1
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Li S, Zhu C, Zhao Q, Zhang ZM, Sun P, Li Z. Ynamide Coupling Reagent for the Chemical Cross-Linking of Proteins in Live Cells. ACS Chem Biol 2023; 18:1405-1415. [PMID: 37231651 DOI: 10.1021/acschembio.3c00149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is a powerful method for the study of protein structure and protein-protein interactions (PPIs). However, the chemical probes used in the CXMS are limited to bidentate reactive warheads, and the available zero-length cross-linkers are restricted to 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride/N-hydroxysuccinimide (EDC/NHS) and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM). To alleviate this issue, an efficient coupling reagent, sulfonyl ynamide, was developed as a new zero-length cross-linker that can connect high-abundance carboxyl residues (D/E) with lysine (K) to form amide bonds in the absence of any catalyst. Significant improvement in the cross-linking efficiency and specificity in comparison with traditional EDC/NHS was achieved with model proteins, which includes inter- and intramolecular conjugations. The cross-linked structures were validated by X-ray crystallography. Importantly, this coupling reagent can be successfully used to capture interacting proteins in the whole proteome and can be a useful reagent for probing potential protein-protein interactions in situ.
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Affiliation(s)
- Shengrong Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Chengjun Zhu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Qian Zhao
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Zhi-Min Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Pinghua Sun
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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2
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Dreyer R, Pfukwa R, Barth S, Hunter R, Klumperman B. The Evolution of SNAP-Tag Labels. Biomacromolecules 2023; 24:517-530. [PMID: 36607253 DOI: 10.1021/acs.biomac.2c01238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The conjugation of proteins with synthetic molecules can be conducted in many different ways. In this Perspective, we focus on tag-based techniques and specifically on the SNAP-tag technology. The SNAP-tag technology makes use of a fusion protein between a protein of interest and an enzyme tag that enables the actual conjugation reaction. The SNAP-tag is based on the O6-alkylguanine-DNA alkyltransferase (AGT) enzyme and is optimized to react selectively with O6-benzylguanine (BG) substrates. BG-containing dye derivatives have frequently been used to introduce a fluorescent tag to a specific protein. We believe that the site-specific conjugation of polymers to proteins can significantly benefit from the SNAP-tag technology. Especially, polymers synthesized via reversible deactivation radical polymerization allow for the facile introduction of a BG end group to enable SNAP-tag conjugation.
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Affiliation(s)
- Rudolf Dreyer
- Stellenbosch University, Department of Chemistry and Polymer Science, Private Bag X1, Matieland 7602, South Africa
| | - Rueben Pfukwa
- Stellenbosch University, Department of Chemistry and Polymer Science, Private Bag X1, Matieland 7602, South Africa
| | - Stefan Barth
- Medical Biotechnology and Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7935, South Africa.,South African Research Chair in Cancer Biotechnology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Observatory 7935, South Africa
| | - Roger Hunter
- Department of Chemistry, Faculty of Science, University of Cape Town, Rondebosch 7701, South Africa
| | - Bert Klumperman
- Stellenbosch University, Department of Chemistry and Polymer Science, Private Bag X1, Matieland 7602, South Africa
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3
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Depke DA, Konken CP, Rösner L, Hermann S, Schäfers M, Rentmeister A. A novel 18F-labeled clickable substrate for targeted imaging of SNAP-tag expressing cells by PET in vivo. Chem Commun (Camb) 2021; 57:9850-9853. [PMID: 34490435 DOI: 10.1039/d1cc03871k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioorthogonal covalent labeling with self-labeling enzymes like SNAP-tag bears a high potential for specific targeting of cells for imaging in vitro and also in vivo. To this end, fluorescent SNAP substrates have been established and used in microscopy and fluorescence imaging while radioactive substrates for the highly sensitive and whole-body positron emission tomography (PET) have been lacking. Here, we show for the first time successful and high-contrast PET imaging of subcutaneous SNAP-tag expressing tumor xenografts by bioorthogonal covalent targeting with a novel 18F-based radioligand in vivo.
