1
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Aleksic M, Meng X. Protein Haptenation and Its Role in Allergy. Chem Res Toxicol 2024. [PMID: 38834188 DOI: 10.1021/acs.chemrestox.4c00062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Humans are exposed to numerous electrophilic chemicals either as medicines, in the workplace, in nature, or through use of many common cosmetic and household products. Covalent modification of human proteins by such chemicals, or protein haptenation, is a common occurrence in cells and may result in generation of antigenic species, leading to development of hypersensitivity reactions. Ranging in severity of symptoms from local cutaneous reactions and rhinitis to potentially life-threatening anaphylaxis and severe hypersensitivity reactions such as Stephen-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN), all these reactions have the same Molecular Initiating Event (MIE), i.e. haptenation. However, not all individuals who are exposed to electrophilic chemicals develop symptoms of hypersensitivity. In the present review, we examine common chemistry behind the haptenation reactions leading to formation of neoantigens. We explore simple reactions involving single molecule additions to a nucleophilic side chain of proteins and complex reactions involving multiple electrophilic centers on a single molecule or involving more than one electrophilic molecule as well as the generation of reactive molecules from the interaction with cellular detoxification mechanisms. Besides generation of antigenic species and enabling activation of the immune system, we explore additional events which result directly from the presence of electrophilic chemicals in cells, including activation of key defense mechanisms and immediate consequences of those reactions, and explore their potential effects. We discuss the factors that work in concert with haptenation leading to the development of hypersensitivity reactions and those that may act to prevent it from developing. We also review the potential harnessing of the specificity of haptenation in the design of potent covalent therapeutic inhibitors.
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Affiliation(s)
- Maja Aleksic
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedford MK44 1LQ, U.K
| | - Xiaoli Meng
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, The University of Liverpool, Liverpool L69 3GE, U.K
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2
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Burton NR, Backus KM. Functionalizing tandem mass tags for streamlining click-based quantitative chemoproteomics. Commun Chem 2024; 7:80. [PMID: 38600184 PMCID: PMC11006884 DOI: 10.1038/s42004-024-01162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
Mapping the ligandability or potential druggability of all proteins in the human proteome is a central goal of mass spectrometry-based covalent chemoproteomics. Achieving this ambitious objective requires high throughput and high coverage sample preparation and liquid chromatography-tandem mass spectrometry analysis for hundreds to thousands of reactive compounds and chemical probes. Conducting chemoproteomic screens at this scale benefits from technical innovations that achieve increased sample throughput. Here we realize this vision by establishing the silane-based cleavable linkers for isotopically-labeled proteomics-tandem mass tag (sCIP-TMT) proteomic platform, which is distinguished by early sample pooling that increases sample preparation throughput. sCIP-TMT pairs a custom click-compatible sCIP capture reagent that is readily functionalized in high yield with commercially available TMT reagents. Synthesis and benchmarking of a 10-plex set of sCIP-TMT reveal a substantial decrease in sample preparation time together with high coverage and high accuracy quantification. By screening a focused set of four cysteine-reactive electrophiles, we demonstrate the utility of sCIP-TMT for chemoproteomic target hunting, identifying 789 total liganded cysteines. Distinguished by its compatibility with established enrichment and quantification protocols, we expect sCIP-TMT will readily translate to a wide range of covalent chemoproteomic applications.
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Affiliation(s)
- Nikolas R Burton
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles CA, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA
| | - Keriann M Backus
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles CA, USA.
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA.
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, USA.
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
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3
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Wang J, Feng X, Liu X, Wang G, Xiong Y, Zhang L, Zhang Y, Lu H. In-Depth Profiling of 4-Hydroxy-2-nonenal Modification via Reversible Thiazolidine Chemistry. Anal Chem 2024; 96:5125-5133. [PMID: 38502245 DOI: 10.1021/acs.analchem.3c05060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Protein modification by lipid-derived electrophiles (LDEs) is associated with various signaling pathways. Among these LDEs, 4-hydroxy-2-nonenal (HNE) is the most toxic, and protein modified with HNE has been linked to various diseases, including Alzheimer's and Parkinson's. However, due to their low abundance, in-depth profiling of HNE modifications still presents challenges. This study introduces a novel strategy utilizing reversible thiazolidine chemistry to selectively capture HNE-modified proteins and a palladium-mediated cleavage reaction to release them. Thousands of HNE-modified sites in different cell lines were identified. Combined with ABPP, we discovered a set of HNE-sensitive sites that offer a new tool for studying LDE modifications in proteomes.
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Affiliation(s)
- Jun Wang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Xiaoxiao Feng
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Xuejiao Liu
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Guoli Wang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Yingying Xiong
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Ying Zhang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai 200032, China
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Haojie Lu
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai 200032, China
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
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4
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Aleksic M, Rajagopal R, de-Ávila R, Spriggs S, Gilmour N. The skin sensitization adverse outcome pathway: exploring the role of mechanistic understanding for higher tier risk assessment. Crit Rev Toxicol 2024; 54:69-91. [PMID: 38385441 DOI: 10.1080/10408444.2024.2308816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/19/2023] [Indexed: 02/23/2024]
Abstract
For over a decade, the skin sensitization Adverse Outcome Pathway (AOP) has served as a useful framework for development of novel in chemico and in vitro assays for use in skin sensitization hazard and risk assessment. Since its establishment, the AOP framework further fueled the existing efforts in new assay development and stimulated a plethora of activities with particular focus on validation, reproducibility and interpretation of individual assays and combination of assay outputs for use in hazard/risk assessment. In parallel, research efforts have also accelerated in pace, providing new molecular and dynamic insight into key events leading to sensitization. In light of novel hypotheses emerging from over a decade of focused research effort, mechanistic evidence relating to the key events in the skin sensitization AOP may complement the tools currently used in risk assessment. We reviewed the recent advances unraveling the complexity of molecular events in sensitization and signpost the most promising avenues for further exploration and development of useful assays.
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Affiliation(s)
- Maja Aleksic
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, UK
| | - Ramya Rajagopal
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, UK
| | - Renato de-Ávila
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, UK
| | - Sandrine Spriggs
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, UK
| | - Nicola Gilmour
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, UK
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5
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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6
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Valgimigli L. Lipid Peroxidation and Antioxidant Protection. Biomolecules 2023; 13:1291. [PMID: 37759691 PMCID: PMC10526874 DOI: 10.3390/biom13091291] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Lipid peroxidation (LP) is the most important type of oxidative-radical damage in biological systems, owing to its interplay with ferroptosis and to its role in secondary damage to other biomolecules, such as proteins. The chemistry of LP and its biological consequences are reviewed with focus on the kinetics of the various processes, which helps understand the mechanisms and efficacy of antioxidant strategies. The main types of antioxidants are discussed in terms of structure-activity rationalization, with focus on mechanism and kinetics, as well as on their potential role in modulating ferroptosis. Phenols, pyri(mi)dinols, antioxidants based on heavy chalcogens (Se and Te), diarylamines, ascorbate and others are addressed, along with the latest unconventional antioxidant strategies based on the double-sided role of the superoxide/hydroperoxyl radical system.
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Affiliation(s)
- Luca Valgimigli
- Department of Chemistry "G. Ciamician", University of Bologna, Via Piero Gobetti 85, 40129 Bologna, Italy
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7
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Huang KT, Poganik JR, Parvez S, Raja S, Miller B, Long MJC, Fetcho JR, Aye Y. Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox responses in larval fish. Nat Protoc 2023; 18:1379-1415. [PMID: 37020146 PMCID: PMC11150335 DOI: 10.1038/s41596-023-00809-8] [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] [Received: 03/24/2017] [Accepted: 12/05/2022] [Indexed: 04/07/2023]
Abstract
This Protocol Extension describes the adaptation of an existing Protocol detailing the use of targetable reactive electrophiles and oxidants, an on-demand redox targeting toolset in cultured cells. The adaptation described here is for use of reactive electrophiles and oxidants technologies in live zebrafish embryos (Z-REX). Zebrafish embryos expressing a Halo-tagged protein of interest (POI)-either ubiquitously or tissue specifically-are treated with a HaloTag-specific small-molecule probe housing a photocaged reactive electrophile (either natural electrophiles or synthetic electrophilic drug-like fragments). The reactive electrophile is then photouncaged at a user-defined time, enabling proximity-assisted electrophile-modification of the POI. Functional and phenotypic ramifications of POI-specific modification can then be monitored, by coupling to standard downstream assays, such as click chemistry-based POI-labeling and target-occupancy quantification; immunofluorescence or live imaging; RNA-sequencing and real-time quantitative polymerase chain reaction analyses of downstream-transcript modulations. Transient expression of requisite Halo-POI in zebrafish embryos is achieved by messenger RNA injection. Procedures associated with generation of transgenic zebrafish expressing a tissue-specific Halo-POI are also described. The Z-REX experiments can be completed in <1 week using standard techniques. To successfully execute Z-REX, researchers should have basic skills in fish husbandry, imaging and pathway analysis. Experience with protein or proteome manipulation is useful. This Protocol Extension is aimed at helping chemical biologists study precision redox events in a model organism and fish biologists perform redox chemical biology.
