1
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Saini G, Parasa MK, Clayton KN, Fraseur JG, Bolton SC, Lin KP, Wereley ST, Kinzer-Ursem TL. Immobilization of azide-functionalized proteins to micro- and nanoparticles directly from cell lysate. Mikrochim Acta 2023; 191:46. [PMID: 38129631 PMCID: PMC10739308 DOI: 10.1007/s00604-023-06068-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/23/2023] [Indexed: 12/23/2023]
Abstract
Immobilization of proteins and enzymes on solid supports has been utilized in a variety of applications, from improved protein stability on supported catalysts in industrial processes to fabrication of biosensors, biochips, and microdevices. A critical requirement for these applications is facile yet stable covalent conjugation between the immobilized and fully active protein and the solid support to produce stable, highly bio-active conjugates. Here, we report functionalization of solid surfaces (gold nanoparticles and magnetic beads) with bio-active proteins using site-specific and biorthogonal labeling and azide-alkyne cycloaddition, a click chemistry. Specifically, we recombinantly express and selectively label calcium-dependent proteins, calmodulin and calcineurin, and cAMP-dependent protein kinase A (PKA) with N-terminal azide-tags for efficient conjugation to nanoparticles and magnetic beads. We successfully immobilized the proteins on to the solid supports directly from the cell lysate with click chemistry, forgoing the step of purification. This approach is optimized to yield low particle aggregation and high levels of protein activity post-conjugation. The entire process enables streamlined workflows for bioconjugation and highly active conjugated proteins.
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Affiliation(s)
- Gunjan Saini
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Mrugesh Krishna Parasa
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Katherine N Clayton
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Julia G Fraseur
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Scott C Bolton
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Kevin P Lin
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47906, USA
| | - Steven T Wereley
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47906, USA
| | - Tamara L Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47906, USA.
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2
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Fedoryshchak RO, Gorelik A, Shen M, Shchepinova MM, Pérez-Dorado I, Tate EW. Discovery of lipid-mediated protein-protein interactions in living cells using metabolic labeling with photoactivatable clickable probes. Chem Sci 2023; 14:2419-2430. [PMID: 36873846 PMCID: PMC9977449 DOI: 10.1039/d2sc06116c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/29/2023] [Indexed: 01/31/2023] Open
Abstract
Protein-protein interactions (PPIs) are essential and pervasive regulatory elements in biology. Despite the development of a range of techniques to probe PPIs in living systems, there is a dearth of approaches to capture interactions driven by specific post-translational modifications (PTMs). Myristoylation is a lipid PTM added to more than 200 human proteins, where it may regulate membrane localization, stability or activity. Here we report the design and synthesis of a panel of novel photocrosslinkable and clickable myristic acid analog probes, and their characterization as efficient substrates for human N-myristoyltransferases NMT1 and NMT2, both biochemically and through X-ray crystallography. We demonstrate metabolic incorporation of probes to label NMT substrates in cell culture and in situ intracellular photoactivation to form a covalent crosslink between modified proteins and their interactors, capturing a snapshot of interactions in the presence of the lipid PTM. Proteomic analyses revealed both known and multiple novel interactors of a series of myristoylated proteins, including ferroptosis suppressor protein 1 (FSP1) and spliceosome-associated RNA helicase DDX46. The concept exemplified by these probes offers an efficient approach for exploring the PTM-specific interactome without the requirement for genetic modification, which may prove broadly applicable to other PTMs.
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Affiliation(s)
- Roman O Fedoryshchak
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - Andrii Gorelik
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - Mengjie Shen
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Maria M Shchepinova
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Inmaculada Pérez-Dorado
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 80 Wood Lane London W12 0BZ UK .,The Francis Crick Institute 1 Midland Road London NW1 1AT UK
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3
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Malarney KP, Chang PV. Chemoproteomic Approaches for Unraveling Prokaryotic Biology. Isr J Chem 2023; 63:e202200076. [PMID: 37842282 PMCID: PMC10575470 DOI: 10.1002/ijch.202200076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 03/07/2023]
Abstract
Bacteria are ubiquitous lifeforms with important roles in the environment, biotechnology, and human health. Many of the functions that bacteria perform are mediated by proteins and enzymes, which catalyze metabolic transformations of small molecules and modifications of proteins. To better understand these biological processes, chemical proteomic approaches, including activity-based protein profiling, have been developed to interrogate protein function and enzymatic activity in physiologically relevant contexts. Here, chemoproteomic strategies and technological advances for studying bacterial physiology, pathogenesis, and metabolism are discussed. The development of chemoproteomic approaches for characterizing protein function and enzymatic activity within bacteria remains an active area of research, and continued innovations are expected to provide breakthroughs in understanding bacterial biology.
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Affiliation(s)
- Kien P Malarney
- Department of Microbiology, Cornell University, Ithaca, NY 14853 (USA)
| | - Pamela V Chang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853 (USA)
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4
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Monassa P, Rivière F, Dian C, Frottin F, Giglione C, Meinnel T. Biochemical and structural analysis of N-myristoyltransferase mediated protein tagging. Methods Enzymol 2023; 684:135-166. [DOI: 10.1016/bs.mie.2023.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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5
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Soupene E, Kuypers FA. Dual Role of ACBD6 in the Acylation Remodeling of Lipids and Proteins. Biomolecules 2022; 12:biom12121726. [PMID: 36551154 PMCID: PMC9775454 DOI: 10.3390/biom12121726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/12/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
The transfer of acyl chains to proteins and lipids from acyl-CoA donor molecules is achieved by the actions of diverse enzymes and proteins, including the acyl-CoA binding domain-containing protein ACBD6. N-myristoyl-transferase (NMT) enzymes catalyze the covalent attachment of a 14-carbon acyl chain from the relatively rare myristoyl-CoA to the N-terminal glycine residue of myr-proteins. The interaction of the ankyrin-repeat domain of ACBD6 with NMT produces an active enzymatic complex for the use of myristoyl-CoA protected from competitive inhibition by acyl donor competitors. The absence of the ACBD6/NMT complex in ACBD6.KO cells increased the sensitivity of the cells to competitors and significantly reduced myristoylation of proteins. Protein palmitoylation was not altered in those cells. The specific defect in myristoyl-transferase activity of the ACBD6.KO cells provided further evidence of the essential functional role of the interaction of ACBD6 with the NMT enzymes. Acyl-CoAs bound to the acyl-CoA binding domain of ACBD6 are acyl donors for the lysophospholipid acyl-transferase enzymes (LPLAT), which acylate single acyl-chain lipids, such as the bioactive molecules LPA and LPC. Whereas the formation of acyl-CoAs was not altered in ACBD6.KO cells, lipid acylation processes were significantly reduced. The defect in PC formation from LPC by the LPCAT enzymes resulted in reduced lipid droplets content. The diversity of the processes affected by ACBD6 highlight its dual function as a carrier and a regulator of acyl-CoA dependent reactions. The unique role of ACBD6 represents an essential common feature of (acyl-CoA)-dependent modification pathways controlling the lipid and protein composition of human cell membranes.
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6
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Hao Z, Zhao P, Xing Q, Wahab A, Gao Z, Gou J, Yu B. Dual Roles of Azide: Dearomative Dimerization of Furfuryl Azides. J Org Chem 2022; 87:10185-10198. [PMID: 35864566 DOI: 10.1021/acs.joc.2c01118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A dearomative dimerization of furfuryl azides for the construction of furfuryl triazoles is developed. As a rare leaving group, azide is capable of initiating the generation of a furfuryl cation under the Lewis acid-catalyzed conditions, followed by reacting with the other azide to realize an intermolecular [3 + 2] cycloaddition/furan ring-opening cascade. By extending the reaction time, a fragmentation reaction of resulting furfuryl triazoles occurs to afford 1H-triazoles in high yield. Control studies demonstrated that key furfuryl cations also can be obtained from furfuryl triazoles. Furthermore, a chemoselective cross-cycloaddition can be achieved between furfuryl azides and a benzyl azide.
