1
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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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2
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Li J, Pan L, Pan W, Li N, Tang B. Recent progress of oxidative stress associated biomarker detection. Chem Commun (Camb) 2023. [PMID: 37194341 DOI: 10.1039/d3cc00878a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Oxidative stress denotes the imbalance between the generation of reactive oxygen species (ROS) and antioxidant defenses in living organisms, participating in various pathophysiological processes and mediating the occurrence of diseases. Typically, the excessive production of ROS under oxidative stress elicits oxidative modification of biomacromolecules, including lipids, proteins and nucleic acids, leading to cell dysfunction and damage. Therefore, the analysis and detection of oxidative stress-associated biomarkers are of considerable importance to accurately reflect and evaluate the oxidative stress status. This review comprehensively elucidates the recent advances and applications of imaging probes for tracking and detecting oxidative stress-related biomarkers such as lipid peroxidation, and protein and DNA oxidation. The existing challenges and future development directions in this field are also discussed.
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Affiliation(s)
- Jingjing Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China.
| | - Limeng Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China.
| | - Wei Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China.
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China.
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China.
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3
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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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4
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Cao R, Zhang W, Zhang H, Wang L, Chen X, Ren X, Cheng B, Xia J. Comprehensive Analysis of the PRDXs Family in Head and Neck Squamous Cell Carcinoma. Front Oncol 2022; 12:798483. [PMID: 35350568 PMCID: PMC8957933 DOI: 10.3389/fonc.2022.798483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/14/2022] [Indexed: 12/24/2022] Open
Abstract
The peroxidase family of peroxiredoxins (PRDXs) plays a vital role in maintaining the intracellular balance of ROS. However, their function in head and neck squamous cell carcinoma (HNSCC) has not been investigated. We therefore explored the value of PRDXs in HNSCC. We found that the expression of PRDX1, PRDX4, and PRDX5 in HNSCC increased while the expression of PRDX2 decreased. Moreover, the high expression of PRDX4/5/6 indicated a poor prognosis. Lower expression of PRDX1/5 was linked to more immune cell infiltration, higher expression of immune-related molecules and a more likely response to anti-PD-1 treatment. Moreover, PRDX5 knockdown inhibited HNSCC cell proliferation, invasion and metastasis and it might promote apoptosis through its antioxidant property. Taken together, our study highlights the potential role of PRDXs in HNSCC. The function of PRDX5 in the development of HNSCC and the formation of the immune microenvironment makes it a promising potential therapeutic target.
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Affiliation(s)
- Ruoyan Cao
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Weilin Zhang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Hongjian Zhang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Lixuan Wang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xijuan Chen
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xianyue Ren
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Bin Cheng
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Juan Xia
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
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5
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Jha JS, Nel C, Haldar T, Peters D, Housh K, Gates KS. Products Generated by Amine-Catalyzed Strand Cleavage at Apurinic/Apyrimidinic Sites in DNA: New Insights from a Biomimetic Nucleoside Model System. Chem Res Toxicol 2022; 35:203-217. [PMID: 35124963 PMCID: PMC9477562 DOI: 10.1021/acs.chemrestox.1c00408] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Abasic sites are common in cellular and synthetic DNA. As a result, it is important to characterize the chemical fate of these lesions. Amine-catalyzed strand cleavage at abasic sites in DNA is an important process in which conversion of small amounts of the ring-opened abasic aldehyde residue to an iminium ion facilitates β-elimination of the 3'-phosphoryl group. This reaction generates a trans-α,β-unsaturated iminium ion on the 3'-terminus of the strand break as an obligate intermediate. The canonical product expected from amine-catalyzed cleavage at an AP site is the corresponding trans-α,β-unsaturated aldehyde sugar remnant resulting from hydrolysis of this iminium ion. Interestingly, a handful of studies have reported noncanonical 3'-sugar remnants generated by amine-catalyzed strand cleavage, but the formation and properties of these products are not well-understood. To address this knowledge gap, a nucleoside system was developed that enabled chemical characterization of the sugar remnants generated by amine-catalyzed β-elimination in the 2-deoxyribose system. The results predict that amine-catalyzed strand cleavage at an AP site under physiological conditions has the potential to reversibly generate noncanonical cleavage products including cis-alkenal, 3-thio-2,3-dideoxyribose, and 2-deoxyribose groups alongside the canonical trans-alkenal residue on the 3'-terminus of the strand break. Thus, the model reactions provide evidence that the products generated by amine-catalyzed strand cleavage at abasic sites in cellular DNA may be more complex that commonly thought, with trans-α,β-unsaturated iminium ion intermediates residing at the hub of interconverting product mixtures. The results expand the list of possible 3'-sugar remnants arising from amine-catalyzed cleavage of abasic sites in DNA that must be chemically or enzymatically removed for the completion of base excision repair and single-strand break repair in cells.