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Affiliation(s)
- Kuan-Ting Huang
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Jesse R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Saba Parvez
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Sruthi Raja
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Brian Miller
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | | | - Joseph R Fetcho
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA.
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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8
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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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9
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Lockridge O. Overview of Adductomics in Toxicology. Curr Protoc 2023; 3:e672. [PMID: 36799690 PMCID: PMC9942099 DOI: 10.1002/cpz1.672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Adductomics is epidemiology at the molecular level. Untargeted adductomics compares levels of chemical adducts on albumin, hemoglobin, and DNA between healthy and exposed individuals. The goal is to determine a cause-and-effect relationship between chemical exposure and illness. Chemical exposures are not necessarily due to synthetic chemicals but are often due to oxidation products of naturally occurring lipids, for example, 4-hydroxynonenal and acrolein produced by lipid peroxidation of arachidonic and linoleic acids. The preferred method used in adductomics is ultra-high pressure liquid chromatography coupled to with nanoelectrospray tandem mass spectrometry. The mass of the adduct indicates its structure and identifies the chemical. The advantages of molecular epidemiology include information about the many toxicants to which a person is exposed over a period of weeks or months and the relative exposure levels. The disadvantage is the absence of information about the mechanism of toxicity. Untargeted adductomics examines albumin and hemoglobin adducts, which serve as biomarkers of exposure but do not identify the proteins and genes responsible for the toxicity. Targeted adductomics is used when the origin of the toxicity is known. This can be either an adducted protein, such as the butyrylcholinesterase protein modified by nerve agents, or a toxicant, such as acetaminophen. Untargeted adductomics methods have identified potential protein adduct biomarkers of breast cancer, colorectal cancer, childhood leukemia, and lung cancer. Adductomics is a new research area that offers structural insights into chemical exposures and a platform for the discovery of disease biomarkers. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
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10
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Leitner A. Probing the secrets of probes. Nat Chem Biol 2022; 18:799-800. [PMID: 35864331 DOI: 10.1038/s41589-022-01092-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.
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11
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A modification-centric assessment tool for the performance of chemoproteomic probes. Nat Chem Biol 2022; 18:904-912. [PMID: 35864333 DOI: 10.1038/s41589-022-01074-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 06/01/2022] [Indexed: 12/29/2022]
Abstract
Chemoproteomics has emerged as a key technology to expand the functional space in complex proteomes for probing fundamental biology and for discovering new small-molecule-based therapies. Here we report a modification-centric computational tool termed pChem to provide a streamlined pipeline for unbiased performance assessment of chemoproteomic probes. The pipeline starts with an experimental setting for isotopically coding probe-derived modifications that can be automatically recognized by pChem, with masses accurately calculated and sites precisely localized. pChem exports on-demand reports by scoring the profiling efficiency, modification homogeneity and proteome-wide residue selectivity of a tested probe. The performance and robustness of pChem were benchmarked by applying it to eighteen bioorthogonal probes. These analyses reveal that the formation of unexpected probe-derived modifications can be driven by endogenous reactive metabolites (for example, bioactive aldehydes and glutathione). pChem is a powerful and user-friendly tool that aims to facilitate the development of probes for the ever-growing field of chemoproteomics.
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12
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Chen Y, Quan B, Li Y, Liu Y, Qin W, Wang C. Quantitative profiling of PTM stoichiometry by resolvable mass tags. RSC Chem Biol 2022; 3:1320-1324. [DOI: 10.1039/d2cb00179a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/21/2022] [Indexed: 11/07/2022] Open
Abstract
Post-translational modifications (PTMs) play important roles in modulating the biological functions of proteins.
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Affiliation(s)
- Ying Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Baiyi Quan
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Yuanpei Li
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Yuan Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Wei Qin
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Chu Wang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
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13
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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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14
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Wang MR, He JY, He JX, Liu KK, Yang J. A Paal-Knorr agent for chemoproteomic profiling of targets of isoketals in cells. Chem Sci 2021; 12:14557-14563. [PMID: 34881007 PMCID: PMC8580055 DOI: 10.1039/d1sc02230j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/14/2021] [Indexed: 12/13/2022] Open
Abstract
Natural systems produce various γ-dicarbonyl-bearing compounds that can covalently modify lysine in protein targets via the classic Paal-Knorr reaction. Among them is a unique class of lipid-derived electrophiles - isoketals that exhibit high chemical reactivity and critical biological functions. However, their target selectivity and profiles in complex proteomes remain unknown. Here we report a Paal-Knorr agent, 4-oxonon-8-ynal (herein termed ONAyne), for surveying the reactivity and selectivity of the γ-dicarbonyl warhead in biological systems. Using an unbiased open-search strategy, we demonstrated the lysine specificity of ONAyne on a proteome-wide scale and characterized six probe-derived modifications, including the initial pyrrole adduct and its oxidative products (i.e., lactam and hydroxylactam adducts), an enlactam adduct from dehydration of hydroxylactam, and two chemotypes formed in the presence of endogenous formaldehyde (i.e., fulvene and aldehyde adducts). Furthermore, combined with quantitative chemoproteomics in a competitive format, ONAyne permitted global, in situ, and site-specific profiling of targeted lysine residues of two specific isomers of isoketals, levuglandin (LG) D2 and E2. The functional analyses reveal that LG-derived adduction drives inhibition of malate dehydrogenase MDH2 and exhibits a crosstalk with two epigenetic marks on histone H2B in macrophages. Our approach should be broadly useful for target profiling of bioactive γ-dicarbonyls in diverse biological contexts.
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Affiliation(s)
- Min-Ran Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics 38 Life Sci. Park Road, Changping District Beijing 102206 China
| | - Jing-Yang He
- State Key Laboratory of Proteomics, National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics 38 Life Sci. Park Road, Changping District Beijing 102206 China
| | - Ji-Xiang He
- State Key Laboratory of Proteomics, National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics 38 Life Sci. Park Road, Changping District Beijing 102206 China
| | - Ke-Ke Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics 38 Life Sci. Park Road, Changping District Beijing 102206 China
| | - Jing Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences - Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics 38 Life Sci. Park Road, Changping District Beijing 102206 China
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15
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Demasi M, Augusto O, Bechara EJH, Bicev RN, Cerqueira FM, da Cunha FM, Denicola A, Gomes F, Miyamoto S, Netto LES, Randall LM, Stevani CV, Thomson L. Oxidative Modification of Proteins: From Damage to Catalysis, Signaling, and Beyond. Antioxid Redox Signal 2021; 35:1016-1080. [PMID: 33726509 DOI: 10.1089/ars.2020.8176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Significance: The systematic investigation of oxidative modification of proteins by reactive oxygen species started in 1980. Later, it was shown that reactive nitrogen species could also modify proteins. Some protein oxidative modifications promote loss of protein function, cleavage or aggregation, and some result in proteo-toxicity and cellular homeostasis disruption. Recent Advances: Previously, protein oxidation was associated exclusively to damage. However, not all oxidative modifications are necessarily associated with damage, as with Met and Cys protein residue oxidation. In these cases, redox state changes can alter protein structure, catalytic function, and signaling processes in response to metabolic and/or environmental alterations. This review aims to integrate the present knowledge on redox modifications of proteins with their fate and role in redox signaling and human pathological conditions. Critical Issues: It is hypothesized that protein oxidation participates in the development and progression of many pathological conditions. However, no quantitative data have been correlated with specific oxidized proteins or the progression or severity of pathological conditions. Hence, the comprehension of the mechanisms underlying these modifications, their importance in human pathologies, and the fate of the modified proteins is of clinical relevance. Future Directions: We discuss new tools to cope with protein oxidation and suggest new approaches for integrating knowledge about protein oxidation and redox processes with human pathophysiological conditions. Antioxid. Redox Signal. 35, 1016-1080.
