1
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Luu T, Gristwood K, Knight JC, Jörg M. Click Chemistry: Reaction Rates and Their Suitability for Biomedical Applications. Bioconjug Chem 2024; 35:715-731. [PMID: 38775705 PMCID: PMC11191409 DOI: 10.1021/acs.bioconjchem.4c00084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024]
Abstract
Click chemistry has become a commonly used synthetic method due to the simplicity, efficiency, and high selectivity of this class of chemical reactions. Since their initial discovery, further click chemistry methods have been identified and added to the toolbox of click chemistry reactions for biomedical applications. However, selecting the most suitable reaction for a specific application is often challenging, as multiple factors must be considered, including selectivity, reactivity, biocompatibility, and stability. Thus, this review provides an overview of the benefits and limitations of well-established click chemistry reactions with a particular focus on the importance of considering reaction rates, an often overlooked criterion with little available guidance. The importance of understanding each click chemistry reaction beyond simply the reaction speed is discussed comprehensively with reference to recent biomedical research which utilized click chemistry. This review aims to provide a practical resource for researchers to guide the selection of click chemistry classes for different biomedical applications.
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Affiliation(s)
- Tracey Luu
- Medicinal
Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Katie Gristwood
- School
of Natural & Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, U.K.
| | - James C. Knight
- School
of Natural & Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, U.K.
| | - Manuela Jörg
- Medicinal
Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- School
of Natural & Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, U.K.
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2
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Ali MY, Bar-Peled L. Chemical proteomics to study metabolism, a reductionist approach applied at the systems level. Cell Chem Biol 2024; 31:446-451. [PMID: 38518745 DOI: 10.1016/j.chembiol.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/02/2023] [Accepted: 02/28/2024] [Indexed: 03/24/2024]
Abstract
Cellular metabolism encompasses a complex array of interconnected biochemical pathways that are required for cellular homeostasis. When dysregulated, metabolism underlies multiple human pathologies. At the heart of metabolic networks are enzymes that have been historically studied through a reductionist lens, and more recently, using high throughput approaches including genomics and proteomics. Merging these two divergent viewpoints are chemical proteomic technologies, including activity-based protein profiling, which combines chemical probes specific to distinct enzyme families or amino acid residues with proteomic analysis. This enables the study of metabolism at the network level with the precision of powerful biochemical approaches. Herein, we provide a primer on how chemical proteomic technologies custom-built for studying metabolism have unearthed fundamental principles in metabolic control. In parallel, these technologies have leap-frogged drug discovery through identification of novel targets and drug specificity. Collectively, chemical proteomics technologies appear to do the impossible: uniting systematic analysis with a reductionist approach.
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Affiliation(s)
- Md Yousuf Ali
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Liron Bar-Peled
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA.
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3
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Ganz D, Geng P, Wagenknecht HA. The Efficiency of Metabolic Labeling of DNA by Diels-Alder Reactions with Inverse Electron Demand: Correlation with the Size of Modified 2'-Deoxyuridines. ACS Chem Biol 2023; 18:1054-1059. [PMID: 36921617 DOI: 10.1021/acschembio.3c00079] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
A selection of four different 2'-deoxyuridines with three different dienophiles of different sizes was synthesized. Their inverse electron demand Diels-Alder reactivity increases from k2 = 0.15 × 10-2 M-1 s-1 to k2 = 105 × 10-2 M-1 s-1 with increasing ring strain of the dienophiles. With a fluorogenic tetrazine-modified cyanine-styryl dye as reactive counterpart the fluorescence turn-on ratios lie in the range of 21-48 suitable for wash-free cellular imaging. The metabolic DNA labeling was visualized by a dot blot on a semiquantitative level and by confocal fluorescence microscopy on a qualitative level. A clear correlation between the steric demand of the dienophiles and the incorporation efficiency of the modified 2'-deoxyuridines into cellular DNA was observed. Even 2'-deoxyuridines with larger dienophiles, such as norbornene and cyclopropene, were incorporated to a detectable level into the nascent genomic DNA. This was achieved by an optimized way of cell culturing. This expands the toolbox of modified nucleosides for metabolic labeling of nucleic acids in general.
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Affiliation(s)
- Dorothée Ganz
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Philipp Geng
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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4
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Wu Q, Dong S, Xuan W. N-Glycan Engineering: Constructing the N-GlcNAc Stump. Chembiochem 2023; 24:e202200388. [PMID: 35977913 DOI: 10.1002/cbic.202200388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/17/2022] [Indexed: 01/05/2023]
Abstract
N-Glycosylation is often essential for the structure and function of proteins. However, N-glycosylated proteins from natural sources exhibit considerable heterogeneity in the appended oligosaccharides, bringing daunting challenges to corresponding basic research and therapeutic applications. To address this issue, various synthetic, enzymatic, and chemoenzymatic approaches have been elegantly designed. Utilizing the endoglycosidase-catalyzed transglycosylation method, a single N-acetylglucosamine (N-GlcNAc, analogous to a tree stump) on proteins can be converted to various homogeneous N-glycosylated forms, thereby becoming the focus of research efforts. In this concept article, we briefly introduce the methods that allow the generation of N-GlcNAc and its close analogues on proteins and peptides and highlight the current challenges and opportunities the scientific community is facing.
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Affiliation(s)
- Qifan Wu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, and, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China.,School of Life Sciences, Tianjin University, Tianjin, 300072, P. R. China
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5
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Sheng A, Yang J, Tang L, Niu L, Cheng L, Zeng Y, Chen X, Zhang J, Li G. Hydrazone chemistry-mediated CRISPR/Cas12a system for bacterial analysis. Nucleic Acids Res 2022; 50:10562-10570. [PMID: 36156138 PMCID: PMC9561268 DOI: 10.1093/nar/gkac809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/21/2022] [Accepted: 09/09/2022] [Indexed: 11/29/2022] Open
Abstract
In this study, a hydrazone chemistry-mediated clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 12a (Cas12a) system has been proposed for the fist time and constructed. In our system, hydrazone chemistry is designed and employed to accelerate the formation of a whole activation strand by taking advantage of the proximity effect induced by complementary base pairing, thus activating the CRISPR/Cas12a system quickly and efficiently. Moreover, the introduction of hydrazone chemistry can improve the specificity of the CRISPR/Cas12a system, allowing it to effectively distinguish single-base mismatches. The established system has been further applied to analyze Pseudomonas aeruginosa by specific recognition of the probe strand with a characteristic fragment in 16S rDNA to release the hydrazine group-modified activation strand. The method shows a wide linear range from 3.8 × 102 colony-forming units (CFU)/ml to 3.8 × 106 CFU/ml, with the lowest detection limit of 24 CFU/ml. Therefore, the introduction of hydrazone chemistry may also broaden the application of the CRISPR/Cas12a system.