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Affiliation(s)
- Dominic Alexej Depke
- European Institute for Molecular Imaging (EIMI), University of Münster, Germany.
| | - Christian Paul Konken
- European Institute for Molecular Imaging (EIMI), University of Münster, Germany. .,Department of Nuclear Medicine, University Hospital Münster, Germany
| | - Lukas Rösner
- Institute of Biochemistry, University of Münster, Germany.
| | - Sven Hermann
- European Institute for Molecular Imaging (EIMI), University of Münster, Germany.
| | - Michael Schäfers
- European Institute for Molecular Imaging (EIMI), University of Münster, Germany. .,Department of Nuclear Medicine, University Hospital Münster, Germany
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4
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Maffei M, Morelli C, Graham E, Patriarca S, Donzelli L, Doleschall B, de Castro Reis F, Nocchi L, Chadick CH, Reymond L, Corrêa IR, Johnsson K, Hackett JA, Heppenstall PA. A ligand-based system for receptor-specific delivery of proteins. Sci Rep 2019; 9:19214. [PMID: 31844114 PMCID: PMC6915567 DOI: 10.1038/s41598-019-55797-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/30/2019] [Indexed: 12/24/2022] Open
Abstract
Gene delivery using vector or viral-based methods is often limited by technical and safety barriers. A promising alternative that circumvents these shortcomings is the direct delivery of proteins into cells. Here we introduce a non-viral, ligand-mediated protein delivery system capable of selectively targeting primary skin cells in-vivo. Using orthologous self-labelling tags and chemical cross-linkers, we conjugate large proteins to ligands that bind their natural receptors on the surface of keratinocytes. Targeted CRE-mediated recombination was achieved by delivery of ligand cross-linked CRE protein to the skin of transgenic reporter mice, but was absent in mice lacking the ligand's cell surface receptor. We further show that ligands mediate the intracellular delivery of Cas9 allowing for CRISPR-mediated gene editing in the skin more efficiently than adeno-associated viral gene delivery. Thus, a ligand-based system enables the effective and receptor-specific delivery of large proteins and may be applied to the treatment of skin-related genetic diseases.
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Affiliation(s)
- Mariano Maffei
- European Molecular Biology Laboratory (EMBL) Rome, Adriano Buzzati-Traverso Campus, 00015, Monterotondo, Italy.
| | - Chiara Morelli
- European Molecular Biology Laboratory (EMBL) Rome, Adriano Buzzati-Traverso Campus, 00015, Monterotondo, Italy.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Ellie Graham
- European Molecular Biology Laboratory (EMBL) Rome, Adriano Buzzati-Traverso Campus, 00015, Monterotondo, Italy
| | - Stefano Patriarca
- European Molecular Biology Laboratory (EMBL) Rome, Adriano Buzzati-Traverso Campus, 00015, Monterotondo, Italy
| | - Laura Donzelli
- European Molecular Biology Laboratory (EMBL) Rome, Adriano Buzzati-Traverso Campus, 00015, Monterotondo, Italy
| | - Balint Doleschall
- European Molecular Biology Laboratory (EMBL) Rome, Adriano Buzzati-Traverso Campus, 00015, Monterotondo, Italy
| | - Fernanda de Castro Reis
- European Molecular Biology Laboratory (EMBL) Rome, Adriano Buzzati-Traverso Campus, 00015, Monterotondo, Italy
| | - Linda Nocchi
- European Molecular Biology Laboratory (EMBL) Rome, Adriano Buzzati-Traverso Campus, 00015, Monterotondo, Italy
| | - Cora H Chadick
- European Molecular Biology Laboratory (EMBL) Rome, Adriano Buzzati-Traverso Campus, 00015, Monterotondo, Italy
| | - Luc Reymond
- Biomolecular Screening Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.,National Center of Competence in Research (NCCR) in Chemical Biology, 1015, Lausanne, Switzerland
| | | | - Kai Johnsson
- Department of Chemical Biology, Max Plank Institute for Medical Research, 69120, Heidelberg, Germany
| | - Jamie A Hackett
- European Molecular Biology Laboratory (EMBL) Rome, Adriano Buzzati-Traverso Campus, 00015, Monterotondo, Italy
| | - Paul A Heppenstall
- European Molecular Biology Laboratory (EMBL) Rome, Adriano Buzzati-Traverso Campus, 00015, Monterotondo, Italy.
