DOI: 10.1016/j.redox.2017.02.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Indexed: 01/13/2023] Open
Abstract
The formation of lipid electrophile-protein adducts is associated with many disorders that involve perturbations of cellular redox status. The identities of adducted proteins and the effects of adduction on protein function are mostly unknown and an increased understanding of these factors may help to define the pathogenesis of various human disorders involving oxidative stress. 7-Dehydrocholesterol (7-DHC), the immediate biosynthetic precursor to cholesterol, is highly oxidizable and gives electrophilic oxysterols that adduct proteins readily, a sequence of events proposed to occur in Smith-Lemli-Opitz syndrome (SLOS), a human disorder resulting from an error in cholesterol biosynthesis. Alkynyl lanosterol (a-Lan) was synthesized and studied in Neuro2a cells, Dhcr7-deficient Neuro2a cells and human fibroblasts. When incubated in control Neuro2a cells and control human fibroblasts, a-Lan completed the sequence of steps involved in cholesterol biosynthesis and alkynyl-cholesterol (a-Chol) was the major product formed. In Dhcr7-deficient Neuro2a cells or fibroblasts from SLOS patients, the biosynthetic transformation was interrupted at the penultimate step and alkynyl-7-DHC (a-7-DHC) was the major product formed. When a-Lan was incubated in Dhcr7-deficient Neuro2a cells and the alkynyl tag was used to ligate a biotin group to alkyne-containing products, protein-sterol adducts were isolated and identified. In parallel experiments with a-Lan and a-7-DHC in Dhcr7-deficient Neuro2a cells, a-7-DHC was found to adduct to a larger set of proteins (799) than a-Lan (457) with most of the a-Lan protein adducts (423) being common to the larger a-7-DHC set. Of the 423 proteins found common to both experiments, those formed from a-7-DHC were more highly enriched compared to a DMSO control than were those derived from a-Lan. The 423 common proteins were ranked according to the enrichment determined for each protein in the a-Lan and a-7-DHC experiments and there was a very strong correlation of protein ranks for the adducts formed in the parallel experiments.
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Affiliation(s)
- Keri A Tallman
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Hye-Young H Kim
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Zeljka Korade
- Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN 37235, United States; Department of Psychiatry, Vanderbilt University, Nashville, TN 37235, United States
| | - Thiago C Genaro-Mattos
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Phillip A Wages
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Wei Liu
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States
| | - Ned A Porter
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, United States; Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN 37235, United States.
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25
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Yuan W, Zhang Y, Xiong Y, Tao T, Wang Y, Yao J, Zhang L, Yan G, Bao H, Lu H. Highly Selective and Large Scale Mass Spectrometric Analysis of 4-Hydroxynonenal Modification via Fluorous Derivatization and Fluorous Solid-Phase Extraction. Anal Chem 2017; 89:3093-3100. [DOI: 10.1021/acs.analchem.6b04850] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Wenjuan Yuan
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Ying Zhang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Yun Xiong
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Tao Tao
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Yi Wang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Jun Yao
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Lei Zhang
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Guoquan Yan
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Huimin Bao
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Haojie Lu
- Shanghai
Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China
- Department
of Chemistry, Fudan University, Shanghai 200433, P. R. China
- Key
Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai 200032, P. R. China
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26
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Abstract
The discovery of the protein targets of small molecule probes is a crucial aspect of activity-based protein profiling and chemical biology. Mass spectrometry is the primary method for target identification, and in the last decade, cleavable linkers have become a popular strategy to facilitate protein enrichment and identification. In this chapter, we provide an overview of cleavable linkers used in chemical proteomics approaches, discuss their different chemistries, and describe how they aid in protein identification.
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Affiliation(s)
- Yinliang Yang
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Marko Fonović
- Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia
| | - Steven H L Verhelst
- Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestr. 49 box 802, 3000 Leuven, Belgium, 3000, Leuven, Belgium.
- Leibniz Institute for AnalyticalSciences ISAS, Otto-Hahn-Str. 6b, 44227, Dortmund, Germany.
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27
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Degani G, Altomare AA, Colzani M, Martino C, Mazzolari A, Fritz G, Vistoli G, Popolo L, Aldini G. A capture method based on the VC1 domain reveals new binding properties of the human receptor for advanced glycation end products (RAGE). Redox Biol 2016; 11:275-285. [PMID: 28013188 PMCID: PMC5198869 DOI: 10.1016/j.redox.2016.12.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 12/16/2016] [Indexed: 12/23/2022] Open
Abstract
The Advanced Glycation and Lipoxidation End products (AGEs and ALEs) are a heterogeneous class of compounds derived from the non-enzymatic glycation or protein adduction by lipoxidation break-down products. The receptor for AGEs (RAGE) is involved in the progression of chronic diseases based on persistent inflammatory state and oxidative stress. RAGE is a pattern recognition receptor (PRR) and the inhibition of the interaction with its ligands or of the ligand accumulation have a potential therapeutic effect. The N-terminal domain of RAGE, the V domain, is the major site of AGEs binding and is stabilized by the adjacent C1 domain. In this study, we set up an affinity assay relying on the extremely specific biological interaction AGEs ligands have for the VC1 domain. A glycosylated form of VC1, produced in the yeast Pichia pastoris, was attached to magnetic beads and used as insoluble affinity matrix (VC1-resin). The VC1 interaction assay was employed to isolate specific VC1 binding partners from in vitro generated AGE-albumins and modifications were identified/localized by mass spectrometry analysis. Interestingly, this method also led to the isolation of ALEs produced by malondialdehyde treatment of albumins. Computational studies provided a rational-based interpretation of the contacts established by specific modified residues and amino acids of the V domain. The validation of VC1-resin in capturing AGE-albumins from complex biological mixtures such as plasma and milk, may lead to the identification of new RAGE ligands potentially involved in pro-inflammatory and pro-fibrotic responses, independently of their structures or physical properties, and without the use of any covalent derivatization process. In addition, the method can be applied to the identification of antagonists of RAGE-ligand interaction. A new VC1 interaction affinity assay was validated using model AGE-albumins. In vitro modifications of the interacting partners were identified/localized by MS. The VC1-pull down assays captures AGE-albumins in simulated complex mixtures ALEs produced by malondialdehyde treatment were mapped in VC1-interacting albumins. The molecular interactions of MDA-induced adduct-VC1 complexes were rationalized.