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Affiliation(s)
- Anzhi Sheng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China.,Department of Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, PR China
| | - Jingyi Yang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Longfei Tang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Lili Niu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Liangfen Cheng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Yujing Zeng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, PR China
| | - Xu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Juan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Genxi Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, PR China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, PR China
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6
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Wu Q, Dong W, Miao H, Wang Q, Dong S, Xuan W. Site‐Specific Protein Modification with Reducing Carbohydrates. Angew Chem Int Ed Engl 2022; 61:e202116545. [DOI: 10.1002/anie.202116545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Indexed: 01/13/2023]
Affiliation(s)
- Qifan Wu
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Weidong Dong
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Hui Miao
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
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7
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Wu Q, Dong W, Miao H, Wang Q, Dong S, Xuan W. Site‐Specific Protein Modification with Reducing Carbohydrates. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qifan Wu
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Weidong Dong
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Hui Miao
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
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8
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Kijewska M, Koch T, Waliczek M, Konieczny A, Stefanowicz P, Szewczuk Z. Selective ESI-MS detection of carbonyl containing compounds by aminooxyacetic acid immobilized on a resin. Anal Chim Acta 2021; 1176:338767. [PMID: 34399903 DOI: 10.1016/j.aca.2021.338767] [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: 04/22/2021] [Revised: 05/28/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
There are numerous examples of bioactive compounds containing carbonyl groups including modified proteins with oxidation of side chain of amino acid residues to aldehyde/ketone groups which are frequently considered as markers of oxidative stress. The carbonyl unit can be also distinguished as a substructure in many illegal drugs including anabolic steroids as well as cations derivatives. Based on chemoselective formation of oximes by solid phase immobilized hydroxylamine derivatives we proposed the protocol for derivatization and selective detection of carbonylated compounds in human serum albumin hydrolysate as a complex peptide mixture and of testosterone in urine samples. This allowed for the removal of the matrix and the qualitative and quantitative analysis of the derivatized analyte by LC-MS/MS (or LC-MRM). Herein we report the preparation and chemical characterization of a novel, ChemMatrix - based resin functionalized with aminooxyacetic acid (AOA). The hydroxylamine moiety in this resin is combined with a peptide linker (GRG) containing an arginine residue to enhance the ionization efficiency. Application of an isotopically labeled carbonylated peptide ((H-Leu-Val-Thr(O)-Asp-Leu-Thr-Lys [13C6,15N2]-OH and testosterone-d3 allowed us to carry out quantitative analyses of detected compounds. Our method is general and may be applied for analysis of carbonylated compounds in biological samples. Our method based on application of functionalized resin allowed to quantify the level of free testosterone in small sample (0.5 mL) of urine, while the non-derivatized testosterone from urine sample was not detected during direct LC-MRM analysis.
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Affiliation(s)
- Monika Kijewska
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland.
| | - Tomasz Koch
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Mateusz Waliczek
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Andrzej Konieczny
- Department of Nephrology and Transplantation Medicine, Wrocław Medical University, Borowska 213, 50-556, Wrocław, Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Zbigniew Szewczuk
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383, Wrocław, Poland
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9
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Chemical (neo)glycosylation of biological drugs. Adv Drug Deliv Rev 2021; 171:62-76. [PMID: 33548302 DOI: 10.1016/j.addr.2021.01.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 02/08/2023]
Abstract
Biological drugs, specifically proteins and peptides, are a privileged class of medicinal agents and are characterized with high specificity and high potency of therapeutic activity. However, biologics are fragile and require special care during storage, and are often modified to optimize their pharmacokinetics in terms of proteolytic stability and blood residence half-life. In this review, we showcase glycosylation as a method to optimize biologics for storage and application. Specifically, we focus on chemical glycosylation as an approach to modify biological drugs. We present case studies that illustrate the success of this methodology and specifically address the highly important question: does connectivity within the glycoconjugate have to be native or not? We then present the innovative methods of chemical glycosylation of biologics and specifically highlight the emerging and established protecting group-free methodologies of glycosylation. We discuss thermodynamic origins of protein stabilization via glycosylation, and analyze in detail stabilization in terms of proteolytic stability, aggregation upon storage and/or heat treatment. Finally, we present a case study of protein modification using sialic acid-containing glycans to avoid hepatic clearance of biological drugs. This review aims to spur interest in chemical glycosylation as a facile, powerful tool to optimize proteins and peptides as medicinal agents.
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10
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Congdon MD, Gildersleeve JC. Enhanced Binding and Reduced Immunogenicity of Glycoconjugates Prepared via Solid-State Photoactivation of Aliphatic Diazirine Carbohydrates. Bioconjug Chem 2020; 32:133-142. [PMID: 33325683 DOI: 10.1021/acs.bioconjchem.0c00555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological conjugation is an important tool employed for many basic research and clinical applications. While useful, common methods of biological conjugation suffer from a variety of limitations, such as (a) requiring the presence of specific surface-exposed residues, such as lysines or cysteines, (b) reducing protein activity, and/or (c) reducing protein stability and solubility. Use of photoreactive moieties including diazirines, azides, and benzophenones provide an alternative, mild approach to conjugation. Upon irradiation with UV and visible light, these functionalities generate highly reactive carbenes, nitrenes, and radical intermediates. Many of these will couple to proteins in a non-amino-acid-specific manner. The main hurdle for photoactivated biological conjugation is very low yield. In this study, we developed a solid-state method to increase conjugation efficiency of diazirine-containing carbohydrates to proteins. Using this methodology, we produced multivalent carbohydrate-protein conjugates with unaltered protein charge and secondary structure. Compared to carbohydrate conjugates prepared with amide linkages to lysine residues using standard NHS conjugation, the photoreactive prepared conjugates displayed up to 100-fold improved binding to lectins and diminished immunogenicity in mice. These results indicate that photoreactive bioconjugation could be especially useful for in vivo applications, such as lectin targeting, where high binding affinity and low immunogenicity are desired.
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Affiliation(s)
- Molly D Congdon
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Jeffrey C Gildersleeve
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
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11
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Jiang T, Laughlin ST. Enzyme- or light-triggered cyclopropenes for bioorthogonal ligation. Methods Enzymol 2020; 641:1-34. [PMID: 32713519 DOI: 10.1016/bs.mie.2020.04.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Since first reported at the beginning of the 21st century, bioorthogonal reactions have become powerful tools for investigating biological systems. Here, we review several classic and current bioorthogonal reactions, including the Staudinger-Bertozzi ligation, strain-promoted azide-alkyne cycloaddition (SPAAC), 1,3-dipolar cycloaddition, and tetrazine-alkene ligation. We discuss the capabilities and limitations of the subset of current bioorthogonal reactions that can be "turned on" by exposure to light or an enzyme. Finally, we focus on our recently developed turn-on cyclopropenes, which can be activated for reaction with tetrazines by exposure to light or enzymes, like nitroreductase, depending on the modular reaction caging group appended to the cyclopropene. We discuss the caged cyclopropene's molecular design and synthesis, and we discuss experiments to evaluate and verify reactivity both in vitro and in vivo.
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Affiliation(s)
- Ting Jiang
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States
| | - Scott T Laughlin
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, United States.
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12
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Wang P, Xue T, Sheng A, Cheng L, Zhang J. Application of Chemoselective Ligation in Biosensing. Crit Rev Anal Chem 2020; 52:170-193. [DOI: 10.1080/10408347.2020.1791044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Pei Wang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
- Shanghai Key Laboratory of Bio-Energy Crops, Shanghai University, Shanghai, P. R. China
| | - Tianxiang Xue
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Anzhi Sheng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Liangfen Cheng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Juan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
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13
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Schilling KM, Ubilla-Rodriguez NC, Wells CW, Millhauser GL. Production of Artificially Doubly Glycosylated, 15N Labeled Prion Protein for NMR Studies Using a pH-Scanning Volatile Buffer System. J Org Chem 2020; 85:1687-1690. [PMID: 31692356 DOI: 10.1021/acs.joc.9b02430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterially expressed proteins used in NMR studies lack glycans, and proteins from other organisms are neither 15N labeled nor glycosylated homogeneously. Here, we add two artificial glycans to uniformly 15N labeled prion protein using a buffer system that evolves over a pH range to accommodate the conflicting pH requirements of the substrate and enzymes without the need to fine-tune buffer conditions. NMR and CD spectroscopy of the protein indicates that the glycans do not influence its fold.
