1
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Maller C, Schedel F, Köhn M. A Modular Approach for the Synthesis of Diverse Heterobifunctional Cyanine Dyes. J Org Chem 2024; 89:3844-3856. [PMID: 38413005 PMCID: PMC10949230 DOI: 10.1021/acs.joc.3c02673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 02/29/2024]
Abstract
Herein, we present a straightforward synthetic route for the design and synthesis of diverse heterobifunctional cyanine 5 dyes. We optimized the workup by harnessing the pH- and functional group-dependent solubility of the asymmetric cyanine 5 dyes. Therefore, purification through chromatography is deferred until the last synthesis step. Demonstrating successful large-scale synthesis, our modular approach prevents functional group degradation by introducing them in the last synthesis step. These modifiable heterobifunctional dyes offer significant utility in advancing biological studies.
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Affiliation(s)
- Corina Maller
- Signalling
Research Centres BIOSS and CIBSS, University
of Freiburg, Freiburg 79104, Germany
- Faculty
of Chemistry and Pharmacy, University of
Freiburg, Freiburg 79104, Germany
- Faculty
of Biology, University of Freiburg, Freiburg 79104, Germany
| | - Franziska Schedel
- Signalling
Research Centres BIOSS and CIBSS, University
of Freiburg, Freiburg 79104, Germany
- Faculty
of Chemistry and Pharmacy, University of
Freiburg, Freiburg 79104, Germany
- Faculty
of Biology, University of Freiburg, Freiburg 79104, Germany
- Spermann
Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg 79104, Germany
| | - Maja Köhn
- Signalling
Research Centres BIOSS and CIBSS, University
of Freiburg, Freiburg 79104, Germany
- Faculty
of Biology, University of Freiburg, Freiburg 79104, Germany
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2
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Du J, Kong Y, Wen Y, Shen E, Xing H. HUH Endonuclease: A Sequence-specific Fusion Protein Tag for Precise DNA-Protein Conjugation. Bioorg Chem 2024; 144:107118. [PMID: 38330720 DOI: 10.1016/j.bioorg.2024.107118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/01/2024] [Accepted: 01/09/2024] [Indexed: 02/10/2024]
Abstract
Synthetic DNA-protein conjugates have found widespread applications in diagnostics and therapeutics, prompting a growing interest in developing chemical biology methodologies for the precise and site-specific preparation of covalent DNA-protein conjugates. In this review article, we concentrate on techniques to achieve precise control over the structural and site-specific aspects of DNA-protein conjugates. We summarize conventional methods involving unnatural amino acids and self-labeling proteins, accompanied by a discussion of their potential limitations. Our primary focus is on introducing HUH endonuclease as a novel generation of fusion protein tags for DNA-protein conjugate preparation. The detailed conjugation mechanisms and structures of representative endonucleases are surveyed, showcasing their advantages as fusion protein tag in sequence selectivity, biological orthogonality, and no requirement for DNA modification. Additionally, we present the burgeoning applications of HUH-tag-based DNA-protein conjugates in protein assembly, biosensing, and gene editing. Furthermore, we delve into the future research directions of the HUH-tag, highlighting its significant potential for applications in the biomedical and DNA nanotechnology fields.
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Affiliation(s)
- Jiajun Du
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China
| | - Yuhan Kong
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China
| | - Yujian Wen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China
| | - Enxi Shen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China.
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3
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Thankarajan E, Oz S, Saady A, Kulbitski K, Kompanets MO, Eisen MS, Berlin S. SNAP-Tag-Targeted MRI-Fluorescent Multimodal Probes. Chembiochem 2023; 24:e202300172. [PMID: 37092744 DOI: 10.1002/cbic.202300172] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/02/2023] [Accepted: 04/24/2023] [Indexed: 04/25/2023]
Abstract
Magnetic resonance imaging (MRI) is a powerful imaging modality, widely employed in research and clinical settings. However, MRI images suffer from low signals and a lack of target specificity. We aimed to develop a multimodal imaging probe to detect targeted cells by MRI and fluorescence microscopy. We synthesized a trifunctional imaging probe consisting of a SNAP-tag substrate for irreversible and specific labelling of cells, cyanine dyes for bright fluorescence, and a chelated GdIII molecule for enhancing MRI contrast. Our probes exhibit specific and efficient labelling of genetically defined cells (expressing SNAP-tag at their membrane), bright fluorescence and MRI signal. Our synthetic approach provides a versatile platform for the production of multimodal imaging probes, particularly for light microscopy and MRI.
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Affiliation(s)
- Ebaston Thankarajan
- Department of Neuroscience, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, 3525422, Israel
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Shimrit Oz
- Department of Neuroscience, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, 3525422, Israel
| | - Abed Saady
- Department of Neuroscience, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, 3525422, Israel
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
- Present address: School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Kseniya Kulbitski
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Mykhail O Kompanets
- L.M. Litvinenko Institute of Physico-Organic Chemistry and Coal Chemistry, National Academy of Sciences of Ukraine, Kyiv, 02660, Ukraine
| | - Moris S Eisen
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Shai Berlin
- Department of Neuroscience, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, 3525422, Israel
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4
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Banerjee A, Anand M, Ganji M. Labeling approaches for DNA-PAINT super-resolution imaging. NANOSCALE 2023; 15:6563-6580. [PMID: 36942769 DOI: 10.1039/d2nr06541j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Super-resolution imaging is becoming a commonly employed tool to visualize biological targets in unprecedented detail. DNA-PAINT is one of the single-molecule localization microscopy-based super-resolution imaging modalities allowing the ultra-high-resolution imaging with superior multiplexing capabilities. We discuss the importance of patterned DNA nanostructures in demonstrating the capabilities of DNA-PAINT and the design of various combinations of imager-docking strand pairs for imaging. Central to the implementation of DNA-PAINT imaging in a biological context is the generation of docking strand-conjugated binders against the target molecules. Several researchers have developed a variety of labelling probes for improving resolution while also providing multiplexing capabilities for the broader application of DNA-PAINT. This review provides a comprehensive summary of the repertoire of labelling probes used for DNA-PAINT in cells and the strategies implemented to chemically modify them with a docking strand.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
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5
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Merlo R, Mattossovich R, Genta M, Valenti A, Di Mauro G, Minassi A, Miggiano R, Perugino G. First thermostable CLIP-tag by rational design applied to an archaeal O-alkyl-guanine-DNA-alkyl-transferase. Comput Struct Biotechnol J 2022; 20:5275-5286. [PMID: 36212535 PMCID: PMC9519396 DOI: 10.1016/j.csbj.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
Self-labelling protein tags (SLPs) are resourceful tools that revolutionized sensor imaging, having the versatile ability of being genetically fused with any protein of interest and undergoing activation with alternative probes specifically designed for each variant (namely, SNAP-tag, CLIP-tag and Halo-tag). Commercially available SLPs are highly useful in studying molecular aspects of mesophilic organisms, while they fail in characterizing model organisms that thrive in harsh conditions. By applying an integrated computational and structural approach, we designed a engineered variant of the alkylguanine-DNA-alkyl-transferase (OGT) from the hyper-thermophilic archaeon Saccharolobus solfataricus (SsOGT), with no DNA-binding activity, able to covalently react with O6-benzyl-cytosine (BC-) derivatives, obtaining the first thermostable CLIP-tag, named SsOGT-MC8. The presented construct is able to recognize and to covalently bind BC- substrates with a marked specificity, displaying a very low activity on orthogonal benzyl-guanine (BG-) substrate and showing a remarkable thermal stability that broadens the applicability of SLPs. The rational mutagenesis that, starting from SsOGT, led to the production of SsOGT-MC8 was first evaluated by structural predictions to precisely design the chimeric construct, by mutating specific residues involved in protein stability and substrate recognition. The final construct was further validated by biochemical characterization and X-ray crystallography, allowing us to present here the first structural model of a CLIP-tag establishing the molecular determinants of its activity, as well as proposing a general approach for the rational engineering of any O6-alkylguanine-DNA-alkyl-transferase turning it into a SNAP- and a CLIP-tag variant.