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Affiliation(s)
- Genny Degani
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milano, Italy; Department of Pharmaceutical Sciences, Via Mangiagalli 25, 20133 Milano, Italy.
| | | | - Mara Colzani
- Department of Pharmaceutical Sciences, Via Mangiagalli 25, 20133 Milano, Italy.
| | - Caterina Martino
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milano, Italy.
| | - Angelica Mazzolari
- Department of Pharmaceutical Sciences, Via Mangiagalli 25, 20133 Milano, Italy.
| | - Guenter Fritz
- University of Freiburg, Institute of Neuropathology Neurozentrum, Breisacher Straße 64, 79106 Freiburg, Germany.
| | - Giulio Vistoli
- Department of Pharmaceutical Sciences, Via Mangiagalli 25, 20133 Milano, Italy.
| | - Laura Popolo
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milano, Italy.
| | - Giancarlo Aldini
- Department of Pharmaceutical Sciences, Via Mangiagalli 25, 20133 Milano, Italy.
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Gebert J, Schnölzer M, Warnken U, Kopitz J. Combining Click Chemistry-Based Proteomics With Dox-Inducible Gene Expression. Methods Enzymol 2016; 585:295-327. [PMID: 28109436 DOI: 10.1016/bs.mie.2016.09.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Inactivating mutations in single genes can trigger, prevent, promote, or alleviate diseases. Identifying such disease-related genes is a main pillar of medical research. Since proteins play a crucial role in mediating these effects, their impact on the diseased cells' proteome including posttranslational modifications has to be elucidated for a detailed understanding of the role of these genes in the disease process. In complex disorders, like cancer, several genes contribute to the disease process, thereby hampering the assignment of a proteomic change to the corresponding causative gene. To enable comprehensive screening for the impact of inactivation of a gene, e.g., loss of a tumor suppressor in cancer, on the cellular proteome, we present a strategy based on combination of three technologies that is recombinase-mediated cassette exchange, click chemistry, and mass spectrometry. The methodology is exemplified by the analysis of the proteomic changes induced by the loss of a tumor suppressor gene in colorectal cancer cells. To demonstrate the applicability to screen for posttranslational modification changes, we also describe the analysis of protein glycosylation changes caused by the tumor suppressor inactivation. In principle, this strategy can be applied to analyze the effects of any gene of interest on protein expression as well as posttranslational modification by glycosylation. Moreover adaptation of the strategy to an appropriate cell culture model has the potential for application on a broad range of diseases where the disease-promoting mutations have been identified.
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Affiliation(s)
- J Gebert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - U Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - J Kopitz
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Parvez S, Long MJC, Lin HY, Zhao Y, Haegele JA, Pham VN, Lee DK, Aye Y. T-REX on-demand redox targeting in live cells. Nat Protoc 2016; 11:2328-2356. [PMID: 27809314 PMCID: PMC5260244 DOI: 10.1038/nprot.2016.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This protocol describes targetable reactive electrophiles and oxidants (T-REX)-a live-cell-based tool designed to (i) interrogate the consequences of specific and time-resolved redox events, and (ii) screen for bona fide redox-sensor targets. A small-molecule toolset comprising photocaged precursors to specific reactive redox signals is constructed such that these inert precursors specifically and irreversibly tag any HaloTag-fused protein of interest (POI) in mammalian and Escherichia coli cells. Syntheses of the alkyne-functionalized endogenous reactive signal 4-hydroxynonenal (HNE(alkyne)) and the HaloTag-targetable photocaged precursor to HNE(alkyne) (also known as Ht-PreHNE or HtPHA) are described. Low-energy light prompts photo-uncaging (t1/2 <1-2 min) and target-specific modification. The targeted modification of the POI enables precisely timed and spatially controlled redox events with no off-target modification. Two independent pathways are described, along with a simple setup to functionally validate known targets or discover novel sensors. T-REX sidesteps mixed responses caused by uncontrolled whole-cell swamping with reactive signals. Modification and downstream response can be analyzed by in-gel fluorescence, proteomics, qRT-PCR, immunofluorescence, fluorescence resonance energy transfer (FRET)-based and dual-luciferase reporters, or flow cytometry assays. T-REX targeting takes 4 h from initial probe treatment. Analysis of targeted redox responses takes an additional 4-24 h, depending on the nature of the pathway and the type of readouts used.
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Affiliation(s)
- Saba Parvez
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Marcus J C Long
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Hong-Yu Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Yi Zhao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Joseph A Haegele
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Vanha N Pham
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Dustin K Lee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Yimon Aye
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, New York, USA
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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]
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Koen YM, Liu K, Shinogle H, Williams TD, Hanzlik RP. Comparative Toxicity and Metabolism of N-Acyl Homologues of Acetaminophen and Its Isomer 3'-Hydroxyacetanilide. Chem Res Toxicol 2016; 29:1857-1864. [PMID: 27680534 DOI: 10.1021/acs.chemrestox.6b00270] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The hepatotoxicity of acetaminophen (APAP) is generally attributed to the formation of a reactive quinoneimine metabolite (NAPQI) that depletes glutathione and covalently binds to hepatocellular proteins. To explore the importance of the N-acyl group in APAP metabolism and toxicity, we synthesized 12 acyl side chain homologues of acetaminophen (APAP) and its 3'-regioisomer (AMAP), including the respective N-(4-pentynoyl) analogues PYPAP and PYMAP. Rat hepatocytes converted APAP, AMAP, PYPAP, and PYMAP extensively to O-glucuronide and O-sulfate conjugates in varying proportions, whereas glutathione or cysteine conjugates were observed only for APAP and PYPAP. PYPAP and PYMAP also underwent N-deacylation followed by O-sulfation and/or N-acetylation to a modest extent. The overall rates of metabolism in hepatocytes varied approximately 2-fold in the order APAP < AMAP ≈ PYPAP < PYMAP. Rat liver microsomes supplemented with NADPH and GSH converted APAP and PYPAP to their respective glutathione conjugates (formed via a reactive quinoneimine intermediate). With PYPAP only, a hydroxylated GSH conjugate was also observed. Thus, differences in biotransformation among these analogues were modest and mostly quantitative in nature. Cytotoxicity was evaluated in cultured hepatocytes by monitoring cell death using time-lapse photomicrography coupled with Hoechst 33342 and CellTox Green dyes to facilitate counting live cells vs dead cells, respectively. Progress curves for cell death and the areas under those curves showed that toxicity was markedly dependent on compound, concentration, and time. AMAP was essentially equipotent with APAP. Homologating the acyl side chain from C-2 to C-5 led to progressive increases in toxicity up to 80-fold in the para series. In conclusion, whereas N- or ring-substitution on APAP decrease metabolism and toxicity, homologating the N-acyl side chain increases metabolism about 2-fold, preserves the chemical reactivity of quinoneimine metabolites, and increases toxicity by up to 80-fold.