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Affiliation(s)
- Kevin M Schilling
- Department of Chemistry and Biochemistry , University of California , Santa Cruz , California 95064 , United States
| | - Natalia C Ubilla-Rodriguez
- Department of Chemistry and Biochemistry , University of California , Santa Cruz , California 95064 , United States
| | - Conner W Wells
- Department of Chemistry and Biochemistry , University of California , Santa Cruz , California 95064 , United States
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry , University of California , Santa Cruz , California 95064 , United States
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14
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Ogunwale MA, Knipp RJ, Evrard CN, Thompson LM, Nantz MH, Fu XA. The Influence of β-Ammonium Substitution on the Reaction Kinetics of Aminooxy Condensations with Aldehydes and Ketones. Chemphyschem 2019; 20:815-822. [PMID: 30725495 DOI: 10.1002/cphc.201801143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/05/2019] [Indexed: 11/06/2022]
Abstract
The click-chemistry capture of volatile aldehydes and ketones by ammonium aminooxy compounds has proven to be an efficient means of analyzing the carbonyl subset in complex mixtures, such as exhaled breath or environmental air. In this work, we examine the carbonyl condensation reaction kinetics of three aminooxy compounds with varying β-ammonium ion substitution using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). We determined the activation energies for the reactions of the aminooxy compounds ATM, ADMH and AMAH with a panel of ketones and aldehydes that included acrolein and crotonaldehyde. The measurements indicate that the activation energies for the oximation reactions are quite low, less than 75 kJ mol-1 . ADMH is observed to react the fastest with the carbonyls studied. We postulate this result may be attributed to the ADMH ammonium proton effecting a Brønsted-Lowry acid-catalyzed elimination of water during the rate-determining step of oxime ether formation. A theoretical study of oxime ether formation is presented to explain the enhanced reactivity of ADMH relative to the tetraalkylammonium analog ATM.
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Affiliation(s)
- Mumiye A Ogunwale
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA
| | - Ralph J Knipp
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA
| | - Clint N Evrard
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA
| | - Lee M Thompson
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA
| | - Michael H Nantz
- Department of Chemistry, University of Louisville, Louisville, KY 40208, USA
| | - Xiao-An Fu
- Department of Chemical Engineering, University of Louisville, Louisville, KY 40208, USA
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15
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Abstract
Delivery remains a major obstacle restricting the potential action of small molecular drugs as well as novel biologics which cannot readily enter cells without the help of a vector. A successful active delivery process involves three steps: (a) tagging the drug with a vector, (b) effective trafficking of this [drug-vector] conjugate through biological barriers, and finally (c) controlled drug release. While covalent bond formation and/or supramolecular association is involved in the making of the [drug-vector] conjugate, the final step requires precisely a controlled dissociation in order to trigger drug release. Therefore, in pursuit of smart, effective, and nontoxic delivery systems, it has become widely recognized that control over dynamic self-assembly could unleash the efficacy of artificial vectors. In this Account, I discuss our endeavors, and those of colleagues, in the recent implementation of Dynamic Covalent Chemistry (DCvC) in delivery applications. DCvC exploits reversible covalent reactions to generate covalent systems that can self-fabricate, adapt, respond, and fall apart in a controlled fashion. A privileged set of reversible covalent reactions has emerged in the community working on delivery applications and is based on condensation reactions (imine, acylhydrazone, oxime), and disulfide and boronate ester formations. The latest developments making this chemistry particularly attractive for such a DCvC approach are discussed. The rational justifying the potential of DCvC in delivery is based on the principle that using such reversible covalent reactions afford transient [drug-vector] conjugates which form spontaneously and chemoselectively, then adapt and self-correct their structure during self-assembly and trafficking thanks to the dynamic nature of the reversible covalent bonds, and finally respond to physicochemical stimuli such as pH and redox changes, thereby enabling controlled dissociation and concomitant drug release. For these reasons, DCvC has recently emerged as a leverage tool with growing prospects for advancing toward smarter delivery systems. The implementation of DCvC can follow three approaches that are discussed herein: (1) dynamic covalent bioconjugates, involving the transient covalent conjugation with a vector, (2) dynamic covalent vectors, involving the controlled dynamic and adaptive assembly and disassembly of vectors that complex drugs through supramolecular association, and (3) dynamic covalent targeting, involving the transient chemoselective formation of covalent bonds with the constituents of cell membranes. While DCvC has already attracted interest in material sciences, the recent results described in this Account showcase the vast potential of DCvC in biological sciences, and in particular in delivery applications where self-fabricated, adaptive, and responsive devices are of utmost importance.
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Affiliation(s)
- Sébastien Ulrich
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
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16
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Abstract
Glycosylation is one of the most prevalent posttranslational modifications that profoundly affects the structure and functions of proteins in a wide variety of biological recognition events. However, the structural complexity and heterogeneity of glycoproteins, usually resulting from the variations of glycan components and/or the sites of glycosylation, often complicates detailed structure-function relationship studies and hampers the therapeutic applications of glycoproteins. To address these challenges, various chemical and biological strategies have been developed for producing glycan-defined homogeneous glycoproteins. This review highlights recent advances in the development of chemoenzymatic methods for synthesizing homogeneous glycoproteins, including the generation of various glycosynthases for synthetic purposes, endoglycosidase-catalyzed glycoprotein synthesis and glycan remodeling, and direct enzymatic glycosylation of polypeptides and proteins. The scope, limitation, and future directions of each method are discussed.
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Affiliation(s)
- Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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17
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Novoa-Carballal R, Carretero A, Pacheco R, Reis RL, Pashkuleva I. Star-Like Glycosaminoglycans with Superior Bioactivity Assemble with Proteins into Microfibers. Chemistry 2018; 24:14341-14345. [DOI: 10.1002/chem.201802243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Ramon Novoa-Carballal
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; University of Minho, Headquarters of the European Institute of, Excellence on Tissue Engineering and Regenerative Medicine, Ave. Park; 4805-017 Barco Guimarães, Portugal. ICVS/3B's-PT, Government Associate Laboratory, Braga/Guimarães Portugal
| | - Agatha Carretero
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; University of Minho, Headquarters of the European Institute of, Excellence on Tissue Engineering and Regenerative Medicine, Ave. Park; 4805-017 Barco Guimarães, Portugal. ICVS/3B's-PT, Government Associate Laboratory, Braga/Guimarães Portugal
| | - Raul Pacheco
- Malvern/Micrcal Products; Enigma Business Park; Grovewood Road Malvern WR141XZ UK
| | - Rui L. Reis
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; University of Minho, Headquarters of the European Institute of, Excellence on Tissue Engineering and Regenerative Medicine, Ave. Park; 4805-017 Barco Guimarães, Portugal. ICVS/3B's-PT, Government Associate Laboratory, Braga/Guimarães Portugal
- The Discoveries Centre for Regenerative and Precision Medicine; Headquarters at University of Minho, Ave. Park; 4805-017 Barco, Guimarães Portugal
| | - Iva Pashkuleva
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; University of Minho, Headquarters of the European Institute of, Excellence on Tissue Engineering and Regenerative Medicine, Ave. Park; 4805-017 Barco Guimarães, Portugal. ICVS/3B's-PT, Government Associate Laboratory, Braga/Guimarães Portugal
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18
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Pifferi C, Daskhan GC, Fiore M, Shiao TC, Roy R, Renaudet O. Aminooxylated Carbohydrates: Synthesis and Applications. Chem Rev 2017; 117:9839-9873. [PMID: 28682060 DOI: 10.1021/acs.chemrev.6b00733] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Among other classes of biomolecules, carbohydrates and glycoconjugates are widely involved in numerous biological functions. In addition to addressing the related synthetic challenges, glycochemists have invested intense efforts in providing access to structures that can be used to study, activate, or inhibit these biological processes. Over the past few decades, aminooxylated carbohydrates have been found to be key building blocks for achieving these goals. This review provides the first in-depth overview covering several aspects related to the syntheses and applications of aminooxylated carbohydrates. After a brief introduction to oxime bonds and their relative stabilities compared to related C═N functions, synthetic aspects of oxime ligation and methodologies for introducing the aminooxy functionality onto both glycofuranosyls and glycopyranosyls are described. The subsequent section focuses on biological applications involving aminooxylated carbohydrates as components for the construcion of diverse architectures. Mimetics of natural structures represent useful tools for better understanding the features that drive carbohydrate-receptor interaction, their biological output and they also represent interesting structures with improved stability and tunable properties. In the next section, multivalent structures such as glycoclusters and glycodendrimers obtained through oxime ligation are described in terms of synthetic design and their biological applications such as immunomodulators. The second-to-last section discusses miscellaneous applications of oxime-based glycoconjugates, such as enantioselective catalysis and glycosylated oligonucleotides, and conclusions and perspectives are provided in the last section.