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Affiliation(s)
- Zhe Hao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Penggang Zhao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Qingzhao Xing
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Abdul Wahab
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Ziwei Gao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Jing Gou
- Shaanxi Key Laboratory for Advanced Energy Devices, Shaanxi Normal University, Xi'an 710062, China
| | - Binxun Yu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.,SCNU Qingyuan Institute of Science and Technology Innovation Co., Ltd., Qingyuan 511517, China
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7
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Sarkar R, Gajurel S, Gupta A, Kumar Pal A. Synergistic Catalysis by Copper Oxide/Graphene Oxide Nanocomposites: A Facile Approach to Prepare Quinazolines and Quinazoline Containing Triazole/Tetrazole Moieties under Mild Reaction Conditions. ChemistrySelect 2022. [DOI: 10.1002/slct.202200297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Rajib Sarkar
- Department of Chemistry, Centre for Advanced Studies North-Eastern Hill University Shillong 793022 India
| | - Sushmita Gajurel
- Department of Chemistry, Centre for Advanced Studies North-Eastern Hill University Shillong 793022 India
| | - Ajay Gupta
- Department of Chemistry, Centre for Advanced Studies North-Eastern Hill University Shillong 793022 India
| | - Amarta Kumar Pal
- Department of Chemistry, Centre for Advanced Studies North-Eastern Hill University Shillong 793022 India
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8
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Hanna CC, Kriegesmann J, Dowman LJ, Becker CFW, Payne RJ. Chemical Synthesis and Semisynthesis of Lipidated Proteins. Angew Chem Int Ed Engl 2022; 61:e202111266. [PMID: 34611966 PMCID: PMC9303669 DOI: 10.1002/anie.202111266] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 11/24/2022]
Abstract
Lipidation is a ubiquitous modification of peptides and proteins that can occur either co- or post-translationally. An array of different lipid classes can adorn proteins and has been shown to influence a number of crucial biological activities, including the regulation of signaling, cell-cell adhesion events, and the anchoring of proteins to lipid rafts and phospholipid membranes. Whereas nature employs a range of enzymes to install lipid modifications onto proteins, the use of these for the chemoenzymatic generation of lipidated proteins is often inefficient or impractical. An alternative is to harness the power of modern synthetic and semisynthetic technologies to access lipid-modified proteins in a pure and homogeneously modified form. This Review aims to highlight significant advances in the development of lipidation and ligation chemistry and their implementation in the synthesis and semisynthesis of homogeneous lipidated proteins that have enabled the influence of these modifications on protein structure and function to be uncovered.
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Affiliation(s)
- Cameron C. Hanna
- School of ChemistryThe University of SydneySydneyNSW2006Australia
| | - Julia Kriegesmann
- Institute of Biological ChemistryFaculty of ChemistryUniversity of ViennaViennaAustria
| | - Luke J. Dowman
- School of ChemistryThe University of SydneySydneyNSW2006Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW2006Australia
| | | | - Richard J. Payne
- School of ChemistryThe University of SydneySydneyNSW2006Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW2006Australia
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9
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Hanna CC, Kriegesmann J, Dowman LJ, Becker CFW, Payne RJ. Chemische Synthese und Semisynthese von lipidierten Proteinen. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202111266. [PMID: 38504765 PMCID: PMC10947004 DOI: 10.1002/ange.202111266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 11/11/2022]
Abstract
AbstractLipidierung ist eine ubiquitäre Modifikation von Peptiden und Proteinen, die entweder co‐ oder posttranslational auftreten kann. Für die Vielzahl von Lipidklassen wurde gezeigt, dass diese viele entscheidende biologische Aktivitäten, z. B. die Regulierung der Signalweiterleitung, Zell‐Zell‐Adhäsion sowie die Anlagerung von Proteinen an Lipid‐Rafts und Phospholipidmembranen, beeinflussen. Während die Natur Enzyme nutzt, um Lipidmodifikationen in Proteine einzubringen, ist ihre Nutzung für die chemoenzymatische Herstellung von lipidierten Proteinen häufig ineffizient. Eine Alternative ist die Kombination moderner synthetischer und semisynthetischer Techniken, um lipidierte Proteine in reiner und homogen modifizierter Form zu erhalten. Dieser Aufsatz erörtert Fortschritte in der Entwicklung der Lipidierungs‐ und Ligationschemie und deren Anwendung in der Synthese und Semisynthese homogen lipidierter Proteine, die es ermöglichen, den Einfluss dieser Modifikationen auf die Proteinstruktur und ‐funktion zu untersuchen.
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Affiliation(s)
- Cameron C. Hanna
- School of ChemistryThe University of SydneySydneyNSW2006Australien
| | - Julia Kriegesmann
- Institut für Biologische ChemieFakultät für ChemieUniversität WienWienÖsterreich
| | - Luke J. Dowman
- School of ChemistryThe University of SydneySydneyNSW2006Australien
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW2006Australien
| | | | - Richard J. Payne
- School of ChemistryThe University of SydneySydneyNSW2006Australien
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW2006Australien
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10
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Rai V, P K, Harmalkar SS, Dhuri SN, Maddani MR. 1,6-Addition of 1,2,3-NH triazoles to para-quinone methides: Facile access to highly selective N 1 and N 2 substituted triazoles. Org Biomol Chem 2022; 20:345-351. [PMID: 34908078 DOI: 10.1039/d1ob01717a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The regioselective syntheses of N1 and N2 substituted triazoles through a 1,6-addition reaction of 1,2,3-NH triazoles to p-quinone methide were achieved under mild reaction conditions. The present reactions showed superior results in terms of selectivity, mild reaction conditions, short reaction time and broad substrate scope with good functional-group compatibility. Considering the high synthetic value of N1- and N2-substituted compounds and p-QM related research, the present strategy will greatly benefit researchers in various fields.
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Affiliation(s)
- Vishakha Rai
- Department of Chemistry, Mangalore University, Mangalagangothri, Mangalore, Karnataka, India.
| | - Kavyashree P
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal, India
| | | | - Sundar N Dhuri
- School of Chemical Sciences, Goa University, Goa 403206, India
| | - Mahagundappa R Maddani
- Department of Chemistry, Mangalore University, Mangalagangothri, Mangalore, Karnataka, India.
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11
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Wang Z, Zhang D, Hu S, Bi X, Lescar J, Tam JP, Liu CF. PAL-Mediated Ligation for Protein and Cell-Surface Modification. Methods Mol Biol 2022; 2530:177-193. [PMID: 35761050 DOI: 10.1007/978-1-0716-2489-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Peptidyl Asx-specific ligases (PALs) effect peptide ligation by catalyzing transpeptidation reactions at Asn/Asp-peptide bonds. Owing to their high efficiency and mild aqueous reaction conditions, these ligases have emerged as powerful biotechnological tools for protein manipulation in recent years. PALs are enzymes of the asparaginyl endopeptidase (AEP) superfamily but have predominant transpeptidase activity as opposed to typical AEPs which are predominantly hydrolases. Butelase-1 and VyPAL2, two PALs discovered by our teams, have been used successfully in a wide range of applications, including macrocyclization of synthetic peptides and recombinant proteins, protein N- or C-terminal modification, and cell-surface labeling. As shown in numerous reports, PAL-mediated ligation is highly efficient at Asn junctions. Although considerably less efficient, Asp-specific ligation has also been shown to be practically useful under suitable conditions. Herein, we describe the methods of using VyPAL2 for protein macrocyclization and labeling at an Asp residue as well as for protein dual labeling through orthogonal Asp- and Asn-directed ligations. We also describe a method for cell-surface protein modification using butelase-1, demonstrating its advantageous features over previous methods.