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Affiliation(s)
- Jay S. Jha
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Christopher Nel
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Tuhin Haldar
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Daniel Peters
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Kurt Housh
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Kent S. Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211,University of Missouri, Department of Biochemistry, Columbia, MO 65211,Corresponding Author: Kent S. Gates – Departments of Chemistry and Biochemistry, 125 Chemistry Bldg. University of Missouri, Columbia, MO 65211, United States; Phone: (573) 882-6763;
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6
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Haldar T, Jha JS, Yang Z, Nel C, Housh K, Cassidy OJ, Gates KS. Unexpected Complexity in the Products Arising from NaOH-, Heat-, Amine-, and Glycosylase-Induced Strand Cleavage at an Abasic Site in DNA. Chem Res Toxicol 2022; 35:218-232. [PMID: 35129338 PMCID: PMC9482271 DOI: 10.1021/acs.chemrestox.1c00409] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hydrolytic loss of nucleobases from the deoxyribose backbone of DNA is one of the most common unavoidable types of damage in synthetic and cellular DNA. The reaction generates abasic sites in DNA, and it is important to understand the properties of these lesions. The acidic nature of the α-protons of the ring-opened abasic aldehyde residue facilitates the β-elimination of the 3'-phosphoryl group. This reaction is expected to generate a DNA strand break with a phosphoryl group on the 5'-terminus and a trans-α,β-unsaturated aldehyde residue on the 3'-terminus; however, a handful of studies have identified noncanonical sugar remnants on the 3'-terminus, suggesting that the products arising from strand cleavage at apurinic/apyrimidinic sites in DNA may be more complex than commonly thought. We characterized the strand cleavage induced by the treatment of an abasic site-containing DNA oligonucleotide with heat, NaOH, piperidine, spermine, and the base excision repair glycosylases Fpg and Endo III. The results showed that under multiple conditions, cleavage at an abasic site in a DNA oligomer generated noncanonical sugar remnants including cis-α,β-unsaturated aldehyde, 2-deoxyribose, and 3-thio-2,3-dideoxyribose products on the 3'-terminus of the strand break.
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Affiliation(s)
- Tuhin Haldar
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Jay S. Jha
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Zhiyu Yang
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Christopher Nel
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Kurt Housh
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Orla J. Cassidy
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211
| | - Kent S. Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211,University of Missouri, Department of Biochemistry, Columbia, MO 65211,Address correspondence to Kent S. Gates – Departments of Chemistry and Biochemistry, 125 Chemistry Bldg. University of Missouri, Columbia, MO 65211, United States; ORCHID ID: 0000-0002-4218-7411; Phone: (573) 882-6763;
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7
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Chen Y, Qin W, Wang C. Functional Proteomics Driven by Chemical and Computational Approaches. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100785] [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)
- Ying Chen
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
- Synthetic and Functional Biomolecules Center Peking University Beijing 100871 China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Wei Qin
- Peking‐Tsinghua Center for Life Science Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
- Synthetic and Functional Biomolecules Center Peking University Beijing 100871 China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Chu Wang
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Peking‐Tsinghua Center for Life Science Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
- Synthetic and Functional Biomolecules Center Peking University Beijing 100871 China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
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8
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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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9
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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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10
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Jennings EQ, Fritz KS, Galligan JJ. Biochemical genesis of enzymatic and non-enzymatic post-translational modifications. Mol Aspects Med 2021; 86:101053. [PMID: 34838336 PMCID: PMC9126990 DOI: 10.1016/j.mam.2021.101053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/07/2021] [Accepted: 11/16/2021] [Indexed: 12/20/2022]
Abstract
Post-translational modifications (PTMs) alter protein structure, function, and localization and play a pivotal role in physiological and pathophysiological conditions. Many PTMs arise from endogenous metabolic intermediates and serve as sensors for metabolic feedback to maintain cell growth and homeostasis. A key feature to PTMs is their biochemical genesis, which can result from either non-enzymatic adduction (nPTMs) or through enzyme-catalyzed reactions (ePTMs). The abundance and site-specificity of PTMs are determined by dedicated classes of enzymes that add (writers) or remove (erasers) the chemical addition. In this review we will highlight the biochemical genesis and regulation of a few of the 700+ PTMs that have been identified.
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Affiliation(s)
- Erin Q Jennings
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Kristofer S Fritz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - James J Galligan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA.
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11
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Long MJC, Ly P, Aye Y. A primer on harnessing non-enzymatic post-translational modifications for drug design. RSC Med Chem 2021; 12:1797-1807. [PMID: 34825181 PMCID: PMC8597429 DOI: 10.1039/d1md00157d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
Abstract
Of the manifold concepts in drug discovery and design, covalent drugs have re-emerged as one of the most promising over the past 20-or so years. All such drugs harness the ability of a covalent bond to drive an interaction between a target biomolecule, typically a protein, and a small molecule. Formation of a covalent bond necessarily prolongs target engagement, opening avenues to targeting shallower binding sites, protein complexes, and other difficult to drug manifolds, amongst other virtues. This opinion piece discusses frameworks around which to develop covalent drugs. Our argument, based on results from our research program on natural electrophile signaling, is that targeting specific residues innately involved in native signaling programs are ideally poised to be targeted by covalent drugs. We outline ways to identify electrophile-sensing residues, and discuss how studying ramifications of innate signaling by endogenous molecules can provide a means to predict drug mechanism and function and assess on- versus off-target behaviors.