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Affiliation(s)
- Carlo Pifferi
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Gour Chand Daskhan
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Michele Fiore
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France
| | - Tze Chieh Shiao
- Pharmaqam, Department of Chemistry, Université du Québec à Montreal , P.O. Box 8888, Succursale Centre-ville, Montréal, Québec H3C 3P8, Canada
| | - René Roy
- Pharmaqam, Department of Chemistry, Université du Québec à Montreal , P.O. Box 8888, Succursale Centre-ville, Montréal, Québec H3C 3P8, Canada
| | - Olivier Renaudet
- Université Grenoble Alpes, CNRS, DCM UMR 5250 , F-38000 Grenoble, France.,Institut Universitaire de France , 103 Boulevard Saint-Michel, 75005 Paris, France
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19
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Villadsen K, Martos-Maldonado MC, Jensen KJ, Thygesen MB. Chemoselective Reactions for the Synthesis of Glycoconjugates from Unprotected Carbohydrates. Chembiochem 2017; 18:574-612. [DOI: 10.1002/cbic.201600582] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Klaus Villadsen
- Department of Chemistry; University of Copenhagen; Faculty of Science; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Manuel C. Martos-Maldonado
- Department of Chemistry; University of Copenhagen; Faculty of Science; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Knud J. Jensen
- Department of Chemistry; University of Copenhagen; Faculty of Science; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
| | - Mikkel B. Thygesen
- Department of Chemistry; University of Copenhagen; Faculty of Science; Thorvaldsensvej 40 1871 Frederiksberg C Denmark
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20
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Chelushkin PS, Leko MV, Dorosh MY, Burov SV. Oxime ligation in acetic acid: efficient synthesis of aminooxy-peptide conjugates. J Pept Sci 2016; 23:13-15. [PMID: 27699914 DOI: 10.1002/psc.2931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/13/2016] [Accepted: 09/15/2016] [Indexed: 11/09/2022]
Abstract
Oxime ligation is a powerful tool in various bioconjugation strategies. Nevertheless, high reaction rates and quantitative yields are typically reported for aldehyde-derived compounds. In contrary, keto groups react much slower, with quantitative yields achieved at 5 h for low-molecular weight compounds and more than 15 h for polymers or dendrimers. In this communication, we report that oxime ligation proceeds rapidly with quantitative (>95%) conversion within 1.5-2 h in pure acetic acid. The practical utility of suggested technique is illustrated by the synthesis of peptide-steroid and peptide-polymer conjugates of model aminooxy-peptides. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Pavel S Chelushkin
- Institute of Macromolecular Compounds, RAS, Bolshoy prospekt 31, Saint Petersburg, 199004, Russia
| | - Maria V Leko
- Institute of Macromolecular Compounds, RAS, Bolshoy prospekt 31, Saint Petersburg, 199004, Russia
| | - Marina Yu Dorosh
- Institute of Macromolecular Compounds, RAS, Bolshoy prospekt 31, Saint Petersburg, 199004, Russia
| | - Sergey V Burov
- Institute of Macromolecular Compounds, RAS, Bolshoy prospekt 31, Saint Petersburg, 199004, Russia
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21
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Russo L, Cipolla L. Glycomics: New Challenges and Opportunities in Regenerative Medicine. Chemistry 2016; 22:13380-8. [DOI: 10.1002/chem.201602156] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Laura Russo
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milano Italy
| | - Laura Cipolla
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milano Italy
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22
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Giddens JP, Lomino JV, Amin MN, Wang LX. Endo-F3 Glycosynthase Mutants Enable Chemoenzymatic Synthesis of Core-fucosylated Triantennary Complex Type Glycopeptides and Glycoproteins. J Biol Chem 2016; 291:9356-70. [PMID: 26966183 DOI: 10.1074/jbc.m116.721597] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 11/06/2022] Open
Abstract
Chemoenzymatic synthesis is emerging as a promising approach to the synthesis of homogeneous glycopeptides and glycoproteins highly demanded for functional glycomics studies, but its generality relies on the availability of a range of enzymes with high catalytic efficiency and well defined substrate specificity. We describe in this paper the discovery of glycosynthase mutants derived from Elizabethkingia meningoseptica endoglycosidase F3 (Endo-F3) of the GH18 family, which are devoid of the inherent hydrolytic activity but are able to take glycan oxazolines for transglycosylation. Notably, the Endo-F3 D165A and D165Q mutants demonstrated high acceptorsubstrate specificity toward α1,6-fucosyl-GlcNAc-Asn or α1,6-fucosyl-GlcNAc-polypeptide in transglycosylation, enabling a highly convergent synthesis of core-fucosylated, complex CD52 glycopeptide antigen. The Endo-F3 mutants were able to use both bi- and triantennary glycan oxazolines as substrates for transglycosylation, in contrast to previously reported endoglycosidases derived from Endo-S, Endo-M, Endo-D, and Endo-A mutants that could not recognize triantennary N-glycans. Using rituximab as a model system, we have further demonstrated that the Endo-F3 mutants are highly efficient for glycosylation remodeling of monoclonal antibodies to produce homogeneous intact antibody glycoforms. Interestingly, the new triantennary glycan glycoform of antibody showed much higher affinity for galectin-3 than that of the commercial antibody. The Endo-F3 mutants represent the first endoglycosidase-based glycosynthases capable of transferring triantennary complex N-glycans, which would be very useful for glycoprotein synthesis and glycosylation remodeling of antibodies.
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Affiliation(s)
- John P Giddens
- From the Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201 and the Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Joseph V Lomino
- From the Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201 and
| | - Mohammed N Amin
- From the Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201 and the Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Lai-Xi Wang
- From the Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201 and the Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
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23
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Liu S, Edgar KJ. Staudinger Reactions for Selective Functionalization of Polysaccharides: A Review. Biomacromolecules 2015; 16:2556-71. [DOI: 10.1021/acs.biomac.5b00855] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Shu Liu
- Departments of †Chemistry, §Sustainable Biomaterials and the Macromolecules and Interfaces Institute, Virginia Tech, 230 Cheatham Hall, Blacksburg, Virginia 24061, United States
| | - Kevin J. Edgar
- Departments of †Chemistry, §Sustainable Biomaterials and the Macromolecules and Interfaces Institute, Virginia Tech, 230 Cheatham Hall, Blacksburg, Virginia 24061, United States
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24
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Yang M, Yu XW, Zheng H, Sha C, Zhao C, Qian M, Xu Y. Role of N-linked glycosylation in the secretion and enzymatic properties of Rhizopus chinensis lipase expressed in Pichia pastoris. Microb Cell Fact 2015; 14:40. [PMID: 25880561 PMCID: PMC4417512 DOI: 10.1186/s12934-015-0225-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/11/2015] [Indexed: 11/29/2022] Open
Abstract
Background The methylotrophic yeast, Pichia pastoris, is widely used as a useful experimental tool in protein engineering and production. It is common for proteins expressed in P. pastoris to exhibit N-glycosylation. In recent years, glycosylation studies in P. pastoris have attracted increasing attention from scholars. Rhizopus chinensis lipase (RCL) is one of the most important industrial lipases, and it has four potential N-linked glycosylation sites. The aim of the present study was to determine whether RCL undergoes asparagine-linked (N-linked) glycosylation and to examine the role of this modification in RCL expression and function. Results In this study, we demonstrated that RCL expressed in Pichia pastoris was N-glycosylated at the sites N-14, N-48 and N-60. The majority of the sites N-14 and N-60 were glycosylated, but the glycosylation degree of the site N-48 was only a very small portion. The glycan on N-60 played a key role in the expression and secretion of RCL. RT-PCR results showed that the mRNA level of proRCLCN60Q remained unchanged even though the protein secretion was hampered. Although the N-glycan on N-14 had no effect on the secretion of RCL, this glycan was beneficial for the lipase catalytic activity. On the other hand, the little amount of N-glycan on N-48 had no effect both on the secretion and activity of RCL in P. pastoris. Moreover, the thermostability analysis of RCL revealed that the lipase with more N-glycan was more thermostable. Conclusions RCL was N-glycosylated when expressed in P. pastoris. The N-glycans of RCL on the different sites had different functions for the secretion and enzymatic properties of the lipase. Our report may also provide theoretical support for the improvement of enzyme expression and stability based on the N-linked glycosylation modification to meet the future needs of the biotechnological industry.
