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Xu J, Zhu N, Du Y, Han T, Zheng X, Li J, Zhu S. Biomimetic NIR-II fluorescent proteins created from chemogenic protein-seeking dyes for multicolor deep-tissue bioimaging. Nat Commun 2024; 15:2845. [PMID: 38565859 PMCID: PMC10987503 DOI: 10.1038/s41467-024-47063-4] [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] [Received: 06/27/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
Near-infrared-I/II fluorescent proteins (NIR-I/II FPs) are crucial for in vivo imaging, yet the current NIR-I/II FPs face challenges including scarcity, the requirement for chromophore maturation, and limited emission wavelengths (typically < 800 nm). Here, we utilize synthetic protein-seeking NIR-II dyes as chromophores, which covalently bind to tag proteins (e.g., human serum albumin, HSA) through a site-specific nucleophilic substitution reaction, thereby creating proof-of-concept biomimetic NIR-II FPs. This chemogenic protein-seeking strategy can be accomplished under gentle physiological conditions without catalysis. Proteomics analysis identifies specific binding site (Cys 477 on DIII). NIR-II FPs significantly enhance chromophore brightness and photostability, while improving biocompatibility, allowing for high-performance NIR-II lymphography and angiography. This strategy is universal and applicable in creating a wide range of spectrally separated NIR-I/II FPs for real-time visualization of multiple biological events. Overall, this straightforward biomimetic approach holds the potential to transform fluorescent protein-based bioimaging and enables in-situ albumin targeting to create NIR-I/II FPs for deep-tissue imaging in live organisms.
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Affiliation(s)
- Jiajun Xu
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, First Hospital of Jilin University, Changchun, 130021, P.R. China
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, P.R. China
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Materials Science, Hebei University, Baoding, 071002, P.R. China
| | - Ningning Zhu
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, First Hospital of Jilin University, Changchun, 130021, P.R. China
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, P.R. China
| | - Yijing Du
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, First Hospital of Jilin University, Changchun, 130021, P.R. China
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, P.R. China
| | - Tianyang Han
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, First Hospital of Jilin University, Changchun, 130021, P.R. China
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, P.R. China
| | - Xue Zheng
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, First Hospital of Jilin University, Changchun, 130021, P.R. China
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, P.R. China
| | - Jia Li
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, First Hospital of Jilin University, Changchun, 130021, P.R. China
| | - Shoujun Zhu
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, First Hospital of Jilin University, Changchun, 130021, P.R. China.
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, P.R. China.
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2
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Bauer N, Kiefer F. Genetically Encoded Reporters to Monitor Hypoxia. Methods Mol Biol 2024; 2755:3-29. [PMID: 38319566 DOI: 10.1007/978-1-0716-3633-6_1] [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: 02/07/2024]
Abstract
Hypoxia resulting from an imbalance of oxygen availability and consumption defines a metabolic cellular state with a profound impact on developmental processes, tissue maintenance, and the development of pathologies. Fluorescence imaging using genetically encoded reporters enables hypoxia and oxygen imaging with cellular resolution. Thereby unrestricted visualization of hypoxic cells and regions essentially relies on the availability of oxygen-independent fluorescent proteins like UnaG, isolated from the Japanese freshwater eel. Here, we describe the application of recently developed members of a UnaG-based hypoxia reporter family to visualize oxygenation patterns by in vitro live-cell imaging and during the ex vivo analysis of intracranial xenografted tumors. Thus, the generation of stably transfected transgenic tumor cell lines, the in vitro calibration of the genetically encoded sensors, the surgical procedures for orthotopic xenografting of tumors in mice, and workflows for the respective sample preparation and microscopy are outlined.
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Affiliation(s)
- Nadine Bauer
- European Institute for Molecular Imaging, University of Münster, Münster, Germany
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Friedemann Kiefer
- European Institute for Molecular Imaging, University of Münster, Münster, Germany.
- Max Planck Institute for Molecular Biomedicine, Münster, Germany.
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3
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Zhang D, Chen Z, Du Z, Bao B, Su N, Chen X, Ge Y, Lin Q, Yang L, Hua Y, Wang S, Hua X, Zuo F, Li N, Liu R, Jiang L, Bao C, Zhao Y, Loscalzo J, Yang Y, Zhu L. Design of a palette of SNAP-tag mimics of fluorescent proteins and their use as cell reporters. Cell Discov 2023; 9:56. [PMID: 37311750 DOI: 10.1038/s41421-023-00546-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/18/2023] [Indexed: 06/15/2023] Open
Abstract
Naturally occurring fluorescent proteins (FPs) are the most widely used tools for tracking cellular proteins and sensing cellular events. Here, we chemically evolved the self-labeling SNAP-tag into a palette of SNAP-tag mimics of fluorescent proteins (SmFPs) that possess bright, rapidly inducible fluorescence ranging from cyan to infrared. SmFPs are integral chemical-genetic entities based on the same fluorogenic principle as FPs, i.e., induction of fluorescence of non-emitting molecular rotors by conformational locking. We demonstrate the usefulness of these SmFPs in real-time tracking of protein expression, degradation, binding interactions, trafficking, and assembly, and show that these optimally designed SmFPs outperform FPs like GFP in many important ways. We further show that the fluorescence of circularly permuted SmFPs is sensitive to the conformational changes of their fusion partners, and that these fusion partners can be used for the development of single SmFP-based genetically encoded calcium sensors for live cell imaging.