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5
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Cassona CP, Pereira F, Serrano M, Henriques AO. A Fluorescent Reporter for Single Cell Analysis of Gene Expression in Clostridium difficile. Methods Mol Biol 2016; 1476:69-90. [PMID: 27507334 DOI: 10.1007/978-1-4939-6361-4_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Genetically identical cells growing under homogeneous growth conditions often display cell-cell variation in gene expression. This variation stems from noise in gene expression and can be adaptive allowing for division of labor and bet-hedging strategies. In particular, for bacterial pathogens, the expression of phenotypes related to virulence can show cell-cell variation. Therefore, understanding virulence-related gene expression requires knowledge of gene expression patterns at the single cell level. We describe protocols for the use of fluorescence reporters for single cell analysis of gene expression in the human enteric pathogen Clostridium difficile, a strict anaerobe. The reporters are based on modified versions of the human DNA repair enzyme O ( 6)-alkylguanine-DNA alkyltransferase, called SNAP-tag and CLIP-tag. SNAP becomes covalently labeled upon reaction with O ( 6)-benzylguanine conjugated to a fluorophore, whereas CLIP is labeled by O ( 6)-benzylcytosine conjugates. SNAP and CLIP labeling is orthogonal allowing for dual labeling in the same cells. SNAP and CLIP cassettes optimized for C. difficile can be used for quantitative studies of gene expression at the single cell level. Both the SNAP and CLIP reporters can also be used for studies of protein subcellular localization in C. difficile.
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Affiliation(s)
- Carolina Piçarra Cassona
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Fátima Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal.
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6
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Rudd AK, Valls Cuevas JM, Devaraj NK. SNAP-Tag-Reactive Lipid Anchors Enable Targeted and Spatiotemporally Controlled Localization of Proteins to Phospholipid Membranes. J Am Chem Soc 2015; 137:4884-7. [DOI: 10.1021/jacs.5b00040] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Andrew K. Rudd
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Joan M. Valls Cuevas
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K. Devaraj
- Department
of Chemistry and
Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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7
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Sun X, Dusserre-Bresson F, Baker B, Zhang A, Xu P, Fibbe C, Noren CJ, Corrêa IR, Xu MQ. Probing homodimer formation of epidermal growth factor receptor by selective crosslinking. Eur J Med Chem 2014; 88:34-41. [PMID: 25042004 DOI: 10.1016/j.ejmech.2014.07.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/11/2014] [Accepted: 07/12/2014] [Indexed: 11/17/2022]
Abstract
Ligand binding promotes conformational rearrangement of the epidermal growth factor receptor (EGFR) leading to receptor autophosphorylation and downstream signaling. However, transient interactions between unstimulated EGFR molecules on the cell surface are not fully understood. In this report, we describe the investigation of homodimer formation of EGFR by means of an SNAP-tag based selective crosslinking approach (S-CROSS). EGFR homodimers were selectively captured in living cells and utilized for analysis of protein receptor interactions on the plasma membrane and ligand-induced activation. We showed that EGFR forms homodimers in unstimulated cells with efficiencies similar to those seen in cells treated with the epidermal growth factor ligand (EGF) supporting the existence of constitutive transient receptor-receptor interactions. EGFR crosslinked homodimers displayed a substantially increase in kinase activation upon ligand stimulation. Interestingly, in unstimulated cells the levels of spontaneous phosphorylation were found to correlate with the yields of the crosslinked homodimers species. In addition, we demonstrated that this crosslinking approach can be applied to interrogate the effect of small molecule inhibitors on receptor dimerization and kinase activity. Our crosslinking assay provides a new tool to dissect ligand-independent dimerization and activation mechanisms of receptor tyrosine kinases, many of which are important anticancer drug targets.
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Affiliation(s)
- Xiaoli Sun
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | | | - Brenda Baker
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Aihua Zhang
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Patrick Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Cassandra Fibbe
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | | | - Ivan R Corrêa
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA.
| | - Ming-Qun Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA.