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6
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An assembly-regulated SNAP-tag fluorogenic probe for long-term super-resolution imaging of mitochondrial dynamics. Biosens Bioelectron 2021; 176:112886. [PMID: 33421760 DOI: 10.1016/j.bios.2020.112886] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022]
Abstract
Super-resolution fluorescence microscopy has emerged as a powerful tool for studying mitochondrial dynamics in living cells. However, the lack of photostable and chemstable probe makes long-term super-resolution imaging of mitochondria still a challenging work. Herein, we reported a 4-azetidinyl-naphthliamide derived SNAP-tag probe AN-BG exhibiting excellent fluorogenicity and photostability for long-term super-resolution imaging of mitochondrial dynamics. The azetidinyl group and naphthalimide fluorophore are in a flat conformation which can effectively suppress twisted intramolecular charge transfer and then effectively improve the brightness and photostability. This planarized molecular structure is conducive to the formation of fluorescence-quenched J-aggregates, and the protein labeling process will depolymerize the probes and restore fluorescence. Fluorescent labeling mitochondrial inner membrane proteins via SNAP tags overcomes the shortcomings that variations in mitochondrial inner membrane potential will release probes attached to mitochondria by electrostatic interactions. Therefore, AN-BG realized the stable labeling of mitochondria and the long-term imaging of mitochondrial dynamics under super-resolution microscopy.
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7
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Reja SI, Minoshima M, Hori Y, Kikuchi K. Near-infrared fluorescent probes: a next-generation tool for protein-labeling applications. Chem Sci 2020; 12:3437-3447. [PMID: 34163617 PMCID: PMC8179524 DOI: 10.1039/d0sc04792a] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/18/2020] [Indexed: 12/21/2022] Open
Abstract
The development of near-infrared (NIR) fluorescent probes over the past few decades has changed the way that biomolecules are imaged, and thus represents one of the most rapidly progressing areas of research. Presently, NIR fluorescent probes are routinely used to visualize and understand intracellular activities. The ability to penetrate tissues deeply, reduced photodamage to living organisms, and a high signal-to-noise ratio characterize NIR fluorescent probes as efficient next-generation tools for elucidating various biological events. The coupling of self-labeling protein tags with synthetic fluorescent probes is one of the most promising research areas in chemical biology. Indeed, at present, protein-labeling techniques are not only used to monitor the dynamics and localization of proteins but also play a more diverse role in imaging applications. For instance, one of the dominant technologies employed in the visualization of protein activity and regulation is based on protein tags and their associated NIR fluorescent probes. In this mini-review, we will discuss the development of several NIR fluorescent probes used for various protein-tag systems.
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Affiliation(s)
- Shahi Imam Reja
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Masafumi Minoshima
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Osaka 565-0871 Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Osaka 565-0871 Japan
- Quantum Information and Quantum Biology Division, Osaka University Suita Osaka 565-0871 Japan
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8
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Carpenter MA, Wang Y, Telmer CA, Schmidt BF, Yang Z, Bruchez MP. Protein Proximity Observed Using Fluorogen Activating Protein and Dye Activated by Proximal Anchoring (FAP-DAPA) System. ACS Chem Biol 2020; 15:2433-2443. [PMID: 32786268 DOI: 10.1021/acschembio.0c00419] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The development and function of tissues, blood, and the immune system is dependent upon proximity for cellular recognition and communication. However, the detection of cell-to-cell contacts is limited due to a lack of reversible, quantitative probes that can function at these dynamic sites of irregular geometry. Described here is a novel chemo-genetic tool developed for fluorescent detection of protein-protein proximity and cell apposition that utilizes the Fluorogen Activating Protein (FAP) in combination with a Dye Activated by Proximal Anchoring (DAPA). The FAP-DAPA system has two protein components, the HaloTag and FAP, expressed on separate protein targets or in separate cells. The proteins function to bind and activate a compound that has the hexyl chloride (HexCl) ligand connected to malachite green (MG), the FAP fluorogen, via a poly(ethylene glycol) spacer spanning up to 28 nm. The dehalogenase protein, HaloTag, covalently binds the HexCl ligand, locally concentrating the attached MG. If the FAP is within range of the anchored fluorogen, it will bind and activate MG specifically when the bath concentration is too low to saturate the FAP receptor. A new FAP variant was isolated with a 1000-fold reduced KD of ∼10-100 nM so that the fluorogen activation reports proximity without artificially enhancing it. The system was characterized using purified FRB and FKBP fusion proteins and showed a doubling of fluorescence upon rapamycin induced complex formation. In cocultured HEK293 cells (HaloTag and FAP-expressing) fluorescence increased at contact sites across a broad range of labeling conditions, more reliably providing contact-specific fluorescence activation with the lower-affinity FAP variant. When combined with suitable targeting and expression constructs, this labeling system may offer significant improvements in on-demand detection of intercellular contacts, potentially applicable in neurological and immunological synapse measurements and other transient, dynamic biological appositions that can be perturbed using other labeling methods that stabilize these interactions.
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Affiliation(s)
- M. Alexandra Carpenter
- Carnegie Mellon University, Department of Chemistry, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Yi Wang
- Carnegie Mellon University, Department of Biological Sciences, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Cheryl A. Telmer
- Carnegie Mellon University, Department of Biological Sciences, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
- Carnegie Mellon University, Molecular Biosensor and Imaging Center, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Brigitte F. Schmidt
- Carnegie Mellon University, Molecular Biosensor and Imaging Center, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Zhipeng Yang
- Carnegie Mellon University, Department of Biological Sciences, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Marcel P. Bruchez
- Carnegie Mellon University, Department of Chemistry, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
- Carnegie Mellon University, Department of Biological Sciences, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
- Carnegie Mellon University, Molecular Biosensor and Imaging Center, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, United States
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9
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Higashi TL, Eickhoff P, Sousa JS, Locke J, Nans A, Flynn HR, Snijders AP, Papageorgiou G, O'Reilly N, Chen ZA, O'Reilly FJ, Rappsilber J, Costa A, Uhlmann F. A Structure-Based Mechanism for DNA Entry into the Cohesin Ring. Mol Cell 2020; 79:917-933.e9. [PMID: 32755595 PMCID: PMC7507959 DOI: 10.1016/j.molcel.2020.07.013] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/05/2020] [Accepted: 07/10/2020] [Indexed: 01/26/2023]
Abstract
Despite key roles in sister chromatid cohesion and chromosome organization, the mechanism by which cohesin rings are loaded onto DNA is still unknown. Here we combine biochemical approaches and cryoelectron microscopy (cryo-EM) to visualize a cohesin loading intermediate in which DNA is locked between two gates that lead into the cohesin ring. Building on this structural framework, we design experiments to establish the order of events during cohesin loading. In an initial step, DNA traverses an N-terminal kleisin gate that is first opened upon ATP binding and then closed as the cohesin loader locks the DNA against the ATPase gate. ATP hydrolysis will lead to ATPase gate opening to complete DNA entry. Whether DNA loading is successful or results in loop extrusion might be dictated by a conserved kleisin N-terminal tail that guides the DNA through the kleisin gate. Our results establish the molecular basis for cohesin loading onto DNA.