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Affiliation(s)
- Yakov M Koen
- Department of Medicinal Chemistry, ‡Microscopy and Analytical Imaging Laboratory, §Mass Spectrometry Laboratory, University of Kansas , Lawrence, Kansas 66045, United States
| | - Ke Liu
- Department of Medicinal Chemistry, ‡Microscopy and Analytical Imaging Laboratory, §Mass Spectrometry Laboratory, University of Kansas , Lawrence, Kansas 66045, United States
| | - Heather Shinogle
- Department of Medicinal Chemistry, ‡Microscopy and Analytical Imaging Laboratory, §Mass Spectrometry Laboratory, University of Kansas , Lawrence, Kansas 66045, United States
| | - Todd D Williams
- Department of Medicinal Chemistry, ‡Microscopy and Analytical Imaging Laboratory, §Mass Spectrometry Laboratory, University of Kansas , Lawrence, Kansas 66045, United States
| | - Robert P Hanzlik
- Department of Medicinal Chemistry, ‡Microscopy and Analytical Imaging Laboratory, §Mass Spectrometry Laboratory, University of Kansas , Lawrence, Kansas 66045, United States
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Speen AM, Kim HYH, Bauer RN, Meyer M, Gowdy KM, Fessler MB, Duncan KE, Liu W, Porter NA, Jaspers I. Ozone-derived Oxysterols Affect Liver X Receptor (LXR) Signaling: A POTENTIAL ROLE FOR LIPID-PROTEIN ADDUCTS. J Biol Chem 2016; 291:25192-25206. [PMID: 27703007 DOI: 10.1074/jbc.m116.732362] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 09/14/2016] [Indexed: 12/25/2022] Open
Abstract
When inhaled, ozone (O3) interacts with cholesterols of airway epithelial cell membranes or the lung-lining fluid, generating chemically reactive oxysterols. The mechanism by which O3-derived oxysterols affect molecular function is unknown. Our data show that in vitro exposure of human bronchial epithelial cells to O3 results in the formation of oxysterols, epoxycholesterol-α and -β and secosterol A and B (Seco A and Seco B), in cell lysates and apical washes. Similarly, bronchoalveolar lavage fluid obtained from human volunteers exposed to O3 contained elevated levels of these oxysterol species. As expected, O3-derived oxysterols have a pro-inflammatory effect and increase NF-κB activity. Interestingly, expression of the cholesterol efflux pump ATP-binding cassette transporter 1 (ABCA1), which is regulated by activation of the liver X receptor (LXR), was suppressed in epithelial cells exposed to O3 Additionally, exposure of LXR knock-out mice to O3 enhanced pro-inflammatory cytokine production in the lung, suggesting LXR inhibits O3-induced inflammation. Using alkynyl surrogates of O3-derived oxysterols, our data demonstrate adduction of LXR with Seco A. Similarly, supplementation of epithelial cells with alkynyl-tagged cholesterol followed by O3 exposure causes observable lipid-LXR adduct formation. Experiments using Seco A and the LXR agonist T0901317 (T09) showed reduced expression of ABCA1 as compared with stimulation with T0901317 alone, indicating that Seco A-LXR protein adduct formation inhibits LXR activation by traditional agonists. Overall, these data demonstrate that O3-derived oxysterols have pro-inflammatory functions and form lipid-protein adducts with LXR, thus leading to suppressed cholesterol regulatory gene expression and providing a biochemical mechanism mediating O3-derived formation of oxidized lipids in the airways and subsequent adverse health effects.
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Affiliation(s)
- Adam M Speen
- From the Curriculum in Toxicology, Departments of Pediatrics and Microbiology and Immunology, Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Hye-Young H Kim
- the Department of Chemistry and Center for Molecular Toxicology, Vanderbilt University, Nashville, Tennessee 37235
| | - Rebecca N Bauer
- From the Curriculum in Toxicology, Departments of Pediatrics and Microbiology and Immunology, Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Megan Meyer
- From the Curriculum in Toxicology, Departments of Pediatrics and Microbiology and Immunology, Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Kymberly M Gowdy
- the Department of Pharmacology and Toxicology, Brody School of Medicine, East Carolina University, Greenville, North Carolina 27834, and
| | - Michael B Fessler
- the Immunity, Inflammation, and Disease Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Kelly E Duncan
- From the Curriculum in Toxicology, Departments of Pediatrics and Microbiology and Immunology, Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Wei Liu
- the Department of Chemistry and Center for Molecular Toxicology, Vanderbilt University, Nashville, Tennessee 37235
| | - Ned A Porter
- the Department of Chemistry and Center for Molecular Toxicology, Vanderbilt University, Nashville, Tennessee 37235
| | - Ilona Jaspers
- From the Curriculum in Toxicology, Departments of Pediatrics and Microbiology and Immunology, Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina, Chapel Hill, North Carolina 27599,
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Federspiel JD, Codreanu SG, Goyal S, Albertolle ME, Lowe E, Teague J, Wong H, Guengerich FP, Liebler DC. Specificity of Protein Covalent Modification by the Electrophilic Proteasome Inhibitor Carfilzomib in Human Cells. Mol Cell Proteomics 2016; 15:3233-3242. [PMID: 27503896 DOI: 10.1074/mcp.m116.059709] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Indexed: 12/25/2022] Open
Abstract
Carfilzomib (CFZ) is a second-generation proteasome inhibitor that is Food and Drug Administration and European Commission approved for the treatment of relapsed or refractory multiple myeloma. CFZ is an epoxomicin derivative with an epoxyketone electrophilic warhead that irreversibly adducts the catalytic threonine residue of the β5 subunit of the proteasome. Although CFZ produces a highly potent, sustained inactivation of the proteasome, the electrophilic nature of the drug could potentially produce off-target protein adduction. To address this possibility, we synthesized an alkynyl analog of CFZ and investigated protein adduction by this analog in HepG2 cells. Using click chemistry coupled with streptavidin based IP and shotgun tandem mass spectrometry (MS/MS), we identified two off-target proteins, cytochrome P450 27A1 (CYP27A1) and glutathione S-transferase omega 1 (GSTO1), as targets of the alkynyl CFZ probe. We confirmed the adduction of CYP27A1 and GSTO1 by streptavidin capture and immunoblotting methodology and then site-specifically mapped the adducts with targeted MS/MS methods. Although CFZ adduction of CYP27A1 and GSTO1 in vitro decreased the activities of these enzymes, the small fraction of these proteins modified by CFZ in intact cells should limit the impact of these off-target modifications. The data support the high selectivity of CFZ for covalent modification of its therapeutic targets, despite the presence of a reactive electrophile. The approach we describe offers a generalizable method to evaluate the safety profile of covalent protein-modifying therapeutics.