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8
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Erhart D, Zimmermann M, Jacques O, Wittwer MB, Ernst B, Constable E, Zvelebil M, Beaufils F, Wymann MP. Chemical development of intracellular protein heterodimerizers. ACTA ACUST UNITED AC 2013; 20:549-57. [PMID: 23601644 DOI: 10.1016/j.chembiol.2013.03.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/13/2013] [Accepted: 03/20/2013] [Indexed: 12/19/2022]
Abstract
Cell activation initiated by receptor ligands or oncogenes triggers complex and convoluted intracellular signaling. Techniques initiating signals at defined starting points and cellular locations are attractive to elucidate the output of selected pathways. Here, we present the development and validation of a protein heterodimerization system based on small molecules cross-linking fusion proteins derived from HaloTags and SNAP-tags. Chemical dimerizers of HaloTag and SNAP-tag (HaXS) show excellent selectivity and have been optimized for intracellular reactivity. HaXS force protein-protein interactions and can translocate proteins to various cellular compartments. Due to the covalent nature of the HaloTag-HaXS-SNAP-tag complex, intracellular dimerization can be easily monitored. First applications include protein targeting to cytoskeleton, to the plasma membrane, to lysosomes, the initiation of the PI3K/mTOR pathway, and multiplexed protein complex formation in combination with the rapamycin dimerization system.
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Affiliation(s)
- Dominik Erhart
- Department of Biomedicine, University of Basel, 4003 Basel, Switzerland
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9
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Hatch AC, Patel A, Beer NR, Lee AP. Passive droplet sorting using viscoelastic flow focusing. LAB ON A CHIP 2013; 13:1308-15. [PMID: 23380996 DOI: 10.1039/c2lc41160a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We present a study of passive hydrodynamic droplet sorting in microfluidic channels based on intrinsic viscoelastic fluid properties. Sorting is achieved by tuning the droplets' intrinsic viscous and viscoelastic properties relative to the continuous oil phase to achieve a positive or negative lateral migration toward high or low shear gradients in the channel. In the presence of weakly viscoelastic fluid behavior, droplets with a viscosity ratio, κ, between 0.5-10 were found to migrate toward a high shear gradient near the channel walls. For all other κ-values, or Newtonian fluids, droplets would migrate toward a low shear gradient at the channel centerline. It was also found that for strongly viscoelastic fluids with low interfacial tension, droplets would migrate toward the edge even with κ-values lower than 0.5. The resulting bi-directional lateral droplet migration between different droplets allows size-independent sorting. Still, their sorting efficiencies are dependent on droplet size, intrinsic fluid elasticity, viscosity, droplet deformability, and overall fluid shear rates. Based on these findings, we demonstrate >200 Hz passive droplet sorting frequencies and achieve >100 fold enrichment factors without the need to actively sense and/or control active mechanisms. Using a low viscosity oil phase of 6.25 cPs, we demonstrate sorting discrimination of 1 cPs and 5 cPs aqueous droplets with κ-values of 0.2 and 0.8 respectively.
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Affiliation(s)
- Andrew C Hatch
- Biomedical Engineering, University of California-Irvine, CA 92697, USA.
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10
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Wasserberg D, Uhlenheuer DA, Neirynck P, Cabanas-Danés J, Schenkel JH, Ravoo BJ, An Q, Huskens J, Milroy LG, Brunsveld L, Jonkheijm P. Immobilization of Ferrocene-Modified SNAP-Fusion Proteins. Int J Mol Sci 2013; 14:4066-80. [PMID: 23429193 PMCID: PMC3588085 DOI: 10.3390/ijms14024066] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/04/2013] [Accepted: 02/04/2013] [Indexed: 12/16/2022] Open
Abstract
The supramolecular assembly of proteins on surfaces has been investigated via the site-selective incorporation of a supramolecular moiety on proteins. To this end, fluorescent proteins have been site-selectively labeled with ferrocenes, as supramolecular guest moieties, via SNAP-tag technology. The assembly of guest-functionalized SNAP-fusion proteins on cyclodextrin- and cucurbit[7]uril-coated surfaces yielded stable monolayers. The binding of all ferrocene fusion proteins is specific as determined by surface plasmon resonance. Micropatterns of the fusion proteins, on patterned cyclodextrin and cucurbituril surfaces, have been visualized using fluorescence microscopy. The SNAP-fusion proteins were also immobilized on cyclodextrin vesicles. The supramolecular SNAP-tag labeling of proteins, thus, allows for the assembly of modified proteins via supramolecular host-guest interaction on different surfaces in a controlled manner. These findings extend the toolbox of fabricating supramolecular protein patterns on surfaces taking advantage of the high labeling efficiency of the SNAP-tag with versatile supramolecular moieties.
