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Zhang D, Lu M, Chen C, Xu Y, Peng T. Fatty Acyl Sulfonyl Fluoride as an Activity-Based Probe for Profiling Fatty Acid-Associated Proteins in Living Cells. Chembiochem 2021; 23:e202100628. [PMID: 34918441 DOI: 10.1002/cbic.202100628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/16/2021] [Indexed: 11/09/2022]
Abstract
Fatty acids play fundamental structural, metabolic, functional, and signaling roles in all biological systems. Altered fatty acid levels and metabolism have been associated with many pathological conditions. Chemical probes have greatly facilitated biological studies on fatty acids. Herein, we report the development and characterization of an alkynyl-functionalized long-chain fatty acid-based sulfonyl fluoride probe for covalent labelling, enrichment, and identification of fatty acid-associated proteins in living cells. Our quantitative chemical proteomics show that this sulfonyl fluoride probe targets diverse classes of fatty acid-associated proteins including many metabolic serine hydrolases that are known to be involved in fatty acid metabolism and modification. We further validate that the probe covalently modifies the catalytically or functionally essential serine or tyrosine residues of its target proteins and enables evaluation of their inhibitors. The sulfonyl fluoride-based chemical probe thus represents a new tool for profiling the expression and activity of fatty acid-associated proteins in living cells.
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Affiliation(s)
- Dong Zhang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Minghao Lu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Chengjie Chen
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Yaxin Xu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
| | - Tao Peng
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, P. R. China
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Abstract
Protein post-translational modifications (PTM) are commonly used to regulate biological processes. Protein S-acylation is an enzymatically regulated reversible modification that has been shown to modulate protein localization, activity and membrane binding. Proteome-scale discovery on Plasmodium falciparum schizonts has revealed a complement of more than 400 palmitoylated proteins, including those essential for host invasion and drug resistance. The wide regulatory affect on this species is endorsed by the presence of 12 proteins containing the conserved DHHC-CRD (DHHC motif within a cysteine-rich domain) that is associated with palmitoyl-transferase activity. Genetic interrogation of these enzymes in Apicomplexa has revealed essentiality and distinct localization at cellular compartments; these features are species specific and are not observed in yeast. It is clear that palmitoylation has an elaborate role in Plasmodium biology and opens intriguing questions on the functional consequence of this group of acylation modifications and how the protein S-acyl transferases (PATs) orchestrate molecular events.
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Yang P, Liu K. Activity-based protein profiling: recent advances in probe development and applications. Chembiochem 2015; 16:712-24. [PMID: 25652106 DOI: 10.1002/cbic.201402582] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 11/08/2022]
Abstract
The completion of the human genome sequencing project has provided a wealth of new information regarding the genomic blueprint of the cell. Although, to date, there are roughly 20,000 genes in the human genome, the functions of only a handful of proteins are clear. The major challenge lies in translating genomic information into an understanding of their cellular functions. The recently developed activity-based protein profiling (ABPP) is an unconventional approach that is complementary for gene expression analysis and an ideal utensil in decoding this overflow of genomic information. This approach makes use of synthetic small molecules that covalently modify a set of related proteins and subsequently facilitates identification of the target protein, enabling rapid biochemical analysis and inhibitor discovery. This tutorial review introduces recent advances in the field of ABPP and its applications.
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Affiliation(s)
- Pengyu Yang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 (USA)
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MacGregor BJ. Click-chemistry tagging of proteins in living cells: new possibilities for microbial (meta) proteomics. Environ Microbiol 2014; 16:2353-6. [PMID: 25040824 DOI: 10.1111/1462-2920.12540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Barbara J MacGregor
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
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Martell J, Weerapana E. Applications of copper-catalyzed click chemistry in activity-based protein profiling. Molecules 2014; 19:1378-93. [PMID: 24473203 PMCID: PMC6270908 DOI: 10.3390/molecules19021378] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/09/2014] [Accepted: 01/17/2014] [Indexed: 12/24/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a chemical proteomic technique that enables the interrogation of protein activity directly within complex proteomes. Given the dominant role of posttranslational modifications in regulating protein function in vivo, ABPP provides a direct readout of activity that is not attained through traditional proteomic methods. ABPP relies on the design of covalent binding probes that either target a specific enzyme or a class of enzymes with related function. These covalent warheads are coupled to either fluorophores or biotin groups for visualization and enrichment of these active proteins. The advent of bioorthogonal chemistries, in particular, the copper (I)-catalyzed azide-alkyne cycloaddition (CuAAC), has benefitted the field of ABPP by achieving the following: (1) replacing bulky reporter groups with smaller alkyne or azide groups to promote cell permeability; (2) adding modularity to the system such that a single probe can be diversified with a variety of reporter groups without the need to develop new synthetic routes; and (3) enabling the conjugation of complex linkers to facilitate quantitative proteomic analyses. Here, we summarize recent examples of CuAAC in ABPP that serve to illustrate the contribution of bioorthogonal chemistry to advancing discoveries in this field.
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Affiliation(s)
- Julianne Martell
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA.
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Kuerschner L, Thiele C. Multiple bonds for the lipid interest. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1031-7. [PMID: 24412758 DOI: 10.1016/j.bbalip.2013.12.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/23/2013] [Accepted: 12/26/2013] [Indexed: 10/25/2022]
Abstract
Polyene lipids and alkyne lipids allow study of lipid organization, dynamics and metabolism. Both types of lipids contain multiple bonds as the essential functional group, leading to minimal disturbance of the hydrophobic properties on which the characteristic behavior of lipids is based. Polyene lipids can directly be traced due to their intrinsic fluorescence, while alkyne lipids need the copper-catalyzed click reaction to an azido-reporter for detection. This review describes recent developments in synthesis and application of both types of lipid analogs with emphasis on metabolic tracing and microscopy imaging. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Lars Kuerschner
- Life & Medical Sciences Institute (LIMES), University of Bonn, Carl-Troll-Str. 31, D-53115 Bonn, Germany.
| | - Christoph Thiele
- Life & Medical Sciences Institute (LIMES), University of Bonn, Carl-Troll-Str. 31, D-53115 Bonn, Germany.