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Affiliation(s)
- Dasheng Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zhengda Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zengmin Du
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Bingkun Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ni Su
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Yihui Ge
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Qiuning Lin
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Lipeng Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yujie Hua
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Wang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xin Hua
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Fangting Zuo
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ningfeng Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Li Jiang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chunyan Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
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4
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Perfilov MM, Zaitseva ER, Baleeva NS, Kublitski VS, Smirnov AY, Bogdanova YA, Krasnova SA, Myasnyanko IN, Mishin AS, Baranov MS. Meta-CF 3-Substituted Analogues of the GFP Chromophore with Remarkable Solvatochromism. Int J Mol Sci 2023; 24:9923. [PMID: 37373071 DOI: 10.3390/ijms24129923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
In this work, we have shown that the introduction of a trifluoromethyl group into the me-ta-position of arylidene imidazolones (GFP chromophore core) leads to a dramatic increase in their fluorescence in nonpolar and aprotic media. The presence of a pronounced solvent-dependent gradation of fluorescence intensity makes it possible to use these substances as fluorescent polarity sensors. In particular, we showed that one of the created compounds could be used for selective labeling of the endoplasmic reticulum of living cells.
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Affiliation(s)
- Maxim M Perfilov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Elvira R Zaitseva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Vadim S Kublitski
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, Moscow 121205, Russia
| | - Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Svetlana A Krasnova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
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5
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Van Thillo T, Van Deuren V, Dedecker P. Smart genetically-encoded biosensors for the chemical monitoring of living systems. Chem Commun (Camb) 2023; 59:520-534. [PMID: 36519509 DOI: 10.1039/d2cc05363b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Genetically-encoded biosensors provide the all-optical and non-invasive visualization of dynamic biochemical events within living systems, which has allowed the discovery of profound new insights. Twenty-five years of biosensor development has steadily improved their performance and has provided us with an ever increasing biosensor repertoire. In this feature article, we present recent advances made in biosensor development and provide a perspective on the future direction of the field.
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Affiliation(s)
- Toon Van Thillo
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Vincent Van Deuren
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
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6
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Bauer N, Maisuls I, Pereira da Graça A, Reinhardt D, Erapaneedi R, Kirschnick N, Schäfers M, Grashoff C, Landfester K, Vestweber D, Strassert CA, Kiefer F. Genetically encoded dual fluorophore reporters for graded oxygen-sensing in light microscopy. Biosens Bioelectron 2022; 221:114917. [DOI: 10.1016/j.bios.2022.114917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/31/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
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7
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Nteroli G, Messa G, Dasa MK, Penttinen A, Härkönen A, Guina M, Podoleanu AG, Koutsikou S, Bradu A. Enhanced resolution optoacoustic microscopy using a picosecond high repetition rate Q-switched microchip laser. JOURNAL OF BIOMEDICAL OPTICS 2022; 27:110501. [PMID: 36458112 PMCID: PMC9705569 DOI: 10.1117/1.jbo.27.11.110501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
Conventional optoacoustic microscopy (OAM) instruments have at their core a nanosecond pulse duration laser. If lasers with a shorter pulse duration are used, broader, higher frequency ultrasound waves are expected to be generated and as a result, the axial resolution of the instrument is improved. Here, we exploit the advantage offered by a picosecond duration pulse laser to enhance the axial resolution of an OAM instrument. In comparison to an instrument equipped with a 2-ns pulse duration laser, an improvement in the axial resolution of 50% is experimentally demonstrated by using excitation pulses of only 85 ps. To illustrate the capability of the instrument to generate high-quality optoacoustic images, en-face, in-vivo images of the brain of Xenopus laevis tadpole are presented with a lateral resolution of 3.8 μ m throughout the entire axial imaging range.
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Affiliation(s)
- Gianni Nteroli
- University of Kent, Applied Optics Group, Canterbury, United Kingdom
| | - Giulia Messa
- University of Kent, Medway School of Pharmacy, Chatham, United Kingdom
| | - Manoj K. Dasa
- Technical University of Denmark, DTU Fotonik, Lyngby, Denmark
| | - Antti Penttinen
- Tampere University, Optoelectronics Research Centre, Physics Unit, Faculty of Engineering and Natural Sciences, Tampere, Finland
| | - Antti Härkönen
- Tampere University, Optoelectronics Research Centre, Physics Unit, Faculty of Engineering and Natural Sciences, Tampere, Finland
| | - Mircea Guina
- Tampere University, Optoelectronics Research Centre, Physics Unit, Faculty of Engineering and Natural Sciences, Tampere, Finland
| | | | - Stella Koutsikou
- University of Kent, Medway School of Pharmacy, Chatham, United Kingdom
| | - Adrian Bradu
- University of Kent, Applied Optics Group, Canterbury, United Kingdom
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8
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Khrulev AA, Baleeva NS, Kamzeeva PN, Baranov MS, Aralov AV. Cyanine Dyes as Fluorogens for FAST and NanoFAST Proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022040112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Bachollet SPJT, Shpinov Y, Broch F, Benaissa H, Gautier A, Pietrancosta N, Mallet JM, Dumat B. An expanded palette of fluorogenic HaloTag probes with enhanced contrast for targeted cellular imaging. Org Biomol Chem 2022; 20:3619-3628. [PMID: 35420083 DOI: 10.1039/d1ob02394b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the development of HaloTag fluorogens based on dipolar flexible molecular rotor structures. By modulating the electron donating and withdrawing groups, we have tuned the absorption and emission wavelengths to design a palette of fluorogens with emissions spanning the green to red range, opening new possibilities for multicolor imaging. The probes were studied in glycerol and in the presence of HaloTag and exhibited good fluorogenic properties thanks to a viscosity-sensitive emission. In live-cell confocal imaging, the fluorogens yielded only a very low non-specific signal that enabled wash-free targeted imaging of intracellular organelles and proteins with good contrast. Combining experimental studies and theoretical investigation of the protein/fluorogen complexes by molecular dynamics, these results offer new insight into the design of molecular rotor-based fluorogenic HaloTag probes in order to improve reaction rates and the imaging contrast.