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Affiliation(s)
| | - Phillippe Ly
- Swiss Federal Institute of Technology in Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology in Lausanne (EPFL) 1015 Lausanne Switzerland
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12
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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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13
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Chen C, Gong L, Liu X, Zhu T, Zhou W, Kong L, Luo J. Identification of peroxiredoxin 6 as a direct target of withangulatin A by quantitative chemical proteomics in non-small cell lung cancer. Redox Biol 2021; 46:102130. [PMID: 34517184 PMCID: PMC8441215 DOI: 10.1016/j.redox.2021.102130] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/05/2021] [Accepted: 09/07/2021] [Indexed: 01/13/2023] Open
Abstract
Peroxiredoxin 6 (PRDX6), as a bifunctional enzyme with glutathione peroxidase activity (GPx) and Ca2+-independent phospholipase A2 (iPLA2) activity, has a higher expression in various cancer cells, which leads to the increase of antioxidant properties and promotes tumorigenesis. However, only a few inhibitors of PRDX6 have been discovered to date, especially the covalent inhibitors of PRDX6. Here, we firstly identified Withangulatin A (WA), a natural small molecule, as a novel covalent inhibitor of PRDX6. SILAC-ABPP identified that WA could directly bind to PRDX6 and inactivate the enzyme activity of PRDX6 by the α, β-unsaturated ketone moiety. Moreover, WA also facilitated the generation of ROS, and inhibited the GPx and iPLA2 activities. However, WA-1, with a reduced α, β-unsaturated ketone moiety, had no significant inhibition of the GPx and iPLA2 activities. Biolayer interferometry and LC-MS/MS analysis further demonstrated the selectively covalent binding of WA to the cysteine 47 residue (Cys47) of PRDX6, while mutation of Cys47 blocked the binding of WA to PRDX6. Notably, WA-mediated cytotoxicity and inhibition of the GPx and iPLA2 activities were almost abolished by the deficiency of PRDX6. Therefore, this study indicates that WA is a novel PRDX6 covalent inhibitor, which could covalently bind to the Cys47 of PRDX6 and holds great potential in developing anti-tumor agents for targeting PRDX6.
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Affiliation(s)
- Chen Chen
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Lijie Gong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiaoqin Liu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Tianyu Zhu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Wuxi Zhou
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Jianguang Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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14
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Viedma-Poyatos Á, González-Jiménez P, Langlois O, Company-Marín I, Spickett CM, Pérez-Sala D. Protein Lipoxidation: Basic Concepts and Emerging Roles. Antioxidants (Basel) 2021; 10:295. [PMID: 33669164 PMCID: PMC7919664 DOI: 10.3390/antiox10020295] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022] Open
Abstract
Protein lipoxidation is a non-enzymatic post-translational modification that consists of the covalent addition of reactive lipid species to proteins. This occurs under basal conditions but increases in situations associated with oxidative stress. Protein targets for lipoxidation include metabolic and signalling enzymes, cytoskeletal proteins, and transcription factors, among others. There is strong evidence for the involvement of protein lipoxidation in disease, including atherosclerosis, neurodegeneration, and cancer. Nevertheless, the involvement of lipoxidation in cellular regulatory mechanisms is less understood. Here we review basic aspects of protein lipoxidation and discuss several features that could support its role in cell signalling, including its selectivity, reversibility, and possibilities for regulation at the levels of the generation and/or detoxification of reactive lipids. Moreover, given the great structural variety of electrophilic lipid species, protein lipoxidation can contribute to the generation of multiple structurally and functionally diverse protein species. Finally, the nature of the lipoxidised proteins and residues provides a frameshift for a complex interplay with other post-translational modifications, including redox and redox-regulated modifications, such as oxidative modifications and phosphorylation, thus strengthening the importance of detailed knowledge of this process.