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Affiliation(s)
- Min Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China.
| | - Xiao-Wei Yu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China. .,State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China.
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility at Robert wood Johnson medical school and Rutgers, the state university of new jersey, Piscataway, NJ 08854, USA.
| | - Chong Sha
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China.
| | - Caifeng Zhao
- Biological Mass Spectrometry Facility at Robert wood Johnson medical school and Rutgers, the state university of new jersey, Piscataway, NJ 08854, USA.
| | - Meiqian Qian
- Biological Mass Spectrometry Facility at Robert wood Johnson medical school and Rutgers, the state university of new jersey, Piscataway, NJ 08854, USA.
| | - Yan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China. .,State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, China.
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25
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Wang LX, Amin MN. Chemical and chemoenzymatic synthesis of glycoproteins for deciphering functions. ACTA ACUST UNITED AC 2015; 21:51-66. [PMID: 24439206 DOI: 10.1016/j.chembiol.2014.01.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 12/31/2013] [Accepted: 01/02/2014] [Indexed: 12/11/2022]
Abstract
Glycoproteins are an important class of biomolecules involved in a number of biological recognition processes. However, natural and recombinant glycoproteins are usually produced as mixtures of glycoforms that differ in the structures of the pendent glycans, which are difficult to separate in pure glycoforms. As a result, synthetic homogeneous glycopeptides and glycoproteins have become indispensable probes for detailed structural and functional studies. A number of elegant chemical and biological strategies have been developed for synthetic construction of tailor-made, full-size glycoproteins to address specific biological problems. In this review, we highlight recent advances in chemical and chemoenzymatic synthesis of homogeneous glycoproteins. Selected examples are given to demonstrate the applications of tailor-made, glycan-defined glycoproteins for deciphering glycosylation functions.
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Affiliation(s)
- Lai-Xi Wang
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Mohammed N Amin
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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26
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Huber T, Sakmar T. Chemical Biology Methods for Investigating G Protein-Coupled Receptor Signaling. ACTA ACUST UNITED AC 2014; 21:1224-37. [DOI: 10.1016/j.chembiol.2014.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/21/2014] [Accepted: 08/20/2014] [Indexed: 11/26/2022]
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27
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Cui JF, Kung KKY, Ko HM, Hui TW, Wong MK. Silver-Catalyzed Transformation of Propargylic AmineN-Oxides to Enones and Acyloxy KetonesviaIsoxazolinium Intermediates. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201400395] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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28
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Seuyep Ntoukam DH, Luinstra GA, Theato P. Postpolymerization modification of reactive polymers derived from vinylcyclopropane. III. Polymer sequential functionalization using a combination of amines with alkoxyamines, hydrazides, isocyanates, or acyl halides. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/pola.27311] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Denis Hervé Seuyep Ntoukam
- University of Hamburg, Institute for Technical and Macromolecular Chemistry; Bundesstr. 45 D-20146 Hamburg Germany
| | - Gerrit Albert Luinstra
- University of Hamburg, Institute for Technical and Macromolecular Chemistry; Bundesstr. 45 D-20146 Hamburg Germany
| | - Patrick Theato
- University of Hamburg, Institute for Technical and Macromolecular Chemistry; Bundesstr. 45 D-20146 Hamburg Germany
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29
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Tian H, Naganathan S, Kazmi MA, Schwartz TW, Sakmar TP, Huber T. Bioorthogonal fluorescent labeling of functional G-protein-coupled receptors. Chembiochem 2014; 15:1820-9. [PMID: 25045132 DOI: 10.1002/cbic.201402193] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Indexed: 11/12/2022]
Abstract
Novel methods are required for site-specific, quantitative fluorescent labeling of G-protein-coupled receptors (GPCRs) and other difficult-to-express membrane proteins. Ideally, fluorescent probes should perturb the native structure and function as little as possible. We evaluated bioorthogonal reactions to label genetically encoded p-acetyl-L-phenylalanine (AcF) or p-azido-L-phenylalanine (azF) residues in receptors heterologously expressed in mammalian cells. We found that keto-selective reagents were not truly bioorthogonal, possibly owing to post-translational protein oxidation reactions. In contrast, the strain-promoted [3+2] azide-alkyne cycloaddition (SpAAC) with dibenzocyclooctyne (DIBO) reagents yielded stoichiometric conjugates with azF-rhodopsin while undergoing negligible background reactions. As one application of this technique, we used Alexa488-rhodopsin to measure the kinetics of ligand uptake and release in membrane-mimetic bicelles using a novel fluorescence-quenching assay.
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Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA)
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30
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Deng K, Takasuka TE, Heins R, Cheng X, Bergeman LF, Shi J, Aschenbrener R, Deutsch S, Singh S, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS). ACS Chem Biol 2014; 9:1470-9. [PMID: 24819174 DOI: 10.1021/cb5000289] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glycoside hydrolases (GHs) are critical to cycling of plant biomass in the environment, digestion of complex polysaccharides by the human gut microbiome, and industrial activities such as deployment of cellulosic biofuels. High-throughput sequencing methods show tremendous sequence diversity among GHs, yet relatively few examples from the over 150,000 unique domain arrangements containing GHs have been functionally characterized. Here, we show how cell-free expression, bioconjugate chemistry, and surface-based mass spectrometry can be used to study glycoside hydrolase reactions with plant biomass. Detection of soluble products is achieved by coupling a unique chemical probe to the reducing end of oligosaccharides in a stable oxime linkage, while the use of (13)C-labeled monosaccharide standards (xylose and glucose) allows quantitation of the derivatized glycans. We apply this oxime-based nanostructure-initiator mass spectrometry (NIMS) method to characterize the functional diversity of GHs secreted by Clostridium thermocellum, a model cellulolytic organism. New reaction specificities are identified, and differences in rates and yields of individual enzymes are demonstrated in reactions with biomass substrates. Numerical analyses of time series data suggests that synergistic combinations of mono- and multifunctional GHs can decrease the complexity of enzymes needed for the hydrolysis of plant biomass during the production of biofuels.
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Affiliation(s)
- Kai Deng
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Taichi E. Takasuka
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Richard Heins
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Xiaoliang Cheng
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lai F. Bergeman
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Jian Shi
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Ryan Aschenbrener
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Sam Deutsch
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Seema Singh
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Kenneth L. Sale
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- University of
California, Berkeley, California 94720, United States
| | - Anup K. Singh
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Brian G. Fox
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Trent R. Northen
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
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31
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Du X, Zhou J, Guvench O, Sangiorgi FO, Li X, Zhou N, Xu B. Supramolecular assemblies of a conjugate of nucleobase, amino acids, and saccharide act as agonists for proliferation of embryonic stem cells and development of zygotes. Bioconjug Chem 2014; 25:1031-5. [PMID: 24798034 PMCID: PMC4068792 DOI: 10.1021/bc500187m] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Indexed: 12/14/2022]
Abstract
The synthetic challenges in glycobiology and glycochemistry hamper the development of glycobiomaterials for biomedicine. Here we report the use of molecular self-assembly to sidestep the laborious synthesis of complex glycans for promoting the proliferation of murine embryonic stem (mES) cells. Our study shows that the supramolecular assemblies of a small molecule conjugate of nucleobase, amino acids, and saccharide, as a de novo glycoconjugate, promote the proliferation of mES cells and the development of zygotes into blastocysts of mouse. Molecular engineering confirms that each motif (i.e., adenine, Arg-Gly-Asp (RGD) domain, and glucosamine) is indispensable for the observed activity of the conjugate. As the first example of using assemblies of the molecular conjugates of multiple fundamental biological building blocks to control cell behaviors, this work illustrates an unprecedented approach to use supramolecular assemblies as multifunctional mimics of glycoconjugates.