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Affiliation(s)
- Sylvestre P J T Bachollet
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Yuriy Shpinov
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Fanny Broch
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Hela Benaissa
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Arnaud Gautier
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France. .,Institut Universitaire de France (IUF), 1 rue Descartes, 75005 Paris, France
| | - Nicolas Pietrancosta
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France. .,Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS) INSERM, CNRS, Sorbonne Université, Paris, France
| | - Jean-Maurice Mallet
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Blaise Dumat
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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10
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Asad M, Laurent AD. Exploring structural dynamics and optical properties of UnaG fluorescent protein upon N57 mutations. Phys Chem Chem Phys 2022; 24:3816-3825. [PMID: 35084408 DOI: 10.1039/d1cp04681k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UnaG is a new class of fluorescence protein in which an endogenous ligand, namely bilirubin (BLR), plays the role of chromophore. Upon photoexcitation, holoUnaG emits green light. A single mutation at residue 57 induces a decrease in the fluorescence quantum yield. To our knowledge, no atomic simulation at the atomic level has been carried out to date to explain this fluorescence decay in N57A and N57Q mutants. Herein molecular dynamics simulations were carried out on wild-type (WT) UnaG and both mutants to investigate the structural impact of the mutation on its global structure, on BLR and the absorption spectra. Our study reveals significant global changes upon mutation at the protein entrance (L3, H2, and, H3) governing a BLR modification. BLR in WT UnaG is rather rigid while when embedded into N57A or N57Q, dihedral angles between endo and exo vinyl moieties and between A and B rings at the entrance of UnaG are strongly modified along with the number of inter-/intramolecular interactions. The water molecules play an important role in the modification of the shape of the binding cavity. For the first time, we show that the structural modifications upon ligand mutations are tightly related to the key structural changes in the protein such as Loop3 (L3), β sheet 2 (B2), and β sheet 3 (B3) dynamics. The present work suggests that the quenching of the fluorescence properties of UnaG mutants is mainly a non-radiative process closely related to the BLR flexibility induced by global structural changes.
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Affiliation(s)
- Mohammad Asad
- Nantes Université, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France.
| | - Adèle D Laurent
- Nantes Université, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France.
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11
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Farrants H, Tebo AG. Fluorescent chemigenetic actuators and indicators for use in living animals. Curr Opin Pharmacol 2022; 62:159-167. [DOI: 10.1016/j.coph.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/03/2021] [Accepted: 12/12/2021] [Indexed: 11/28/2022]
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12
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Frei MS, Tarnawski M, Roberti MJ, Koch B, Hiblot J, Johnsson K. Engineered HaloTag variants for fluorescence lifetime multiplexing. Nat Methods 2022; 19:65-70. [PMID: 34916672 PMCID: PMC8748199 DOI: 10.1038/s41592-021-01341-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/02/2021] [Indexed: 12/03/2022]
Abstract
Self-labeling protein tags such as HaloTag are powerful tools that can label fusion proteins with synthetic fluorophores for use in fluorescence microscopy. Here we introduce HaloTag variants with either increased or decreased brightness and fluorescence lifetime compared with HaloTag7 when labeled with rhodamines. Combining these HaloTag variants enabled live-cell fluorescence lifetime multiplexing of three cellular targets in one spectral channel using a single fluorophore and the generation of a fluorescence lifetime-based biosensor. Additionally, the brightest HaloTag variant showed up to 40% higher brightness in live-cell imaging applications.
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Affiliation(s)
- Michelle S Frei
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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13
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Innard N, Chong JPJ. The challenges of monitoring and manipulating anaerobic microbial communities. BIORESOURCE TECHNOLOGY 2022; 344:126326. [PMID: 34780902 DOI: 10.1016/j.biortech.2021.126326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.
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Affiliation(s)
- Nathan Innard
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - James P J Chong
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK.