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Affiliation(s)
- Marilene Demasi
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, Brazil
| | - Ohara Augusto
- Departamento de Bioquímica and Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Etelvino J H Bechara
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Renata N Bicev
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda M Cerqueira
- CENTD, Centre of Excellence in New Target Discovery, Instituto Butantan, São Paulo, Brazil
| | - Fernanda M da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Denicola
- Laboratorios Fisicoquímica Biológica-Enzimología, Facultad de Ciencias, Instituto de Química Biológica, Universidad de la República, Montevideo, Uruguay
| | - Fernando Gomes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Sayuri Miyamoto
- Departamento de Bioquímica and Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Luis E S Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Lía M Randall
- Laboratorios Fisicoquímica Biológica-Enzimología, Facultad de Ciencias, Instituto de Química Biológica, Universidad de la República, Montevideo, Uruguay
| | - Cassius V Stevani
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Leonor Thomson
- Laboratorios Fisicoquímica Biológica-Enzimología, Facultad de Ciencias, Instituto de Química Biológica, Universidad de la República, Montevideo, Uruguay
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16
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Li G, Peng X, Guo Y, Gong S, Cao S, Qiu F. Currently Available Strategies for Target Identification of Bioactive Natural Products. Front Chem 2021; 9:761609. [PMID: 34660543 PMCID: PMC8515416 DOI: 10.3389/fchem.2021.761609] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
In recent years, biologically active natural products have gradually become important agents in the field of drug research and development because of their wide availability and variety. However, the target sites of many natural products are yet to be identified, which is a setback in the pharmaceutical industry and has seriously hindered the translation of research findings of these natural products as viable candidates for new drug exploitation. This review systematically describes the commonly used strategies for target identification via the application of probe and non-probe approaches. The merits and demerits of each method were summarized using recent examples, with the goal of comparing currently available methods and selecting the optimum techniques for identifying the targets of bioactive natural products.
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Affiliation(s)
- Gen Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xuling Peng
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yajing Guo
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shaoxuan Gong
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shijie Cao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Feng Qiu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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17
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Fang MY, Huang KH, Tu WJ, Chen YT, Pan PY, Hsiao WC, Ke YY, Tsou LK, Zhang MM. Chemoproteomic profiling reveals cellular targets of nitro-fatty acids. Redox Biol 2021; 46:102126. [PMID: 34509914 PMCID: PMC8441202 DOI: 10.1016/j.redox.2021.102126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 02/02/2023] Open
Abstract
Nitro-fatty acids are a class of endogenous electrophilic lipid mediators with anti-inflammatory and cytoprotective effects in a wide range of inflammatory and fibrotic disease models. While these beneficial biological effects of nitro-fatty acids are mainly attributed to their ability to form covalent adducts with proteins, only a small number of proteins are known to be nitro-alkylated and the scope of protein nitro-alkylation remains undetermined. Here we describe the synthesis and application of a clickable nitro-fatty acid probe for the detection and first global identification of mammalian proteins that are susceptible to nitro-alkylation. 184 high confidence nitro-alkylated proteins were identified in THP1 macrophages, majority of which are novel targets of nitro-fatty acids, including extended synaptotagmin 2 (ESYT2), signal transducer and activator of transcription 3 (STAT3), toll-like receptor 2 (TLR2), retinoid X receptor alpha (RXRα) and glucocorticoid receptor (NR3C1). In particular, we showed that 9-nitro-oleate covalently modified and inhibited dexamethasone binding to NR3C1. Bioinformatic analyses revealed that nitro-alkylated proteins are highly enriched in endoplasmic reticulum and transmembrane proteins, and are overrepresented in lipid metabolism and transport pathways. This study significantly expands the scope of protein substrates targeted by nitro-fatty acids in living cells and provides a useful resource towards understanding the pleiotropic biological roles of nitro-fatty acids as signaling molecules or as multi-target therapeutic agents.
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Affiliation(s)
- Ming-Yu Fang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Kuan-Hsun Huang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Wei-Ju Tu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Ting Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Pei-Yun Pan
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Wan-Chi Hsiao
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan; Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yi-Yu Ke
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Lun K Tsou
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan
| | - Mingzi M Zhang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, 35053, Taiwan.
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18
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Tola AJ, Jaballi A, Missihoun TD. Protein Carbonylation: Emerging Roles in Plant Redox Biology and Future Prospects. PLANTS (BASEL, SWITZERLAND) 2021; 10:1451. [PMID: 34371653 PMCID: PMC8309296 DOI: 10.3390/plants10071451] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/26/2021] [Accepted: 07/09/2021] [Indexed: 12/15/2022]
Abstract
Plants are sessile in nature and they perceive and react to environmental stresses such as abiotic and biotic factors. These induce a change in the cellular homeostasis of reactive oxygen species (ROS). ROS are known to react with cellular components, including DNA, lipids, and proteins, and to interfere with hormone signaling via several post-translational modifications (PTMs). Protein carbonylation (PC) is a non-enzymatic and irreversible PTM induced by ROS. The non-enzymatic feature of the carbonylation reaction has slowed the efforts to identify functions regulated by PC in plants. Yet, in prokaryotic and animal cells, studies have shown the relevance of protein carbonylation as a signal transduction mechanism in physiological processes including hydrogen peroxide sensing, cell proliferation and survival, ferroptosis, and antioxidant response. In this review, we provide a detailed update on the most recent findings pertaining to the role of PC and its implications in various physiological processes in plants. By leveraging the progress made in bacteria and animals, we highlight the main challenges in studying the impacts of carbonylation on protein functions in vivo and the knowledge gap in plants. Inspired by the success stories in animal sciences, we then suggest a few approaches that could be undertaken to overcome these challenges in plant research. Overall, this review describes the state of protein carbonylation research in plants and proposes new research avenues on the link between protein carbonylation and plant redox biology.
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Affiliation(s)
| | | | - Tagnon D. Missihoun
- Groupe de Recherche en Biologie Végétale (GRBV), Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, QC G9A 5H7, Canada; (A.J.T.); (A.J.)
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19
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Das AB, Seddon AR, O'Connor KM, Hampton MB. Regulation of the epigenetic landscape by immune cell oxidants. Free Radic Biol Med 2021; 170:131-149. [PMID: 33444713 DOI: 10.1016/j.freeradbiomed.2020.12.453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/21/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022]
Abstract
Excessive production of microbicidal oxidants by neutrophils can damage host tissue. The short-term response of cells to oxidative stress is well understood, but the mechanisms behind long-term consequences require further clarification. Epigenetic pathways mediate cellular adaptation, and are therefore a potential target of oxidative stress. Indeed, there is evidence that many proteins and metabolites involved in epigenetic pathways are redox sensitive. In this review we provide an overview of the epigenetic landscape and discuss the potential for redox regulation. Using this information, we highlight specific examples where neutrophil oxidants react with epigenetic pathway components. We also use published data from redox proteomics to map out known intersections between oxidative stress and epigenetics that may signpost helpful directions for future investigation. Finally, we discuss the role neutrophils play in adaptive pathologies with a focus on tumour initiation and progression. We hope this information will stimulate further discourse on the emerging field of redox epigenomics.
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Affiliation(s)
- Andrew B Das
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Annika R Seddon
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Karina M O'Connor
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
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20
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Zhang HW, Lv C, Zhang LJ, Guo X, Shen YW, Nagle DG, Zhou YD, Liu SH, Zhang WD, Luan X. Application of omics- and multi-omics-based techniques for natural product target discovery. Biomed Pharmacother 2021; 141:111833. [PMID: 34175822 DOI: 10.1016/j.biopha.2021.111833] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023] Open
Abstract
Natural products continue to be an unparalleled source of pharmacologically active lead compounds because of their unprecedented structures and unique biological activities. Natural product target discovery is a vital component of natural product-based medicine translation and development and is required to understand and potentially reduce mechanisms that may be associated with off-target side effects and toxicity. Omics-based techniques, including genomics, transcriptomics, proteomics, metabolomics, and bioinformatics, have become recognized as effective tools needed to construct innovative strategies to discover natural product targets. Although considerable progress has been made, the successful discovery of natural product targets remains a challenging time-consuming process that has come to increasingly rely on the effective integration of multi-omics-based technologies to create emerging panomics (a.k.a., integrative omics, pan-omics, multiomics)-based strategies. This review summarizes a series of successful studies regarding the application of integrative omics-based methods in natural product target discovery. The advantages and disadvantages of each technique are discussed, with a particular focus on the systematic integration of multi-omics strategies. Further, emerging micro-scale single-cell-based techniques are introduced, especially to deal with minute natural product samples.