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Affiliation(s)
- Xuewen Du
- Department of Chemistry, Brandeis
University, 415 South
Street, Waltham, Massachusetts 02454, United States
- Department of Pharmaceutical
Sciences, University of New England College
of Pharmacy, 716 Stevens
Avenue, Portland, Maine 04102, United States
| | - Jie Zhou
- Department of Chemistry, Brandeis
University, 415 South
Street, Waltham, Massachusetts 02454, United States
- Department of Pharmaceutical
Sciences, University of New England College
of Pharmacy, 716 Stevens
Avenue, Portland, Maine 04102, United States
| | - Olgun Guvench
- Department of Chemistry, Brandeis
University, 415 South
Street, Waltham, Massachusetts 02454, United States
- Department of Pharmaceutical
Sciences, University of New England College
of Pharmacy, 716 Stevens
Avenue, Portland, Maine 04102, United States
| | - Frank O. Sangiorgi
- Department of Chemistry, Brandeis
University, 415 South
Street, Waltham, Massachusetts 02454, United States
- Department of Pharmaceutical
Sciences, University of New England College
of Pharmacy, 716 Stevens
Avenue, Portland, Maine 04102, United States
| | - Xinming Li
- Department of Chemistry, Brandeis
University, 415 South
Street, Waltham, Massachusetts 02454, United States
- Department of Pharmaceutical
Sciences, University of New England College
of Pharmacy, 716 Stevens
Avenue, Portland, Maine 04102, United States
| | - Ning Zhou
- Department of Chemistry, Brandeis
University, 415 South
Street, Waltham, Massachusetts 02454, United States
- Department of Pharmaceutical
Sciences, University of New England College
of Pharmacy, 716 Stevens
Avenue, Portland, Maine 04102, United States
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32
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Sanapala SR, Kulkarni SS. Chemical synthesis of asparagine-linked archaeal N-glycan from Methanothermus fervidus. Chemistry 2014; 20:3578-83. [PMID: 24616211 DOI: 10.1002/chem.201304950] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/02/2014] [Indexed: 12/12/2022]
Abstract
Several N-linked glycoproteins have been identified in archaea and there is growing evidence that the N-glycan is involved in survival and functioning of archaea in extreme conditions. Chemical synthesis of the archaeal N-glycans represents a crucial step towards understanding the putative function of protein glycosylation in archaea. Herein the first total synthesis of the archaeal L-asparagine linked hexasaccharide from Methanothermus fervidus is reported using a highly convergent [3+3] glycosylation approach in high overall yields. The synthesis relies on efficient preparation of regioselectively protected thioglycoside building blocks for orthogonal glycosylations and late stage N-aspartylation.
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Affiliation(s)
- Someswara Rao Sanapala
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076 (India)
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Li C, Key JA, Jia F, Dandapat A, Hur S, Cairo CW. Practical labeling methodology for choline-derived lipids and applications in live cell fluorescence imaging. Photochem Photobiol 2014; 90:686-95. [PMID: 24383866 DOI: 10.1111/php.12234] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 12/24/2013] [Indexed: 12/18/2022]
Abstract
Lipids of the plasma membrane participate in a variety of biological processes, and methods to probe their function and cellular location are essential to understanding biochemical mechanisms. Previous reports have established that phosphocholine-containing lipids can be labeled by alkyne groups through metabolic incorporation. Herein, we have tested alkyne, azide and ketone-containing derivatives of choline as metabolic labels of choline-containing lipids in cells. We also show that 17-octadecynoic acid can be used as a complementary metabolic label for lipid acyl chains. We provide methods for the synthesis of cyanine-based dyes that are reactive with alkyne, azide and ketone metabolic labels. Using an improved method for fluorophore conjugation to azide or alkyne-modified lipids by Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC), we apply this methodology in cells. Lipid-labeled cell membranes were then interrogated using flow cytometry and fluorescence microscopy. Furthermore, we explored the utility of this labeling strategy for use in live cell experiments. We demonstrate measurements of lipid dynamics (lateral mobility) by fluorescence photobleaching recovery (FPR). In addition, we show that adhesion of cells to specific surfaces can be accomplished by chemically linking membrane lipids to a functionalized surface. The strategies described provide robust methods for introducing bioorthogonal labels into native lipids.
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Affiliation(s)
- Caishun Li
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton Alberta, T6G 2G2, Canada
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Ulrich S, Boturyn D, Marra A, Renaudet O, Dumy P. Oxime Ligation: A Chemoselective Click-Type Reaction for Accessing Multifunctional Biomolecular Constructs. Chemistry 2013; 20:34-41. [DOI: 10.1002/chem.201302426] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Pandey BK, Enck S, Price JL. Stabilizing impact of N-glycosylation on the WW domain depends strongly on the Asn-GlcNAc linkage. ACS Chem Biol 2013; 8:2140-4. [PMID: 23937634 DOI: 10.1021/cb4004496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-glycans play important roles in many cellular processes and can increase protein conformational stability in specific structural contexts. Glycosylation (with a single GlcNAc) of the reverse turn sequence Phe-Yyy-Asn-Xxx-Thr at Asn stabilizes the Pin 1 WW domain by -0.85 ± 0.12 kcal mol(-1). Alternative methods exist for attaching carbohydrates to proteins; some occur naturally (e.g., the O-linkage), whereas others use chemoselective ligation reactions to mimic the natural N- or O-linkages. Here, we assess the energetic consequences of replacing the Asn linkage in the glycosylated WW domain with a Gln linkage, with two natural O-linkages, with two unnatural triazole linkages, and with an unnatural α-mercaptoacetamide linkage. Of these alternatives, only glycosylation of the triazole linkages stabilizes WW, and by a smaller amount than N-glycosylation, highlighting the need for caution when using triazole- or α-mercaptoacetamide-linked carbohydrates to mimic native N-glycans, especially where the impact of glycosylation on protein conformational stability is important.
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Affiliation(s)
- Brijesh K. Pandey
- Department of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
| | - Sebastian Enck
- Department of Chemistry and
Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California
92037, United States
| | - Joshua L. Price
- Department of Chemistry and
Biochemistry, Brigham Young University,
Provo, Utah 84602, United States
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Li D, Chiu H, Zhang H, Chan DW. Analysis of serum protein glycosylation by a differential lectin immunosorbant assay (dLISA). Clin Proteomics 2013; 10:12. [PMID: 24015777 PMCID: PMC3847486 DOI: 10.1186/1559-0275-10-12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 08/08/2013] [Indexed: 12/16/2022] Open
Abstract
Background Lectin immunosorbant assays (LISAs) have been widely used for analyzing protein glycosylation. However, the analysis of serum samples by LISAs could suffer from high sample-dependent background noise. The aim of this study is to develop a differential lectin immunosorbant assay (dLISA) with reduced background interferences. Methods For the analysis of protein glycosylation, dLISA establishes a dose–response curve for every serum sample. The sample is split into five aliquots. Four aliquots undergo differential removal of the glycoprotein of interest by immunoprecipitation. Then, all five aliquots are subject to two measurements: protein by immunoassay and protein glycans by LISA. A dose–response curve is established by plotting glycans signals on the y-axis and protein levels on the x-axis for all the aliquots. Slope of the curve, calculated by linear progression analysis and expressed as fluorescence per concentration of protein, is used for the measurement of protein glycosylation in the serum sample. Results/conclusions To demonstrate the feasibility of the dLISA approach, we used recombinant, fucosylated tissue inhibitor of metallopeptidase 1 (TIMP-1) as the target glycoprotein. Magnetic beads based TIMP1 immunoassay and TIMP-1 UEA LISA were developed for the measurement of TIMP1 protein and terminal α1, 2 fucosylated glycans on TIMP1, respectively. Serum samples supplemented with differentially fucosylated recombinant TIMP-1 were used to demonstrate that the slopes measured the TIMP-1 fucosylation, and were less prone to background interference.