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14
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Wu Y, Shi C, Wang G, Sun H, Yin S. Recent Advances in the Development and Applications of Conjugated Polymer dots. J Mater Chem B 2022; 10:2995-3015. [DOI: 10.1039/d1tb02816b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conjugated polymer dots or semiconducting polymer nanoparticles (Pdots) are nanoparticles prepared based on organic polymers. Pdots have the advantages of lower cost, simple preparation process, good biocompatibility, excellent stability, easy...
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15
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Chia HE, Koebke KJ, Rangarajan AA, Koropatkin NM, Marsh ENG, Biteen JS. New Orange Ligand-Dependent Fluorescent Reporter for Anaerobic Imaging. ACS Chem Biol 2021; 16:2109-2115. [PMID: 34652894 PMCID: PMC11180495 DOI: 10.1021/acschembio.1c00391] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Bilin-binding fluorescent proteins like UnaG-bilirubin are noncovalent ligand-dependent reporters for oxygen-free microscopy but are restricted to blue and far-red fluorescence. Here we describe a high-throughput screening approach to provide a new UnaG-ligand pair that can be excited in the 532 nm green excitation microscopy channel. We identified a novel orange UnaG-ligand pair that maximally emits at 581 nm. Whereas the benzothiazole-based ligand itself is nominally fluorescent, the compound binds UnaG with high affinity (Kd = 3 nM) to induce a 2.5-fold fluorescence intensity enhancement and a 10 nm red shift. We demonstrated this pair in the anaerobic fluorescence microscopy of the prevalent gut bacterium Bacteroides thetaiotaomicron and in Escherichia coli. This UnaG-ligand pair can also be coupled to IFP2.0-biliverdin to differentiate cells in mixed-species two-color imaging. Our results demonstrate the versatility of the UnaG ligand-binding pocket and extend the ability to image cells at longer wavelengths in anoxic environments.
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Affiliation(s)
- Hannah E Chia
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Aathmaja A Rangarajan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - E Neil G Marsh
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Julie S Biteen
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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16
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Baleeva NS, Smirnov AY, Myasnyanko IN, Gavrikov AS, Baranov MS. A Thiophene Analog of the GFP Chromophore As Fluorogen for FAST Protein. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021050198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Fan J, Cheney PP, Bloch S, Xu B, Liang K, Odonkor CA, Edwards WB, Basak S, Mintz R, Biswas P, Achilefu S. Multifunctional Thio-Stabilized Gold Nanoparticles for Near-Infrared Fluorescence Detection and Imaging of Activated Caspase-3. CURR ANAL CHEM 2021; 17:1182-1193. [PMID: 34393690 DOI: 10.2174/1573411017999210112175743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background Gold nanoparticles (AuNPs) are commonly used in nanomedicine because of their unique spectral properties, chemical and biological stability, and ability to quench the fluorescence of organic dyes attached to their surfaces. However, the utility of spherical AuNPs for activatable fluorescence sensing of molecular processes have been confined to resonance-matched fluorophores in the 500 nm to 600 nm spectral range to maximize dye fluorescence quenching efficiency. Expanding the repertoire of fluorophore systems into the NIR fluorescence regimen with emission >800 nm will facilitate the analysis of multiple biological events with high detection sensitivity. Objective The primary goal of this study is to determine if spherical AuNP-induced radiative rate suppression of non-resonant near-infrared (NIR) fluorescent probes can serve as a versatile nanoconstruct for highly sensitive detection and imaging of activated caspase-3 in aqueous media and cancer cells. This required the development of activatable NIR fluorescence sensors of caspase-3 designed to overcome the nonspecific degradation and release of the surface coatings in aqueous media. Method We harnessed the fluorescence-quenching properties and multivalency of spherical AuNPs to develop AuNP-templated activatable NIR fluorescent probes to detect activated caspase-3, an intracellular reporter of early cell death. Freshly AuNPs were coated with a multifunctional NIR fluorescent dye-labeled peptide (LS422) consisting of an RGD peptide sequence that targets αvβ3-integrin protein (αvβ3) on the surface of cancer cells to mediate the uptake and internalization of the sensors in tumor cells; a DEVD peptide sequence for reporting the induction of cell death through caspase-3 mediated NIR fluorescence enhancement; and a multidentate hexacysteine sequence for enhancing self-assembly and stabilizing the multifunctional construct on AuNPs. The integrin binding affinity of LS422 and caspase-3 kinetics were determined by a radioligand competitive binding and fluorogenic peptide assays, respectively. Detection of intracellular caspase-3, cell viability, and the internalization of LS422 in cancer cells were determined by confocal NIR fluorescence spectroscopy and microscopy. Results Narrow size AuNPs (13 nm) were prepared and characterized by transmission electron microscopy and dynamic light scattering. When assembled on the AuNPs, the binding constant of LS422 for αvβ3 improved 11-fold from 13.2 nM to 1.2 nM. Whereas the catalytic turnover of caspase-3 by LS422-AuNPs was similar to the reference fluorogenic peptide, the binding affinity for the enzyme increased by a factor of 2. Unlike the αvβ3 positive, but caspase-3 negative breast cancer MCF-7 cells, treatment of the αvβ3 and caspase-3 positive lung cancer A549 cells with Paclitaxel showed significant fluorescence enhancement within 30 minutes, which correlated with caspase-3 specific activation of LS422-AuNPs fluorescence. Incorporation of a 3.5 mW NIR laser source into our spectrofluorometer increased the detection sensitivity by an order of magnitude (limit of detection ~0.1 nM of cypate) and significantly decreased the signal noise relative to a xenon lamp. This gain in sensitivity enabled the detection of substrate hydrolysis at a broad range of inhibitor concentrations without photobleaching the cypate dye. Conclusion The multifunctional AuNPs demonstrate the use of a non-resonant quenching strategy to design activatable NIR fluorescence molecular probes. The nanoconstruct offers a selective reporting method for detecting activated caspase-3, imaging of cell viability, identifying dying cells, and visualizing the functional status of intracellular enzymes. Performing these tasks with NIR fluorescent probes creates an opportunity to translate the in vitro and cellular analysis of enzymes into in vivo interrogation of their functional status using deep tissue penetrating NIR fluorescence analytical methods.