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Affiliation(s)
- Zhen Wang
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
| | - Dingpeng Zhang
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
| | - Side Hu
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
| | - Xiaobao Bi
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Zhejiang, China
| | - Julien Lescar
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
| | - James P Tam
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
| | - Chuan-Fa Liu
- School of Biological Science, Nanyang Technological University, Singapore, Singapore.
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12
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Giglione C, Meinnel T. Mapping the myristoylome through a complete understanding of protein myristoylation biochemistry. Prog Lipid Res 2021; 85:101139. [PMID: 34793862 DOI: 10.1016/j.plipres.2021.101139] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 12/22/2022]
Abstract
Protein myristoylation is a C14 fatty acid modification found in all living organisms. Myristoylation tags either the N-terminal alpha groups of cysteine or glycine residues through amide bonds or lysine and cysteine side chains directly or indirectly via glycerol thioester and ester linkages. Before transfer to proteins, myristate must be activated into myristoyl coenzyme A in eukaryotes or, in bacteria, to derivatives like phosphatidylethanolamine. Myristate originates through de novo biosynthesis (e.g., plants), from external uptake (e.g., human tissues), or from mixed origins (e.g., unicellular organisms). Myristate usually serves as a molecular anchor, allowing tagged proteins to be targeted to membranes and travel across endomembrane networks in eukaryotes. In this review, we describe and discuss the metabolic origins of protein-bound myristate. We review strategies for in vivo protein labeling that take advantage of click-chemistry with reactive analogs, and we discuss new approaches to the proteome-wide discovery of myristate-containing proteins. The machineries of myristoylation are described, along with how protein targets can be generated directly from translating precursors or from processed proteins. Few myristoylation catalysts are currently described, with only N-myristoyltransferase described to date in eukaryotes. Finally, we describe how viruses and bacteria hijack and exploit myristoylation for their pathogenicity.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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13
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Kallemeijn WW, Lanyon-Hogg T, Panyain N, Goya Grocin A, Ciepla P, Morales-Sanfrutos J, Tate EW. Proteome-wide analysis of protein lipidation using chemical probes: in-gel fluorescence visualization, identification and quantification of N-myristoylation, N- and S-acylation, O-cholesterylation, S-farnesylation and S-geranylgeranylation. Nat Protoc 2021; 16:5083-5122. [PMID: 34707257 DOI: 10.1038/s41596-021-00601-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 07/05/2021] [Indexed: 02/08/2023]
Abstract
Protein lipidation is one of the most widespread post-translational modifications (PTMs) found in nature, regulating protein function, structure and subcellular localization. Lipid transferases and their substrate proteins are also attracting increasing interest as drug targets because of their dysregulation in many disease states. However, the inherent hydrophobicity and potential dynamic nature of lipid modifications makes them notoriously challenging to detect by many analytical methods. Chemical proteomics provides a powerful approach to identify and quantify these diverse protein modifications by combining bespoke chemical tools for lipidated protein enrichment with quantitative mass spectrometry-based proteomics. Here, we report a robust and proteome-wide approach for the exploration of five major classes of protein lipidation in living cells, through the use of specific chemical probes for each lipid PTM. In-cell labeling of lipidated proteins is achieved by the metabolic incorporation of a lipid probe that mimics the specific natural lipid, concomitantly wielding an alkyne as a bio-orthogonal labeling tag. After incorporation, the chemically tagged proteins can be coupled to multifunctional 'capture reagents' by using click chemistry, allowing in-gel fluorescence visualization or enrichment via affinity handles for quantitative chemical proteomics based on label-free quantification (LFQ) or tandem mass-tag (TMT) approaches. In this protocol, we describe the application of lipid probes for N-myristoylation, N- and S-acylation, O-cholesterylation, S-farnesylation and S-geranylgeranylation in multiple cell lines to illustrate both the workflow and data obtained in these experiments. We provide detailed workflows for method optimization, sample preparation for chemical proteomics and data processing. A properly trained researcher (e.g., technician, graduate student or postdoc) can complete all steps from optimizing metabolic labeling to data processing within 3 weeks. This protocol enables sensitive and quantitative analysis of lipidated proteins at a proteome-wide scale at native expression levels, which is critical to understanding the role of lipid PTMs in health and disease.
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Affiliation(s)
- Wouter W Kallemeijn
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- The Francis Crick Institute, London, UK
| | - Thomas Lanyon-Hogg
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Nattawadee Panyain
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- Global Health Institute, Faculty of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Andrea Goya Grocin
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- The Francis Crick Institute, London, UK
| | - Paulina Ciepla
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- Institute of Chemical Sciences and Engineering (ISIC), Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Julia Morales-Sanfrutos
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
- Proteomics Unit, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK.
- The Francis Crick Institute, London, UK.
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14
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Xing Q, Zhou C, Jiang S, Chen S, Deng GJ. Acid-catalyzed three-component addition of carbonyl compounds with 1,2,3-triazoles and indoles. Org Biomol Chem 2021; 19:7838-7842. [PMID: 34549239 DOI: 10.1039/d1ob01451j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A facile and efficient acid-catalyzed three-component reaction of indoles, 1-tosyl-1,2,3-triazoles and carbonyl compounds has been developed. The use of TsOH with a small amount of water significantly promoted the reaction yield. This method provided a general and one-pot approach for the synthesis of structurally diverse C3-alkylated indole derivatives. The alkylation exclusively occurred at the N2 position of triazoles. Various functional groups were tolerated under the optimized simple reaction conditions.
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Affiliation(s)
- Qiaoyan Xing
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China.
| | - Chunlan Zhou
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China.
| | - Shuxin Jiang
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China.
| | - Shanping Chen
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China.
| | - Guo-Jun Deng
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China.
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15
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Suazo KF, Park KY, Distefano MD. A Not-So-Ancient Grease History: Click Chemistry and Protein Lipid Modifications. Chem Rev 2021; 121:7178-7248. [PMID: 33821625 PMCID: PMC8820976 DOI: 10.1021/acs.chemrev.0c01108] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein lipid modification involves the attachment of hydrophobic groups to proteins via ester, thioester, amide, or thioether linkages. In this review, the specific click chemical reactions that have been employed to study protein lipid modification and their use for specific labeling applications are first described. This is followed by an introduction to the different types of protein lipid modifications that occur in biology. Next, the roles of click chemistry in elucidating specific biological features including the identification of lipid-modified proteins, studies of their regulation, and their role in diseases are presented. A description of the use of protein-lipid modifying enzymes for specific labeling applications including protein immobilization, fluorescent labeling, nanostructure assembly, and the construction of protein-drug conjugates is presented next. Concluding remarks and future directions are presented in the final section.
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Affiliation(s)
- Kiall F. Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Keun-Young Park
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
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16
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De Rosa L, Di Stasi R, Romanelli A, D’Andrea LD. Exploiting Protein N-Terminus for Site-Specific Bioconjugation. Molecules 2021; 26:3521. [PMID: 34207845 PMCID: PMC8228110 DOI: 10.3390/molecules26123521] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 11/29/2022] Open
Abstract
Although a plethora of chemistries have been developed to selectively decorate protein molecules, novel strategies continue to be reported with the final aim of improving selectivity and mildness of the reaction conditions, preserve protein integrity, and fulfill all the increasing requirements of the modern applications of protein conjugates. The targeting of the protein N-terminal alpha-amine group appears a convenient solution to the issue, emerging as a useful and unique reactive site universally present in each protein molecule. Herein, we provide an updated overview of the methodologies developed until today to afford the selective modification of proteins through the targeting of the N-terminal alpha-amine. Chemical and enzymatic strategies enabling the selective labeling of the protein N-terminal alpha-amine group are described.