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Affiliation(s)
- Dorothee Wasserberg
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
| | - Dana A. Uhlenheuer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands; E-Mails: (D.A.U.); (P.N.); (L.-G.M.)
| | - Pauline Neirynck
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands; E-Mails: (D.A.U.); (P.N.); (L.-G.M.)
| | - Jordi Cabanas-Danés
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
| | - Jan Hendrik Schenkel
- Institute of Organic Chemistry, Westfaelische Wilhelms-Universität Muenster, Corrensstrasse 40, 48149 Münster, Germany; E-Mails: (J.H.S.); (B.J.R.)
| | - Bart Jan Ravoo
- Institute of Organic Chemistry, Westfaelische Wilhelms-Universität Muenster, Corrensstrasse 40, 48149 Münster, Germany; E-Mails: (J.H.S.); (B.J.R.)
| | - Qi An
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
| | - Jurriaan Huskens
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands; E-Mails: (D.A.U.); (P.N.); (L.-G.M.)
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands; E-Mails: (D.A.U.); (P.N.); (L.-G.M.)
- Authors to whom correspondence should be addressed; E-Mails: (L.B.); (P.J.); Tel.: +31-53-489-2987 (P.J.); Fax: +31-53-489-4546 (P.J.)
| | - Pascal Jonkheijm
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
- Authors to whom correspondence should be addressed; E-Mails: (L.B.); (P.J.); Tel.: +31-53-489-2987 (P.J.); Fax: +31-53-489-4546 (P.J.)
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11
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Petkau-Milroy K, Uhlenheuer DA, Spiering AJH, Vekemans JAJM, Brunsveld L. Dynamic and bio-orthogonal protein assembly along a supramolecular polymer. Chem Sci 2013. [DOI: 10.1039/c3sc50891a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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12
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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13
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Foraker AB, Camus SM, Evans TM, Majeed SR, Chen CY, Taner SB, Corrêa IR, Doxsey SJ, Brodsky FM. Clathrin promotes centrosome integrity in early mitosis through stabilization of centrosomal ch-TOG. ACTA ACUST UNITED AC 2012; 198:591-605. [PMID: 22891263 PMCID: PMC3514040 DOI: 10.1083/jcb.201205116] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Clathrin inactivation during S phase destabilizes the microtubule-binding protein
ch-TOG, affecting its centrosomal localization and centrosome integrity during
early mitosis. Clathrin depletion by ribonucleic acid interference (RNAi) impairs mitotic
spindle stability and cytokinesis. Depletion of several clathrin-associated
proteins affects centrosome integrity, suggesting a further cell cycle function
for clathrin. In this paper, we report that RNAi depletion of CHC17 (clathrin
heavy chain 17) clathrin, but not the CHC22 clathrin isoform, induced centrosome
amplification and multipolar spindles. To stage clathrin function within the
cell cycle, a cell line expressing SNAP-tagged clathrin light chains was
generated. Acute clathrin inactivation by chemical dimerization of the SNAP-tag
during S phase caused reduction of both clathrin and ch-TOG (colonic, hepatic
tumor overexpressed gene) at metaphase centrosomes, which became fragmented.
This was phenocopied by treatment with Aurora A kinase inhibitor, suggesting a
centrosomal role for the Aurora A–dependent complex of clathrin, ch-TOG,
and TACC3 (transforming acidic coiled-coil protein 3). Clathrin inactivation in
S phase also reduced total cellular levels of ch-TOG by metaphase. Live-cell
imaging showed dynamic clathrin recruitment during centrosome maturation.
Therefore, we propose that clathrin promotes centrosome maturation by
stabilizing the microtubule-binding protein ch-TOG, defining a novel role for
the clathrin–ch-TOG–TACC3 complex.