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Affiliation(s)
- J Fan
- Departments of Radiology, Washington University School of Medicine, St Louis, United States
| | - P P Cheney
- Departments of Radiology, Washington University School of Medicine, St Louis, United States
| | - S Bloch
- Departments of Radiology, Washington University School of Medicine, St Louis, United States
| | - B Xu
- Departments of Radiology, Washington University School of Medicine, St Louis, United States
| | - K Liang
- Departments of Radiology, Washington University School of Medicine, St Louis, United States
| | - C A Odonkor
- Departments of Radiology, Washington University School of Medicine, St Louis, United States
| | - W B Edwards
- Departments of Radiology, Washington University School of Medicine, St Louis, United States
| | - S Basak
- Department of Energy, Environmental & Chemical Engineering, Washington University, St Louis, United States
| | - R Mintz
- Departments of Radiology, Washington University School of Medicine, St Louis, United States.,Department of Energy, Environmental & Chemical Engineering, Washington University, St Louis, United States.,Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St Louis, United States.,Department of Biomedical Engineering, Washington University, St Louis, United States.,Department of Medicine, Washington University, St Louis, United States
| | - P Biswas
- Department of Energy, Environmental & Chemical Engineering, Washington University, St Louis, United States
| | - S Achilefu
- Departments of Radiology, Washington University School of Medicine, St Louis, United States.,Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St Louis, United States.,Department of Biomedical Engineering, Washington University, St Louis, United States.,Department of Medicine, Washington University, St Louis, United States
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18
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Kirschnick N, Drees D, Redder E, Erapaneedi R, Pereira da Graca A, Schäfers M, Jiang X, Kiefer F. Rapid methods for the evaluation of fluorescent reporters in tissue clearing and the segmentation of large vascular structures. iScience 2021; 24:102650. [PMID: 34151237 PMCID: PMC8192726 DOI: 10.1016/j.isci.2021.102650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/23/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
Light sheet fluorescence microscopy (LSFM) of large tissue samples does not require mechanical sectioning and allows efficient visualization of spatially complex or rare structures. Therefore, LSFM has become invaluable in developmental and biomedical research. Because sample size may limit whole-mount staining, LSFM benefits from transgenic reporter organisms expressing fluorescent proteins (FPs) and, however, requires optical clearing and computational data visualization and analysis. The former often interferes with FPs, while the latter requires massive computing resources. Here, we describe 3D-polymerized cell dispersions, a rapid and straightforward method, based on recombinant FP expression in freely selectable tester cells, to evaluate and compare fluorescence retention in different tissue-clearing protocols. For the analysis of large LSFM data, which usually requires huge computing resources, we introduce a refined, interactive, hierarchical random walker approach that is capable of efficient segmentation of the vasculature in data sets even on a consumer grade PC.
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Affiliation(s)
- Nils Kirschnick
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Dominik Drees
- Institute of Computer Science, University of Münster, Einsteinstraße 62, 48149 Münster, Germany
| | - Esther Redder
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Raghu Erapaneedi
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Abel Pereira da Graca
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Michael Schäfers
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Xiaoyi Jiang
- Institute of Computer Science, University of Münster, Einsteinstraße 62, 48149 Münster, Germany
| | - Friedemann Kiefer
- European Institute of Molecular Imaging, University of Münster, Waldeyerstraße 15, 48149 Münster, Germany
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19
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Suss O, Motiei L, Margulies D. Broad Applications of Thiazole Orange in Fluorescent Sensing of Biomolecules and Ions. Molecules 2021; 26:2828. [PMID: 34068759 PMCID: PMC8126248 DOI: 10.3390/molecules26092828] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
Fluorescent sensing of biomolecules has served as a revolutionary tool for studying and better understanding various biological systems. Therefore, it has become increasingly important to identify fluorescent building blocks that can be easily converted into sensing probes, which can detect specific targets with increasing sensitivity and accuracy. Over the past 30 years, thiazole orange (TO) has garnered great attention due to its low fluorescence background signal and remarkable 'turn-on' fluorescence response, being controlled only by its intramolecular torsional movement. These features have led to the development of numerous molecular probes that apply TO in order to sense a variety of biomolecules and metal ions. Here, we highlight the tremendous progress made in the field of TO-based sensors and demonstrate the different strategies that have enabled TO to evolve into a versatile dye for monitoring a collection of biomolecules.