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Affiliation(s)
- Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy; (L.D.R.); (R.D.S.)
| | - Rossella Di Stasi
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy; (L.D.R.); (R.D.S.)
| | - Alessandra Romanelli
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy;
| | - Luca Domenico D’Andrea
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR Via M. Bianco 9, 20131 Milano, Italy
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17
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Main A, Fuller W. Protein S-Palmitoylation: advances and challenges in studying a therapeutically important lipid modification. FEBS J 2021; 289:861-882. [PMID: 33624421 DOI: 10.1111/febs.15781] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/01/2021] [Accepted: 02/22/2021] [Indexed: 12/11/2022]
Abstract
The lipid post-translational modification S-palmitoylation is a vast developing field, with the modification itself and the enzymes that catalyse the reversible reaction implicated in a number of diseases. In this review, we discuss the past and recent advances in the experimental tools used in this field, including pharmacological tools, animal models and techniques to understand how palmitoylation controls protein localisation and function. Additionally, we discuss the obstacles to overcome in order to advance the field, particularly to the point at which modulating palmitoylation may be achieved as a therapeutic strategy.
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Affiliation(s)
- Alice Main
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
| | - William Fuller
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
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18
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Fedoryshchak RO, Ocasio CA, Strutton B, Mattocks J, Corran AJ, Tate EW. Wheat pathogen Zymoseptoria tritici N-myristoyltransferase inhibitors: on-target antifungal activity and an unusual metabolic defense mechanism. RSC Chem Biol 2020; 1:68-78. [PMID: 34458749 PMCID: PMC8341946 DOI: 10.1039/d0cb00020e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022] Open
Abstract
Zymoseptoria tritici is the causative agent of Septoria tritici blotch (STB), which costs billions of dollars annually to major wheat-producing countries in terms of both fungicide use and crop loss. Agricultural pathogenic fungi have acquired resistance to most commercially available fungicide classes, and the rate of discovery and development of new fungicides has stalled, demanding new approaches and insights. Here we investigate a potential mechanism of targeting an important wheat pathogen Z. tritici via inhibition of N-myristoyltransferase (NMT). We characterize Z. tritici NMT biochemically for the first time, profile the in vivo Z. tritici myristoylated proteome and identify and validate the first Z. tritici NMT inhibitors. Proteomic investigation of the downstream effects of NMT inhibition identified an unusual and novel mechanism of defense against chemical toxicity in Z. tritici through the application of comparative bioinformatics to deconvolute function from the previously largely unannotated Z. tritici proteome. Research into novel fungicidal modes-of-action is essential to satisfy an urgent unmet need for novel fungicide targets, and we anticipate that this study will serve as a useful proteomics and bioinformatics resource for researchers studying Z. tritici.
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Affiliation(s)
- Roman O Fedoryshchak
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub Wood Lane London W12 0BZ UK
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
| | - Cory A Ocasio
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
| | | | - Jo Mattocks
- Syngenta AG, Jealott's Hill Research Centre Bracknell UK
| | | | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub Wood Lane London W12 0BZ UK
- The Francis Crick Institute 1 Midland Rd London NW1 1AT UK
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19
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Affiliation(s)
- Christin Bednarek
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Ilona Wehl
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Nicole Jung
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
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20
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Ejendal KFK, Fraseur JG, Kinzer-Ursem TL. Protein Labeling and Bioconjugation Using N-Myristoyltransferase. Methods Mol Biol 2019; 2033:149-165. [PMID: 31332753 DOI: 10.1007/978-1-4939-9654-4_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Methods that allow for labeling of proteins cotranslationally within protein expression systems have had wide-ranging applications in health, engineering, and medicine. Bioorthogonal chemistries that allow for conjugation of proteins or biomolecules of interest to substrates (fluorophores, gold nanoparticles, polymers, etc.) in living cells without prior enrichment or purification have likewise enabled advances in technology to study and engineer cellular and biomolecular systems. At the intersection of these, chemoenzymatic labeling of proteins at specific sites of interest and their subsequent selective bioconjugation to substrates without prior purification has dramatically streamlined workflows that allow proteins to reside in the native expression volumes as long as possible prior to conjugation, be readily isolated upon conjugation, and remain functionally active after conjugation. Here we present methods and protocols to express and label proteins of interest at the N-terminus with azide derivatives of myristic acid, a small, soluble, 14-carbon fatty acid, and conjugate the labeled protein to fluorophores and gold nanoparticle substrates. These methods can be extended to label proteins with other myristoyl derivatives and to conjugation to other solid or polymeric substrates of interest.
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Affiliation(s)
- Karin F K Ejendal
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Julia G Fraseur
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Tamara L Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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21
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Ho SH, Tirrell DA. N-Myristoyl Transferase (NMT)-Catalyzed Labeling of Bacterial Proteins for Imaging in Fixed and Live Cells. Methods Mol Biol 2019; 2012:315-326. [PMID: 31161515 DOI: 10.1007/978-1-4939-9546-2_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Methods for selective protein imaging are critical for elucidating how cells orchestrate fundamental biological processes. We recently developed a chemoenzymatic method to modify bacterial proteins in situ for fluorescence imaging using N-myristoyl transferase (NMT). Target proteins outfitted with an N-terminal NMT recognition sequence are covalently modified with an azido fatty acid. Subsequent strain-promoted azide-alkyne cycloaddition allows for conjugation to cell-permeant fluorophores and imaging by fluorescence microscopy. Here we describe sample preparation and labeling protocols for imaging bacterial proteins in fixed and live cells.
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Affiliation(s)
- Samuel H Ho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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22
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Zhang Y, Park KY, Suazo KF, Distefano MD. Recent progress in enzymatic protein labelling techniques and their applications. Chem Soc Rev 2018; 47:9106-9136. [PMID: 30259933 PMCID: PMC6289631 DOI: 10.1039/c8cs00537k] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein-based conjugates are valuable constructs for a variety of applications. Conjugation of proteins to fluorophores is commonly used to study their cellular localization and the protein-protein interactions. Modification of therapeutic proteins with either polymers or cytotoxic moieties greatly enhances their pharmacokinetics or potency. To label a protein of interest, conventional direct chemical reaction with the side-chains of native amino acids often yields heterogeneously modified products. This renders their characterization complicated, requires difficult separation steps and may impact protein function. Although modification can also be achieved via the insertion of unnatural amino acids bearing bioorthogonal functional groups, these methods can have lower protein expression yields, limiting large scale production. As a site-specific modification method, enzymatic protein labelling is highly efficient and robust under mild reaction conditions. Significant progress has been made over the last five years in modifying proteins using enzymatic methods for numerous applications, including the creation of clinically relevant conjugates with polymers, cytotoxins or imaging agents, fluorescent or affinity probes to study complex protein interaction networks, and protein-linked materials for biosensing. This review summarizes developments in enzymatic protein labelling over the last five years for a panel of ten enzymes, including sortase A, subtiligase, microbial transglutaminase, farnesyltransferase, N-myristoyltransferase, phosphopantetheinyl transferases, tubulin tyrosin ligase, lipoic acid ligase, biotin ligase and formylglycine generating enzyme.
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Affiliation(s)
- Yi Zhang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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23
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Joachimiak Ł, Błażewska KM. Phosphorus-Based Probes as Molecular Tools for Proteome Studies: Recent Advances in Probe Development and Applications. J Med Chem 2018; 61:8536-8562. [DOI: 10.1021/acs.jmedchem.8b00249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Łukasz Joachimiak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
| | - Katarzyna M. Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
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24
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Jiang H, Zhang X, Chen X, Aramsangtienchai P, Tong Z, Lin H. Protein Lipidation: Occurrence, Mechanisms, Biological Functions, and Enabling Technologies. Chem Rev 2018; 118:919-988. [PMID: 29292991 DOI: 10.1021/acs.chemrev.6b00750] [Citation(s) in RCA: 291] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein lipidation, including cysteine prenylation, N-terminal glycine myristoylation, cysteine palmitoylation, and serine and lysine fatty acylation, occurs in many proteins in eukaryotic cells and regulates numerous biological pathways, such as membrane trafficking, protein secretion, signal transduction, and apoptosis. We provide a comprehensive review of protein lipidation, including descriptions of proteins known to be modified and the functions of the modifications, the enzymes that control them, and the tools and technologies developed to study them. We also highlight key questions about protein lipidation that remain to be answered, the challenges associated with answering such questions, and possible solutions to overcome these challenges.