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Affiliation(s)
- Danni Li
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
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Lopez M, Bornaghi LF, Poulsen SA. Synthesis of sulfonamide-conjugated glycosyl-amino acid building blocks. Carbohydr Res 2013; 386:78-85. [PMID: 24491845 DOI: 10.1016/j.carres.2013.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 08/16/2013] [Accepted: 08/17/2013] [Indexed: 10/26/2022]
Abstract
The efficient synthesis of novel glycoconjugate amino acid building blocks wherein the amino acid and carbohydrate moieties are linked via a sulfonamide functional group is reported. The general reaction sequence consists of coupling a glycosyl thioacetate to an amino acid methyl ester followed by oxidation and deprotection of the carbohydrate moiety. We demonstrate the synthesis of derivatives from a range of amino acids, with reaction at either the α-amino group of amino acid precursors or the sidechain ε-amino group of lysine precursors.
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Affiliation(s)
- Marie Lopez
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
| | - Laurent F Bornaghi
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
| | - Sally-Ann Poulsen
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia.
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38
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Naganathan S, Ye S, Sakmar TP, Huber T. Site-specific epitope tagging of G protein-coupled receptors by bioorthogonal modification of a genetically encoded unnatural amino acid. Biochemistry 2013; 52:1028-36. [PMID: 23317030 DOI: 10.1021/bi301292h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We developed a general strategy for labeling expressed membrane proteins with a peptide epitope tag and detecting the tagged proteins in native cellular membranes. First, we genetically encoded the unnatural amino acid p-azido-L-phenylalanine (azF) at various specific sites in a G protein-coupled receptor (GPCR), C-C chemokine receptor 5 (CCR5). The reactive azido moiety facilitates Staudinger ligation to a triarylphosphine-conjugated FLAG peptide. We then developed a whole-cell-based enzyme-linked immunosorbent assay approach to detect the modified azF-CCR5 using anti-FLAG mAb. We optimized conditions to achieve labeling and detection of low-abundance GPCRs in live cells. We also performed an accessibility screen to identify azF positions on CCR5 amenable to labeling. Finally, we demonstrate a preparative strategy for obtaining pure bioorthogonally modified GPCRs suitable for single-molecule detection fluorescence experiments. This peptide epitope tagging strategy, which employs genetic encoding and bioorthogonal labeling of azF in live cells, should be useful for studying biogenesis of polytopic membrane proteins and GPCR signaling mechanisms.
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Affiliation(s)
- Saranga Naganathan
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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39
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Paramelle D, Miralles G, Subra G, Martinez J. Chemical cross-linkers for protein structure studies by mass spectrometry. Proteomics 2013; 13:438-56. [PMID: 23255214 DOI: 10.1002/pmic.201200305] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 10/12/2012] [Accepted: 10/22/2012] [Indexed: 12/24/2022]
Abstract
The cross-linking approach combined with MS for protein structure determination is one of the most striking examples of multidisciplinary success. Indeed, it has become clear that the bottleneck of the method was the detection and the identification of low-abundance cross-linked peptides in complex mixtures. Sample treatment or chromatography separation partially addresses these issues. However, the main problem comes from over-represented unmodified peptides, which do not yield any structural information. A real breakthrough was provided by high mass accuracy measurement, because of the outstanding technical developments in MS. This improvement greatly simplified the identification of cross-linked peptides, reducing the possible combinations matching with an observed m/z value. In addition, the huge amount of data collected has to be processed with dedicated software whose role is to propose distance constraints or ideally a structural model of the protein. In addition to instrumentation and algorithms efficiency, significant efforts have been made to design new cross-linkers matching all the requirements in terms of reactivity and selectivity but also displaying probes or reactive systems facilitating the isolation, the detection of cross-links, or the interpretation of MS data. These chemical features are reviewed and commented on in the light of the more recent strategies.
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Affiliation(s)
- David Paramelle
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 3 Research Link, Singapore
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40
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On-Yee Chan A, Lui-Lui Tsai J, Kar-Yan Lo V, Li GL, Wong MK, Che CM. Gold-mediated selective cysteine modification of peptides using allenes. Chem Commun (Camb) 2013; 49:1428-30. [DOI: 10.1039/c2cc38214h] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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41
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Hemantha HP, Narendra N, Sureshbabu VV. Total chemical synthesis of polypeptides and proteins: chemistry of ligation techniques and beyond. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.08.059] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Abstract
Imaging technologies developed in the early 20th century achieved contrast solely by relying on macroscopic and morphological differences between the tissues of interest and the surrounding tissues. Since then, there has been a movement toward imaging at the cellular and molecular level in order to visualize biological processes. This rapidly growing field is known as molecular imaging. In the last decade, many methodologies for imaging proteins have emerged. However, most of these approaches cannot be extended to imaging beyond the proteome. Here, we highlight some of the recently developed technologies that enable imaging of non-proteinaceous molecules in the cell: lipids, signalling molecules, inorganic ions, glycans, nucleic acids, small-molecule metabolites, and protein post-translational modifications such as phosphorylation and methylation.
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Affiliation(s)
- Pamela V. Chang
- Department of Chemistry, University of California, Berkeley, 94720, USA
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, U.S.A
- Howard Hughes Medical Institute, University of California, Berkeley, U.S.A
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43
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Gorityala BK, Lu Z, Leow ML, Ma J, Liu XW. Design of a “Turn-Off/Turn-On” Biosensor: Understanding Carbohydrate-Lectin Interactions for Use in Noncovalent Drug Delivery. J Am Chem Soc 2012; 134:15229-32. [DOI: 10.1021/ja306288p] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Bala Kishan Gorityala
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Zhiqiang Lu
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Min Li Leow
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Jimei Ma
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Xue-Wei Liu
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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44
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Zhang Y, Liu Y, Wang Z, Wang Z, Huang L. The Synthesis of a 2-Deoxy-2-Acetonyl Sugar from its Corresponding Natural Saccharide. JOURNAL OF CHEMICAL RESEARCH 2012. [DOI: 10.3184/174751912x13326765667344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An efficient synthesis of a 2-deoxy-2-acetonyl sugar from its corresponding natural sugar by methallylation of the 2–iodo sugar is reported. The simplified procedure eliminated the need to carry out the reaction under strictly controlled conditions, giving an efficient route for the synthesis of 2-deoxy-2-acetonyl sugar under ordinary laboratory conditions.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences
| | - Yang Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences
| | - Zhijun Wang
- Department of Chemistry, Northwest University, Xi'an 710069, P. R. China
| | - Zhongfu Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences
| | - Linjuan Huang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences
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45
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Wang LX, Lomino JV. Emerging technologies for making glycan-defined glycoproteins. ACS Chem Biol 2012; 7:110-22. [PMID: 22141574 DOI: 10.1021/cb200429n] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein glycosylation is a common and complex posttranslational modification of proteins, which expands functional diversity while boosting structural heterogeneity. Glycoproteins, the end products of such a modification, are typically produced as mixtures of glycoforms possessing the same polypeptide backbone but differing in the site of glycosylation and/or in the structures of pendant glycans, from which single glycoforms are difficult to isolate. The urgent need for glycan-defined glycoproteins in both detailed structure-function relationship studies and therapeutic applications has stimulated an extensive interest in developing various methods for manipulating protein glycosylation. This review highlights emerging technologies that hold great promise in making a variety of glycan-defined glycoproteins, with a particular emphasis in the following three areas: specific glycoengineering of host biosynthetic pathways, in vitro chemoenzymatic glycosylation remodeling, and chemoselective and site-specific glycosylation of proteins.