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Affiliation(s)
- Álvaro Viedma-Poyatos
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (C.S.I.C.), 28040 Madrid, Spain
| | - Patricia González-Jiménez
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (C.S.I.C.), 28040 Madrid, Spain
| | - Ophélie Langlois
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Idoia Company-Marín
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Corinne M Spickett
- College of Health & Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Dolores Pérez-Sala
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (C.S.I.C.), 28040 Madrid, Spain
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15
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Allihn PWA, Hackl MW, Ludwig C, Hacker SM, Sieber SA. A tailored phosphoaspartate probe unravels CprR as a response regulator in Pseudomonas aeruginosa interkingdom signaling. Chem Sci 2021; 12:4763-4770. [PMID: 34168754 PMCID: PMC8179651 DOI: 10.1039/d0sc06226j] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/07/2021] [Indexed: 01/06/2023] Open
Abstract
Pseudomonas aeruginosa is a difficult-to-treat Gram-negative bacterial pathogen causing life-threatening infections. Adaptive resistance (AR) to cationic peptide antibiotics such as polymyxin B impairs the therapeutic success. This self-protection is mediated by two component systems (TCSs) consisting of a membrane-bound histidine kinase and an intracellular response regulator (RR). As phosphorylation of the key RR aspartate residue is transient during signaling and hydrolytically unstable, the study of these systems is challenging. Here, we apply a tailored reverse polarity chemical proteomic strategy to capture this transient modification and read-out RR phosphorylation in complex proteomes using a nucleophilic probe. In-depth mechanistic insights into an ideal trapping strategy were performed with a recombinant RR demonstrating the importance of fine-tuned acidic pH values to facilitate the attack on the aspartate carbonyl C-atom and prevent unproductive hydrolysis. Analysis of Bacillus subtilis and P. aeruginosa proteomes revealed the detection of multiple annotated phosphoaspartate (pAsp) sites of known RRs in addition to many new potential pAsp sites. With this validated strategy we dissected the signaling of dynorphin A, a human peptide stress hormone, which is sensed by P. aeruginosa to prepare AR. Intriguingly, our methodology identified CprR as an unprecedented RR in dynorphin A interkingdom signaling.
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Affiliation(s)
- Patrick W A Allihn
- TUM Center for Functional Protein Assemblies (CPA), Department of Chemistry and Chair of Organic Chemistry II, Technical University of Munich Lichtenbergstraße 4 85748 Garching Germany
| | - Mathias W Hackl
- TUM Center for Functional Protein Assemblies (CPA), Department of Chemistry and Chair of Organic Chemistry II, Technical University of Munich Lichtenbergstraße 4 85748 Garching Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich 85354 Freising Germany
| | - Stephan M Hacker
- Department of Chemistry, Technical University of Munich 85748 Garching Germany
| | - Stephan A Sieber
- TUM Center for Functional Protein Assemblies (CPA), Department of Chemistry and Chair of Organic Chemistry II, Technical University of Munich Lichtenbergstraße 4 85748 Garching Germany
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16
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Lyu X, Li S, Jiang C, He N, Chen Z, Zou Y, Li L. DeepCSO: A Deep-Learning Network Approach to Predicting Cysteine S-Sulphenylation Sites. Front Cell Dev Biol 2020; 8:594587. [PMID: 33335901 PMCID: PMC7736615 DOI: 10.3389/fcell.2020.594587] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/12/2020] [Indexed: 01/02/2023] Open
Abstract
Cysteine S-sulphenylation (CSO), as a novel post-translational modification (PTM), has emerged as a potential mechanism to regulate protein functions and affect signal networks. Because of its functional significance, several prediction approaches have been developed. Nevertheless, they are based on a limited dataset from Homo sapiens and there is a lack of prediction tools for the CSO sites of other species. Recently, this modification has been investigated at the proteomics scale for a few species and the number of identified CSO sites has significantly increased. Thus, it is essential to explore the characteristics of this modification across different species and construct prediction models with better performances based on the enlarged dataset. In this study, we constructed several classifiers and found that the long short-term memory model with the word-embedding encoding approach, dubbed LSTMWE, performs favorably to the traditional machine-learning models and other deep-learning models across different species, in terms of cross-validation and independent test. The area under the receiver operating characteristic (ROC) curve for LSTMWE ranged from 0.82 to 0.85 for different organisms, which was superior to the reported CSO predictors. Moreover, we developed the general model based on the integrated data from different species and it showed great universality and effectiveness. We provided the on-line prediction service called DeepCSO that included both species-specific and general models, which is accessible through http://www.bioinfogo.org/DeepCSO.
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Affiliation(s)
- Xiaru Lyu
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Shuhao Li
- College of Life Sciences, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Chunyang Jiang
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Ningning He
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Zhen Chen
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, China.,Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Yang Zou
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Lei Li
- School of Basic Medicine, Qingdao University, Qingdao, China.,School of Data Science and Software Engineering, Qingdao University, Qingdao, China
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17
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Sun DE, Fan X, Shi Y, Zhang H, Huang Z, Cheng B, Tang Q, Li W, Zhu Y, Bai J, Liu W, Li Y, Wang X, Lei X, Chen X. Click-ExM enables expansion microscopy for all biomolecules. Nat Methods 2020; 18:107-113. [PMID: 33288959 DOI: 10.1038/s41592-020-01005-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 10/28/2020] [Indexed: 12/11/2022]
Abstract
Expansion microscopy (ExM) allows super-resolution imaging on conventional fluorescence microscopes, but has been limited to proteins and nucleic acids. Here we develop click-ExM, which integrates click labeling into ExM to enable a 'one-stop-shop' method for nanoscale imaging of various types of biomolecule. By click labeling with biotin and staining with fluorescently labeled streptavidin, a large range of biomolecules can be imaged by the standard ExM procedure normally used for proteins. Using 18 clickable labels, we demonstrate click-ExM on lipids, glycans, proteins, DNA, RNA and small molecules. We demonstrate that click-ExM is applicable in cell culture systems and for tissue imaging. We further show that click-ExM is compatible with signal-amplification techniques and two-color imaging. Click-ExM thus provides a convenient and versatile method for super-resolution imaging, which may be routinely used for cell and tissue samples.