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Affiliation(s)
- Amy B Foraker
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143, USA
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14
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White BR, Carlson JCT, Kerns JL, Wagner CR. Protein interface remodeling in a chemically induced protein dimer. J Mol Recognit 2012; 25:393-403. [DOI: 10.1002/jmr.2196] [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)
- Brian R. White
- Department of Medicinal Chemistry, College of Pharmacy; University of Minnesota; Minneapolis; MN; 55455; USA
| | - Jonathan C. T. Carlson
- Department of Medicinal Chemistry, College of Pharmacy; University of Minnesota; Minneapolis; MN; 55455; USA
| | - Jessie L. Kerns
- Department of Medicinal Chemistry, College of Pharmacy; University of Minnesota; Minneapolis; MN; 55455; USA
| | - Carston R. Wagner
- Department of Medicinal Chemistry, College of Pharmacy; University of Minnesota; Minneapolis; MN; 55455; USA
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15
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Rutkowska A, Schultz C. Protein Tango: The Toolbox to Capture Interacting Partners. Angew Chem Int Ed Engl 2012; 51:8166-76. [DOI: 10.1002/anie.201201717] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Indexed: 11/07/2022]
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16
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17
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Rutkowska A, Haering CH, Schultz C. A FlAsH-Based Cross-Linker to Study Protein Interactions in Living Cells. Angew Chem Int Ed Engl 2011; 50:12655-8. [DOI: 10.1002/anie.201106404] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Indexed: 11/11/2022]
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18
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Rutkowska A, Haering CH, Schultz C. FlAsH-basierte Verknüpfungen von Proteinen in lebenden Zellen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106404] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Sun X, Zhang A, Baker B, Sun L, Howard A, Buswell J, Maurel D, Masharina A, Johnsson K, Noren CJ, Xu MQ, Corrêa IR. Development of SNAP-tag fluorogenic probes for wash-free fluorescence imaging. Chembiochem 2011; 12:2217-26. [PMID: 21793150 PMCID: PMC3213346 DOI: 10.1002/cbic.201100173] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Indexed: 12/22/2022]
Abstract
The ability to specifically attach chemical probes to individual proteins represents a powerful approach to the study and manipulation of protein function in living cells. It provides a simple, robust and versatile approach to the imaging of fusion proteins in a wide range of experimental settings. However, a potential drawback of detection using chemical probes is the fluorescence background from unreacted or nonspecifically bound probes. In this report we present the design and application of novel fluorogenic probes for labeling SNAP-tag fusion proteins in living cells. SNAP-tag is an engineered variant of the human repair protein O(6)-alkylguanine-DNA alkyltransferase (hAGT) that covalently reacts with benzylguanine derivatives. Reporter groups attached to the benzyl moiety become covalently attached to the SNAP tag while the guanine acts as a leaving group. Incorporation of a quencher on the guanine group ensures that the benzylguanine probe becomes highly fluorescent only upon labeling of the SNAP-tag protein. We describe the use of intramolecularly quenched probes for wash-free labeling of cell surface-localized epidermal growth factor receptor (EGFR) fused to SNAP-tag and for direct quantification of SNAP-tagged β-tubulin in cell lysates. In addition, we have characterized a fast-labeling variant of SNAP-tag, termed SNAP(f), which displays up to a tenfold increase in its reactivity towards benzylguanine substrates. The presented data demonstrate that the combination of SNAP(f) and the fluorogenic substrates greatly reduces the background fluorescence for labeling and imaging applications. This approach enables highly sensitive spatiotemporal investigation of protein dynamics in living cells.