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Affiliation(s)
- Torahiko L Higashi
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Patrik Eickhoff
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Joana S Sousa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Julia Locke
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Andrea Nans
- Structural Biology STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Helen R Flynn
- Proteomics STP, The Francis Crick Institute, London NW1 1AT, UK
| | | | | | - Nicola O'Reilly
- Peptide Chemistry STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Zhuo A Chen
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Francis J O'Reilly
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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10
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Li C, Tebo AG, Thauvin M, Plamont M, Volovitch M, Morin X, Vriz S, Gautier A. A Far‐Red Emitting Fluorescent Chemogenetic Reporter for In Vivo Molecular Imaging. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006576] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chenge Li
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
- Present address: Department of Obstetrics and Gynecology Ren Ji Hospital School of Medicine Shanghai Jiao Tong University China
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Ren Ji Hospital School of Medicine Shanghai Jiao Tong University China
| | - Alison G. Tebo
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
- Sorbonne Université École Normale Supérieure Université PSL CNRS, Laboratoire des biomolécules, LBM 75005 Paris France
| | - Marion Thauvin
- Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France
- Sorbonne Université Paris France
| | - Marie‐Aude Plamont
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
| | - Michel Volovitch
- Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France
- École Normale Supérieure Université PSL Department of biology Paris France
| | - Xavier Morin
- Institut de Biologie de l'ENS (IBENS) École Normale Supérieure CNRS INSERM Université PSL 75005 Paris France
| | - Sophie Vriz
- Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France
- Université de Paris Faculty of Science 75006 Paris France
| | - Arnaud Gautier
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
- Sorbonne Université École Normale Supérieure Université PSL CNRS, Laboratoire des biomolécules, LBM 75005 Paris France
- Institut Universitaire de France France
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11
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Li C, Tebo AG, Thauvin M, Plamont M, Volovitch M, Morin X, Vriz S, Gautier A. A Far‐Red Emitting Fluorescent Chemogenetic Reporter for In Vivo Molecular Imaging. Angew Chem Int Ed Engl 2020; 59:17917-17923. [DOI: 10.1002/anie.202006576] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Chenge Li
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
- Present address: Department of Obstetrics and Gynecology Ren Ji Hospital School of Medicine Shanghai Jiao Tong University China
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Ren Ji Hospital School of Medicine Shanghai Jiao Tong University China
| | - Alison G. Tebo
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
- Sorbonne Université École Normale Supérieure Université PSL CNRS, Laboratoire des biomolécules, LBM 75005 Paris France
| | - Marion Thauvin
- Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France
- Sorbonne Université Paris France
| | - Marie‐Aude Plamont
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
| | - Michel Volovitch
- Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France
- École Normale Supérieure Université PSL Department of biology Paris France
| | - Xavier Morin
- Institut de Biologie de l'ENS (IBENS) École Normale Supérieure CNRS INSERM Université PSL 75005 Paris France
| | - Sophie Vriz
- Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France
- Université de Paris Faculty of Science 75006 Paris France
| | - Arnaud Gautier
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
- Sorbonne Université École Normale Supérieure Université PSL CNRS, Laboratoire des biomolécules, LBM 75005 Paris France
- Institut Universitaire de France France
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12
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Macias-Contreras M, He H, Little KN, Lee JP, Campbell RP, Royzen M, Zhu L. SNAP/CLIP-Tags and Strain-Promoted Azide–Alkyne Cycloaddition (SPAAC)/Inverse Electron Demand Diels–Alder (IEDDA) for Intracellular Orthogonal/Bioorthogonal Labeling. Bioconjug Chem 2020; 31:1370-1381. [DOI: 10.1021/acs.bioconjchem.0c00107] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Miguel Macias-Contreras
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Huan He
- Translational Science Laboratory, College of Medicine, Florida State University, Tallahassee, Florida 32306-4300, United States
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306-4380, United States
| | - Kevin N. Little
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Justin P. Lee
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Ryan P. Campbell
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306-4380, United States
| | - Maksim Royzen
- Department of Chemistry, University at Albany, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Lei Zhu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
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13
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Leung PKK, Lo KKW. Modulation of emission and singlet oxygen photosensitisation in live cells utilising bioorthogonal phosphorogenic probes and protein tag technology. Chem Commun (Camb) 2020; 56:6074-6077. [DOI: 10.1039/d0cc02056g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We developed a strategy to exploit the bioorthogonal reactivity and phosphorogenic property of iridium(iii) polypyridine nitrone complexes and SNAP-tag protein for the modulation of emission and single oxygen photosensitisation in live cells.