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Affiliation(s)
- Lai-Xi Wang
- Institute of Human Virology and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Joseph V. Lomino
- Institute of Human Virology and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
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46
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Presolski SI, Hong VP, Finn M. Copper-Catalyzed Azide-Alkyne Click Chemistry for Bioconjugation. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2011; 3:153-162. [PMID: 22844652 PMCID: PMC3404492 DOI: 10.1002/9780470559277.ch110148] [Citation(s) in RCA: 262] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The copper-catalyzed azide-alkyne cycloaddition reaction is widely used for the connection of molecular entities of all sizes. A protocol is provided here for the process with biomolecules. Ascorbate is used as reducing agent to maintain the required cuprous oxidation state. Since these convenient conditions produce reactive oxygen species, five equivalents of a copper-binding ligand is used with respect to metal. The ligand both accelerates the reaction and serves as a sacrificial reductant, protecting the biomolecules from oxidation. A procedure is also described for testing the efficiency of the reaction under desired conditions for purposes of optimization, before expensive biological reagents are used.
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Affiliation(s)
| | - Vu Phong Hong
- Department of Chemistry, The Scripps Research Institute, La Jolla, California
| | - M.G. Finn
- Department of Chemistry, The Scripps Research Institute, La Jolla, California
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47
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Thon V, Li Y, Yu H, Lau K, Chen X. PmST3 from Pasteurella multocida encoded by Pm1174 gene is a monofunctional α2-3-sialyltransferase. Appl Microbiol Biotechnol 2011; 94:977-85. [PMID: 22075637 DOI: 10.1007/s00253-011-3676-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/06/2011] [Accepted: 10/26/2011] [Indexed: 01/07/2023]
Abstract
Pasteurella multocida (Pm) strain Pm70 has three putative sialyltransferase genes including Pm0188, Pm0508, and Pm1174. A Pm0188 gene homolog in Pm strain P-1059 encodes a multifunctional α2-3-sialyltransferase, PmST1, that prefers oligosaccharide acceptors. A Pm0508 gene homolog in the same strain encodes a monofunctional sialyltransferase PmST2 that prefers glycolipid acceptors. Here, we report that the third sialyltransferase from Pm (PmST3) encoded by gene Pm1174 in strain Pm70 is a monofunctional α2-3-sialyltransferase that can use both oligosaccharides and glycolipids as efficient acceptors. Despite the existence of both Pm0188 and Pm0508 gene homologs encoding PmST1 and PmST2, respectively, in Pm strain P-1059, a Pm1174 gene homolog appears to be absent from Pm strains P-1059 and P-934. PmST3 was successfully obtained by cloning and expression using a synthetic gene of Pm1174 with codons optimized for Escherichia coli expression system as the DNA template for polymer chain reactions. Truncation of 35 amino acid residues from the carboxyl terminus was shown to improve the expression of a soluble and active enzyme in E. coli as a C-His(6)-tagged fusion protein. This sialidase-free monofunctional α2-3-sialyltransferase is a useful tool for synthesizing sialylated oligosaccharides and glycolipids.
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Affiliation(s)
- Vireak Thon
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
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48
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Buré C, Marceau P, Meudal H, Delmas AF. Synthesis and analytical investigation of C-terminally modified peptide aldehydes and ketone: application to oxime ligation. J Pept Sci 2011; 18:147-54. [DOI: 10.1002/psc.1429] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 10/11/2011] [Accepted: 10/14/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Corinne Buré
- Centre de Biophysique Moléculaire CNRS UPR4301; affiliated to the University of Orléans and INSERM; rue Charles Sadron 45071 Orléans cedex 2 France
- Present address: Chimie et Biologie des Membranes et des Nanoobjets (CBMN) - UMR 5248 Centre de Génomique Fonctionnelle BP 68; Université Bordeaux 2 Victor Segalen; 146, rue Léo Saignat 33076 Bordeaux Cedex France
| | - Philippe Marceau
- Centre de Biophysique Moléculaire CNRS UPR4301; affiliated to the University of Orléans and INSERM; rue Charles Sadron 45071 Orléans cedex 2 France
| | - Hervé Meudal
- Centre de Biophysique Moléculaire CNRS UPR4301; affiliated to the University of Orléans and INSERM; rue Charles Sadron 45071 Orléans cedex 2 France
| | - Agnès F. Delmas
- Centre de Biophysique Moléculaire CNRS UPR4301; affiliated to the University of Orléans and INSERM; rue Charles Sadron 45071 Orléans cedex 2 France
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49
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Hang HC, Wilson JP, Charron G. Bioorthogonal chemical reporters for analyzing protein lipidation and lipid trafficking. Acc Chem Res 2011; 44:699-708. [PMID: 21675729 DOI: 10.1021/ar200063v] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein lipidation and lipid trafficking control many key biological functions in all kingdoms of life. The discovery of diverse lipid species and their covalent attachment to many proteins has revealed a complex and regulated network of membranes and lipidated proteins that are central to fundamental aspects of physiology and human disease. Given the complexity of lipid trafficking and the protein targeting mechanisms involved with membrane lipids, precise and sensitive methods are needed to monitor and identify these hydrophobic molecules in bacteria, yeast, and higher eukaryotes. Although many analytical methods have been developed for characterizing membrane lipids and covalently modified proteins, traditional reagents and approaches have limited sensitivity, do not faithfully report on the lipids of interest, or are not readily accessible. The invention of bioorthogonal ligation reactions, such as the Staudinger ligation and azide-alkyne cycloadditions, has provided new tools to address these limitations, and their use has begun to yield fresh insight into the biology of protein lipidation and lipid trafficking. In this Account, we discuss how these new bioorthogonal ligation reactions and lipid chemical reporters afford new opportunities for exploring the biology of lipid-modified proteins and lipid trafficking. Lipid chemical reporters from our laboratory and several other research groups have enabled improved detection and large-scale proteomic analysis of fatty-acylated and prenylated proteins. For example, fatty acid and isoprenoid chemical reporters in conjunction with bioorthogonal ligation methods have circumvented the limited sensitivity and hazards of radioactive analogues, allowing rapid and robust fluorescent detection of lipidated proteins in all organisms tested. These chemical tools have revealed alterations in protein lipidation in different cellular states and are beginning to provide unique insights in mechanisms of regulation. Notably, the purification of proteins labeled with lipid chemical reporters has allowed both the large-scale analysis of lipidated proteins as well as the discovery of new lipidated proteins involved in metabolism, gene expression, and innate immunity. Specific lipid reporters have also been developed to monitor the trafficking of soluble lipids; these species are enabling bioorthogonal imaging of membranes in cells and tissues. Future advances in bioorthogonal chemistry, specific lipid reporters, and spectroscopy should provide important new insight into the functional roles of lipidated proteins and membranes in biology.
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Affiliation(s)
- Howard C. Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - John P. Wilson
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
| | - Guillaume Charron
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, New York 10065, United States
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50
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Dere RT, Kumar A, Kumar V, Zhu X, Schmidt RR. Synthesis of Glycosylthiols and Reactivity Studies. J Org Chem 2011; 76:7539-45. [DOI: 10.1021/jo200624e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ravindra T. Dere
- Fachbereich Chemie, Universität Konstanz, Fach 725, D-78457 Konstanz, Germany
| | - Amit Kumar
- Fachbereich Chemie, Universität Konstanz, Fach 725, D-78457 Konstanz, Germany
| | - Vipin Kumar
- Fachbereich Chemie, Universität Konstanz, Fach 725, D-78457 Konstanz, Germany
| | - Xiangming Zhu
- College of Chemistry & Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Richard R. Schmidt
- Fachbereich Chemie, Universität Konstanz, Fach 725, D-78457 Konstanz, Germany
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