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Broch F, El Hajji L, Pietrancosta N, Gautier A. Engineering of Tunable Allosteric-like Fluorogenic Protein Sensors. ACS Sens 2023; 8:3933-3942. [PMID: 37830919 DOI: 10.1021/acssensors.3c01536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Optical protein sensors that enable detection of relevant biomolecules of interest play central roles in biological research. Coupling fluorescent reporters with protein sensing units has enabled the development of a wide range of biosensors that recognize analytes with high selectivity. In these sensors, analyte recognition induces a conformational change in the protein sensing unit that can modulate the optical signal of the fluorescent reporter. Here, we explore various designs for the creation of tunable allosteric-like fluorogenic protein sensors through incorporation of sensing protein units within the chemogenetic fluorescence-activating and absorption-shifting tag (FAST) that selectively binds and stabilizes the fluorescent state of 4-hydroxybenzylidene rhodanine (HBR) analogs. Conformational coupling allowed us to design analyte-responsive optical protein sensors through allosteric-like modulation of fluorogen binding.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Lina El Hajji
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Nicolas Pietrancosta
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Neuroscience Paris Seine-Institut de Biologie Paris Seine (NPS-IBPS) INSERM, CNRS, Sorbonne Université, 75005 Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Institut Universitaire de France, 75231 Paris, France
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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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Broch F, Gautier A. Illuminating Cellular Biochemistry: Fluorogenic Chemogenetic Biosensors for Biological Imaging. Chempluschem 2020; 85:1487-1497. [PMID: 32644262 DOI: 10.1002/cplu.202000413] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/18/2020] [Indexed: 12/19/2022]
Abstract
Cellular activity is defined by the precise spatiotemporal regulation of various components, such as ions, small molecules, or proteins. Studying cell physiology consequently requires the optical recording of these processes, notably by using fluorescent biosensors. The recent development of various fluorogenic systems greatly expanded the palette of reporters to be included in these sensors design. Fluorogenic reporters consist of a protein or RNA tag that can complex either an endogenous or a synthetic fluorogenic dye (so-called fluorogen). The intrinsic nature of these tags, along with the high tunability of their cognate chromophore provide interesting features such as far-red to near-infrared emission, oxygen independence, or unprecedented color versatility. These engineered photoreceptors, self-labelling proteins, or noncovalent aptamers and protein tags were rapidly identified as promising reporters to observe biological events. This Minireview focuses on the new perspectives they offer to design unique and innovative biosensors, thus pushing the boundaries of cellular imaging.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France.,Institut Universitaire de France, France
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Gallo E. Fluorogen-Activating Proteins: Next-Generation Fluorescence Probes for Biological Research. Bioconjug Chem 2019; 31:16-27. [DOI: 10.1021/acs.bioconjchem.9b00710] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Eugenio Gallo
- Department of Molecular Genetics, University of Toronto, Charles Best Institute, 112 College Street, Toronto, Ontario M5G 1L6, Canada
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Ackerman DS, Altun B, Kolodieznyi D, Bruchez MP, Tsourkas A, Jarvik JW. Antibody-Linked Fluorogen-Activating Proteins for Antigen Detection and Cell Ablation. Bioconjug Chem 2018; 30:63-69. [PMID: 30543409 DOI: 10.1021/acs.bioconjchem.8b00720] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate selective labeling of cell surface proteins using fluorogen-activating proteins (FAPs) conjugated to standard immunoglobulins (IgGs). Conjugation was achieved with a polypeptide reagent comprised of an N-terminal photoactivatable Fc-binding domain and a C-terminal FAP domain. The resulting FAP-antibody conjugates were effective agents for protein detection and cell ablation in cultured mammalian cells and for visualizing cell-cell contacts using a tethered fluorogen assay. Because our approach allows FAP-antibody conjugates to be generated for most currently available IgGs, it should have broad utility for experimental and therapeutic applications.
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Affiliation(s)
| | - Burcin Altun
- Department of Bioengineering , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | | | | | - Andrew Tsourkas
- Department of Bioengineering , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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Zeng G, Wang Y, Bruchez MP, Liang FS. Self-Reporting Chemically Induced Protein Proximity System Based on a Malachite Green Derivative and the L5** Fluorogen Activating Protein. Bioconjug Chem 2018; 29:3010-3015. [PMID: 30016083 DOI: 10.1021/acs.bioconjchem.8b00415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A unique chemically induced proximity method is engineered based on mutant antibody VL domain using a fluorogenic malachite green derivative as the inducer, which gives fluorescent signals upon VL domain dimerization while simultaneously inducing downstream biological effects.
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Affiliation(s)
- Guihua Zeng
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , United States
| | - Yi Wang
- Department of Chemistry, Department of Biological Sciences, and Molecular Biosensor and Imaging Center , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Marcel P Bruchez
- Department of Chemistry, Department of Biological Sciences, and Molecular Biosensor and Imaging Center , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , United States
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Xu S, Hu HY. Fluorogen-activating proteins: beyond classical fluorescent proteins. Acta Pharm Sin B 2018; 8:339-348. [PMID: 29881673 PMCID: PMC5989828 DOI: 10.1016/j.apsb.2018.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/11/2018] [Accepted: 02/18/2018] [Indexed: 01/09/2023] Open
Abstract
Fluorescence imaging is a powerful technique for the real-time noninvasive monitoring of protein dynamics. Recently, fluorogen activating proteins (FAPs)/fluorogen probes for protein imaging were developed. Unlike the traditional fluorescent proteins (FPs), FAPs do not fluoresce unless bound to their specific small-molecule fluorogens. When using FAPs/fluorogen probes, a washing step is not required for the removal of free probes from the cells, thus allowing rapid and specific detection of proteins in living cells with high signal-to-noise ratio. Furthermore, with different fluorogens, living cell multi-color proteins labeling system was developed. In this review, we describe about the discovery of FAPs, the design strategy of FAP fluorogens, the application of the FAP technology and the advances of FAP technology in protein labeling systems.
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Affiliation(s)
- Shengnan Xu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Hai-Yu Hu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
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A cell surface display fluorescent biosensor for measuring MMP14 activity in real-time. Sci Rep 2018; 8:5916. [PMID: 29651043 PMCID: PMC5897415 DOI: 10.1038/s41598-018-24080-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/23/2018] [Indexed: 01/16/2023] Open
Abstract
Despite numerous recent advances in imaging technologies, one continuing challenge for cell biologists and microscopists is the visualization and measurement of endogenous proteins as they function within living cells. Achieving this goal will provide a tool that investigators can use to associate cellular outcomes with the behavior and activity of many well-studied target proteins. Here, we describe the development of a plasmid-based fluorescent biosensor engineered to measure the location and activity of matrix metalloprotease-14 (MMP14). The biosensor design uses fluorogen-activating protein technology coupled with a MMP14-selective protease sequence to generate a binary, “switch-on” fluorescence reporter capable of measuring MMP14 location, activity, and temporal dynamics. The MMP14-fluorogen activating protein biosensor approach is applicable to both short and long-term imaging modalities and contains an adaptable module that can be used to study many membrane-bound proteases. This MMP14 biosensor promises to serve as a tool for the advancement of a broad range of investigations targeting MMP14 activity during cell migration in health and disease.
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Conner JW. Fluorogens: Generating Receptor-Specific Turn-On Fluorescence. Aust J Chem 2018. [DOI: 10.1071/ch17492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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