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Affiliation(s)
- Joel D Federspiel
- From the ‡Department of Biochemistry, Vanderbilt University School of MedicineNashville, Tennessee
| | - Simona G Codreanu
- From the ‡Department of Biochemistry, Vanderbilt University School of MedicineNashville, Tennessee
| | - Sandeep Goyal
- From the ‡Department of Biochemistry, Vanderbilt University School of MedicineNashville, Tennessee
| | - Matthew E Albertolle
- From the ‡Department of Biochemistry, Vanderbilt University School of MedicineNashville, Tennessee
| | - Eric Lowe
- §Onyx Pharmaceuticals, an Amgen subsidiary, San Francisco, California 94080
| | - Juli Teague
- §Onyx Pharmaceuticals, an Amgen subsidiary, San Francisco, California 94080
| | - Hansen Wong
- §Onyx Pharmaceuticals, an Amgen subsidiary, San Francisco, California 94080
| | - F Peter Guengerich
- From the ‡Department of Biochemistry, Vanderbilt University School of MedicineNashville, Tennessee
| | - Daniel C Liebler
- From the ‡Department of Biochemistry, Vanderbilt University School of MedicineNashville, Tennessee;
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Chacko BK, Wall SB, Kramer PA, Ravi S, Mitchell T, Johnson MS, Wilson L, Barnes S, Landar A, Darley-Usmar VM. Pleiotropic effects of 4-hydroxynonenal on oxidative burst and phagocytosis in neutrophils. Redox Biol 2016; 9:57-66. [PMID: 27393890 PMCID: PMC4939321 DOI: 10.1016/j.redox.2016.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 01/09/2023] Open
Abstract
Metabolic control of cellular function is significant in the context of inflammation-induced metabolic dysregulation in immune cells. Generation of reactive oxygen species (ROS) such as hydrogen peroxide and superoxide are one of the critical events that modulate the immune response in neutrophils. When activated, neutrophil NADPH oxidases consume large quantities of oxygen to rapidly generate ROS, a process that is referred to as the oxidative burst. These ROS are required for the efficient removal of phagocytized cellular debris and pathogens. In chronic inflammatory diseases, neutrophils are exposed to increased levels of oxidants and pro-inflammatory cytokines that can further prime oxidative burst responses and generate lipid oxidation products such as 4-hydroxynonenal (4-HNE). In this study we hypothesized that since 4-HNE can target glycolysis then this could modify the oxidative burst. To address this the oxidative burst was determined in freshly isolated healthy subject neutrophils using 13-phorbol myristate acetate (PMA) and the extracellular flux analyzer. Neutrophils pretreated with 4-HNE exhibited a significant decrease in the oxidative burst response and phagocytosis. Mass spectrometric analysis of alkyne-HNE treated neutrophils followed by click chemistry detected modification of a number of cytoskeletal, metabolic, redox and signaling proteins that are critical for the NADPH oxidase mediated oxidative burst. These modifications were confirmed using a candidate immunoblot approach for critical proteins of the active NADPH oxidase enzyme complex (Nox2 gp91phox subunit and Rac1 of the NADPH oxidase) and glyceraldehyde phosphate dehydrogenase, a critical enzyme in the metabolic regulation of oxidative burst. Taken together, these data suggest that 4-HNE-induces a pleiotropic mechanism to inhibit neutrophil function. These mechanisms may contribute to the immune dysregulation associated with chronic pathological conditions where 4-HNE is generated. Phagocytosis and glycolysis are inhibited in neutrophils by 4-hydroxynonenal. Click chemistry with alkyne-HNE identifies over 100 potential protein targets. Rac1, NOX2 and GAPDH are modified by 4-HNE. The 4-HNE-dependent inhibition of neutrophil function is mediated by a pleiotropic mechanism.
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Affiliation(s)
- Balu K Chacko
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, United States; Department of Pathology, University of Alabama at Birmingham, United States
| | - Stephanie B Wall
- Department of Pathology, University of Alabama at Birmingham, United States
| | - Philip A Kramer
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, United States; Department of Pathology, University of Alabama at Birmingham, United States
| | - Saranya Ravi
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, United States; Department of Pathology, University of Alabama at Birmingham, United States
| | - Tanecia Mitchell
- Department of Urology, University of Alabama at Birmingham, United States
| | - Michelle S Johnson
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, United States; Department of Pathology, University of Alabama at Birmingham, United States
| | - Landon Wilson
- Department of Pharmacology and Toxicology, The Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, United States
| | - Stephen Barnes
- Department of Pharmacology and Toxicology, The Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, United States
| | - Aimee Landar
- Department of Pathology, University of Alabama at Birmingham, United States
| | - Victor M Darley-Usmar
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, United States; Department of Pathology, University of Alabama at Birmingham, United States.