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Affiliation(s)
- Xiaoli Sun
- New England Biolabs, Inc240 County Road, Ipswich, MA 01938 (USA)
| | - Aihua Zhang
- New England Biolabs, Inc240 County Road, Ipswich, MA 01938 (USA)
| | - Brenda Baker
- New England Biolabs, Inc240 County Road, Ipswich, MA 01938 (USA)
| | - Luo Sun
- New England Biolabs, Inc240 County Road, Ipswich, MA 01938 (USA)
| | - Angela Howard
- New England Biolabs, Inc240 County Road, Ipswich, MA 01938 (USA)
| | - John Buswell
- New England Biolabs, Inc240 County Road, Ipswich, MA 01938 (USA)
| | - Damien Maurel
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Federal de Lausanne (EPFL)1015 Lausanne (Switzerland)
| | - Anastasiya Masharina
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Federal de Lausanne (EPFL)1015 Lausanne (Switzerland)
| | - Kai Johnsson
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Federal de Lausanne (EPFL)1015 Lausanne (Switzerland)
| | | | - Ming-Qun Xu
- New England Biolabs, Inc240 County Road, Ipswich, MA 01938 (USA)
| | - Ivan R Corrêa
- New England Biolabs, Inc240 County Road, Ipswich, MA 01938 (USA)
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20
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Campos C, Kamiya M, Banala S, Johnsson K, González-Gaitán M. Labelling cell structures and tracking cell lineage in zebrafish using SNAP-tag. Dev Dyn 2011; 240:820-7. [DOI: 10.1002/dvdy.22574] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2010] [Indexed: 01/30/2023] Open
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21
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Hinner MJ, Johnsson K. How to obtain labeled proteins and what to do with them. Curr Opin Biotechnol 2010; 21:766-76. [PMID: 21030243 DOI: 10.1016/j.copbio.2010.09.011] [Citation(s) in RCA: 227] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 09/10/2010] [Accepted: 09/21/2010] [Indexed: 12/20/2022]
Abstract
We review new and established methods for the chemical modification of proteins in living cells and highlight recent applications. The review focuses on tag-mediated protein labeling methods, such as the tetracysteine tag and SNAP-tag, and new developments in this field such as intracellular labeling with lipoic acid ligase. Recent promising advances in the incorporation of unnatural amino acids into proteins are also briefly discussed. We describe new tools using tag-mediated labeling methods including the super-resolution microscopy of tagged proteins, the study of the interactions of proteins and protein domains, the subcellular targeting of synthetic ion sensors, and the generation of new semisynthetic metabolite sensors. We conclude with a view on necessary future developments, with one example being the selective labeling of non-tagged, native proteins in complex protein mixtures.
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Affiliation(s)
- Marlon J Hinner
- Institute of Chemical Sciences and Engineering, Laboratory of Protein Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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22
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Fegan A, White B, Carlson JCT, Wagner CR. Chemically controlled protein assembly: techniques and applications. Chem Rev 2010; 110:3315-36. [PMID: 20353181 DOI: 10.1021/cr8002888] [Citation(s) in RCA: 229] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Adrian Fegan
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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23
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Gautier A, Nakata E, Lukinavičius G, Tan KT, Johnsson K. Selective Cross-Linking of Interacting Proteins Using Self-Labeling Tags. J Am Chem Soc 2009; 131:17954-62. [DOI: 10.1021/ja907818q] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Arnaud Gautier
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Eiji Nakata
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Gražvydas Lukinavičius
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Kui-Thong Tan
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Kai Johnsson
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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24
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Brun MA, Tan KT, Nakata E, Hinner MJ, Johnsson K. Semisynthetic fluorescent sensor proteins based on self-labeling protein tags. J Am Chem Soc 2009; 131:5873-84. [PMID: 19348459 DOI: 10.1021/ja900149e] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetically encoded fluorescent sensor proteins offer the possibility to probe the concentration of key metabolites in living cells. The approaches currently used to generate such fluorescent sensor proteins lack generality, as they require a protein that undergoes a conformational change upon metabolite binding. Here we present an approach that overcomes this limitation. Our biosensors consist of SNAP-tag, a fluorescent protein and a metabolite-binding protein. SNAP-tag is specifically labeled with a synthetic molecule containing a ligand of the metabolite-binding protein and a fluorophore. In the labeled sensor, the metabolite of interest displaces the intramolecular ligand from the binding protein, thereby shifting the sensor protein from a closed to an open conformation. The readout is a concomitant ratiometric change in the fluorescence intensities of the fluorescent protein and the tethered fluorophore. The observed ratiometric changes compare favorably with those achieved in genetically encoded fluorescent sensor proteins. Furthermore, the modular design of our sensors permits the facile generation of ratiometric fluorescent sensors at wavelengths not covered by autofluorescent proteins. These features should allow semisynthetic fluorescent sensor proteins based on SNAP-tag to become important tools for probing previously inaccessible metabolites.