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Affiliation(s)
| | - Kenneth Kam-Wing Lo
- Department of Chemistry
- City University of Hong Kong
- Kowloon
- P. R. China
- State Key Laboratory of Terahertz and Millimeter Waves
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14
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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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15
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Kuzmenkov AI, Vassilevski AA. Labelled animal toxins as selective molecular markers of ion channels: Applications in neurobiology and beyond. Neurosci Lett 2018; 679:15-23. [DOI: 10.1016/j.neulet.2017.10.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 12/12/2022]
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16
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Rossi F, Morrone C, Massarotti A, Ferraris DM, Valenti A, Perugino G, Miggiano R. Crystal structure of a thermophilic O6-alkylguanine-DNA alkyltransferase-derived self-labeling protein-tag in covalent complex with a fluorescent probe. Biochem Biophys Res Commun 2018; 500:698-703. [DOI: 10.1016/j.bbrc.2018.04.139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 04/17/2018] [Indexed: 02/07/2023]
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17
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Chen HJ, Chew CY, Chang EH, Tu YW, Wei LY, Wu BH, Chen CH, Yang YT, Huang SC, Chen JK, Chen IC, Tan KT. S-Cis Diene Conformation: A New Bathochromic Shift Strategy for Near-Infrared Fluorescence Switchable Dye and the Imaging Applications. J Am Chem Soc 2018; 140:5224-5234. [DOI: 10.1021/jacs.8b01159] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | | | | | | | - Chien-Hung Chen
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan (ROC)
| | - Ya-Ting Yang
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan (ROC)
| | - Su-Chin Huang
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan (ROC)
| | - Jen-Kun Chen
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Miaoli 35053, Taiwan (ROC)
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18
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Leng S, Qiao QL, Gao Y, Miao L, Deng WG, Xu ZC. SNAP-tag fluorogenic probes for wash free protein labeling. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2017.03.034] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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19
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Wu Q, Ploegh HL, Truttmann MC. Hepta-Mutant Staphylococcus aureus Sortase A (SrtA 7m) as a Tool for in Vivo Protein Labeling in Caenorhabditis elegans. ACS Chem Biol 2017; 12:664-673. [PMID: 28098972 DOI: 10.1021/acschembio.6b00998] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In vivo protein ligation is of emerging interest as a means of endowing proteins with new properties in a controlled fashion. Tools to site-specifically and covalently modify proteins with small molecules, peptides, or other proteins in living cells are few and far between. Here, we describe the development of a Staphylococcus aureus sortase (SrtA)-based protein ligation approach for site-specific conjugation of fluorescent dyes and ubiquitin (Ub) to modify proteins in Caenorhabditis elegans. Hepta-mutant SrtA (SrtA7m) expressed in C. elegans is functional and supports in vitro sortase reactions in a low-Ca2+ environment. Feeding SrtA7m-expressing C. elegans with small peptide-based probes such as (Gly)3- biotin or (Gly)3-fluorophores enables in vivo target protein modification. SrtA7m also catalyzes the circularization of suitably modified linear target proteins in vivo and allows the installation of F-box domains on targets to induce their degradation in a ubiquitin-dependent manner. This is a noninvasive method to achieve in vivo protein labeling, protein circularization, and targeted degradation in C. elegans. This technique should improve our ability to monitor and alter the function of intracellular proteins in vivo.
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Affiliation(s)
- Qin Wu
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Hidde L. Ploegh
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, United States
- Department
of Biology, Massachusetts Institute of Technology (MIT), 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Matthias C. Truttmann
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, United States
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20
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Chen X, Li F, Wu YW. Chemical labeling of intracellular proteins via affinity conjugation and strain-promoted cycloadditions in live cells. Chem Commun (Camb) 2016; 51:16537-40. [PMID: 26421329 DOI: 10.1039/c5cc05208d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A versatile chemical labeling approach was developed, where intracellular proteins were first incorporated with a bioorthogonal group via affinity conjugation, and subsequently labeled via strain-promoted cycloaddition reactions in live cells.
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Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund, Germany. and Max-Planck Institute for Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Fu Li
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund, Germany. and Max-Planck Institute for Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund, Germany. and Max-Planck Institute for Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
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21
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Hou TC, Wu YY, Chiang PY, Tan KT. Near-infrared fluorescence activation probes based on disassembly-induced emission cyanine dye. Chem Sci 2015; 6:4643-4649. [PMID: 28717479 PMCID: PMC5500852 DOI: 10.1039/c5sc01330e] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/22/2015] [Indexed: 02/02/2023] Open
Abstract
Currently most of the fluorogenic probes are designed for the detection of enzymes which work by converting the non-fluorescence substrate into the fluorescence product via an enzymatic reaction. On the other hand, the design of fluorogenic probes for non-enzymatic proteins remains a great challenge. Herein, we report a general strategy to create near-IR fluorogenic probes, where a small molecule ligand is conjugated to a novel γ-phenyl-substituted Cy5 fluorophore, for the selective detection of proteins through a non-enzymatic process. Detail mechanistic studies reveal that the probes self-assemble to form fluorescence-quenched J-type aggregate. In the presence of target analyte, bright fluorescence in the near-IR region is emitted through the recognition-induced disassembly of the probe aggregate. This Cy5 fluorophore is a unique self-assembly/disassembly dye as it gives remarkable fluorescence enhancement. Based on the same design, three different fluorogenic probes were constructed and one of them was applied for the no-wash imaging of tumor cells for the detection of hypoxia-induced cancer-specific biomarker, transmembrane-type carbonic anhydrase IX.
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Affiliation(s)
- Tai-Cheng Hou
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of china . ; Tel: +886-3-5715131
| | - Ying-Yi Wu
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of china . ; Tel: +886-3-5715131
| | - Po-Yi Chiang
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of china . ; Tel: +886-3-5715131
| | - Kui-Thong Tan
- Department of Chemistry , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of china . ; Tel: +886-3-5715131
- Frontier Research Center on Fundamental and Applied Sciences of Matters , National Tsing Hua University , 101 Sec. 2, Kuang Fu Rd , Hsinchu 30013 , Taiwan , Republic of china
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22
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Ishitsuka Y, Azadfar N, Kobitski AY, Nienhaus K, Johnsson N, Nienhaus GU. Evaluation of Genetically Encoded Chemical Tags as Orthogonal Fluorophore Labeling Tools for Single-Molecule FRET Applications. J Phys Chem B 2015; 119:6611-9. [PMID: 25978145 DOI: 10.1021/acs.jpcb.5b03584] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fluorescence resonance energy transfer (FRET) is a superb technique for measuring conformational changes of proteins on the single molecule level (smFRET) in real time. It requires introducing a donor and acceptor fluorophore pair at specific locations on the protein molecule of interest, which has often been a challenging task. By using two different self-labeling chemical tags, such as Halo-, TMP-, SNAP- and CLIP-tags, orthogonal labeling may be achieved rapidly and reliably. However, these comparatively large tags add extra distance and flexibility between the desired labeling location on the protein and the fluorophore position, which may affect the results. To systematically characterize chemical tags for smFRET measurement applications, we took the SNAP-tag/CLIP-tag combination as a model system and fused a flexible unstructured peptide, rigid polyproline peptides of various lengths, and the calcium sensor protein calmodulin between the tags. We could reliably identify length variations as small as four residues in the polyproline peptide. In the calmodulin system, the added length introduced by these tags was even beneficial for revealing subtle conformational changes upon variation of the buffer conditions. This approach opens up new possibilities for studying conformational dynamics, especially in large protein systems that are difficult to specifically conjugate with fluorophores.
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Affiliation(s)
- Yuji Ishitsuka
- †Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Naghmeh Azadfar
- †Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Andrei Yu Kobitski
- †Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Karin Nienhaus
- †Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany
| | - Nils Johnsson
- §Institute of Molecular Genetics and Cell Biology, Ulm University, James Franck Ring N27, 89081 Ulm, Germany
| | - G Ulrich Nienhaus
- †Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1, 76131 Karlsruhe, Germany.,∥Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,⊥Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
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23
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Yan Q, Bruchez MP. Advances in chemical labeling of proteins in living cells. Cell Tissue Res 2015; 360:179-94. [PMID: 25743694 PMCID: PMC4380784 DOI: 10.1007/s00441-015-2145-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 02/02/2015] [Indexed: 01/07/2023]
Abstract
The pursuit of quantitative biological information via imaging requires robust labeling approaches that can be used in multiple applications and with a variety of detectable colors and properties. In addition to conventional fluorescent proteins, chemists and biologists have come together to provide a range of approaches that combine dye chemistry with the convenience of genetic targeting. This hybrid-tagging approach amalgamates the rational design of properties available through synthetic dye chemistry with the robust biological targeting available with genetic encoding. In this review, we discuss the current range of approaches that have been exploited for dye targeting or for targeting and activation and some of the recent applications that are uniquely permitted by these hybrid-tagging approaches.