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Affiliation(s)
- Hong Jiang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiaoyu Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiao Chen
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Pornpun Aramsangtienchai
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Zhen Tong
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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25
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Gao X, Hannoush RN. A Decade of Click Chemistry in Protein Palmitoylation: Impact on Discovery and New Biology. Cell Chem Biol 2017; 25:236-246. [PMID: 29290622 DOI: 10.1016/j.chembiol.2017.12.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/10/2017] [Accepted: 11/30/2017] [Indexed: 12/17/2022]
Abstract
Protein palmitoylation plays diverse roles in regulating the trafficking, stability, and activity of cellular proteins. The advent of click chemistry has propelled the field of protein palmitoylation forward by providing specific, sensitive, rapid, and easy-to-handle methods for studying protein palmitoylation. This year marks the 10th anniversary since the first click chemistry-based fatty acid probes for detecting protein lipid modifications were reported. The goal of this review is to highlight key biological advancements in the field of protein palmitoylation during the past 10 years. In particular, we discuss the impact of click chemistry on enabling protein palmitoylation proteomics methods, uncovering novel lipid modifications on proteins and elucidating their functions, as well as the development of non-radioactive biochemical and enzymatic assays. In addition, this review provides context for building and exploring new research avenues in protein palmitoylation through the use of clickable fatty acid probes.
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Affiliation(s)
- Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.
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26
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Shala-Lawrence A, Blanden MJ, Krylova SM, Gangopadhyay SA, Beloborodov SS, Hougland JL, Krylov SN. Simultaneous Analysis of a Non-Lipidated Protein and Its Lipidated Counterpart: Enabling Quantitative Investigation of Protein Lipidation’s Impact on Cellular Regulation. Anal Chem 2017; 89:13502-13507. [DOI: 10.1021/acs.analchem.7b03846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Agnesa Shala-Lawrence
- Department
of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Melanie J. Blanden
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Svetlana M. Krylova
- Department
of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | | | - Stanislav S. Beloborodov
- Department
of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - James L. Hougland
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Sergey N. Krylov
- Department
of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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27
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Luginbuhl KM, Mozhdehi D, Dzuricky M, Yousefpour P, Huang FC, Mayne NR, Buehne KL, Chilkoti A. Recombinant Synthesis of Hybrid Lipid-Peptide Polymer Fusions that Self-Assemble and Encapsulate Hydrophobic Drugs. Angew Chem Int Ed Engl 2017; 56:13979-13984. [PMID: 28879687 PMCID: PMC5909378 DOI: 10.1002/anie.201704625] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/14/2017] [Indexed: 11/06/2022]
Abstract
Inspired by biohybrid molecules that are synthesized in Nature through post-translational modification (PTM), we have exploited a eukaryotic PTM to recombinantly synthesize lipid-polypeptide hybrid materials. By co-expressing yeast N-myristoyltransferase with an elastin-like polypeptide (ELP) fused to a short recognition sequence in E. coli, we show robust and high-yield modification of the ELP with myristic acid. The ELP's reversible phase behavior is retained upon myristoylation and can be tuned to span a 30-60 °C. Myristoylated ELPs provide a versatile platform for genetically pre-programming self-assembly into micelles of varied size and shape. Their lipid cores can be loaded with hydrophobic small molecules by passive diffusion. Encapsulated doxorubicin and paclitaxel exhibit cytotoxic effects on 4T1 and PC3-luc cells, respectively, with potencies similar to chemically conjugated counterparts, and longer plasma circulation than free drug upon intravenous injection in mice.
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Affiliation(s)
- Kelli M Luginbuhl
- Department of Biomedical Engineering, Duke University, 1427 FCIEMAS, Box 90281, USA
- NSF Research Triangle Materials Research Science and Engineering Center, Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Davoud Mozhdehi
- Department of Biomedical Engineering, Duke University, 1427 FCIEMAS, Box 90281, USA
- NSF Research Triangle Materials Research Science and Engineering Center, Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Michael Dzuricky
- Department of Biomedical Engineering, Duke University, 1427 FCIEMAS, Box 90281, USA
- NSF Research Triangle Materials Research Science and Engineering Center, Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Parisa Yousefpour
- Department of Biomedical Engineering, Duke University, 1427 FCIEMAS, Box 90281, USA
| | - Fred C Huang
- Department of Biomedical Engineering, Duke University, 1427 FCIEMAS, Box 90281, USA
| | - Nicholas R Mayne
- Department of Biomedical Engineering, Duke University, 1427 FCIEMAS, Box 90281, USA
| | - Kristen L Buehne
- Department of Biomedical Engineering, Duke University, 1427 FCIEMAS, Box 90281, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, 1427 FCIEMAS, Box 90281, USA
- NSF Research Triangle Materials Research Science and Engineering Center, Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
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28
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Luginbuhl KM, Mozhdehi D, Dzuricky M, Yousefpour P, Huang FC, Mayne NR, Buehne KL, Chilkoti A. Recombinant Synthesis of Hybrid Lipid–Peptide Polymer Fusions that Self‐Assemble and Encapsulate Hydrophobic Drugs. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kelli M. Luginbuhl
- Department of Biomedical Engineering Duke University 1427 FCIEMAS, Box 90281 USA
- NSF Research Triangle Materials Research Science and Engineering Center Department of Biomedical Engineering Duke University Durham NC 27708 USA
| | - Davoud Mozhdehi
- Department of Biomedical Engineering Duke University 1427 FCIEMAS, Box 90281 USA
- NSF Research Triangle Materials Research Science and Engineering Center Department of Biomedical Engineering Duke University Durham NC 27708 USA
| | - Michael Dzuricky
- Department of Biomedical Engineering Duke University 1427 FCIEMAS, Box 90281 USA
- NSF Research Triangle Materials Research Science and Engineering Center Department of Biomedical Engineering Duke University Durham NC 27708 USA
| | - Parisa Yousefpour
- Department of Biomedical Engineering Duke University 1427 FCIEMAS, Box 90281 USA
| | - Fred C. Huang
- Department of Biomedical Engineering Duke University 1427 FCIEMAS, Box 90281 USA
| | - Nicholas R. Mayne
- Department of Biomedical Engineering Duke University 1427 FCIEMAS, Box 90281 USA
| | - Kristen L. Buehne
- Department of Biomedical Engineering Duke University 1427 FCIEMAS, Box 90281 USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering Duke University 1427 FCIEMAS, Box 90281 USA
- NSF Research Triangle Materials Research Science and Engineering Center Department of Biomedical Engineering Duke University Durham NC 27708 USA
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29
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Li LH, Jiang Y, Hao J, Wei Y, Shi M. N
2
-Selective Autocatalytic Ditriazolylation Reactions of Cyclopropenones and Tropone with N
1
-Sulfonyl-1,2,3-triazoles. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700936] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Long-Hai Li
- Department of Chemistry; Shanghai University; 99 Shangda Road Shanghai 200444 People's Republic of China
| | - Yu Jiang
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Mei Long Road Shanghai 200237 People's Republic of China
| | - Jian Hao
- Department of Chemistry; Shanghai University; 99 Shangda Road Shanghai 200444 People's Republic of China
| | - Yin Wei
- State Key Laboratory of Organometallic Chemistry; University of Chinese Academy of Sciences; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 People's Republic of China
| | - Min Shi
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Mei Long Road Shanghai 200237 People's Republic of China
- State Key Laboratory of Organometallic Chemistry; University of Chinese Academy of Sciences; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 People's Republic of China
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30
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Deng X, Lei X, Nie G, Jia L, Li Y, Chen Y. Copper-Catalyzed Cross-Dehydrogenative N 2-Coupling of NH-1,2,3-Triazoles with N,N -Dialkylamides: N-Amidoalkylation of NH-1,2,3-Triazoles. J Org Chem 2017; 82:6163-6171. [PMID: 28558242 DOI: 10.1021/acs.joc.7b00752] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
An efficient copper-catalyzed C-N bond formation by N-H/C-H cross-dehydrogenative coupling (CDC) between NH-1,2,3-triazoles and N,N-dialkylamides has been developed. The method provided N-amidoalkylated 1,2,3-triazoles with moderate to high yields, and the reactions showed high N2-selectivities when 4,5-disubstituted NH-1,2,3-triazoles served as the substrates.