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Affiliation(s)
| | | | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (O.S.); (L.M.)
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20
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Yu Q, Ren K, You M. Genetically encoded RNA nanodevices for cellular imaging and regulation. NANOSCALE 2021; 13:7988-8003. [PMID: 33885099 PMCID: PMC8122502 DOI: 10.1039/d0nr08301a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nucleic acid-based nanodevices have been widely used in the fields of biosensing and nanomedicine. Traditionally, the majority of these nanodevices were first constructed in vitro using synthetic DNA or RNA oligonucleotides and then delivered into cells. Nowadays, the emergence of genetically encoded RNA nanodevices has provided a promising alternative approach for intracellular analysis and regulation. These genetically encoded RNA-based nanodevices can be directly transcribed and continuously produced inside living cells. A variety of highly precise and programmable nanodevices have been constructed in this way during the last decade. In this review, we will summarize the recent advances in the design and function of these artificial genetically encoded RNA nanodevices. In particular, we will focus on their applications in regulating cellular gene expression, imaging, logic operation, structural biology, and optogenetics. We believe these versatile RNA-based nanodevices will be broadly used in the near future to probe and program cells and other biological systems.
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Affiliation(s)
- Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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21
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Abstract
Technologies for RNA imaging in live cells play an important role in understanding the function and regulatory process of RNAs. One approach for genetically encoded fluorescent RNA imaging involves fluorescent light-up aptamers (FLAPs), which are short RNA sequences that can bind cognate fluorogens and activate their fluorescence greatly. Over the past few years, FLAPs have emerged as genetically encoded RNA-based fluorescent biosensors for the cellular imaging and detection of various targets of interest. In this review, we first give a brief overview of the development of the current FLAPs based on various fluorogens. Then we further discuss on the photocycles of the reversibly photoswitching properties in FLAPs and their photostability. Finally, we focus on the applications of FLAPs as genetically encoded RNA-based fluorescent biosensors in biosensing and bioimaging, including RNA, non-nucleic acid molecules, metal ions imaging and quantitative imaging. Their design strategies and recent cellular applications are emphasized and summarized in detail.
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Affiliation(s)
- Huangmei Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, China.,NYU-ECNU Institute of Physics at NYU Shanghai, Shanghai, China
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22
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Mineev KS, Goncharuk SA, Goncharuk MV, Povarova NV, Sokolov AI, Baleeva NS, Smirnov AY, Myasnyanko IN, Ruchkin DA, Bukhdruker S, Remeeva A, Mishin A, Borshchevskiy V, Gordeliy V, Arseniev AS, Gorbachev DA, Gavrikov AS, Mishin AS, Baranov MS. NanoFAST: structure-based design of a small fluorogen-activating protein with only 98 amino acids. Chem Sci 2021; 12:6719-6725. [PMID: 34040747 PMCID: PMC8132994 DOI: 10.1039/d1sc01454d] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/08/2021] [Indexed: 12/31/2022] Open
Abstract
One of the essential characteristics of any tag used in bioscience and medical applications is its size. The larger the label, the more it may affect the studied object, and the more it may distort its behavior. In this paper, using NMR spectroscopy and X-ray crystallography, we have studied the structure of fluorogen-activating protein FAST both in the apo form and in complex with the fluorogen. We showed that significant change in the protein occurs upon interaction with the ligand. While the protein is completely ordered in the complex, its apo form is characterized by higher mobility and disordering of its N-terminus. We used structural information to design the shortened FAST (which we named nanoFAST) by truncating 26 N-terminal residues. Thus, we created the shortest genetically encoded tag among all known fluorescent and fluorogen-activating proteins, which is composed of only 98 amino acids.
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Affiliation(s)
- Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Marina V Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Natalia V Povarova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Anatolii I Sokolov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Dmitry A Ruchkin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Sergey Bukhdruker
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH Jülich 52425 Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH Jülich 52425 Germany
- ESRF - The European Synchrotron Grenoble 38000 France
| | - Alina Remeeva
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Alexey Mishin
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Valentin Borshchevskiy
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH Jülich 52425 Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH Jülich 52425 Germany
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH Jülich 52425 Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH Jülich 52425 Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes, CEA, CNRS Grenoble France
| | - Alexander S Arseniev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Dmitriy A Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Pirogov Russian National Research Medical University Ostrovitianov 1 Moscow 117997 Russia
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23
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Schenk R, Bachmaier S, Bringaud F, Boshart M. Efficient flavinylation of glycosomal fumarate reductase by its own ApbE domain in Trypanosoma brucei. FEBS J 2021; 288:5430-5445. [PMID: 33755328 DOI: 10.1111/febs.15812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/08/2021] [Accepted: 03/09/2021] [Indexed: 01/26/2023]
Abstract
A subset of flavoproteins has a covalently attached flavin prosthetic group enzymatically attached via phosphoester bonding. In prokaryotes, this is catalysed by alternative pyrimidine biosynthesis E (ApbE) flavin transferases. ApbE-like domains are present in few eukaryotic taxa, for example the N-terminal domain of fumarate reductase (FRD) of Trypanosoma, a parasitic protist known as a tropical pathogen causing African sleeping sickness. We use the versatile reverse genetic tools available for Trypanosoma to investigate the flavinylation of glycosomal FRD (FRDg) in vivo in the physiological and organellar context. Using direct in-gel fluorescence detection of covalently attached flavin as proxy for activity, we show that the ApbE-like domain of FRDg has flavin transferase activity in vivo. The ApbE domain is preceded by a consensus flavinylation target motif at the extreme N terminus of FRDg, and serine 9 in this motif is essential as flavin acceptor. The preferred mode of flavinylation in the glycosome was addressed by stoichiometric expression and comparison of native and catalytically inactive ApbE domains. In addition to the trans-flavinylation activity, the ApbE domain catalyses the intramolecular cis-flavinylation with at least fivefold higher efficiency. We discuss how the higher efficiency due to unusual fusion of the ApbE domain to its substrate protein FRD may provide a selective advantage by faster FRD biogenesis during rapid metabolic adaptation of trypanosomes. The first 37 amino acids of FRDg, including the consensus motif, are sufficient as flavinylation target upon fusion to other proteins. We propose FRDg(1-37) as 4-kDa heat-stable, detergent-resistant fluorescent protein tag and suggest its use as a new tool to study glycosomal protein import.