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Affiliation(s)
- De-En Sun
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Xinqi Fan
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Yujie Shi
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Hao Zhang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Zhimin Huang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Bo Cheng
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Qi Tang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Wei Li
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Yuntao Zhu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China.,Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Jinyi Bai
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Wei Liu
- School of Life Sciences, Peking University, Beijing, China
| | - Yuan Li
- School of Life Sciences, Peking University, Beijing, China
| | - Xiaoting Wang
- School of Life Sciences, Peking University, Beijing, China
| | - Xiaoguang Lei
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life 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
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China. .,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China. .,Peking-Tsinghua Center for Life 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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18
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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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19
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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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20
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Carlström KE, Zhu K, Ewing E, Krabbendam IE, Harris RA, Falcão AM, Jagodic M, Castelo-Branco G, Piehl F. Gsta4 controls apoptosis of differentiating adult oligodendrocytes during homeostasis and remyelination via the mitochondria-associated Fas-Casp8-Bid-axis. Nat Commun 2020; 11:4071. [PMID: 32792491 PMCID: PMC7426940 DOI: 10.1038/s41467-020-17871-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 07/23/2020] [Indexed: 01/20/2023] Open
Abstract
Arrest of oligodendrocyte (OL) differentiation and remyelination following myelin damage in multiple sclerosis (MS) is associated with neurodegeneration and clinical worsening. We show that Glutathione S-transferase 4α (Gsta4) is highly expressed during adult OL differentiation and that Gsta4 loss impairs differentiation into myelinating OLs in vitro. In addition, we identify Gsta4 as a target of both dimethyl fumarate, an existing MS therapy, and clemastine fumarate, a candidate remyelinating agent in MS. Overexpression of Gsta4 reduces expression of Fas and activity of the mitochondria-associated Casp8-Bid-axis in adult oligodendrocyte precursor cells, leading to improved OL survival during differentiation. The Gsta4 effect on apoptosis during adult OL differentiation was corroborated in vivo in both lysolecithin-induced demyelination and experimental autoimmune encephalomyelitis models, where Casp8 activity was reduced in Gsta4-overexpressing OLs. Our results identify Gsta4 as an intrinsic regulator of OL differentiation, survival and remyelination, as well as a potential target for future reparative MS therapies.
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Affiliation(s)
- Karl E Carlström
- Department of Clinical Neurosciences, Karolinska Institutet, Center for Molecular Medicine, Karolinska Hospital at Solna, 17177, Stockholm, Sweden.
| | - Keying Zhu
- Department of Clinical Neurosciences, Karolinska Institutet, Center for Molecular Medicine, Karolinska Hospital at Solna, 17177, Stockholm, Sweden
| | - Ewoud Ewing
- Department of Clinical Neurosciences, Karolinska Institutet, Center for Molecular Medicine, Karolinska Hospital at Solna, 17177, Stockholm, Sweden
| | - Inge E Krabbendam
- Department of Clinical Neurosciences, Karolinska Institutet, Center for Molecular Medicine, Karolinska Hospital at Solna, 17177, Stockholm, Sweden
| | - Robert A Harris
- Department of Clinical Neurosciences, Karolinska Institutet, Center for Molecular Medicine, Karolinska Hospital at Solna, 17177, Stockholm, Sweden
| | - Ana Mendanha Falcão
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, 17177, Stockholm, Sweden
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Minho, Portugal
| | - Maja Jagodic
- Department of Clinical Neurosciences, Karolinska Institutet, Center for Molecular Medicine, Karolinska Hospital at Solna, 17177, Stockholm, Sweden
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Biomedicum, Karolinska Institutet, 17177, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Piehl
- Department of Clinical Neurosciences, Karolinska Institutet, Center for Molecular Medicine, Karolinska Hospital at Solna, 17177, Stockholm, Sweden
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21
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Shao X, Zhang H, Yang Z, Zhu L, Cai Z. Quantitative Profiling of Protein-Derived Electrophilic Cofactors in Bacterial Cells with a Hydrazine-Derived Probe. Anal Chem 2020; 92:4484-4490. [PMID: 32093472 DOI: 10.1021/acs.analchem.9b05607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Post-translational modification of proteins can form electrophilic cofactors that serve as a catalytic center. The derived electrophilic cofactors greatly expand protein activities and functions. However, there are few studies concerning how to profile the electrophiles in bacteria. Herein, we utilized a clickable probe called propargyl hydrazine to profile the protein-derived electrophilic cofactors in Escherichia coli (E. coli) cells. Since the cofactors are mostly carbonyl groups, the hydrazine-based probe can specifically react with the cofactors to form a Schiff base. The labeled proteins were then pulled down for mass spectrometry (MS) analysis. Fourteen proteins were shown to undergo enrichment by the probe and competitive binding by its analogue, propyl hydrazine. The identified proteins were further analyzed with targeted proteomics based on parallel reaction monitoring (PRM). Using this strategy, we obtained a global portrait of protein electrophiles in bacterial cells, among which the proteins of speD and panD were previously reported to derive pyruvoyl group as an electrophilic center while lpp can retain N-terminal formyl methionine. This quantitative chemical proteomics strategy can be used to find out protein electrophiles in bacteria and holds great potential to further characterize the protein functions.