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Ballard TE, Dahal UP, Bessire AJ, Schneider RP, Geoghegan KF, Vaz ADN. A tag-free collisionally induced fragmentation approach to detect drug-adducted proteins by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:2175-2183. [PMID: 26467230 DOI: 10.1002/rcm.7375] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 08/10/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE The covalent modification of proteins by toxicants, new chemical entities or drug molecules, either by metabolic activation or the presence of inherently reactive functional groups, is commonly implicated in organ toxicity and idiosyncratic reactions. In efforts to better prosecute protein modifications, we investigated a tag-free technique capable of detecting protein-small molecule adducts based solely on the collision-induced dissociation (CID) of the protein-small molecule complex. Detection of proteins using unique CID small molecule (SM) product ions would mitigate common issues associated with tagging technologies (e.g., altered reactivity/affinity of the protein-SM complex). METHODS A Waters SYNAPT G2 mass spectrometer (MS) was operated in MS(e) mode with appropriate collision energy conditions during the MS(2) acquisition for fragmentation of protein-small molecule adducts to generate characteristic small molecule product ions. RESULTS Ibrutinib, an acrylamide-containing small molecule drug, was shown to form adducts with rat serum albumin in ex vivo experiments and these adducts were detected by relying solely on the CID product ions generated from ibrutinib. Additionally, ibrutinib produced three CID product ions, one of which was a selective protein-ibrutinib fragment ion not produced by the compound alone. CONCLUSIONS Herein we describe a tag-free mass spectral detection technique for protein-small molecule conjugates that relies on the unique product ion fragmentation profile of the small molecule. This technique allows the detection of macromolecular ions containing the adducted small molecule from complex protein matrices through mass range selection for the unique product ions in the CID spectra.
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Affiliation(s)
- T Eric Ballard
- Pharmacokinetics, Dynamics and Metabolism, Pfizer, Inc., Groton, CT, 06340, USA
| | - Upendra P Dahal
- Pharmacokinetics, Dynamics and Metabolism, Pfizer, Inc., Groton, CT, 06340, USA
| | - Andrew J Bessire
- Pharmacokinetics, Dynamics and Metabolism, Pfizer, Inc., Groton, CT, 06340, USA
| | - Richard P Schneider
- Pharmacokinetics, Dynamics and Metabolism, Pfizer, Inc., Groton, CT, 06340, USA
| | | | - Alfin D N Vaz
- Pharmacokinetics, Dynamics and Metabolism, Pfizer, Inc., Groton, CT, 06340, USA
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Chen Y, Qin W, Wang C. Chemoproteomic profiling of protein modifications by lipid-derived electrophiles. Curr Opin Chem Biol 2015; 30:37-45. [PMID: 26625013 DOI: 10.1016/j.cbpa.2015.10.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 01/21/2023]
Abstract
Lipid-derived electrophiles (LDEs) are a group of endogenous reactive metabolites generated as products of lipid peroxidation when cells are under oxidative stress. LDEs are able to covalently modify nucleophilic residues in proteins to alter their structures and activities, either resulting in irreversible functional damage or triggering aberrant signaling pathways. Traditional biochemical methods have revealed individual protein targets modified by LDEs, however, deciphering the toxicity and/or signaling roles of LDEs requires systematic studies of these modifications in a high-throughput fashion. Here we survey recent progress in developing chemical proteomic strategies to globally profile protein-LDE interactions directly from complex proteomes. These powerful chemoproteomic methods have yielded a rich inventory of proteins and residue sites that are sensitive to LDE modification, serving as valuable resources to investigate mechanisms of their cellular toxicity at the molecular level.
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Affiliation(s)
- Ying Chen
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China; Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering and Peking University, Beijing 100871, China
| | - Wei Qin
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China; Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chu Wang
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China; Synthetic and Functional Biomolecules Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering and Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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Abstract
Protein S-sulfenylation is the reversible oxidative modification of cysteine thiol groups to form cysteine S-sulfenic acids. Mapping the specific sites of protein S-sulfenylation onto complex proteomes is crucial to understanding the molecular mechanisms controlling redox signaling and regulation. This protocol describes global, in situ, site-specific analysis of protein S-sulfenylation using sulfenic acid-specific chemical probes and mass spectrometry (MS)-based proteomics. The major steps in this protocol are as follows: (i) optimization of conditions for selective labeling of cysteine S-sulfenic acids in intact cells with the commercially available dimedone-based probe, DYn-2; (ii) tagging the modified cysteines with a functionalized biotin reagent containing a cleavable linker via Cu(I)-catalyzed azide-alkyne cycloaddition reaction; (iii) enrichment of the biotin-tagged tryptic peptides with streptavidin; (iv) liquid chromatography-tandem MS (LC-MS/MS)-based shotgun proteomics; and (v) computational data analysis. We also outline strategies for quantitative analysis of this modification in cells responding to redox perturbations and discuss special issues pertaining to experimental design of thiol redox studies. Our chemoproteomic platform should be broadly applicable to the investigation of other bio-orthogonal chemically engineered post-translational modifications. The entire analysis protocol takes ∼1 week to complete.
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Codreanu SG, Liebler DC. Novel approaches to identify protein adducts produced by lipid peroxidation. Free Radic Res 2015; 49:881-7. [PMID: 25819163 DOI: 10.3109/10715762.2015.1019348] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lipid peroxidation is responsible for the generation of chemically reactive, diffusible lipid-derived electrophiles (LDEs) that covalently modify cellular protein targets. These protein modifications modulate protein activity and macromolecular interactions and induce adaptive and toxic cell signaling. Protein modifications induced by LDEs can be identified and quantified by affinity enrichment and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based techniques. Tagged LDE analog probes with different electrophilic groups can be covalently captured by click chemistry for LC-MS/MS analyses, thereby enabling in-depth studies of proteome damage at the protein and peptide sequence levels. Conversely, click-reactive, thiol-directed probes can be used to evaluate thiol damage caused by LDE by difference. These analytical approaches permit systematic study of the dynamics of protein damage caused by LDE and mechanisms by which oxidative stress contribute to toxicity and diseases.