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Affiliation(s)
- Matthias A Brun
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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25
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Yang L, Zhang H, Bruce JE. Optimizing the detergent concentration conditions for immunoprecipitation (IP) coupled with LC-MS/MS identification of interacting proteins. Analyst 2009; 134:755-62. [PMID: 19305927 DOI: 10.1039/b813335b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Immunoprecipitation (IP) coupled with LC-MS/MS is a widely used method in proteomics research to identify proteins and to study protein-protein interactions. IP techniques allow purification of proteins of interest and reduce sample complexity before introduction to the mass spectrometer. The effectiveness of IP experiments is an important factor for identification of proteins and protein-protein interactions. In this paper, a variety of IP conditions were studied systematically to improve IP-based protein interaction identification capabilities. Low concentration detergent (around 0.05% NP40/PBS) was found to improve IP effectiveness by decreasing non-specific binding. However, higher concentration detergent (e.g. 1% NP40/PBS) was detrimental. Furthermore, with lower protein concentrations, the IP system showed lower tolerance to detergent. For example, with a detergent concentration higher than 0.05% NP40/PBS, IP experiments were unsuccessful with low protein concentration (e.g. 0.28 microM ADH). In some cases the observed results were even worse than the results obtained without detergent. However, when the protein concentration was high (e.g. 1.12 microM ADH), this effect was not obvious and the high detergent (higher than 0.1%) experimental results were similar to those from low detergent concentration experiments (around 0.05%). Another application of this strategy to a more general system based on FLAG-Bacterial Alkaline Phosphatase (BAP) and anti-FLAG antibody was also performed. These results also suggested that low detergent concentration (0.05% NP40) is helpful for IP experiments, especially for the experiments with low protein concentrations. Considering that in most real applications, the proteins of interest are usually present in low abundance, a low amount of detergent is recommended to be used. The optimized detergent concentration was determined to be 0.05% in these studies. However, the key result presented here illustrates that both detergent and protein concentrations should be carefully considered when one is trying to optimize IP prior to mass spectrometry experiments.
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Affiliation(s)
- Li Yang
- Department of Genome Sciences, The University of Washington, Seattle, WA 98195-5065, USA
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26
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Sunbul M, Yin J. Site specific protein labeling by enzymatic posttranslational modification. Org Biomol Chem 2009; 7:3361-71. [DOI: 10.1039/b908687k] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Corson TW, Aberle N, Crews CM. Design and Applications of Bifunctional Small Molecules: Why Two Heads Are Better Than One. ACS Chem Biol 2008; 3:677-692. [PMID: 19112665 DOI: 10.1021/cb8001792] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Induction of protein--protein interactions is a daunting challenge, but recent studies show promise for small molecules that specifically bring two or more protein molecules together for enhanced or novel biological effect. The first such bifunctional molecules were the rapamycin- and FK506-based "chemical inducers of dimerization", but the field has since expanded with new molecules and new applications in chemical genetics and cell biology. Examples include coumermycin-mediated gyrase B dimerization, proteolysis targeting chimeric molecules (PROTACs), drug hybrids, and strategies for exploiting multivalency in toxin binding and antibody recruitment. This Review discusses these and other advances in the design and use of bifunctional small molecules and potential strategies for future systems.
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Affiliation(s)
| | | | - Craig M. Crews
- Department of Molecular, Cellular & Developmental Biology
- Departments of Chemistry and Pharmacology, Yale University, New Haven, Connecticut 06511
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28
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Banala S, Arnold A, Johnsson K. Caged substrates for protein labeling and immobilization. Chembiochem 2008; 9:38-41. [PMID: 18033718 DOI: 10.1002/cbic.200700472] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Sambashiva Banala
- Ecole Polytechnique Fédéral de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, 1015 Lausanne, Switzerland
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29
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Gautier A, Juillerat A, Heinis C, Corrêa IR, Kindermann M, Beaufils F, Johnsson K. An Engineered Protein Tag for Multiprotein Labeling in Living Cells. ACTA ACUST UNITED AC 2008; 15:128-36. [DOI: 10.1016/j.chembiol.2008.01.007] [Citation(s) in RCA: 609] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Revised: 01/12/2008] [Accepted: 01/17/2008] [Indexed: 10/22/2022]
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30
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Dijkstra HP, Sprong H, Aerts BNH, Kruithof CA, Egmond MR, Klein Gebbink RJM. Selective and diagnostic labelling of serine hydrolases with reactive phosphonate inhibitors. Org Biomol Chem 2008; 6:523-31. [DOI: 10.1039/b717345h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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