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Affiliation(s)
- Hong-Wei Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Chao Lv
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Li-Jun Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xin Guo
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yi-Wen Shen
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Dale G Nagle
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Department of BioMolecular Sciences and Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University-1848, MS 38677-1848, USA
| | - Yu-Dong Zhou
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - San-Hong Liu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Wei-Dong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
| | - Xin Luan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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21
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Wang Y, Li S, Rentfrow G, Chen J, Zhu H, Suman SP. Myoglobin Post-Translational Modifications Influence Color Stability of Beef Longissimus Lumborum. MEAT AND MUSCLE BIOLOGY 2021. [DOI: 10.22175/mmb.11689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Post-translational modifications (PTM) of proteins play critical roles in biological processes. PTM of muscle proteins influence meat quality. Nonetheless, myoglobin (Mb) PTM and their impact on fresh beef color stability have not been characterized yet. Therefore, our objectives were to identify Mb PTM in beef longissimus lumborum muscle during postmortem aging and to characterize their influence on color stability. The longissimus lumborum muscles from 9 (n = 9) beef carcasses (24 h postmortem) were subjected to wet aging for 0, 7, 14, and 21 d. At the end of each wet-aging period, steaks were fabricated. One steak for analyses of PTM was immediately frozen at −80°C, whereas other steaks were assigned to refrigerated storage in the darkness under aerobic packaging. Instrumental color and biochemical attributes were evaluated on day 0, 3, or 6 of storage. Mb PTM were analyzed using two-dimensional electrophoresis and tandem mass spectrometry. Surface redness (a* value), color stability, and Mb concentration decreased (P < 0.05) upon aging. Gel image analyses identified 6 Mb spots with similar molecular weight (17 kDa) but different isoelectric pH. Tandem mass spectrometry identified multiple PTM (phosphorylation, methylation, carboxymethylation, acetylation, and 4-hydroxynonenal alkylation) in these 6 isoforms. The amino acids susceptible to phosphorylation were serine (S), threonine (T), and tyrosine, whereas other PTM were detected in lysine (K), arginine (R), and histidine residues. Additionally, distal histidine (position 64), critical to heme stability, was found to be alkylated. Overall, Mb PTM increased with aging. The aging-induced PTM, especially those occurring close to hydrophobic heme pocket, could disrupt Mb tertiary structure, influence heme affinity, and compromise oxygen binding capacity, leading to decreased color stability of fresh beef. Furthermore, PTM at K45, K47, and K87 were unique to Mb from non-aged beef, whereas PTM at R31, T51, K96, K98, S121, R139, and K147 were unique to Mb from aged counterparts, indicating that these Mb PTM could be used as novel biomarkers for fresh beef color stability.
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Affiliation(s)
- Yifei Wang
- University of Kentucky Department of Animal and Food Sciences
| | - Shuting Li
- University of Kentucky Department of Animal and Food Sciences
| | - Gregg Rentfrow
- University of Kentucky Department of Animal and Food Sciences
| | - Jing Chen
- University of Kentucky Proteomics Core Facility
| | - Haining Zhu
- University of Kentucky Proteomics Core Facility
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22
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Spradlin JN, Zhang E, Nomura DK. Reimagining Druggability Using Chemoproteomic Platforms. Acc Chem Res 2021; 54:1801-1813. [PMID: 33733731 DOI: 10.1021/acs.accounts.1c00065] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
One of the biggest bottlenecks in modern drug discovery efforts is in tackling the undruggable proteome. Currently, over 85% of the proteome is still considered undruggable because most proteins lack well-defined binding pockets that can be functionally targeted with small molecules. Tackling the undruggable proteome necessitates innovative approaches for ligand discovery against undruggable proteins as well as the development of new therapeutic modalities to functionally manipulate proteins of interest. Chemoproteomic platforms, in particular activity-based protein profiling (ABPP), have arisen to tackle the undruggable proteome by using reactivity-based chemical probes and advanced quantitative mass spectrometry-based proteomic approaches to enable the discovery of "ligandable hotspots" or proteome-wide sites that can be targeted with small-molecule ligands. These sites can subsequently be pharmacologically targeted with covalent ligands to rapidly discover functional or nonfunctional binders against therapeutic proteins of interest. Chemoproteomic approaches have also revealed unique insights into ligandability such as the discovery of unique allosteric sites or intrinsically disordered regions of proteins that can be pharmacologically and selectively targeted for biological modulation and therapeutic benefit. Chemoproteomic platforms have also expanded the scope of emerging therapeutic modalities for targeted protein degradation and proteolysis-targeting chimeras (PROTACs) through the discovery of several new covalent E3 ligase recruiters. Looking into the future, chemoproteomic approaches will unquestionably have a major impact in further expansion of existing efforts toward proteome-wide ligandability mapping, targeted ligand discovery efforts against high-value undruggable therapeutic targets, further expansion of the scope of targeted protein degradation platforms, the discovery of new molecular glue scaffolds that enable unique modulation of protein function, and perhaps most excitingly the development of next-generation small-molecule induced-proximity-based therapeutic modalities that go beyond degradation. Exciting days lie ahead in this field as chemical biology becomes an increasingly major driver in drug discovery, and chemoproteomic approaches are sure to be a mainstay in developing next-generation therapeutics.
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Affiliation(s)
- Jessica N. Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, California 94720, United States
| | - Erika Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, California 94720, United States
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, California 94720, United States
- Departments of Molecular and Cell Biology and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
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23
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In-Depth AGE and ALE Profiling of Human Albumin in Heart Failure: Ex Vivo Studies. Antioxidants (Basel) 2021; 10:antiox10030358. [PMID: 33673523 PMCID: PMC7997412 DOI: 10.3390/antiox10030358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/08/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023] Open
Abstract
Advanced glycation end-products (AGEs) and advanced lipoxidation end-products (ALEs), particularly carboxymethyl-lysine (CML), have been largely proposed as factors involved in the establishment and progression of heart failure (HF). Despite this evidence, the current literature lacks the comprehensive identification and characterization of the plasma AGEs/ALEs involved in HF (untargeted approach). This work provides the first ex vivo high-resolution mass spectrometry (HR-MS) profiling of AGEs/ALEs occurring in human serum albumin (HSA), the most abundant protein in plasma, characterized by several nucleophilic sites and thus representing the main protein substrate for AGE/ALE formation. A set of AGE/ALE adducts in pooled HF-HSA samples was defined, and a semi-quantitative analysis was carried out in order to finally select those presenting in increased amounts in the HF samples with respect to the control condition. These adducts were statistically confirmed by monitoring their content in individual HF samples by applying a targeted approach. Selected AGEs/ALEs proved to be mostly CML derivatives on Lys residues (i.e., CML-Lys12, CML-Lys378, CML-Lys402), and one deoxy-fructosyl derivative on the Lys 389 (DFK-Lys 389). The nature of CML adducts was finally confirmed using immunological methods and in vitro production of such adducts further confirmed by mass spectrometry.