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Affiliation(s)
- Qi Yan
- Sharp Edge Laboratories, Inc. Pittsburgh, PA
| | - Marcel P. Bruchez
- Sharp Edge Laboratories, Inc. Pittsburgh, PA
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA
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24
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Schifferer M, Feng S, Stein F, Tischer C, Schultz C. Reversible chemical dimerizer-induced recovery of PIP2 levels moves clathrin to the plasma membrane. Bioorg Med Chem 2015; 23:2862-7. [PMID: 25840797 DOI: 10.1016/j.bmc.2015.03.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 12/24/2022]
Abstract
Chemical dimerizers are powerful non-invasive tools for bringing molecules together inside intact cells. We recently introduced a rapidly reversible chemical dimerizer system which enables transient translocation of enzymes to and from the plasma membrane (PM). Here we have applied this system to transiently activate phosphatidylinositol 4,5-bisphosphate (PIP2) breakdown at the PM via translocation of phosphoinositide 5-phosphatase (5Ptase). We found that the PIP2 sensor phospholipase C-δ PH domain (PLCδ-PH) is released from the PM upon addition of the reversible chemical dimerizer rCD1. By outcompeting rCD1, rapid release of the 5Ptase from the PM is followed by PIP2 recovery. This permits the observation of the PIP2-dependent clathrin assembly at the PM.
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Affiliation(s)
- Martina Schifferer
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Suihan Feng
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Christian Tischer
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany.
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25
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Lukinavičius G, Reymond L, Johnsson K. Fluorescent labeling of SNAP-tagged proteins in cells. Methods Mol Biol 2015; 1266:107-118. [PMID: 25560070 DOI: 10.1007/978-1-4939-2272-7_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
One of the most prominent self-labeling tags is SNAP-tag. It is an in vitro evolution product of the human DNA repair protein O (6)-alkylguanine-DNA alkyltransferase (hAGT) that reacts specifically with benzylguanine (BG) and benzylchloropyrimidine (CP) derivatives, leading to covalent labeling of SNAP-tag with a synthetic probe (Gronemeyer et al., Protein Eng Des Sel 19:309-316, 2006; Curr Opin Biotechnol 16:453-458, 2005; Keppler et al., Nat Biotechnol 21:86-89, 2003; Proc Natl Acad Sci U S A 101:9955-9959, 2004). SNAP-tag is well suited for the analysis and quantification of fused target protein using fluorescence microscopy techniques. It provides a simple, robust, and versatile approach to the imaging of fusion proteins under a wide range of experimental conditions.
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Affiliation(s)
- Gražvydas Lukinavičius
- Institute of Chemical Sciences and Engineering, NCCR Chemical Biology, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
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26
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Abstract
Chemists and biologists have long recognized small molecule probes as powerful tools for functional genomics and proteomics studies. The possibility of specifically attaching chemical probes to individual proteins with spatial and temporal resolution has greatly improved our ability to visualize and characterize proteins in their native environment. The continued development of novel molecular probes for protein labeling is, therefore, of fundamental importance to gain new insights into biological processes in living cells and organisms. Several excellent approaches for the site-specific labeling of fusion proteins with chemical probes exist. Herein I discuss the design and generation of chemical probes for the SNAP-tag and CLIP-tag systems. The first part of this chapter is dedicated to reviewing the principles of the SNAP-tag technology, followed by a section dedicated to the development of chemical probes for unique applications, such as super-resolution imaging, protein trafficking and recycling, protein-protein interactions, and biomolecular sensing. The last part of the chapter contains experimental protocols and technical notes for the synthesis of selected SNAP-tag substrates and labeling of SNAP-tag fusion proteins in vitro and in living cells.
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Affiliation(s)
- Ivan R Corrêa
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA,
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27
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Liu TK, Hsieh PY, Zhuang YD, Hsia CY, Huang CL, Lai HP, Lin HS, Chen IC, Hsu HY, Tan KT. A rapid SNAP-tag fluorogenic probe based on an environment-sensitive fluorophore for no-wash live cell imaging. ACS Chem Biol 2014; 9:2359-65. [PMID: 25105835 DOI: 10.1021/cb500502n] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
One major limitation of labeling proteins with synthetic fluorophores is the high fluorescence background, which necessitates extensive washing steps to remove unreacted fluorophores. In this paper, we describe a novel fluorogenic probe based on an environment-sensitive fluorophore for labeling with SNAP-tag proteins. The probe exhibits dramatic fluorescence turn-on of 280-fold upon being labeled to SNAP-tag. The major advantages of our fluorogenic probe are the dramatic fluorescence turn-on, ease of synthesis, high selectivity, and rapid labeling with SNAP-tag. No-wash labeling of both intracellular and cell surface proteins was successfully achieved in living cells, and the localization of these proteins was specifically visualized.
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Affiliation(s)
- Tao-Kai Liu
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Pei-Ying Hsieh
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Yu-De Zhuang
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Chi-Yang Hsia
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Chi-Ling Huang
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Hsiu-Ping Lai
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Hung-Sheung Lin
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - I-Chia Chen
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Hsin-Yun Hsu
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
| | - Kui-Thong Tan
- Department of Chemistry and ‡Frontier Research Center on Fundamental
and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang-Fu Rd., Hsinchu 30013, Taiwan (ROC)
- Department of Applied Chemistry and Institute of Molecular Science and ∥Center for Interdisciplinary
Science (CIS), National Chiao-Tung University, No.1001 Ta-Hsueh Road, Hsinchu 30010, Taiwan (ROC)
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28
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Bio-orthogonal labeling as a tool to visualize and identify newly synthesized proteins in Caenorhabditis elegans. Nat Protoc 2014; 9:2237-55. [DOI: 10.1038/nprot.2014.150] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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29
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Wueseke O, Bunkenborg J, Hein MY, Zinke A, Viscardi V, Woodruff JB, Oegema K, Mann M, Andersen JS, Hyman AA. The Caenorhabditis elegans pericentriolar material components SPD-2 and SPD-5 are monomeric in the cytoplasm before incorporation into the PCM matrix. Mol Biol Cell 2014; 25:2984-92. [PMID: 25103243 PMCID: PMC4230587 DOI: 10.1091/mbc.e13-09-0514] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Centrosomes are the main microtubule-organizing centers in animal cells. Centrosomes consist of a pair of centrioles surrounded by a matrix of pericentriolar material (PCM) that assembles from cytoplasmic components. In Caenorhabditis elegans embryos, interactions between the coiled-coil proteins SPD-5 and SPD-2 and the kinase PLK-1 are critical for PCM assembly. However, it is not known whether these interactions promote the formation of cytoplasmic complexes that are added to the PCM or whether the components interact only during incorporation into the PCM matrix. Here we address this problem by using a combination of live-cell fluorescence correlation spectroscopy, mass spectrometry, and hydrodynamic techniques to investigate the native state of PCM components in the cytoplasm. We show that SPD-2 is monomeric, and neither SPD-2 nor SPD-5 exists in complex with PLK-1. SPD-5 exists mostly as a monomer but also forms complexes with the PP2A-regulatory proteins RSA-1 and RSA-2, which are required for microtubule organization at centrosomes. These results suggest that the interactions between SPD-2, SPD-5, and PLK-1 do not result in formation of cytoplasmic complexes, but instead occur in the context of PCM assembly.