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Affiliation(s)
- Xiaojian Shao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Hailei Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zhu Yang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Lin Zhu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
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22
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Poganik JR, Aye Y. Electrophile Signaling and Emerging Immuno- and Neuro-modulatory Electrophilic Pharmaceuticals. Front Aging Neurosci 2020; 12:1. [PMID: 32116644 PMCID: PMC7019031 DOI: 10.3389/fnagi.2020.00001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022] Open
Abstract
With a lipid-rich environment and elevated oxygen consumption, the central nervous system (CNS) is subject to intricate regulation by lipid-derived electrophiles (LDEs). Investigations into oxidative damage and chronic LDE generation in neural disorders have spurred the development of tools that can detect and catalog the gamut of LDE-adducted proteins. Despite these advances, deconstructing the precise consequences of individual protein-specific LDE modifications remained largely impossible until recently. In this perspective, we first overview emerging toolsets that can decode electrophile-signaling events in a protein/context-specific manner, and how the accumulating mechanistic insights brought about by these tools have begun to offer new means to modulate pathways relevant to multiple sclerosis (MS). By surveying the latest data surrounding the blockbuster MS drug dimethyl fumarate that functions through LDE-signaling-like mechanisms, we further provide a vision for how chemical biology tools probing electrophile signaling may be leveraged toward novel interventions in CNS disease.
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Affiliation(s)
- Jesse R Poganik
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
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23
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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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24
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Abstract
Aim: Advanced glycation end products (AGE) are the biomarkers of aging and diabetes which are formed via reactions between glycating agents and biomacromolecules. However, no proteomic study has been reported to systematically investigate the protein substrates of AGEs. Results: In this paper, we used an aniline-based probe to capture the glyoxal-imine intermediate which is the transition sate of glyoxal-derived AGEs. Combined with the tandem orthogonal proteolysis activity-based protein profiling strategy, we successfully identified 962 lysines modified by glyoxal. Conclusion: Enzymes in glycolysis are heavily modified by glyoxal and our biochemical experiments showed that glyoxal can significantly inhibit the activity of GAPDH and glycolysis. These data indicated that AGEs modifications may contribute to pathological processes through impairing the glycolytic process.
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25
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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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26
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Nunes J, Charneira C, Morello J, Rodrigues J, Pereira SA, Antunes AMM. Mass Spectrometry-Based Methodologies for Targeted and Untargeted Identification of Protein Covalent Adducts (Adductomics): Current Status and Challenges. High Throughput 2019; 8:ht8020009. [PMID: 31018479 PMCID: PMC6631461 DOI: 10.3390/ht8020009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 12/12/2022] Open
Abstract
Protein covalent adducts formed upon exposure to reactive (mainly electrophilic) chemicals may lead to the development of a wide range of deleterious health outcomes. Therefore, the identification of protein covalent adducts constitutes a huge opportunity for a better understanding of events underlying diseases and for the development of biomarkers which may constitute effective tools for disease diagnosis/prognosis, for the application of personalized medicine approaches and for accurately assessing human exposure to chemical toxicants. The currently available mass spectrometry (MS)-based methodologies, are clearly the most suitable for the analysis of protein covalent modifications, providing accuracy, sensitivity, unbiased identification of the modified residue and conjugates along with quantitative information. However, despite the huge technological advances in MS instrumentation and bioinformatics tools, the identification of low abundant protein covalent adducts is still challenging. This review is aimed at summarizing the MS-based methodologies currently used for the identification of protein covalent adducts and the strategies developed to overcome the analytical challenges, involving not only sample pre-treatment procedures but also distinct MS and data analysis approaches.