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24
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Altomare A, Baron G, Gianazza E, Banfi C, Carini M, Aldini G. Lipid peroxidation derived reactive carbonyl species in free and conjugated forms as an index of lipid peroxidation: limits and perspectives. Redox Biol 2021; 42:101899. [PMID: 33642248 PMCID: PMC8113032 DOI: 10.1016/j.redox.2021.101899] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/01/2021] [Accepted: 02/12/2021] [Indexed: 02/08/2023] Open
Abstract
Reactive carbonyl species (RCS) formed by lipidperoxidation as free forms or as enzymatic and non-enzymatic conjugates are widely used as an index of oxidative stress. Besides general measurements based on derivatizing reactions, more selective and sensitive MS based analyses have been proposed in the last decade. Untargeted and targeted methods for the measurement of free RCS and adducts have been described and their applications to in vitro and ex vivo samples have permitted the identification of many biological targets, reaction mechanisms and adducted moieties with a particular relevance to RCS protein adducts. The growing interest in protein carbonylation can be explained by considering that protein adducts are now recognized as being involved in the damaging action of oxidative stress so that their measurement is performed not only to obtain an index of lipid peroxidation but also to gain a deeper insight into the molecular mechanisms of oxidative stress. The aim of the review is to discuss the most novel analytical approaches and their application for profiling reactive carbonyl species and their enzymatic and non-enzymatic metabolites as an index of lipid-oxidation and oxidative stress. Limits and perspectives will be discussed.
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Affiliation(s)
- Alessandra Altomare
- Department of Pharmaceutical Sciences (DISFARM), Università Degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy
| | - Giovanna Baron
- Department of Pharmaceutical Sciences (DISFARM), Università Degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy
| | - Erica Gianazza
- Centro Cardiologico Monzino, IRCCS, Via Parea 4, 20138, Milan, Italy
| | - Cristina Banfi
- Centro Cardiologico Monzino, IRCCS, Via Parea 4, 20138, Milan, Italy
| | - Marina Carini
- Department of Pharmaceutical Sciences (DISFARM), Università Degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy
| | - Giancarlo Aldini
- Department of Pharmaceutical Sciences (DISFARM), Università Degli Studi di Milano, Via Mangiagalli 25, 20133, Milan, Italy.
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25
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Modification of proteins by reactive lipid oxidation products and biochemical effects of lipoxidation. Essays Biochem 2020; 64:19-31. [PMID: 31867621 DOI: 10.1042/ebc20190058] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023]
Abstract
Lipid oxidation results in the formation of many reactive products, such as small aldehydes, substituted alkenals, and cyclopentenone prostaglandins, which are all able to form covalent adducts with nucleophilic residues of proteins. This process is called lipoxidation, and the resulting adducts are called advanced lipoxidation end products (ALEs), by analogy with the formation of advanced glycoxidation end products from oxidized sugars. Modification of proteins by reactive oxidized lipids leads to structural changes such as increased β-sheet conformation, which tends to result in amyloid-like structures and oligomerization, or unfolding and aggregation. Reaction with catalytic cysteines is often responsible for the loss of enzymatic activity in lipoxidized proteins, although inhibition may also occur through conformational changes at more distant sites affecting substrate binding or regulation. On the other hand, a few proteins are activated by lipoxidation-induced oligomerization or interactions, leading to increased downstream signalling. At the cellular level, it is clear that some proteins are much more susceptible to lipoxidation than others. ALEs affect cell metabolism, protein-protein interactions, protein turnover via the proteasome, and cell viability. Evidence is building that they play roles in both physiological and pathological situations, and inhibiting ALE formation can have beneficial effects.
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26
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Abstract
Aims: Cysteine persulfidation (also called sulfhydration or sulfuration) has emerged as a potential redox mechanism to regulate protein functions and diverse biological processes in hydrogen sulfide (H2S) signaling. Due to its intrinsically unstable nature, working with this modification has proven to be challenging. Although methodological progress has expanded the inventory of persulfidated proteins, there is a continued need to develop methods that can directly and unequivocally identify persulfidated cysteine residues in complex proteomes. Results: A quantitative chemoproteomic method termed as low-pH quantitative thiol reactivity profiling (QTRP) was developed to enable direct site-specific mapping and reactivity profiling of proteomic persulfides and thiols in parallel. The method was first applied to cell lysates treated with NaHS, resulting in the identification of overall 1547 persulfidated sites on 994 proteins. Structural analysis uncovered unique consensus motifs that might define this distinct type of modification. Moreover, the method was extended to profile endogenous protein persulfides in cells expressing H2S-generating enzyme, mouse tissues, and human serum, which led to additional insights into mechanistic, structural, and functional features of persulfidation events, particularly on human serum albumin. Innovation and Conclusion: Low-pH QTRP represents the first method that enables direct and unbiased proteomic mapping of cysteine persulfidation. Our method allows to generate the most comprehensive inventory of persulfidated targets of NaHS so far and to perform the first analysis of in vivo persulfidation events, providing a valuable tool to dissect the biological functions of this important modification.
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Affiliation(s)
- Ling Fu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences • Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Keke Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences • Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Jingyang He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences • Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Caiping Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences • Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences • Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Jing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences • Beijing, Beijing Institute of Lifeomics, Beijing, China
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27
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Foret MK, Lincoln R, Do Carmo S, Cuello AC, Cosa G. Connecting the "Dots": From Free Radical Lipid Autoxidation to Cell Pathology and Disease. Chem Rev 2020; 120:12757-12787. [PMID: 33211489 DOI: 10.1021/acs.chemrev.0c00761] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Our understanding of lipid peroxidation in biology and medicine is rapidly evolving, as it is increasingly implicated in various diseases but also recognized as a key part of normal cell function, signaling, and death (ferroptosis). Not surprisingly, the root and consequences of lipid peroxidation have garnered increasing attention from multiple disciplines in recent years. Here we "connect the dots" between the fundamental chemistry underpinning the cascade reactions of lipid peroxidation (enzymatic or free radical), the reactive nature of the products formed (lipid-derived electrophiles), and the biological targets and mechanisms associated with these products that culminate in cellular responses. We additionally bring light to the use of highly sensitive, fluorescence-based methodologies. Stemming from the foundational concepts in chemistry and biology, these methodologies enable visualizing and quantifying each reaction in the cascade in a cellular and ultimately tissue context, toward deciphering the connections between the chemistry and physiology of lipid peroxidation. The review offers a platform in which the chemistry and biomedical research communities can access a comprehensive summary of fundamental concepts regarding lipid peroxidation, experimental tools for the study of such processes, as well as the recent discoveries by leading investigators with an emphasis on significant open questions.
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Affiliation(s)
- Morgan K Foret
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 1Y6
| | - Richard Lincoln
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Sonia Do Carmo
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 1Y6
| | - A Claudio Cuello
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G 1Y6.,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada H3A 0C7.,Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada H3A 2B4
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
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28
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Abstract
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The biological responses to dienone compounds with a 1,5-diaryl-3-oxo-1,4-pentadienyl
pharmacophore have been studied extensively. Despite their expected
general thiol reactivity, these compounds display considerable degrees
of tumor cell selectivity. Here we review in vitro and preclinical studies of dienone compounds including b-AP15, VLX1570,
RA-9, RA-190, EF24, HO-3867, and MCB-613. A common property of these
compounds is their targeting of the ubiquitin–proteasome system
(UPS), known to be essential for the viability of tumor cells. Gene
expression profiling experiments have shown induction of responses
characteristic of UPS inhibition, and experiments using cellular reporter
proteins have shown that proteasome inhibition is associated with
cell death. Other mechanisms of action such as reactivation of mutant
p53, stimulation of steroid receptor coactivators, and induction of
protein cross-linking have also been described. Although unsuitable
as biological probes due to widespread reactivity, dienone compounds
are cytotoxic to apoptosis-resistant tumor cells and show activity
in animal tumor models.