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Affiliation(s)
- Oliver Wueseke
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Jakob Bunkenborg
- Department of Clinical Biochemistry, Copenhagen University Hospital Hvidovre, 2650 Hvidovre, Denmark Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Marco Y Hein
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Andrea Zinke
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Valeria Viscardi
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093
| | - Jeffrey B Woodruff
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Karen Oegema
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Anthony A Hyman
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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Tsukiji S, Hamachi I. Ligand-directed tosyl chemistry for in situ native protein labeling and engineering in living systems: from basic properties to applications. Curr Opin Chem Biol 2014; 21:136-43. [DOI: 10.1016/j.cbpa.2014.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/11/2014] [Accepted: 07/14/2014] [Indexed: 11/17/2022]
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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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Karabasheva D, Cole NB, Donaldson JG. Roles for trafficking and O-linked glycosylation in the turnover of model cell surface proteins. J Biol Chem 2014; 289:19477-90. [PMID: 24891503 DOI: 10.1074/jbc.m114.564666] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins targeted to the plasma membrane (PM) of cells are degraded at different rates. Sorting motifs contained within the cytoplasmic domains of transmembrane proteins, post-translational modifications (e.g. ubiquitination), and assembly into multiprotein or protein-lipid complexes all may affect the efficiency of endocytosis and recycling and influence the delivery to degradative compartments. Using the SNAP-tag labeling system, we examined the turnover of a model PM protein, the α chain of the interleukin-2 receptor (Tac). The surface lifetimes of SNAP-Tac fusions were influenced by their mode of entry into cells (clathrin-dependent versus clathrin-independent), their orientation in the PM (transmembrane versus glycosylphosphatidylinositol-anchored), and ubiquitination in their cytosolic domains. In addition, shedding of SNAP-Tac into the medium was greatly influenced by its O-linked glycosylation status. For a number of PM proteins, delivery to lysosomes and ectodomain shedding represent distinct parallel mechanisms to determine protein half-life.
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Affiliation(s)
- Darya Karabasheva
- From the Cell Biology and Physiology Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Nelson B Cole
- From the Cell Biology and Physiology Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Julie G Donaldson
- From the Cell Biology and Physiology Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
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Corrêa IR. Live-cell reporters for fluorescence imaging. Curr Opin Chem Biol 2014; 20:36-45. [PMID: 24835389 DOI: 10.1016/j.cbpa.2014.04.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 01/14/2023]
Abstract
Advances in the development of new fluorescent reporters and imaging techniques have revolutionized our ability to directly visualize biological processes in living systems. Real-time analysis of protein localization, dynamics, and interactions has been made possible by site-specific protein labeling with custom designed probes. This review outlines some of the most recent advances in the design and application of live-cell imaging probes, with a particular focus on SNAP-tag technology. Specific examples illustrating applications in superresolution and single-molecule imaging, protein trafficking and recycling, and protein-protein interactions are presented.
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Affiliation(s)
- Ivan R Corrêa
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
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Rostgaard KR, Frederiksen RS, Liu YCC, Berthing T, Madsen MH, Holm J, Nygård J, Martinez KL. Vertical nanowire arrays as a versatile platform for protein detection and analysis. NANOSCALE 2013; 5:10226-35. [PMID: 24062006 DOI: 10.1039/c3nr03113f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein microarrays are valuable tools for protein assays. Reducing spot sizes from micro- to nano-scale facilitates miniaturization of platforms and consequently decreased material consumption, but faces inherent challenges in the reduction of fluorescent signals and compatibility with complex solutions. Here we show that vertical arrays of nanowires (NWs) can overcome several bottlenecks of using nanoarrays for extraction and analysis of proteins. The high aspect ratio of the NWs results in a large surface area available for protein immobilization and renders passivation of the surface between the NWs unnecessary. Fluorescence detection of proteins allows quantitative measurements and spatial resolution, enabling us to track individual NWs through several analytical steps, thereby allowing multiplexed detection of different proteins immobilized on different regions of the NW array. We use NW arrays for on-chip extraction, detection and functional analysis of proteins on a nano-scale platform that holds great promise for performing protein analysis on minute amounts of material. The demonstration made here on highly ordered arrays of indium arsenide (InAs) NWs is generic and can be extended to many high aspect ratio nanostructures.
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Affiliation(s)
- Katrine R Rostgaard
- Bio-Nanotechnology and Nanomedicine Laboratory, Department of Chemistry & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.
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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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36
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Selective chemical crosslinking reveals a Cep57-Cep63-Cep152 centrosomal complex. Curr Biol 2013; 23:265-70. [PMID: 23333316 DOI: 10.1016/j.cub.2012.12.030] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 07/12/2012] [Accepted: 12/14/2012] [Indexed: 11/23/2022]
Abstract
The centrosome functions as the main microtubule-organizing center of animal cells and is crucial for several fundamental cellular processes. Abnormalities in centrosome number and composition correlate with tumor progression and other diseases. Although proteomic studies have identified many centrosomal proteins, their interactions are incompletely characterized. The lack of information on the precise localization and interaction partners for many centrosomal proteins precludes comprehensive understanding of centrosome biology. Here, we utilize a combination of selective chemical crosslinking and superresolution microscopy to reveal novel functional interactions among a set of 31 centrosomal proteins. We reveal that Cep57, Cep63, and Cep152 are parts of a ring-like complex localizing around the proximal end of centrioles. Furthermore, we identify that STIL, together with HsSAS-6, resides at the proximal end of the procentriole, where the cartwheel is located. Our studies also reveal that the known interactors Cep152 and Plk4 reside in two separable structures, suggesting that the kinase Plk4 contacts its substrate Cep152 only transiently, at the centrosome or within the cytoplasm. Our findings provide novel insights into protein interactions critical for centrosome biology and establish a toolbox for future studies of centrosomal proteins.
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37
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Wymann MP, Schultz C. The chemical biology of phosphoinositide 3-kinases. Chembiochem 2012; 13:2022-35. [PMID: 22965647 DOI: 10.1002/cbic.201200089] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 07/13/2012] [Indexed: 01/14/2023]
Abstract
Since its discovery in the late 1980s, phosphoinositide 3-kinase (PI3K), and its isoforms have arguably reached the forefront of signal transduction research. Regulation of this lipid kinase, its functions, its effectors, in short its entire signaling network, has been extensively studied. PI3K inhibitors are frequently used in biochemistry and cell biology. In addition, many pharmaceutical companies have launched drug-discovery programs to identify modulators of PI3Ks. Despite these efforts and a fairly good knowledge of the PI3K signaling network, we still have only a rudimentary picture of the signaling dynamics of PI3K and its lipid products in space and time. It is therefore essential to create and use novel biological and chemical tools to manipulate the phosphoinositide signaling network with spatial and temporal resolution. In this review, we discuss the current and potential future tools that are available and necessary to unravel the various functions of PI3K and its isoforms.