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Affiliation(s)
- Robin Schenk
- Biozentrum, Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München (LMU), Martinsried, Germany
| | - Sabine Bachmaier
- Biozentrum, Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München (LMU), Martinsried, Germany
| | - Frédéric Bringaud
- CNRS, Microbiologie Fondamentale et Pathogénicité (MFP), UMR 5234, Université de Bordeaux, France
| | - Michael Boshart
- Biozentrum, Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München (LMU), Martinsried, Germany
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24
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Myasnyanko IN, Gavrikov AS, Zaitseva SO, Smirnov AY, Zaitseva ER, Sokolov AI, Malyshevskaya KK, Baleeva NS, Mishin AS, Baranov MS. Color Tuning of Fluorogens for FAST Fluorogen‐Activating Protein. Chemistry 2021; 27:3986-3990. [DOI: 10.1002/chem.202004760] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/16/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Ivan N. Myasnyanko
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexey S. Gavrikov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Snizhana O. Zaitseva
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander Yu. Smirnov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Elvira R. Zaitseva
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Anatolii I. Sokolov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Kseniya K. Malyshevskaya
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Nadezhda S. Baleeva
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander S. Mishin
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Pirogov Russian National Research Medical University Ostrovitianov 1 Moscow 117997 Russia
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25
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Camarca A, Varriale A, Capo A, Pennacchio A, Calabrese A, Giannattasio C, Murillo Almuzara C, D’Auria S, Staiano M. Emergent Biosensing Technologies Based on Fluorescence Spectroscopy and Surface Plasmon Resonance. SENSORS (BASEL, SWITZERLAND) 2021; 21:906. [PMID: 33572812 PMCID: PMC7866296 DOI: 10.3390/s21030906] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/23/2022]
Abstract
The purpose of this work is to provide an exhaustive overview of the emerging biosensor technologies for the detection of analytes of interest for food, environment, security, and health. Over the years, biosensors have acquired increasing importance in a wide range of applications due to synergistic studies of various scientific disciplines, determining their great commercial potential and revealing how nanotechnology and biotechnology can be strictly connected. In the present scenario, biosensors have increased their detection limit and sensitivity unthinkable until a few years ago. The most widely used biosensors are optical-based devices such as surface plasmon resonance (SPR)-based biosensors and fluorescence-based biosensors. Here, we will review them by highlighting how the progress in their design and development could impact our daily life.
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Affiliation(s)
- Alessandra Camarca
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Antonio Varriale
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
- URT-ISA at Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
| | - Alessandro Capo
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Angela Pennacchio
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Alessia Calabrese
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Cristina Giannattasio
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Carlos Murillo Almuzara
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Sabato D’Auria
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
| | - Maria Staiano
- Institute of Food Science, CNR Italy, 83100 Avellino, Italy; (A.C.); (A.V.); (A.C.); (A.P.); (A.C.); (C.G.); (C.M.A.); (M.S.)
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Chekli Y, Peron-Cane C, Dell'Arciprete D, Allemand JF, Li C, Ghigo JM, Gautier A, Lebreton A, Desprat N, Beloin C. Visualizing the dynamics of exported bacterial proteins with the chemogenetic fluorescent reporter FAST. Sci Rep 2020; 10:15791. [PMID: 32978420 PMCID: PMC7519654 DOI: 10.1038/s41598-020-72498-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023] Open
Abstract
Bacterial proteins exported to the cell surface play key cellular functions. However, despite the interest to study the localisation of surface proteins such as adhesins, transporters or hydrolases, monitoring their dynamics in live imaging remains challenging, due to the limited availability of fluorescent probes remaining functional after secretion. In this work, we used the Escherichia coli intimin and the Listeria monocytogenes InlB invasin as surface exposed scaffolds fused with the recently developed chemogenetic fluorescent reporter protein FAST. Using both membrane permeant (HBR-3,5DM) and non-permeant (HBRAA-3E) fluorogens that fluoresce upon binding to FAST, we demonstrated that fully functional FAST can be exposed at the cell surface and used to specifically tag the external side of the bacterial envelop in both diderm and monoderm bacteria. Our work opens new avenues to study the organization and dynamics of the bacterial cell surface proteins.