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Affiliation(s)
- Martina Bazzaro
- Masonic Cancer Center and Department of Obstetrics, Gynecology and Women's Heath, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Stig Linder
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, SE-58183 Linköping, Sweden.,Department of Oncology and Pathology, Karolinska Institute, SE-17176 Stockholm, Sweden
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29
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Geib T, Iacob C, Jribi R, Fernandes J, Benderdour M, Sleno L. Identification of 4-hydroxynonenal-modified proteins in human osteoarthritic chondrocytes. J Proteomics 2020; 232:104024. [PMID: 33122130 DOI: 10.1016/j.jprot.2020.104024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 11/19/2022]
Abstract
The α,β-unsaturated aldehyde 4-hydroxynonenal (HNE) is formed through lipid peroxidation during oxidative stress. As a highly reactive electrophile, it is able to form adducts with various biomolecules, including proteins. These protein modifications could modulate many signaling pathways, as well as cell differentiation and proliferation, and thus could be highly important in the context of the extracellular matrix and degradation of articular cartilage. This study specifically investigated the role of HNE as a bioactive molecule in chondrocytes of osteoarthritis (OA) patients. Chondrocyte extracts of OA and non-OA patients were analyzed for HNE binding using Western blot and bottom-up LC-MS/MS analyses. HNE-modified histones, H2A and H2B, and histone deacetylase were identified using anti-HNE antibodies. Furthermore, peptide sequencing and database searching revealed 95 distinct HNE-modified proteins and their exact modification sites, with 88 protein adducts being unique to OA chondrocytes. HNE-proteins of specific interest included histone H2A, H2B and H4, collagen alpha-3(VI) chain, eukaryotic initiation factor 4A-I, and nucleolar RNA helicase 2. Comparing their MS/MS spectra to those of HNE-modified standard peptides further validated the six HNE-proteins. SIGNIFICANCE: HNE binding to proteins has been shown to result in multiple abnormalities of chondrocyte phenotype and function, suggesting its contribution in OA development. Considering the increased levels of HNE in OA cartilage, this reactive aldehyde could play a role in OA. This work represents a clinically-relevant in vivo study to demonstrate the pathophysiological role of HNE in human OA. Since HNE binding can alter protein conformation and function, it remains highly relevant to study the effects of this modification in OA.
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Affiliation(s)
- Timon Geib
- Chemistry Department, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Cristiana Iacob
- Orthopaedic Research Laboratory, Hôpital du Sacré-Coeur, University of Montréal, Montréal, Québec, Canada
| | - Rihab Jribi
- Orthopaedic Research Laboratory, Hôpital du Sacré-Coeur, University of Montréal, Montréal, Québec, Canada
| | - Julio Fernandes
- Orthopaedic Research Laboratory, Hôpital du Sacré-Coeur, University of Montréal, Montréal, Québec, Canada
| | - Mohamed Benderdour
- Orthopaedic Research Laboratory, Hôpital du Sacré-Coeur, University of Montréal, Montréal, Québec, Canada.
| | - Lekha Sleno
- Chemistry Department, Université du Québec à Montréal, Montréal, Québec, Canada.
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30
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Yang F, Wang C. Profiling of post-translational modifications by chemical and computational proteomics. Chem Commun (Camb) 2020; 56:13506-13519. [PMID: 33084662 DOI: 10.1039/d0cc05447j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational modifications (PTMs) diversify the molecular structures of proteins and play essential roles in regulating their functions. Abnormal PTM status has been linked to a variety of developmental disorders and human diseases, highlighting the importance of studying PTMs in understanding physiological processes and discovering novel nodes and links with therapeutic intervention potential. Classical biochemical methods are suitable for studying PTMs on individual proteins; however, global profiling of PTMs in proteomes remains a challenging task. In this feature article, we start with a brief review of the traditional affinity-based strategies and shift the emphasis to summarizing recent progress in the development and application of chemical and computational proteomic strategies to delineate the global landscapes of functional PTMs. Finally, we discuss current challenges in PTM detection and provide future perspectives on how the field can be further advanced.
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Affiliation(s)
- Fan Yang
- 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 100871, China.
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31
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Yuan W, Wang J, Zhang Y, Lu H. Sample preparation approaches for qualitative and quantitative analysis of lipid-derived electrophile modified proteomes by mass spectrometry. Mol Omics 2020; 16:511-520. [PMID: 33079115 DOI: 10.1039/d0mo00099j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lipid-derived electrophile (LDE) modifications, which are covalent modifications of proteins by endogenous LDEs, are essential types of protein posttranslational modifications. LDE modifications alter the protein structure and regulate their biological processes in cells. LDE modifications of proteins are also closely associated with several diseases and function as potential biomarkers for clinical diagnosis. The crucial step in studying the LDE modifications is to enrich the LDE modified proteins/peptides from complex biological samples with high efficiency and high selectivity and quantify modified proteins/peptides with high accuracy. In this review, we summarize the recent progress in MS-based proteomic technologies to globally identify and quantify LDE modified proteomes, mainly focusing on discussing the qualitative and quantitative technologies.
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Affiliation(s)
- Wenjuan Yuan
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China.
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32
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Zhang H, Liu J, Sun YQ, Liu M, Guo W. Carbon–Dipyrromethenes: Bright Cationic Fluorescent Dyes and Potential Application in Revealing Cellular Trafficking of Mitochondrial Glutathione Conjugates. J Am Chem Soc 2020; 142:17069-17078. [DOI: 10.1021/jacs.0c06916] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hongxing Zhang
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Jing Liu
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Yuan-Qiang Sun
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou University, Zhengzhou 450001, China
| | - Mengxing Liu
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Wei Guo
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
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A quantitative thiol reactivity profiling platform to analyze redox and electrophile reactive cysteine proteomes. Nat Protoc 2020; 15:2891-2919. [PMID: 32690958 DOI: 10.1038/s41596-020-0352-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/05/2020] [Indexed: 02/08/2023]
Abstract
Cysteine is unique among all protein-coding amino acids, owing to its intrinsically high nucleophilicity. The cysteinyl thiol group can be covalently modified by a broad range of redox mechanisms or by various electrophiles derived from exogenous or endogenous sources. Measuring the response of protein cysteines to redox perturbation or electrophiles is critical for understanding the underlying mechanisms involved. Activity-based protein profiling based on thiol-reactive probes has been the method of choice for such analyses. We therefore adapted this approach and developed a new chemoproteomic platform, termed 'QTRP' (quantitative thiol reactivity profiling), that relies on the ability of a commercially available thiol-reactive probe IPM (2-iodo-N-(prop-2-yn-1-yl)acetamide) to covalently label, enrich and quantify the reactive cysteinome in cells and tissues. Here, we provide a detailed and updated workflow of QTRP that includes procedures for (i) labeling of the reactive cysteinome from cell or tissue samples (e.g., control versus treatment) with IPM, (ii) processing the protein samples into tryptic peptides and tagging the probe-modified peptides with isotopically labeled azido-biotin reagents containing a photo-cleavable linker via click chemistry reaction, (iii) capturing biotin-conjugated peptides with streptavidin beads, (iv) identifying and quantifying the photo-released peptides by mass spectrometry (MS)-based shotgun proteomics and (v) interpreting MS data by a streamlined informatic pipeline using a proteomics software, pFind 3, and an automatic post-processing algorithm. We also exemplified here how to use QTRP for mining H2O2-sensitive cysteines and for determining the intrinsic reactivity of cysteines in a complex proteome. We anticipate that this protocol should find broad applications in redox biology, chemical biology and the pharmaceutical industry. The protocol for sample preparation takes 3 d, whereas MS measurements and data analyses require 75 min and <30 min, respectively, per sample.
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Zhou J, Wang W, Zhang J, Du Z, Yang H, Zhang G. Click chemistry-based imaging to study the tissue distribution of the curcumin-protein complex in mice. Food Funct 2020; 11:1684-1691. [PMID: 32037431 DOI: 10.1039/c9fo02012h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Previous studies have shown that curcumin, a bioactive dietary compound with a thiol-reactive α,β-unsaturated carbonyl moiety, can covalently modify protein thiols. However, most of the previous studies were performed in cultured cells or cell-free enzyme systems, and so it remains unknown whether curcumin could covalently modify proteins after oral administration in vivo. Using click chemistry-based fluorescence imaging, here we show that oral administration of dialkyne-curcumin (Di-Cur), a "click" probe mimicking curcumin, results in covalent modifications of cellular proteins in colon and liver tissues, but not in other tissues, in mice. This result suggests that oral administration of curcumin leads to the formation of the curcumin-protein complex in a tissue-specific manner, which could contribute to the biological effects and/or pharmacokinetics of curcumin. Further studies to elucidate the identities of curcumin-binding proteins could greatly help us to better understand the molecular mechanisms of curcumin, and develop novel strategies for disease prevention.
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Affiliation(s)
- Jingyi Zhou
- Department of Food Science, University of Massachusetts, Amherst, MA, USA.
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35
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Qin W, Yang F, Wang C. Chemoproteomic profiling of protein-metabolite interactions. Curr Opin Chem Biol 2019; 54:28-36. [PMID: 31812894 DOI: 10.1016/j.cbpa.2019.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/23/2019] [Accepted: 11/03/2019] [Indexed: 12/29/2022]
Abstract
Small molecule metabolites play important roles in regulating protein functions, which are acted through either covalent non-enzymatic post-translational modifications or non-covalent binding interactions. Chemical proteomic strategies can help delineate global landscapes of cellular protein-metabolite interactions and provide molecular insights about their mechanisms of action. In this review, we summarized the recent progress in developments and applications of chemoproteomic strategies to profile protein-metabolite interactions.