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Affiliation(s)
- S G Codreanu
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, TN , USA
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Boronat S, García-Santamarina S, Hidalgo E. Gel-free proteomic methodologies to study reversible cysteine oxidation and irreversible protein carbonyl formation. Free Radic Res 2015; 49:494-510. [PMID: 25782062 DOI: 10.3109/10715762.2015.1009053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Oxidative modifications in proteins have been traditionally considered as hallmarks of damage by oxidative stress and aging. However, oxidants can generate a huge variety of reversible and irreversible modifications in amino acid side chains as well as in the protein backbones, and these post-translational modifications can contribute to the activation of signal transduction pathways, and also mediate the toxicity of oxidants. Among the reversible modifications, the most relevant ones are those arising from cysteine oxidation. Thus, formation of sulfenic acid or disulfide bonds is known to occur in many enzymes as part of their catalytic cycles, and it also participates in the activation of signaling cascades. Furthermore, these reversible modifications have been usually attributed with a protective role, since they may prevent the formation of irreversible damage by scavenging reactive oxygen species. Among irreversible modifications, protein carbonyl formation has been linked to damage and death, since it cannot be repaired and can lead to protein loss-of-function and to the formation of protein aggregates. This review is aimed at researchers interested on the biological consequences of oxidative stress, both at the level of signaling and toxicity. Here we are providing a concise overview on current mass-spectrometry-based methodologies to detect reversible cysteine oxidation and irreversible protein carbonyl formation in proteomes. We do not pretend to impose any of the different methodologies, but rather to provide an objective catwalk on published gel-free approaches to detect those two types of modifications, from a biologist's point of view.
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Affiliation(s)
- S Boronat
- Departament de Ciències Experimentals i de la Salut, Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra , C/Dr. Aiguader 88, E-08003 Barcelona , Spain
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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.
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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.
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Yang J, Tallman KA, Porter NA, Liebler DC. Quantitative chemoproteomics for site-specific analysis of protein alkylation by 4-hydroxy-2-nonenal in cells. Anal Chem 2015; 87:2535-41. [PMID: 25654326 PMCID: PMC4350606 DOI: 10.1021/ac504685y] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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Protein alkylation by 4-hydroxy-2-nonenal
(HNE), an endogenous
lipid derived electrophile, contributes to stress signaling and cellular
toxicity. Although previous work has identified protein targets for
HNE alkylation, the sequence specificity of alkylation and dynamics
in a cellular context remain largely unexplored. We developed a new
quantitative chemoproteomic platform, which uses isotopically tagged,
photocleavable azido-biotin reagents to selectively capture and quantify
the cellular targets labeled by the alkynyl analogue of HNE (aHNE).
Our analyses site-specifically identified and quantified 398 aHNE
protein alkylation events (386 cysteine sites and 12 histidine sites)
in intact cells. This data set expands by at least an order of magnitude
the number of such modification sites previously reported. Although
adducts formed by Michael addition are thought to be largely irreversible,
we found that most aHNE modifications are lost rapidly in
situ. Moreover, aHNE adduct turnover occurs only in intact
cells and loss rates are site-selective. This quantitative chemoproteomics
platform provides a versatile general approach to map bioorthogonal-chemically
engineered post-translational modifications and their cellular dynamics
in a site-specific and unbiased manner.
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Affiliation(s)
- Jing Yang
- Department of Biochemistry, Vanderbilt University School of Medicine , 465 21st Avenue South, U1213 MRB III, Nashville, Tennessee 37232, United States
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42
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Reimann O, Smet‐Nocca C, Hackenberger CPR. Spurlose Aufreinigung und Desulfurierung von Ligationsprodukten des Tau‐Proteins. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408674] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Oliver Reimann
- Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Straße 10, 13125 Berlin (Deutschland)
- Humboldt Universität zu Berlin, Department Chemie, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland)
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustraße 3, 14195 Berlin (Deutschland)
| | - Caroline Smet‐Nocca
- UMR CNRS 8576, Lille 1 Science and Technology University, 59655 Villeneuve d'Ascq Cedex (Frankreich)
| | - Christian P. R. Hackenberger
- Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Straße 10, 13125 Berlin (Deutschland)
- Humboldt Universität zu Berlin, Department Chemie, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland)
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustraße 3, 14195 Berlin (Deutschland)
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43
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Reimann O, Smet‐Nocca C, Hackenberger CPR. Traceless Purification and Desulfurization of Tau Protein Ligation Products. Angew Chem Int Ed Engl 2014; 54:306-10. [DOI: 10.1002/anie.201408674] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Oliver Reimann
- Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Strasse 10, 13125 Berlin (Germany)
- Humboldt Universität zu Berlin, Department Chemie, Brook‐Taylor‐Strasse 2, 12489 Berlin (Germany)
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, 14195 Berlin (Germany)
| | - Caroline Smet‐Nocca
- UMR CNRS 8576—Lille 1 Science and Technology University, 59655 Villeneuve d'Ascq Cedex (France)
| | - Christian P. R. Hackenberger
- Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Strasse 10, 13125 Berlin (Germany)
- Humboldt Universität zu Berlin, Department Chemie, Brook‐Taylor‐Strasse 2, 12489 Berlin (Germany)
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, 14195 Berlin (Germany)
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44
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Couvertier SM, Zhou Y, Weerapana E. Chemical-proteomic strategies to investigate cysteine posttranslational modifications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2315-30. [PMID: 25291386 DOI: 10.1016/j.bbapap.2014.09.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 01/10/2023]
Abstract
The unique combination of nucleophilicity and redox-sensitivity that is characteristic of cysteine residues results in a variety of posttranslational modifications (PTMs), including oxidation, nitrosation, glutathionylation, prenylation, palmitoylation and Michael adducts with lipid-derived electrophiles (LDEs). These PTMs regulate the activity of diverse protein families by modulating the reactivity of cysteine nucleophiles within active sites of enzymes, and governing protein localization between soluble and membrane-bound forms. Many of these modifications are highly labile, sensitive to small changes in the environment, and dynamic, rendering it difficult to detect these modified species within a complex proteome. Several chemical-proteomic platforms have evolved to study these modifications and enable a better understanding of the diversity of proteins that are regulated by cysteine PTMs. These platforms include: (1) chemical probes to selectively tag PTM-modified cysteines; (2) differential labeling platforms that selectively reveal and tag PTM-modified cysteines; (3) lipid, isoprene and LDE derivatives containing bioorthogonal handles; and (4) cysteine-reactivity profiling to identify PTM-induced decreases in cysteine nucleophilicity. Here, we will provide an overview of these existing chemical-proteomic strategies and their effectiveness at identifying PTM-modified cysteine residues within native biological systems.