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Thirumurugan P, Matosiuk D, Jozwiak K. Click Chemistry for Drug Development and Diverse Chemical–Biology Applications. Chem Rev 2013; 113:4905-79. [DOI: 10.1021/cr200409f] [Citation(s) in RCA: 1309] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Prakasam Thirumurugan
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Dariusz Matosiuk
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Krzysztof Jozwiak
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
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Agüera-González S, Gross CC, Fernández-Messina L, Ashiru O, Esteso G, Hang HC, Reyburn HT, Long EO, Valés-Gómez M. Palmitoylation of MICA, a ligand for NKG2D, mediates its recruitment to membrane microdomains and promotes its shedding. Eur J Immunol 2011; 41:3667-76. [PMID: 21928280 PMCID: PMC3709245 DOI: 10.1002/eji.201141645] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 08/08/2011] [Accepted: 09/15/2011] [Indexed: 11/05/2022]
Abstract
MICA and MICB (MHC-class-I-related chain A/B) are transmembrane proteins expressed in pathological conditions that are ligands for NKG2D, an activating receptor found on cytotoxic lymphocytes. The recognition on target cells of NKG2D ligands leads to the activation of lysis and cytokine secretion by NK cells and T cells. Besides being expressed at the cell surface, MICA/B can be released as soluble proteins. Soluble NKG2D ligands downmodulate expression of the NKG2D receptor on lymphocytes, leading to a diminished cytotoxic response. Prior studies suggested that recruitment of MICA/B molecules to cholesterol-enriched microdomains was an important factor regulating the proteolytic release of these molecules. We now show that recruitment of MICA to these microdomains depends on palmitoylation of two cysteine residues that allow MICA molecules to reside in the membrane in the same domains as caveolin-1. Compared with WT molecules, nonpalmitoylated mutant MICA molecules were shed to the supernatant with low efficiency; however, both WT and mutant MICA were able to trigger NK cell cytotoxicity. These data suggest that the presence of NKG2D ligands at the plasma membrane is sufficient to activate cytotoxicity and reflect the need of different ligands to exploit different cellular pathways to reach the cell surface upon different stress situations.
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Affiliation(s)
- Sonia Agüera-González
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Catharina C. Gross
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Lola Fernández-Messina
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK
- Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Omodele Ashiru
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Gloria Esteso
- Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Howard C. Hang
- The Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY, USA
| | - Hugh T. Reyburn
- Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Eric O. Long
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Mar Valés-Gómez
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK
- Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
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Truong TH, Garcia FJ, Seo YH, Carroll KS. Isotope-coded chemical reporter and acid-cleavable affinity reagents for monitoring protein sulfenic acids. Bioorg Med Chem Lett 2011; 21:5015-20. [PMID: 21601453 DOI: 10.1016/j.bmcl.2011.04.115] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 04/21/2011] [Accepted: 04/25/2011] [Indexed: 12/27/2022]
Abstract
We have developed an approach that allows relative quantification of protein sulfenic acids using a pair of light and heavy isotope labled probes, DAz-2 and d(6)-DAz-2. In conjunction with a new complementary acid-cleavable linker, Yn-ACL, we demonstrate that tagged peptides are successfully labeled, enriched, and fully characterized by LC-MS/MS analysis. Overall, this method can be applied to map sites of cysteine oxidation and compare protein sulfenylation in normal and disease states.
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Affiliation(s)
- Thu H Truong
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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Garner AL, Janda KD. cat-ELCCA: a robust method to monitor the fatty acid acyltransferase activity of ghrelin O-acyltransferase (GOAT). Angew Chem Int Ed Engl 2010; 49:9630-4. [PMID: 20845345 PMCID: PMC3485397 DOI: 10.1002/anie.201003387] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Assays armed with catalytic signal amplification have arisen as superior systems for ultrasensitive detection of analytes. Here we describe a conceptually new enzyme assay based on cat-ELISA, catalytic assay using enzyme-linked click chemistry assay (cat-ELCCA), where an enzyme-linked azide is utilized to arm the assay with catalytic fluorescence signal amplification. Using this assay technology, we have developed the first potentially high-throughput screen for the recently disclosed acyltransferase, ghrelin O -acyltransferase (GOAT).
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Affiliation(s)
- Amanda L. Garner
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology and The Worm Institute for Research and Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 (USA) Fax: (+1) 858-784-2595
| | - Kim D. Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology and The Worm Institute for Research and Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 (USA) Fax: (+1) 858-784-2595
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Garner AL, Janda KD. cat-ELCCA: A Robust Method To Monitor the Fatty Acid Acyltransferase Activity of Ghrelin O-Acyltransferase (GOAT). Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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13
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Schittmayer M, Birner-Gruenberger R. Functional proteomics in lipid research: Lipases, lipid droplets and lipoproteins. J Proteomics 2009; 72:1006-18. [DOI: 10.1016/j.jprot.2009.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 05/06/2009] [Accepted: 05/19/2009] [Indexed: 01/22/2023]
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Raghavan AS, Hang HC. Seeing small molecules in action with bioorthogonal chemistry. Drug Discov Today 2009; 14:178-84. [DOI: 10.1016/j.drudis.2008.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 09/17/2008] [Accepted: 09/30/2008] [Indexed: 10/21/2022]
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