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Affiliation(s)
- Wei Qin
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Fan Yang
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China; College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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36
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37
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Wang Y, Dattmore DA, Wang W, Pohnert G, Wolfram S, Zhang J, Yang R, Decker EA, Lee KSS, Zhang G. trans, trans-2,4-Decadienal, a lipid peroxidation product, induces inflammatory responses via Hsp90- or 14-3-3ζ-dependent mechanisms. J Nutr Biochem 2019; 76:108286. [PMID: 31918337 DOI: 10.1016/j.jnutbio.2019.108286] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/14/2019] [Accepted: 11/07/2019] [Indexed: 12/24/2022]
Abstract
Peroxidation of polyunsaturated fatty acids leads to the formation of a large array of lipid-derived electrophiles (LDEs), many of which are important signaling molecules involved in the pathogenesis of human diseases. Previous research has shown that one of such LDEs, trans, trans-2,4-decadienal (tt-DDE), increases inflammation, however, the underlying mechanisms are not well understood. Here we used click chemistry-based proteomics to identify the cellular targets which are required for the pro-inflammatory effects of tt-DDE. We found that treatment with tt-DDE increased cytokine production, JNK phosphorylation, and activation of NF-κB signaling in macrophage cells, and increased severity of dextran sulfate sodium (DSS)-induced colonic inflammation in mice, demonstrating its pro-inflammatory effects in vitro and in vivo. Using click chemistry-based proteomics, we found that tt-DDE directly interacts with Hsp90 and 14-3-3ζ, which are two important proteins involved in inflammation and tumorigenesis. Furthermore, siRNA knockdown of Hsp90 or 14-3-3ζ abolished the pro-inflammatory effects of tt-DDE in macrophage cells. Together, our results support that tt-DDE increases inflammatory responses via Hsp90- and 14-3-3ζ-dependent mechanisms.
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Affiliation(s)
- Yuxin Wang
- College of Life Science, Northwest University, Xi'an, Shaanxi, China; Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Devon A Dattmore
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
| | - Weicang Wang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Stefanie Wolfram
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Jianan Zhang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Ran Yang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Eric A Decker
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Kin Sing Stephen Lee
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA.
| | - Guodong Zhang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA.
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38
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Mining for protein S-sulfenylation in Arabidopsis uncovers redox-sensitive sites. Proc Natl Acad Sci U S A 2019; 116:21256-21261. [PMID: 31578252 DOI: 10.1073/pnas.1906768116] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hydrogen peroxide (H2O2) is an important messenger molecule for diverse cellular processes. H2O2 oxidizes proteinaceous cysteinyl thiols to sulfenic acid, also known as S-sulfenylation, thereby affecting the protein conformation and functionality. Although many proteins have been identified as S-sulfenylation targets in plants, site-specific mapping and quantification remain largely unexplored. By means of a peptide-centric chemoproteomics approach, we mapped 1,537 S-sulfenylated sites on more than 1,000 proteins in Arabidopsis thaliana cells. Proteins involved in RNA homeostasis and metabolism were identified as hotspots for S-sulfenylation. Moreover, S-sulfenylation frequently occurred on cysteines located at catalytic sites of enzymes or on cysteines involved in metal binding, hinting at a direct mode of action for redox regulation. Comparison of human and Arabidopsis S-sulfenylation datasets provided 155 conserved S-sulfenylated cysteines, including Cys181 of the Arabidopsis MITOGEN-ACTIVATED PROTEIN KINASE4 (AtMAPK4) that corresponds to Cys161 in the human MAPK1, which has been identified previously as being S-sulfenylated. We show that, by replacing Cys181 of recombinant AtMAPK4 by a redox-insensitive serine residue, the kinase activity decreased, indicating the importance of this noncatalytic cysteine for the kinase mechanism. Altogether, we quantitatively mapped the S-sulfenylated cysteines in Arabidopsis cells under H2O2 stress and thereby generated a comprehensive view on the S-sulfenylation landscape that will facilitate downstream plant redox studies.
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39
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S-glycosylation-based cysteine profiling reveals regulation of glycolysis by itaconate. Nat Chem Biol 2019; 15:983-991. [DOI: 10.1038/s41589-019-0323-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 06/12/2019] [Indexed: 01/19/2023]
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40
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Zhang S, Fang C, Yuan W, Zhang Y, Yan G, Zhang L, Di Y, Cai Y, Lu H. Selective Identification and Site-Specific Quantification of 4-Hydroxy-2-nonenal-Modified Proteins. Anal Chem 2019; 91:5235-5243. [DOI: 10.1021/acs.analchem.8b05970] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Caiyun Fang
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | | | | | | | | | | | | | - Haojie Lu
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
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41
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Chen Y, Liu Y, Hou X, Ye Z, Wang C. Quantitative and Site-Specific Chemoproteomic Profiling of Targets of Acrolein. Chem Res Toxicol 2019; 32:467-473. [PMID: 30604966 DOI: 10.1021/acs.chemrestox.8b00343] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Acrolein exists in common pollutants, such as cigarette smoke and car exhaust, which has been implicated with many pathological processes. It is also one type of endogenous lipid-derived electrophile (LDE) generated from lipid peroxidation when cells are under oxidative stress. Chemically, acrolein is able to covalently modify nucleophilic residues in proteins so as to influence their structures and functions, and identification of targets of acrolein modification in proteomes is critical for understanding its biological roles. Here, we report a quantitative chemoproteomic method to globally profile acrolein modifications using an aldehyde-directed aniline-based probe. Collectively, we identified >2300 proteins and >500 cysteine sites that are targeted by acrolein. Our data provide valuable information for understanding acrolein-mediated toxicity and expanding our knowledge of oxidative stress-mediated damage and signaling.
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42
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Greene LE, Lincoln R, Cosa G. Spatio-temporal monitoring of lipid peroxyl radicals in live cell studies combining fluorogenic antioxidants and fluorescence microscopy methods. Free Radic Biol Med 2018; 128:124-136. [PMID: 29649566 DOI: 10.1016/j.freeradbiomed.2018.04.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 12/28/2022]
Abstract
Lipid peroxidation of polyunsaturated fatty acids in cells may occur via their catalytic autoxidation through peroxyl radicals under oxidative stress conditions. Lipid peroxidation is related to a number of pathologies, and may be invoked in new forms of regulated cell death, yet it may also have beneficial roles in cell signaling cascades. Antioxidants are a natural line of defense against lipid peroxidation, and may accordingly impact the biological outcome associated with the redox chemistry of lipid peroxidation. Critical to unraveling the physiological and pathological role of lipid peroxidation is the development of novel probes with the partition, chemical sensitivity and more importantly, molecular specificity, enabling the spatial and temporal imaging of peroxyl radicals in the lipid membranes of live cells, reporting on the redox status of the cell membrane. This review describes our recent progress to visualize lipid peroxidation in model membrane systems and in live cell studies. Our work portrays the mechanistic insight leading to the development of a highly sensitive probe to monitor lipid peroxyl radicals (LOO•). It also describes technical aspects including reagents and fluorescence microscopy methodologies to consider in order to achieve the much sought after monitoring of rates of lipid peroxyl radical production in live cell studies, be it under oxidative stress but also under cell homeostasis. This review seeks to bring attention to the study of lipid redox reactions and to lay the groundwork for the adoption of fluorogenic antioxidant probeshancement and maximum intensity recorded in turn provide a benchmark to estimate, when compared to the control BODIPY dye lacking the intramolecular PeT based switch, the overall exte and related fluorescence microscopy methods toward gaining rich spatiotemporal information on lipid peroxidation in live cells.
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Affiliation(s)
- Lana E Greene
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM/CQMF), McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 0B8
| | - Richard Lincoln
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM/CQMF), McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 0B8
| | - Gonzalo Cosa
- Department of Chemistry and Quebec Center for Advanced Materials (QCAM/CQMF), McGill University, 801 Sherbrooke Street West, Montreal, QC, Canada H3A 0B8.