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Affiliation(s)
- Matthias P Wymann
- Institute of Biochemistry & Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
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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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Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation. N Biotechnol 2012; 30:144-52. [PMID: 22664266 DOI: 10.1016/j.nbt.2012.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/14/2012] [Accepted: 05/17/2012] [Indexed: 11/22/2022]
Abstract
While antibodies currently play a dominant role as affinity reagents in biological research and for diagnostics, a broad range of recombinant proteins are emerging as promising alternative affinity reagents in detection assays and quantification. DNA-mediated affinity-based assays, such as immuno-PCR and proximity ligation assays (PLA), use oligonucleotides attached to affinity reagents as reporter molecules. Conjugation of oligonucleotides to affinity reagents generally employs chemistries that target primary amines or cysteines. Because of the random nature of these processes neither the number of oligonucleotides conjugated per molecule nor their sites of attachment can be accurately controlled for affinity reagents with several available amines and cysteines. Here, we present a straightforward and convenient approach to functionalize recombinant affinity reagents for PLA by expressing the reagents as fusion partners with SNAP protein tags. This allowed us to conjugate oligonucleotides in a site-specific fashion, yielding precisely one oligonucleotide per affinity reagent. We demonstrate this method using designed ankyrin repeat proteins (DARPins) recognizing the tumor antigen HER2 and we apply the conjugates in different assay formats. We also show that SNAP or CLIP tags, expressed as fusion partners of transfected genes, allow oligonucleotide conjugations to be performed in fixed cells, with no need for specific affinity reagents. The approach is used to demonstrate induced interactions between the fusion proteins FKBP and FRB by allowing the in situ conjugated oligonucleotides to direct the production of templates for localized rolling circle amplification reactions.
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Haruki H, Gonzalez MR, Johnsson K. Exploiting ligand-protein conjugates to monitor ligand-receptor interactions. PLoS One 2012; 7:e37598. [PMID: 22701522 PMCID: PMC3365113 DOI: 10.1371/journal.pone.0037598] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 04/23/2012] [Indexed: 01/12/2023] Open
Abstract
We introduce three assays for analyzing ligand-receptor interactions based on the specific conjugation of ligands to SNAP-tag fusion proteins. Conjugation of ligands to different SNAP-tag fusions permits the validation of suspected interactions in cell extracts and fixed cells as well as the establishment of high-throughput assays. The different assays allow the analysis of strong and weak interactions. Conversion of ligands into SNAP-tag substrates thus provides access to a powerful toolbox for the analysis of their interactions with proteins.
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Affiliation(s)
- Hirohito Haruki
- École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research (NCCR) in Chemical Biology, Lausanne, Switzerland
| | - Monica Rengifo Gonzalez
- École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research (NCCR) in Chemical Biology, Lausanne, Switzerland
| | - Kai Johnsson
- École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research (NCCR) in Chemical Biology, Lausanne, Switzerland
- * E-mail:
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Putyrski M, Schultz C. Protein translocation as a tool: The current rapamycin story. FEBS Lett 2012; 586:2097-105. [DOI: 10.1016/j.febslet.2012.04.061] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/27/2012] [Accepted: 04/29/2012] [Indexed: 01/08/2023]
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Mollwitz B, Brunk E, Schmitt S, Pojer F, Bannwarth M, Schiltz M, Rothlisberger U, Johnsson K. Directed Evolution of the Suicide Protein O6-Alkylguanine-DNA Alkyltransferase for Increased Reactivity Results in an Alkylated Protein with Exceptional Stability. Biochemistry 2012; 51:986-94. [DOI: 10.1021/bi2016537] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Birgit Mollwitz
- Laboratory of Protein
Engineering, Institute of Chemical Sciences and Engineering, ‡Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, §Chair of Microbial Pathogenesis,
Global Health Institute, School of Life Sciences, and ∥Laboratory of Crystallography, Institute
of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne, CH-1015
Lausanne, Switzerland
| | - Elizabeth Brunk
- Laboratory of Protein
Engineering, Institute of Chemical Sciences and Engineering, ‡Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, §Chair of Microbial Pathogenesis,
Global Health Institute, School of Life Sciences, and ∥Laboratory of Crystallography, Institute
of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne, CH-1015
Lausanne, Switzerland
| | - Simone Schmitt
- Laboratory of Protein
Engineering, Institute of Chemical Sciences and Engineering, ‡Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, §Chair of Microbial Pathogenesis,
Global Health Institute, School of Life Sciences, and ∥Laboratory of Crystallography, Institute
of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne, CH-1015
Lausanne, Switzerland
| | - Florence Pojer
- Laboratory of Protein
Engineering, Institute of Chemical Sciences and Engineering, ‡Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, §Chair of Microbial Pathogenesis,
Global Health Institute, School of Life Sciences, and ∥Laboratory of Crystallography, Institute
of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne, CH-1015
Lausanne, Switzerland
| | - Michael Bannwarth
- Laboratory of Protein
Engineering, Institute of Chemical Sciences and Engineering, ‡Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, §Chair of Microbial Pathogenesis,
Global Health Institute, School of Life Sciences, and ∥Laboratory of Crystallography, Institute
of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne, CH-1015
Lausanne, Switzerland
| | - Marc Schiltz
- Laboratory of Protein
Engineering, Institute of Chemical Sciences and Engineering, ‡Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, §Chair of Microbial Pathogenesis,
Global Health Institute, School of Life Sciences, and ∥Laboratory of Crystallography, Institute
of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne, CH-1015
Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Protein
Engineering, Institute of Chemical Sciences and Engineering, ‡Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, §Chair of Microbial Pathogenesis,
Global Health Institute, School of Life Sciences, and ∥Laboratory of Crystallography, Institute
of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne, CH-1015
Lausanne, Switzerland
| | - Kai Johnsson
- Laboratory of Protein
Engineering, Institute of Chemical Sciences and Engineering, ‡Laboratory of Computational
Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, §Chair of Microbial Pathogenesis,
Global Health Institute, School of Life Sciences, and ∥Laboratory of Crystallography, Institute
of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne, CH-1015
Lausanne, Switzerland
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Cottet M, Faklaris O, Maurel D, Scholler P, Doumazane E, Trinquet E, Pin JP, Durroux T. BRET and Time-resolved FRET strategy to study GPCR oligomerization: from cell lines toward native tissues. Front Endocrinol (Lausanne) 2012; 3:92. [PMID: 22837753 PMCID: PMC3401989 DOI: 10.3389/fendo.2012.00092] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/03/2012] [Indexed: 11/13/2022] Open
Abstract
The concept of oligomerization of G protein-coupled receptor (GPCR) opens new perspectives regarding physiological function regulation. The capacity of one GPCR to modify its binding and coupling properties by interacting with a second one can be at the origin of regulations unsuspected two decades ago. Although the concept is interesting, its validation at a physiological level is challenging and probably explains why receptor oligomerization is still controversial. Demonstrating direct interactions between two proteins is not trivial since few techniques present a spatial resolution allowing this precision. Resonance energy transfer (RET) strategies are actually the most convenient ones. During the last two decades, bioluminescent resonance energy transfer and time-resolved fluorescence resonance energy transfer (TR-FRET) have been widely used since they exhibit high signal-to-noise ratio. Most of the experiments based on GPCR labeling have been performed in cell lines and it has been shown that all GPCRs have the propensity to form homo- or hetero-oligomers. However, whether these data can be extrapolated to GPCRs expressed in native tissues and explain receptor functioning in real life, remains an open question. Native tissues impose different constraints since GPCR sequences cannot be modified. Recently, a fluorescent ligand-based GPCR labeling strategy combined to a TR-FRET approach has been successfully used to prove the existence of GPCR oligomerization in native tissues. Although the RET-based strategies are generally quite simple to implement, precautions have to be taken before concluding to the absence or the existence of specific interactions between receptors. For example, one should exclude the possibility of collision of receptors diffusing throughout the membrane leading to a specific FRET signal. The advantages and the limits of different approaches will be reviewed and the consequent perspectives discussed.