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Affiliation(s)
- Yankel Chekli
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Caroline Peron-Cane
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Dario Dell'Arciprete
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France
| | - Jean-François Allemand
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Chenge Li
- École Normale Supérieure, Université PSL, CNRS, Laboratoire Des Biomolécules (LBM), Sorbonne Université, 75005, Paris, France
| | - Jean-Marc Ghigo
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France
| | - Arnaud Gautier
- École Normale Supérieure, Université PSL, CNRS, Laboratoire Des Biomolécules (LBM), Sorbonne Université, 75005, Paris, France
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
- Institut Universitaire de France, Paris, France
| | - Alice Lebreton
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- INRAE, IBENS, 75005, Paris, France
| | - Nicolas Desprat
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France.
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
| | - Christophe Beloin
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France.
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27
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Dallas SL, Moore DS. Using confocal imaging approaches to understand the structure and function of osteocytes and the lacunocanalicular network. Bone 2020; 138:115463. [PMID: 32512167 PMCID: PMC7423610 DOI: 10.1016/j.bone.2020.115463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 05/29/2020] [Indexed: 02/07/2023]
Abstract
Although overlooked in the past, osteocytes have come to the forefront of skeletal biology and are now recognized as a key cell type that integrates hormonal, mechanical and other signals to control bone mass through regulation of both osteoblast and osteoclast activity. With the surge of recent interest in osteocytes as bone regulatory cells and the discovery that they also function as endocrine regulators of phosphate homeostasis, there has been renewed interest in understanding the structure and function of these unique and relatively inaccessible cells. Osteocytes are embedded within the mineralized bone matrix and are housed within a complex lacunocanalicular system which connects them with the circulation and with other organ systems. This has presented unique challenges for imaging these cells. This review summarizes recent advances in confocal imaging approaches for visualizing osteocytes and their lacunocanalicular networks in both living and fixed bone specimens and discusses how computational approaches can be combined with live and fixed cell imaging techniques to generate quantitative outputs and predictive models. The integration of advanced imaging with computational approaches promises to lead to a more in depth understanding of the structure and function of osteocyte networks and the lacunocanalicular system in the healthy and aging state as well as in pathological conditions in bone.
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Affiliation(s)
- Sarah L Dallas
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri Kansas City, Kansas City, MO 64108, United States of America.
| | - David S Moore
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri Kansas City, Kansas City, MO 64108, United States of America
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28
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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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29
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Gautier A, Tebo AG. Sensing cellular biochemistry with fluorescent chemical-genetic hybrids. Curr Opin Chem Biol 2020; 57:58-64. [PMID: 32580134 DOI: 10.1016/j.cbpa.2020.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/19/2020] [Accepted: 04/08/2020] [Indexed: 11/26/2022]
Abstract
Fluorescent biosensors are powerful tools for the detection of biochemical events inside cells with high spatiotemporal resolution. Biosensors based on fluorescent proteins often suffer from issues with photostability and brightness. On the other hand, hybrid, chemical-genetic systems present unique opportunities to combine the strengths of synthetic, organic chemistry with biological macromolecules to generate exquisitely tailored semisynthetic sensors.
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Affiliation(s)
- Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France; Institut Universitaire de France, France.
| | - Alison G Tebo
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France.
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30
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Moeyaert B, Dedecker P. Genetically encoded biosensors based on innovative scaffolds. Int J Biochem Cell Biol 2020; 125:105761. [PMID: 32504671 DOI: 10.1016/j.biocel.2020.105761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
Abstract
Genetically encoded biosensors are indispensable tools for visualizing the spatiotemporal dynamics of analytes or processes in living cells in vitro and in vivo. Their widespread adaptation has gone hand in hand with the development of sensors for new analytes or processes and improved functionality and robustness. In this review, we highlight some of the recent advances in genetically encoded biosensor development, with a special focus on novel and innovative scaffolds that will lead to new possibilities in the future.
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Affiliation(s)
- Benjamien Moeyaert
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium.
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31
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Perkins LA, Bruchez MP. Fluorogen activating protein toolset for protein trafficking measurements. Traffic 2020; 21:333-348. [PMID: 32080949 PMCID: PMC7462100 DOI: 10.1111/tra.12722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/11/2022]
Abstract
Throughout the past decade the use of fluorogen activating proteins (FAPs) has expanded with several unique reporter dyes that support a variety of methods to specifically quantify protein trafficking events. The platform's capabilities have been demonstrated in several systems and shared for widespread use. This review will highlight the current FAP labeling techniques for protein traffic measurements and focus on the use of the different designed fluorogenic dyes for selective and specific labeling applications.
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Affiliation(s)
- Lydia A. Perkins
- School of MedicineUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Marcel P. Bruchez
- The Department of Biological SciencesCarnegie MellonPittsburghPennsylvaniaUSA
- Department of ChemistryCarnegie MellonPittsburghPennsylvaniaUSA
- Molecular and Biosensor Imaging CenterCarnegie MellonPittsburghPennsylvaniaUSA
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