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Affiliation(s)
- João Nunes
- Centro de Química Estrutural, Instituto Superior Técnico, ULisboa, 1049-001 Lisboa, Portugal.
| | - Catarina Charneira
- Centro de Química Estrutural, Instituto Superior Técnico, ULisboa, 1049-001 Lisboa, Portugal.
| | - Judit Morello
- Centro de Química Estrutural, Instituto Superior Técnico, ULisboa, 1049-001 Lisboa, Portugal.
| | - João Rodrigues
- Clarify Analytical, Rua dos Mercadores 128A, 7000-872 Évora, Portugal.
| | - Sofia A Pereira
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-006 Lisboa, Portugal.
| | - Alexandra M M Antunes
- Centro de Química Estrutural, Instituto Superior Técnico, ULisboa, 1049-001 Lisboa, Portugal.
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27
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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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28
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Reactive-cysteine profiling for drug discovery. Curr Opin Chem Biol 2019; 50:29-36. [PMID: 30897495 DOI: 10.1016/j.cbpa.2019.02.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 01/10/2023]
Abstract
The recognition that only a small percentage of known human gene products are druggable using traditional modes of non-covalent ligand design, has led to a resurgence in targeted covalent inhibitors. Covalent inhibitors offer advantages over non-covalent inhibitors in engaging otherwise challenging targets. Reactive cysteine residues on proteins are a common target for covalent inhibitors, whereby the high nucleophilicity of the cysteine thiol under physiological conditions provides an ideal anchoring site for electrophilic small molecules. A chemical-proteomic platform, termed isoTOP-ABPP, allows for profiling cysteine reactivity in complex proteomes and is one of many techniques that can aid in two aspects of the covalent-inhibitor development process: (1) to identify functional cysteines that lead to modulation of protein activity through covalent modification; and, (2) to determine cellular targets and evaluate promiscuity of electrophilic fragments, small molecules, and natural products. Herein, we discuss recent advances in isoTOP-ABPP and potential applications of this technology in the drug-discovery pipeline.
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29
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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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30
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Gesslbauer B, Kuerzl D, Valpatic N, Bochkov VN. Unbiased Identification of Proteins Covalently Modified by Complex Mixtures of Peroxidized Lipids Using a Combination of Electrophoretic Mobility Band Shift with Mass Spectrometry. Antioxidants (Basel) 2018; 7:antiox7090116. [PMID: 30200198 PMCID: PMC6162613 DOI: 10.3390/antiox7090116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 12/15/2022] Open
Abstract
Covalent modification of functionally important cell proteins by lipid oxidation products (LOPs) is a known mechanism initiating pathological consequences of oxidative stress. Identification of new proteins covalently modified by electrophilic lipids can be performed by a combination of chemical, immunological, and mass spectrometry-based methods, but requires prior knowledge either on the exact molecular structure of LOPs (e.g., 4-hydroxynonenal) or candidate protein targets. However, under the conditions of oxidative stress in vivo, a complex mixture of proteins (e.g., cytosolic proteome) reacts with a complex mixture of LOPs. Here we describe a method for detection of lipid-modified proteins that does not require an a priori knowledge on the chemical structure of LOPs or identity of target proteins. The method is based on the change of electrophoretic mobility of lipid-modified proteins, which is induced by conformational changes and cross-linking with other proteins. Abnormally migrating proteins are detected by mass spectrometry-based protein peptide sequencing. We applied this method to study effects of oxidized palmitoyl-arachidonoyl-phosphatidylcholine (OxPAPC) on endothelial cells. Several known, but also many new, OxPAPC-binding proteins were identified. We expect that this technically relatively simple method can be widely applied for label-free analysis of lipid-protein interactions in complex protein samples treated with different LOPs.
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Affiliation(s)
- Bernd Gesslbauer
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Humboldtstrasse 46, 8010 Graz, Austria.
| | - David Kuerzl
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Humboldtstrasse 46, 8010 Graz, Austria.
| | - Niko Valpatic
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Humboldtstrasse 46, 8010 Graz, Austria.
| | - Valery N Bochkov
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Humboldtstrasse 46, 8010 Graz, Austria.