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Affiliation(s)
- Xiaocong Deng
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology , Wuhan 430073, People's Republic of China
| | - Xue Lei
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology , Wuhan 430073, People's Republic of China
| | - Gang Nie
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology , Wuhan 430073, People's Republic of China
| | - Lihui Jia
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology , Wuhan 430073, People's Republic of China
| | - Yuanxiang Li
- College of Chemistry and Materials Engineering, Huaihua University , Huaihua 418008, People's Republic of China
| | - Yunfeng Chen
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology , Wuhan 430073, People's Republic of China
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31
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Sun C, Yuan X, Li Y, Li X, Zhao Z. N 1-Selective alkenylation of 1-sulfonyl-1,2,3-triazoles with alkynes via gold catalysis. Org Biomol Chem 2017; 15:2721-2724. [PMID: 28281720 DOI: 10.1039/c7ob00142h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A N1-selective alkenylation of 1-sulfonyl-1,2,3-triazoles with alkynes via gold catalysis is reported. N1-Vinyl substituted 1,2,3-triazoles were selectively prepared in up to 92% yield through the sulfonyl group of 1,2,3-triazole derivatives transformed to alkenyl groups in a "one-pot two steps" manner. This method provided a new method for the synthesis of potentially biological-active vinyl-triazole building blocks.
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Affiliation(s)
- Chenyang Sun
- College of Chemistry and Environmental Protection Engineering, Southwest University for Nationalities, Chengdu 610041, PR China.
| | - Xiao Yuan
- College of Chemistry and Environmental Protection Engineering, Southwest University for Nationalities, Chengdu 610041, PR China.
| | - Yan Li
- College of Chemistry and Environmental Protection Engineering, Southwest University for Nationalities, Chengdu 610041, PR China.
| | - Xiaoxiao Li
- College of Chemistry and Environmental Protection Engineering, Southwest University for Nationalities, Chengdu 610041, PR China.
| | - Zhigang Zhao
- College of Chemistry and Environmental Protection Engineering, Southwest University for Nationalities, Chengdu 610041, PR China.
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32
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New developments in probing and targeting protein acylation in malaria, leishmaniasis and African sleeping sickness. Parasitology 2017; 145:157-174. [PMID: 28270257 DOI: 10.1017/s0031182017000282] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Infections by protozoan parasites, such as Plasmodium falciparum or Leishmania donovani, have a significant health, social and economic impact and threaten billions of people living in tropical and sub-tropical regions of developing countries worldwide. The increasing range of parasite strains resistant to frontline therapeutics makes the identification of novel drug targets and the development of corresponding inhibitors vital. Post-translational modifications (PTMs) are important modulators of biology and inhibition of protein lipidation has emerged as a promising therapeutic strategy for treatment of parasitic diseases. In this review we summarize the latest insights into protein lipidation in protozoan parasites. We discuss how recent chemical proteomic approaches have delivered the first global overviews of protein lipidation in these organisms, contributing to our understanding of the role of this PTM in critical metabolic and cellular functions. Additionally, we highlight the development of new small molecule inhibitors to target parasite acyl transferases.
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Demetriadou A, Morales-Sanfrutos J, Nearchou M, Baba O, Kyriacou K, Tate EW, Drousiotou A, Petrou PP. Mouse Stbd1 is N-myristoylated and affects ER-mitochondria association and mitochondrial morphology. J Cell Sci 2017; 130:903-915. [PMID: 28137759 PMCID: PMC5358331 DOI: 10.1242/jcs.195263] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/16/2017] [Indexed: 12/17/2022] Open
Abstract
Starch binding domain-containing protein 1 (Stbd1) is a carbohydrate-binding protein that has been proposed to be a selective autophagy receptor for glycogen. Here, we show that mouse Stbd1 is a transmembrane endoplasmic reticulum (ER)-resident protein with the capacity to induce the formation of organized ER structures in HeLa cells. In addition to bulk ER, Stbd1 was found to localize to mitochondria-associated membranes (MAMs), which represent regions of close apposition between the ER and mitochondria. We demonstrate that N-myristoylation and binding of Stbd1 to glycogen act as major determinants of its subcellular targeting. Moreover, overexpression of non-myristoylated Stbd1 enhanced the association between ER and mitochondria, and further induced prominent mitochondrial fragmentation and clustering. Conversely, shRNA-mediated Stbd1 silencing resulted in an increase in the spacing between ER and mitochondria, and an altered morphology of the mitochondrial network, suggesting elevated fusion and interconnectivity of mitochondria. Our data unravel the molecular mechanism underlying Stbd1 subcellular targeting, support and expand its proposed function as a selective autophagy receptor for glycogen and uncover a new role for the protein in the physical association between ER and mitochondria.
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Affiliation(s)
- Anthi Demetriadou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, Nicosia 1683, Cyprus
- The Cyprus School of Molecular Medicine, P. O. Box 23462, Nicosia 1683, Cyprus
| | | | - Marianna Nearchou
- Department of Electron Microscopy / Molecular Pathology, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, Nicosia 1683, Cyprus
| | - Otto Baba
- Oral and Maxillofacial Anatomy, Faculty of Dentistry, Tokushima University, Tokushima 770-8504, Japan
| | - Kyriacos Kyriacou
- The Cyprus School of Molecular Medicine, P. O. Box 23462, Nicosia 1683, Cyprus
- Department of Electron Microscopy / Molecular Pathology, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, Nicosia 1683, Cyprus
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Anthi Drousiotou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, Nicosia 1683, Cyprus
- The Cyprus School of Molecular Medicine, P. O. Box 23462, Nicosia 1683, Cyprus
| | - Petros P Petrou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, P. O. Box 23462, Nicosia 1683, Cyprus
- The Cyprus School of Molecular Medicine, P. O. Box 23462, Nicosia 1683, Cyprus
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34
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Ozer I, Chilkoti A. Site-Specific and Stoichiometric Stealth Polymer Conjugates of Therapeutic Peptides and Proteins. Bioconjug Chem 2017; 28:713-723. [PMID: 27998056 DOI: 10.1021/acs.bioconjchem.6b00652] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
As potent and selective therapeutic agents, peptides and proteins are an important class of drugs, but they typically have suboptimal pharmacokinetic profiles. One approach to solve this problem is their conjugation with "stealth" polymers. Conventional methods for conjugation of this class of polymers to peptides and proteins are typically carried out by reactions that have poor yield and provide limited control over the site of conjugation and the stoichiometry of the conjugate. To address these limitations, new chemical and biological approaches have been developed that provide new molecular tools in the bioconjugation toolbox to create stealth polymer conjugates of peptides and proteins with exquisite control over their properties. This review article highlights these recent advances in the synthesis of therapeutic peptide- and protein-stealth polymer conjugates.