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Affiliation(s)
| | - Yani Zhou
- Boston College, Chestnut Hill, MA 02467, USA
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45
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Yang J, Gupta V, Carroll KS, Liebler DC. Site-specific mapping and quantification of protein S-sulphenylation in cells. Nat Commun 2014; 5:4776. [PMID: 25175731 PMCID: PMC4167403 DOI: 10.1038/ncomms5776] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/22/2014] [Indexed: 02/06/2023] Open
Abstract
Cysteine S-sulphenylation provides redox regulation of protein functions, but the global cellular impact of this transient post-translational modification remains unexplored. We describe a chemoproteomic workflow to map and quantify over 1,000 S-sulphenylation sites on more than 700 proteins in intact cells. Quantitative analysis of human cells stimulated with hydrogen peroxide or epidermal growth factor measured hundreds of site selective redox changes. Different cysteines in the same proteins displayed dramatic differences in susceptibility to S-sulphenylation. Newly discovered S-sulphenylations provided mechanistic support for proposed cysteine redox reactions and suggested novel redox mechanisms, including S-sulphenyl-mediated redox regulation of the transcription factor HIF1A by SIRT6. S-sulphenylation is favored at solvent-exposed protein surfaces and is associated with sequence motifs that are distinct from those for other thiol modifications. S-sulphenylations affect regulators of phosphorylation, acetylation and ubiquitylation, which suggest regulatory crosstalk between redox control and signalling pathways.
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Affiliation(s)
- Jing Yang
- 1] Departmemt of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6350, USA [2] Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6350, USA
| | - 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
| | - Daniel C Liebler
- 1] Departmemt of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6350, USA [2] Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6350, USA
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46
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Beavers W, Serwa R, Shimozu Y, Tallman KA, Vaught M, Dalvie ED, Marnett LJ, Porter NA. ω-Alkynyl lipid surrogates for polyunsaturated fatty acids: free radical and enzymatic oxidations. J Am Chem Soc 2014; 136:11529-39. [PMID: 25034362 PMCID: PMC4140476 DOI: 10.1021/ja506038v] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Indexed: 12/22/2022]
Abstract
Lipid and lipid metabolite profiling are important parameters in understanding the pathogenesis of many diseases. Alkynylated polyunsaturated fatty acids are potentially useful probes for tracking the fate of fatty acid metabolites. The nonenzymatic and enzymatic oxidations of ω-alkynyl linoleic acid and ω-alkynyl arachidonic acid were compared to that of linoleic and arachidonic acid. There was no detectable difference in the primary products of nonenzymatic oxidation, which comprised cis,trans-hydroxy fatty acids. Similar hydroxy fatty acid products were formed when ω-alkynyl linoleic acid and ω-alkynyl arachidonic acid were reacted with lipoxygenase enzymes that introduce oxygen at different positions in the carbon chains. The rates of oxidation of ω-alkynylated fatty acids were reduced compared to those of the natural fatty acids. Cyclooxygenase-1 and -2 did not oxidize alkynyl linoleic but efficiently oxidized alkynyl arachidonic acid. The products were identified as alkynyl 11-hydroxy-eicosatetraenoic acid, alkynyl 11-hydroxy-8,9-epoxy-eicosatrienoic acid, and alkynyl prostaglandins. This deviation from the metabolic profile of arachidonic acid may limit the utility of alkynyl arachidonic acid in the tracking of cyclooxygenase-based lipid oxidation. The formation of alkynyl 11-hydroxy-8,9-epoxy-eicosatrienoic acid compared to alkynyl prostaglandins suggests that the ω-alkyne group causes a conformational change in the fatty acid bound to the enzyme, which reduces the efficiency of cyclization of dioxalanyl intermediates to endoperoxide intermediates. Overall, ω-alkynyl linoleic acid and ω-alkynyl arachidonic acid appear to be metabolically competent surrogates for tracking the fate of polyunsaturated fatty acids when looking at models involving autoxidation and oxidation by lipoxygenases.