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Affiliation(s)
- Martin Cottet
- Institut de Génomique Fonctionnelle CNRS, UMR 5203,Montpellier, France
- INSERM, U.661, Montpellier and Université Montpellier 1,2,Montpellier, France
| | - Orestis Faklaris
- Institut de Génomique Fonctionnelle CNRS, UMR 5203,Montpellier, France
- INSERM, U.661, Montpellier and Université Montpellier 1,2,Montpellier, France
| | - Damien Maurel
- Institut de Génomique Fonctionnelle CNRS, UMR 5203,Montpellier, France
- INSERM, U.661, Montpellier and Université Montpellier 1,2,Montpellier, France
| | - Pauline Scholler
- Institut de Génomique Fonctionnelle CNRS, UMR 5203,Montpellier, France
- INSERM, U.661, Montpellier and Université Montpellier 1,2,Montpellier, France
| | - Etienne Doumazane
- Institut de Génomique Fonctionnelle CNRS, UMR 5203,Montpellier, France
- INSERM, U.661, Montpellier and Université Montpellier 1,2,Montpellier, France
| | | | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle CNRS, UMR 5203,Montpellier, France
- INSERM, U.661, Montpellier and Université Montpellier 1,2,Montpellier, France
| | - Thierry Durroux
- Institut de Génomique Fonctionnelle CNRS, UMR 5203,Montpellier, France
- INSERM, U.661, Montpellier and Université Montpellier 1,2,Montpellier, France
- *Correspondence: Thierry Durroux, Institut de Génomique Fonctionnelle CNRS, UMR 5203, Montpellier, France; INSERM U661, Montpellier and Université Montpellier 1,2, 141 Rue de la Cardonille, 34094 Montpellier Cedex 5, France. e-mail:
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Lowder MA, Appelbaum JS, Hobert EM, Schepartz A. Visualizing protein partnerships in living cells and organisms. Curr Opin Chem Biol 2011; 15:781-8. [PMID: 22104179 DOI: 10.1016/j.cbpa.2011.10.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 10/25/2011] [Accepted: 10/25/2011] [Indexed: 11/25/2022]
Abstract
In recent years, scientists have expanded their focus from cataloging genes to characterizing the multiple states of their translated products. One anticipated result is a dynamic map of the protein association networks and activities that occur within the cellular environment. While in vitro-derived network maps can illustrate which of a multitude of possible protein-protein associations could exist, they supply a falsely static picture lacking the subtleties of subcellular location (where) or cellular state (when). Generating protein association network maps that are informed by both subcellular location and cell state requires novel approaches that accurately characterize the state of protein associations in living cells and provide precise spatiotemporal resolution. In this review, we highlight recent advances in visualizing protein associations and networks under increasingly native conditions. These advances include second generation protein complementation assays (PCAs), chemical and photo-crosslinking techniques, and proximity-induced ligation approaches. The advances described focus on background reduction, signal optimization, rapid and reversible reporter assembly, decreased cytotoxicity, and minimal functional perturbation. Key breakthroughs have addressed many challenges and should expand the repertoire of tools useful for generating maps of protein interactions resolved in both time and space.
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Affiliation(s)
- Melissa A Lowder
- Yale University, Department of Molecular Biophysics and Biochemistry, 60 Whitney Ave., New Haven, CT 06520-8114, USA
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Abstract
To build on the last century's tremendous strides in understanding the workings of individual proteins in the test tube, we now face the challenge of understanding how macromolecular machines, signaling pathways, and other biological networks operate in the complex environment of the living cell. The fluorescent proteins (FPs) revolutionized our ability to study protein function directly in the cell by enabling individual proteins to be selectively labeled through genetic encoding of a fluorescent tag. Although FPs continue to be invaluable tools for cell biology, they show limitations in the face of the increasingly sophisticated dynamic measurements of protein interactions now called for to unravel cellular mechanisms. Therefore, just as chemical methods for selectively labeling proteins in the test tube significantly impacted in vitro biophysics in the last century, chemical tagging technologies are now poised to provide a breakthrough to meet this century's challenge of understanding protein function in the living cell. With chemical tags, the protein of interest is attached to a polypeptide rather than an FP. The polypeptide is subsequently modified with an organic fluorophore or another probe. The FlAsH peptide tag was first reported in 1998. Since then, more refined protein tags, exemplified by the TMP- and SNAP-tag, have improved selectivity and enabled imaging of intracellular proteins with high signal-to-noise ratios. Further improvement is still required to achieve direct incorporation of powerful fluorophores, but enzyme-mediated chemical tags show promise for overcoming the difficulty of selectively labeling a short peptide tag. In this Account, we focus on the development and application of chemical tags for studying protein function within living cells. Thus, in our overview of different chemical tagging strategies and technologies, we emphasize the challenge of rendering the labeling reaction sufficiently selective and the fluorophore probe sufficiently well behaved to image intracellular proteins with high signal-to-noise ratios. We highlight recent applications in which the chemical tags have enabled sophisticated biophysical measurements that would be difficult or even impossible with FPs. Finally, we conclude by looking forward to (i) the development of high-photon-output chemical tags compatible with living cells to enable high-resolution imaging, (ii) the realization of the potential of the chemical tags to significantly reduce tag size, and (iii) the exploitation of the modular chemical tag label to go beyond fluorescent imaging.
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Affiliation(s)
- Chaoran Jing
- Department of Chemistry, Columbia University, 550 West 120th Street, MC 4854, NWC Building, New York, New York 10027, United States
| | - Virginia W. Cornish
- Department of Chemistry, Columbia University, 550 West 120th Street, MC 4854, NWC Building, New York, New York 10027, United States
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48
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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: 207] [Impact Index Per Article: 15.9] [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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49
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Site-specific in vitro and in vivo incorporation of molecular probes to study G-protein-coupled receptors. Curr Opin Chem Biol 2011; 15:392-8. [DOI: 10.1016/j.cbpa.2011.03.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/15/2011] [Accepted: 03/17/2011] [Indexed: 12/20/2022]
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50
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Plass T, Schultz C. Covalent Labeling of Biomolecules in Living Cells. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY III 2011. [DOI: 10.1007/978-3-642-18035-4_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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