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Affiliation(s)
- Imran Ozer
- Department of Biomedical Engineering, Duke University , 101 Science Drive, Durham, North Carolina 27708, United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University , 101 Science Drive, Durham, North Carolina 27708, United States
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35
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Gao H, Sun W, Song Z, Yu Y, Wang L, Chen X, Zhang Q. A Method to Generate and Analyze Modified Myristoylated Proteins. Chembiochem 2017; 18:324-330. [PMID: 27925692 DOI: 10.1002/cbic.201600608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 11/07/2022]
Abstract
Covalent lipid modification of proteins is essential to their cellular localizations and functions. Engineered lipid motifs, coupled with bio-orthogonal chemistry, have been utilized to identify myristoylated or palmitoylated proteins in cells. However, whether modified proteins have similar properties as endogenous ones has not been well investigated mainly due to lack of methods to generate and analyze purified proteins. We have developed a method that utilizes metabolic interference and mass spectrometry to produce and analyze modified, myristoylated small GTPase ADP-ribosylation factor 1 (Arf1). The capacities of these recombinant proteins to bind liposomes and load and hydrolyze GTP were measured and compared with the unmodified myristoylated Arf1. The ketone-modified myristoylated Arf1 could be further labeled by fluorophore-coupled hydrazine and subsequently visualized through fluorescence imaging. This methodology provides an effective model system to characterize lipid-modified proteins with additional functions before applying them to cellular systems.
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Affiliation(s)
- Huanyao Gao
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Wei Sun
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Zhiquan Song
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Yanbao Yu
- Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Li Wang
- Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Qisheng Zhang
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
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36
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Ma T, Sun C, Yuan X, Li X, Zhao Z. N-2-Selective gold-catalyzed alkylation of 1-sulfonyl-1,2,3-trizoles. RSC Adv 2017. [DOI: 10.1039/c6ra26521a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An efficient new method was developed to synthesis N-2-alkyl-1,2,3-trizoles via gold catalyzed alkylation of 1-sulfonyl-1,2,3-trizoles with vinyl ethers.
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Affiliation(s)
- Ting Ma
- College of Chemistry and Environmental Protection Engineering
- Southwest University for Nationalities
- Chengdu 610041
- PR China
| | - Chenyang Sun
- College of Chemistry and Environmental Protection Engineering
- Southwest University for Nationalities
- Chengdu 610041
- PR China
| | - Xiao Yuan
- College of Chemistry and Environmental Protection Engineering
- Southwest University for Nationalities
- Chengdu 610041
- PR China
| | - Xiaoxiao Li
- College of Chemistry and Environmental Protection Engineering
- Southwest University for Nationalities
- Chengdu 610041
- PR China
| | - Zhigang Zhao
- College of Chemistry and Environmental Protection Engineering
- Southwest University for Nationalities
- Chengdu 610041
- PR China
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37
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Hentschel A, Zahedi RP, Ahrends R. Protein lipid modifications--More than just a greasy ballast. Proteomics 2016; 16:759-82. [PMID: 26683279 DOI: 10.1002/pmic.201500353] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 10/24/2015] [Accepted: 12/14/2015] [Indexed: 12/21/2022]
Abstract
Covalent lipid modifications of proteins are crucial for regulation of cellular plasticity, since they affect the chemical and physical properties and therefore protein activity, localization, and stability. Most recently, lipid modifications on proteins are increasingly attracting important regulatory entities in diverse signaling events and diseases. In all cases, the lipid moiety of modified proteins is essential to allow water-soluble proteins to strongly interact with membranes or to induce structural changes in proteins that are critical for elemental processes such as respiration, transport, signal transduction, and motility. Until now, roughly about ten lipid modifications on different amino acid residues are described at the UniProtKB database and even well-known modifications are underrepresented. Thus, it is of fundamental importance to develop a better understanding of this emerging and so far under-investigated type of protein modification. Therefore, this review aims to give a comprehensive and detailed overview about enzymatic and nonenzymatic lipidation events, will report their role in cellular biology, discuss their relevancy for diseases, and describe so far available bioanalytical strategies to analyze this highly challenging type of modification.
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Affiliation(s)
- Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
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38
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Ho SH, Tirrell DA. Chemoenzymatic Labeling of Proteins for Imaging in Bacterial Cells. J Am Chem Soc 2016; 138:15098-15101. [PMID: 27933886 DOI: 10.1021/jacs.6b07067] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Reliable methods to determine the subcellular localization of bacterial proteins are needed for the study of prokaryotic cell biology. We describe here a simple and general technique for imaging of bacterial proteins in situ by fluorescence microscopy. The method uses the eukaryotic enzyme N-myristoyltransferase to modify the N-terminus of the protein of interest with an azido fatty acid. Subsequent strain-promoted azide-alkyne cycloaddition allows conjugation of dyes and imaging of tagged proteins by confocal fluorescence microscopy. We demonstrate the method by labeling the chemotaxis proteins Tar and CheA and the cell division proteins FtsZ and FtsA in Escherichia coli. We observe distinct spatial patterns for each of these proteins in both fixed and live cells. The method should prove broadly useful for protein imaging in bacteria.
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Affiliation(s)
- Samuel H Ho
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
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39
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Chuh KN, Batt AR, Pratt MR. Chemical Methods for Encoding and Decoding of Posttranslational Modifications. Cell Chem Biol 2016; 23:86-107. [PMID: 26933738 DOI: 10.1016/j.chembiol.2015.11.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/25/2015] [Accepted: 11/25/2015] [Indexed: 12/13/2022]
Abstract
A large array of posttranslational modifications can dramatically change the properties of proteins and influence different aspects of their biological function such as enzymatic activity, binding interactions, and proteostasis. Despite the significant knowledge that has been gained about the function of posttranslational modifications using traditional biological techniques, the analysis of the site-specific effects of a particular modification, the identification of the full complement of modified proteins in the proteome, and the detection of new types of modifications remains challenging. Over the years, chemical methods have contributed significantly in both of these areas of research. This review highlights several posttranslational modifications where chemistry-based approaches have made significant contributions to our ability to both prepare homogeneously modified proteins and identify and characterize particular modifications in complex biological settings. As the number and chemical diversity of documented posttranslational modifications continues to rise, we believe that chemical strategies will be essential to advance the field in years to come.
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Affiliation(s)
- Kelly N Chuh
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Anna R Batt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
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40
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Shi J, Zhu L, Wen J, Chen Z. Brönsted acid catalyzed addition of N 1 - p -methyl toluenesulfonyl triazole to olefins for the preparation of N 2 -alkyl 1,2,3-triazoles with high N 2 -selectivity. CHINESE JOURNAL OF CATALYSIS 2016. [DOI: 10.1016/s1872-2067(15)61107-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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41
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Glasgow JE, Salit ML, Cochran JR. In Vivo Site-Specific Protein Tagging with Diverse Amines Using an Engineered Sortase Variant. J Am Chem Soc 2016; 138:7496-9. [PMID: 27280683 DOI: 10.1021/jacs.6b03836] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Chemoenzymatic modification of proteins is an attractive option to create highly specific conjugates for therapeutics, diagnostics, or materials under gentle biological conditions. However, these methods often suffer from expensive specialized substrates, bulky fusion tags, low yields, and extra purification steps to achieve the desired conjugate. Staphylococcus aureus sortase A and its engineered variants are used to attach oligoglycine derivatives to the C-terminus of proteins expressed with a minimal LPXTG tag. This strategy has been used extensively for bioconjugation in vitro and for protein-protein conjugation in living cells. Here we show that an enzyme variant recently engineered for higher activity on oligoglycine has promiscuous activity that allows proteins to be tagged using a diverse array of small, commercially available amines, including several bioorthogonal functional groups. This technique can also be carried out in living Escherichia coli, enabling simple, inexpensive production of chemically functionalized proteins with no additional purification steps.