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Affiliation(s)
- William
N. Beavers
- A.B. Hancock Memorial Laboratory for
Cancer Research, Departments of Chemistry, Biochemistry, and Pharmacology, Vanderbilt Institute for Chemical Biology, Vanderbilt
Center in Molecular Toxicology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Remigiusz Serwa
- A.B. Hancock Memorial Laboratory for
Cancer Research, Departments of Chemistry, Biochemistry, and Pharmacology, Vanderbilt Institute for Chemical Biology, Vanderbilt
Center in Molecular Toxicology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yuki Shimozu
- A.B. Hancock Memorial Laboratory for
Cancer Research, Departments of Chemistry, Biochemistry, and Pharmacology, Vanderbilt Institute for Chemical Biology, Vanderbilt
Center in Molecular Toxicology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Keri A. Tallman
- A.B. Hancock Memorial Laboratory for
Cancer Research, Departments of Chemistry, Biochemistry, and Pharmacology, Vanderbilt Institute for Chemical Biology, Vanderbilt
Center in Molecular Toxicology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Melissa Vaught
- A.B. Hancock Memorial Laboratory for
Cancer Research, Departments of Chemistry, Biochemistry, and Pharmacology, Vanderbilt Institute for Chemical Biology, Vanderbilt
Center in Molecular Toxicology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Esha D. Dalvie
- A.B. Hancock Memorial Laboratory for
Cancer Research, Departments of Chemistry, Biochemistry, and Pharmacology, Vanderbilt Institute for Chemical Biology, Vanderbilt
Center in Molecular Toxicology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Lawrence J. Marnett
- A.B. Hancock Memorial Laboratory for
Cancer Research, Departments of Chemistry, Biochemistry, and Pharmacology, Vanderbilt Institute for Chemical Biology, Vanderbilt
Center in Molecular Toxicology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ned A. Porter
- A.B. Hancock Memorial Laboratory for
Cancer Research, Departments of Chemistry, Biochemistry, and Pharmacology, Vanderbilt Institute for Chemical Biology, Vanderbilt
Center in Molecular Toxicology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
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47
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Butterfield DA, Gu L, Di Domenico F, Robinson RAS. Mass spectrometry and redox proteomics: applications in disease. MASS SPECTROMETRY REVIEWS 2014; 33:277-301. [PMID: 24930952 DOI: 10.1002/mas.21374] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/07/2013] [Accepted: 02/07/2013] [Indexed: 06/03/2023]
Abstract
Proteomics techniques are continuously being developed to further understanding of biology and disease. Many of the pathways that are relevant to disease mechanisms rely on the identification of post-translational modifications (PTMs) such as phosphorylation, acetylation, and glycosylation. Much attention has also been focused on oxidative PTMs which include protein carbonyls, protein nitration, and the incorporation of fatty acids and advanced glycation products to amino acid side chains, amongst others. The introduction of these PTMs in the cell can occur due to the attack of reactive oxygen and nitrogen species (ROS and RNS, respectively) on proteins. ROS and RNS can be present as a result of normal metabolic processes as well as external factors such as UV radiation, disease, and environmental toxins. The imbalance of ROS and RNS with antioxidant cellular defenses leads to a state of oxidative stress, which has been implicated in many diseases. Redox proteomics techniques have been used to characterize oxidative PTMs that result as a part of normal cell signaling processes as well as oxidative stress conditions. This review highlights many of the redox proteomics techniques which are currently available for several oxidative PTMs and brings to the reader's attention the application of redox proteomics for understanding disease pathogenesis in neurodegenerative disorders and others such as cancer, kidney, and heart diseases.
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Affiliation(s)
- D Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences, Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, 40506
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48
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Miyazaki A, Asanuma M, Dodo K, Egami H, Sodeoka M. A "catch-and-release" protocol for alkyne-tagged molecules based on a resin-bound cobalt complex for peptide enrichment in aqueous media. Chemistry 2014; 20:8116-28. [PMID: 24788842 DOI: 10.1002/chem.201400056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Indexed: 01/09/2023]
Abstract
The development of new and mild protocols for the specific enrichment of biomolecules is of significant interest from the perspective of chemical biology. A cobalt-phosphine complex immobilised on a solid-phase resin has been found to selectively bind to a propargyl carbamate tag, that is, "catch", under dilute aqueous conditions (pH 7) at 4 °C. Upon acidic treatment of the resulting resin-bound alkyne-cobalt complex, the Nicholas reaction was induced to "release" the alkyne-tagged molecule from the resin as a free amine. Model studies revealed that selective enrichment of the alkyne-tagged molecule could be achieved with high efficiency at 4 °C. The proof-of-concept was applied to an alkyne-tagged amino acid and dipeptide. Studies using an alkyne-tagged dipeptide proved that this protocol is compatible with various amino acids bearing a range of functionalities in the side-chain. In addition, selective enrichment and detection of an amine derived from the "catch and release" of an alkyne-tagged dipeptide in the presence of various peptides has been accomplished under highly dilute conditions, as determined by mass spectrometry.
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Affiliation(s)
- Ayako Miyazaki
- Sodeoka Live Cell Chemistry Project, ERATO, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan) and Synthetic Organic Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Current address: Institute of Transformative, Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan)
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49
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Codreanu SG, Ullery JC, Zhu J, Tallman KA, Beavers WN, Porter NA, Marnett LJ, Zhang B, Liebler DC. Alkylation damage by lipid electrophiles targets functional protein systems. Mol Cell Proteomics 2014; 13:849-59. [PMID: 24429493 PMCID: PMC3945913 DOI: 10.1074/mcp.m113.032953] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Protein alkylation by reactive electrophiles contributes to chemical toxicities and oxidative stress, but the functional impact of alkylation damage across proteomes is poorly understood. We used Click chemistry and shotgun proteomics to profile the accumulation of proteome damage in human cells treated with lipid electrophile probes. Protein target profiles revealed three damage susceptibility classes, as well as proteins that were highly resistant to alkylation. Damage occurred selectively across functional protein interaction networks, with the most highly alkylation-susceptible proteins mapping to networks involved in cytoskeletal regulation. Proteins with lower damage susceptibility mapped to networks involved in protein synthesis and turnover and were alkylated only at electrophile concentrations that caused significant toxicity. Hierarchical susceptibility of proteome systems to alkylation may allow cells to survive sublethal damage while protecting critical cell functions.
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Affiliation(s)
- Simona G Codreanu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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50
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Wang C, Weerapana E, Blewett MM, Cravatt BF. A chemoproteomic platform to quantitatively map targets of lipid-derived electrophiles. Nat Methods 2013; 11:79-85. [PMID: 24292485 PMCID: PMC3901407 DOI: 10.1038/nmeth.2759] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 10/11/2013] [Indexed: 02/07/2023]
Abstract
Cells produce electrophilic products with the potential to modify and affect the function of proteins. Chemoproteomic methods have provided a means to qualitatively inventory proteins targeted by endogenous electrophiles; however, ascertaining the potency and specificity of these reactions to identify the most sensitive sites in the proteome to electrophilic modification requires more quantitative methods. Here, we describe a competitive activity-based profiling method for quantifying the reactivity of electrophilic compounds against 1000+ cysteines in parallel in the human proteome. Using this approach, we identify a select set of proteins that constitute “hot spots” for modification by various lipid-derived electrophiles, including the oxidative stress product 4-hydroxynonenal (HNE). We show that one of these proteins, ZAK kinase, is labeled by HNE on a conserved, active site-proximal cysteine, resulting in enzyme inhibition to create a negative feedback mechanism that can suppress the activation of JNK pathways by oxidative stress.
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Affiliation(s)
- Chu Wang
- 1] The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - Eranthie Weerapana
- 1] The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - Megan M Blewett
- 1] The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
| | - Benjamin F Cravatt
- 1] The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
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