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31
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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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32
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Gao X, Sun JZ, Tang BZ. Reaction-based AIE-active Fluorescent Probes for Selective Detection and Imaging. Isr J Chem 2018. [DOI: 10.1002/ijch.201800035] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xiaoying Gao
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering; Zhejiang University; Hangzhou 310027 China
| | - Jing Zhi Sun
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering; Zhejiang University; Hangzhou 310027 China
| | - Ben Zhong Tang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering; Zhejiang University; Hangzhou 310027 China
- Department of Chemistry, Division of Biomedical Engineering, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, State Key Laboratory of Molecular Neuroscience, Institute of Molecular Functional Materials, Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Kowloon, Hong Kong China
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33
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Ye Z, Zhang X, Zhu Y, Song T, Chen X, Lei X, Wang C. Chemoproteomic Profiling Reveals Ethacrynic Acid Targets Adenine Nucleotide Translocases to Impair Mitochondrial Function. Mol Pharm 2018; 15:2413-2422. [PMID: 29763317 DOI: 10.1021/acs.molpharmaceut.8b00250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Ethacrynic acid (EA) is a diuretic drug that is widely used to treat high-blood pressure and swelling caused by congestive heart failure or kidney failure. It acts through noncovalent inhibition of the Na+-K+-2Cl- cotransporter in the thick ascending limb of Henle's loop. Chemically, EA contains a Michael acceptor group that can react covalently with nucleophilic residues in proteins; however, the proteome reactivity of EA remains unexplored. Herein, we took a quantitative chemoproteomic approach to globally profile EA's targets in cancer cells. We discovered that EA induces impaired mitochondrial function accompanied by increased ROS production. Our profiling revealed that EA targets functional proteins on mitochondrial membranes, including adenine nucleotide translocases (ANTs). Site-specific mapping identified that EA covalently modifies a functional cysteine in ANTs, a mutation of which resulted in the rescuing effect on EA-induced mitochondrial dysfunction. The newly discovered modes of action offer valuable information to repurpose EA for cancer treatment.
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Affiliation(s)
- Zi Ye
- 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.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies , Peking University , Beijing 100871 , China
| | - Xiaoyun Zhang
- 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
| | - Yuangang Zhu
- Institute of Molecular Medicine , Peking University , Beijing 100871 , China
| | - Tong Song
- 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
| | - Xiaowei Chen
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies , Peking University , Beijing 100871 , China.,Institute of Molecular Medicine , Peking University , Beijing 100871 , China
| | - Xiaoguang Lei
- 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.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies , Peking University , Beijing 100871 , 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 100871 , China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies , Peking University , Beijing 100871 , China
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34
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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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35
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Chen Y, Liu Y, Lan T, Qin W, Zhu Y, Qin K, Gao J, Wang H, Hou X, Chen N, Friedmann Angeli JP, Conrad M, Wang C. Quantitative Profiling of Protein Carbonylations in Ferroptosis by an Aniline-Derived Probe. J Am Chem Soc 2018; 140:4712-4720. [PMID: 29569437 DOI: 10.1021/jacs.8b01462] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ferroptosis is a regulated form of necrotic cell death implicated in carcinogenesis and neurodegeneration that is driven by phospholipid peroxidation. Lipid-derived electrophiles (LDEs) generated during this process can covalently modify proteins ("carbonylation") and affect their functions. Here we report the development of a quantitative chemoproteomic method to profile carbonylations in ferroptosis by an aniline-derived probe. Using the method, we established a global portrait of protein carbonylations in ferroptosis with >400 endogenously modified proteins and for the first time, identified >20 residue sites with endogenous LDE modifications in ferroptotic cells. Specifically, we discovered and validated a novel cysteine site of modification on voltage-dependent anion-selective channel protein 2 (VDAC2) that might play an important role in sensitizing LDE signals and mediating ferroptosis. Our results will contribute to the understanding of ferroptotic signaling and pathogenesis and provide potential biomarkers for ferroptosis detection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Marcus Conrad
- Institute of Developmental Genetics , Helmholtz Zentrum Munchen , Munchen , Germany
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36
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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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37
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Sun R, Fu L, Liu K, Tian C, Yang Y, Tallman KA, Porter NA, Liebler DC, Yang J. Chemoproteomics Reveals Chemical Diversity and Dynamics of 4-Oxo-2-nonenal Modifications in Cells. Mol Cell Proteomics 2017; 16:1789-1800. [PMID: 28814509 DOI: 10.1074/mcp.ra117.000116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
4-Oxo-2-nonenal (ONE) derived from lipid peroxidation modifies nucleophiles and transduces redox signaling by its reactions with proteins. However, the molecular interactions between ONE and complex proteomes and their dynamics in situ remain largely unknown. Here we describe a quantitative chemoproteomic analysis of protein adduction by ONE in cells, in which the cellular target profile of ONE is mimicked by its alkynyl surrogate. The analyses reveal four types of ONE-derived modifications in cells, including ketoamide and Schiff-base adducts to lysine, Michael adducts to cysteine, and a novel pyrrole adduct to cysteine. ONE-derived adducts co-localize and exhibit crosstalk with many histone marks and redox sensitive sites. All four types of modifications derived from ONE can be reversed site-specifically in cells. Taken together, our study provides much-needed mechanistic insights into the cellular signaling and potential toxicities associated with this important lipid derived electrophile.
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Affiliation(s)
- Rui Sun
- From the ‡State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China.,§State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Ling Fu
- §State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Keke Liu
- §State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Caiping Tian
- §State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yong Yang
- From the ‡State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Keri A Tallman
- ¶Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - Ned A Porter
- ¶Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - Daniel C Liebler
- ‖Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Jing Yang
- §State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China;
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