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Affiliation(s)
- Jeff E Glasgow
- National Institute of Standards and Technology , Stanford, California 94305, United States
| | - Marc L Salit
- National Institute of Standards and Technology , Stanford, California 94305, United States
| | - Jennifer R Cochran
- Departments of Bioengineering and Chemical Engineering, Stanford University , Stanford, California 94305, United States
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42
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Zhu LL, Xu XQ, Shi JW, Chen BL, Chen Z. N2-Selective Iodofunctionalization of Olefins with NH-1,2,3-Triazoles to provide N2-Alkyl-Substituted 1,2,3-Triazoles. J Org Chem 2016; 81:3568-75. [DOI: 10.1021/acs.joc.6b00185] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li-Li Zhu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Xiao-Qi Xu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Jin-Wei Shi
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Bai-Ling Chen
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Zili Chen
- Department of Chemistry, Renmin University of China, Beijing 100872, China
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43
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Lehmann J, Wright MH, Sieber SA. Making a Long Journey Short: Alkyne Functionalization of Natural Product Scaffolds. Chemistry 2016; 22:4666-78. [PMID: 26752308 DOI: 10.1002/chem.201504419] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Indexed: 01/09/2023]
Abstract
Biological selection makes natural products promising scaffolds for drug development and the ever growing number of newly identified, structurally diverse molecules helps to fill the gaps in chemical space. Elucidating the function of a small molecule, such as identifying its protein binding partners, its on- and off-targets, is becoming increasingly important. Activity- and affinity-based protein profiling are modern strategies to acquire such molecular-level information. Introduction of a molecular handle (azide, alkyne, biotin) can shed light on the mode of action of small molecules. This Concept article covers central points on synthetic methodology for integrating a terminal alkyne into a molecule of interest.
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Affiliation(s)
- Johannes Lehmann
- Center for Integrated Protein Science, Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Megan H Wright
- Center for Integrated Protein Science, Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Stephan A Sieber
- Center for Integrated Protein Science, Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany.
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44
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Abstract
Proteins are acylated by a variety of metabolites that regulates many important cellular pathways in all kingdoms of life. Acyl groups in cells can vary in structure from the smallest unit, acetate, to modified long-chain fatty acids, all of which can be activated and covalently attached to diverse amino acid side chains and consequently modulate protein function. For example, acetylation of Lys residues can alter the charge state of proteins and generate new recognition elements for protein-protein interactions. Alternatively, long-chain fatty-acylation targets proteins to membranes and enables spatial control of cell signalling. To facilitate the analysis of protein acylation in biology, acyl analogues bearing alkyne or azide tags have been developed that enable fluorescent imaging and proteomic profiling of modified proteins using bioorthogonal ligation methods. Herein, we summarize the currently available acylation chemical reporters and highlight their utility to discover and quantify the roles of protein acylation in biology.
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45
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Jung S, Kwon I. Expansion of bioorthogonal chemistries towards site-specific polymer–protein conjugation. Polym Chem 2016. [DOI: 10.1039/c6py00856a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bioorthogonal chemistries have been used to achieve polymer-protein conjugation with the retained critical properties.
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Affiliation(s)
- Secheon Jung
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
| | - Inchan Kwon
- School of Materials Science and Engineering
- Gwangju Institute of Science and Technology (GIST)
- Gwangju 61005
- Republic of Korea
- Department of Chemical Engineering
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46
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Kulkarni C, Lo M, Fraseur JG, Tirrell DA, Kinzer-Ursem TL. Bioorthogonal Chemoenzymatic Functionalization of Calmodulin for Bioconjugation Applications. Bioconjug Chem 2015; 26:2153-60. [PMID: 26431265 DOI: 10.1021/acs.bioconjchem.5b00449] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Calmodulin (CaM) is a widely studied Ca(2+)-binding protein that is highly conserved across species and involved in many biological processes, including vesicle release, cell proliferation, and apoptosis. To facilitate biophysical studies of CaM, researchers have tagged and mutated CaM at various sites, enabling its conjugation to fluorophores, microarrays, and other reactive partners. However, previous attempts to add a reactive label to CaM for downstream studies have generally employed nonselective labeling methods or resulted in diminished CaM function. Here we report the first engineered CaM protein that undergoes site-specific and bioorthogonal labeling while retaining wild-type activity levels. By employing a chemoenzymatic labeling approach, we achieved selective and quantitative labeling of the engineered CaM protein with an N-terminal 12-azidododecanoic acid tag; notably, addition of the tag did not interfere with the ability of CaM to bind Ca(2+) or a partner protein. The specificity of our chemoenzymatic labeling approach also allowed for selective conjugation of CaM to reactive partners in bacterial cell lysates, without intermediate purification of the engineered protein. Additionally, we prepared CaM-affinity resins that were highly effective in purifying a representative CaM-binding protein, demonstrating that the engineered CaM remains active even after surface capture. Beyond studies of CaM and CaM-binding proteins, the protein engineering and surface capture methods described here should be translatable to other proteins and other bioconjugation applications.
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Affiliation(s)
- Chethana Kulkarni
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States
| | - Megan Lo
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States
| | - Julia G Fraseur
- Weldon School of Biomedical Engineering, Purdue University , 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States
| | - Tamara L Kinzer-Ursem
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States.,Weldon School of Biomedical Engineering, Purdue University , 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
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47
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Hannoush RN. Synthetic protein lipidation. Curr Opin Chem Biol 2015; 28:39-46. [DOI: 10.1016/j.cbpa.2015.05.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/26/2015] [Indexed: 12/19/2022]
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48
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Walper SA, Turner KB, Medintz IL. Enzymatic bioconjugation of nanoparticles: developing specificity and control. Curr Opin Biotechnol 2015; 34:232-41. [PMID: 25955793 DOI: 10.1016/j.copbio.2015.04.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 12/31/2022]
Abstract
Nanoparticles are finding increasing roles in biotechnology for applications as contrast agents, probes, sensors, therapeutics and increasingly new value-added hybrid materials such as molecular logic devices. In most cases these materials must be conjugated to different types of biologicals such as proteins or DNA to accomplish this. However, most traditional methods of bioconjugation result in heterogeneous attachment and loss of activity. Bioorthogonal chemistries and in particular enzymatic labeling chemistries offer new strategies for catalyzing specific biomolecular attachment. We highlight current enzymatic labeling methods available for bioconjugating nanoparticles, some materials they have been used with, and how the resulting bioconjugates were applied. A discussion of the benefits and remaining issues associated with this type of bioconjugation chemistry and a brief perspective on how this field will develop is also provided.
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Affiliation(s)
- Scott A Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue, S.W., Washington, DC 20375, USA
| | - Kendrick B Turner
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue, S.W., Washington, DC 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue, S.W., Washington, DC 20375, USA.
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49
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Chen Y, Tsao K, Keillor JW. Fluorogenic protein labelling: a review of photophysical quench mechanisms and principles of fluorogen design. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0405] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fluorescent labelling of specific proteins in complex biological systems remains an important challenge in chemical biology. One promising approach comprises the use of small molecules designed to react specifically with a targeted protein of interest and to increase in fluorescent intensity following this reaction. This kind of fluorogenic reaction generally derives from fluorescence quenching in the unreacted probe that is abrogated over the course of the reaction. Herein, we review the mechanistic principles of three major photophysical quenching mechanisms involving Förster resonance energy transfer (FRET), through-bond energy transfer (TBET), and photoinduced electron transfer (PeT). We then present design principles for novel fluorogenic probes based on an understanding of these quench mechanisms, with emphasis on the emerging utility of density functional theory (DFT) calculations in the design process.
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Affiliation(s)
- Yingche Chen
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - Kelvin Tsao
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - Jeffrey W. Keillor
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
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Hassan S, Müller TJJ. Multicomponent Syntheses based upon Copper-Catalyzed Alkyne-Azide Cycloaddition. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201400904] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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