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43
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Proteomics and Beyond: Cell Decision-Making Shaped by Reactive Electrophiles. Trends Biochem Sci 2018; 44:75-89. [PMID: 30327250 DOI: 10.1016/j.tibs.2018.09.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/21/2018] [Accepted: 09/19/2018] [Indexed: 12/11/2022]
Abstract
Revolutionary proteomic strategies have enabled rapid profiling of the cellular targets of electrophilic small molecules. However, precise means to directly interrogate how these individual electrophilic modifications at low occupancy functionally reshape signaling networks have until recently been largely limited. We highlight here new methods that transcend proteomic platforms to forge a quantitative link between protein target-selective engagement and downstream signaling. We focus on recent progress in the study of non-enzyme-assisted signaling mechanisms and crosstalk choreographed by native reactive electrophilic species (RES). Using this as a model, we offer a long-term vision of how these toolsets together with fundamental biochemical knowledge of precision electrophile signaling may be harnessed to assist covalent ligand-target matching and ultimately amend disease-specific signaling dysfunction.
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44
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Fu L, Liu K, Ferreira RB, Carroll KS, Yang J. Proteome-Wide Analysis of Cysteine S-Sulfenylation Using a Benzothiazine-Based Probe. ACTA ACUST UNITED AC 2018; 95:e76. [PMID: 30312022 DOI: 10.1002/cpps.76] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Oxidation of a protein cysteinyl thiol (Cys-SH) to S-sulfenic acid (Cys-SOH) by a reactive oxygen species (e.g., hydrogen peroxide), which is termed protein S-sulfenylation, is a reversible post-translational modification that plays a crucial role in redox regulation of protein function in various biological processes. Due to its intrinsically labile nature, protein S-sulfenylation cannot be directly detected or analyzed. Chemoselective probing has been the method of choice for analyzing S-sulfenylated proteins either in vitro or in situ, as it allows stabilization and direct detection of this transient oxidative intermediate. However, it remains challenging to globally pinpoint the specific S-sulfenylated cysteine sites on complex proteomes and to quantify their dynamic changes upon oxidative stress. This unit describes how a benzothiazine-based chemoselective probe called BTD and mass spectrometry based chemoproteomics can be used to globally and site-specifically identify and quantify protein S-sulfenylation. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ling Fu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Keke Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
| | - Renan B Ferreira
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida
| | - Kate S Carroll
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida
| | - Jing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Lifeomics, Beijing, China
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45
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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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46
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Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X. Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker. ACS Chem Biol 2018; 13:1983-1989. [PMID: 30059200 DOI: 10.1021/acschembio.8b00414] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Large-scale quantification of protein O-linked β- N-acetylglucosamine (O-GlcNAc) modification in a site-specific manner remains a key challenge in studying O-GlcNAc biology. Herein, we developed an isotope-tagged cleavable linker (isoTCL) strategy, which enabled isotopic labeling of O-GlcNAc through bioorthogonal conjugation of affinity tags. We demonstrated the application of the isoTCL in mapping and quantification of O-GlcNAcylation sites in HeLa cells. Furthermore, we investigated the O-GlcNAcylation sensitivity to the sugar donor by quantifying the levels of modification under different concentrations of the O-GlcNAc labeling probe in a site-specific manner. In addition, we applied isoTCL to compare the O-GlcNAcylation stoichiometry levels of more than 100 modification sites between placenta samples from male and female mice and confirmed site-specifically that female placenta has a higher O-GlcNAcylation than its male counterpart. The isoTCL platform provides a powerful tool for quantitative profiling of O-GlcNAc modification.
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Affiliation(s)
| | | | | | | | - Xuan Shao
- State Key Laboratory of Stem Cells and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan-ling Wang
- State Key Laboratory of Stem Cells and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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47
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Yang F, Gao J, Che J, Jia G, Wang C. A Dimethyl-Labeling-Based Strategy for Site-Specifically Quantitative Chemical Proteomics. Anal Chem 2018; 90:9576-9582. [PMID: 29989794 DOI: 10.1021/acs.analchem.8b02426] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Activity-based protein profiling (ABPP) has emerged as a powerful functional chemoproteomic strategy which enables global profiling of proteome reactivity toward bioactive small molecules in complex biological and/or pathological processes. To quantify the degree of reactivity in a site-specific manner, an isotopic tandem orthogonal proteolysis (isoTOP)-ABPP strategy has been developed; however, the high cost and long workflow associated with the synthesis of isotopically labeled cleavable tags limit its wide use. Herein, we combined reductive dimethyl labeling with TOP-ABPP to develop a fast, affordable, and efficient method, termed "rdTOP-ABPP", for quantitative chemical proteomics with site-specific precision and triplex quantification. The rdTOP-ABPP method shows high accuracy and precision, good reproducibility, and better capacity for site identification and quantification and is highly compatible with many commercially available cleavable tags. We demonstrated the power of rdTOP-ABPP by profiling the target of (1 S,3 R)-RSL3, a canonical inducer for cell ferroptosis, and provided the first global portrait of its proteome reactivity in a quantitative and site-specific manner.
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48
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Poganik JR, Long MJC, Aye Y. Getting the Message? Native Reactive Electrophiles Pass Two Out of Three Thresholds to be Bona Fide Signaling Mediators. Bioessays 2018; 40:e1700240. [PMID: 29603288 PMCID: PMC6488019 DOI: 10.1002/bies.201700240] [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] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/24/2018] [Indexed: 12/11/2022]
Abstract
Precision cell signaling activities of reactive electrophilic species (RES) are arguably among the most poorly-understood means to transmit biological messages. Latest research implicates native RES to be a chemically-distinct subset of endogenous redox signals that influence cell decision making through non-enzyme-assisted modifications of specific proteins. Yet, fundamental questions remain regarding the role of RES as bona fide second messengers. Here, we lay out three sets of criteria we feel need to be met for RES to be considered as true cellular signals that directly mediate information transfer by modifying "first-responding" sensor proteins. We critically assess the available evidence and define the extent to which each criterion has been fulfilled. Finally, we offer some ideas on the future trajectories of the electrophile signaling field taking inspiration from work that has been done to understand canonical signaling mediators. Also see the video abstract here: https://youtu.be/rG7o0clVP0c.
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Affiliation(s)
- Jesse R. Poganik
- Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853, USA
| | - Marcus J. C. Long
- Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853, USA
| | - Yimon Aye
- Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853, USA
- Department of Biochemistry Weill Cornell Medicine New York, NY 10065, USA
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49
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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: 122] [Impact Index Per Article: 20.3] [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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50
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Tian C, Liu K, Sun R, Fu L, Yang J. Chemoproteomics Reveals Unexpected Lysine/Arginine-Specific Cleavage of Peptide Chains as a Potential Protein Degradation Machinery. Anal Chem 2017; 90:794-800. [PMID: 29207244 DOI: 10.1021/acs.analchem.7b03237] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins can undergo oxidative cleavage by in vitro metal-catalyzed oxidation (MCO) in either the α-amidation or the diamide pathway. However, whether oxidative cleavage of polypeptide-chain occurs in biological systems remains unexplored. We describe a chemoproteomic approach to globally and site-specifically profile electrophilic protein degradants formed from peptide backbone cleavages in human proteomes, including the known N-terminal α-ketoacyl products and >1000 unexpected N-terminal formyl products. Strikingly, such cleavages predominantly occur at the carboxyl side of lysine (K) and arginine (R) residues across native proteomes in situ, while MCO-induced oxidative cleavages randomly distribute on peptide/protein sequences in vitro. Furthermore, ionizing radiation-induced reactive oxygen species (ROS) also generate random oxidative cleavages in situ. These findings suggest that the endogenous formation of N-formyl and N-α-ketoacyl degradants in biological systems is more likely regulated by a previously unknown mechanism with a trypsin-like specificity, rather than the random oxidative damage as previously thought. More generally, our study highlights the utility of quantitative chemoproteomics in combination with unrestricted search tools as a viable strategy to discover unexpected chemical modifications of proteins labeled with active-based probes.
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Affiliation(s)
- Caiping Tian
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics , Beijing 102206, China
| | - Keke Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics , Beijing 102206, China
| | - Rui Sun
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics , Beijing 102206, China
| | - Ling Fu
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics , Beijing 102206, China
| | - Jing Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics , Beijing 102206, China
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