1
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Khan TA, Stoldt S, Bossi ML, Belov VN, Hell SW. β-Galactosidase- and Photo-Activatable Fluorescent Probes for Protein Labeling and Super-Resolution STED Microscopy in Living Cells. Molecules 2024; 29:3596. [PMID: 39125001 PMCID: PMC11314211 DOI: 10.3390/molecules29153596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
We report on the synthesis of two fluorescent probes which can be activated by β-Galactosidase (β-Gal) enzymes and/or light. The probes contained 2-nitro-4-oxybenzyl and 3-nitro-4-oxybenzyl fragments, with β-Gal residues linked to C-4. We performed the enzymatic and photoactivation of the probes in a cuvette and compared them, prior to the labeling of Vimentin-Halo fusion protein in live cells with overexpressed β-galactosidase. The dye fluorescence afforded the observation of enzyme activity by means of confocal and super-resolution optical microscopy based on stimulated emission depletion (STED). The tracing of enzymatic activity with the retention of activated fluorescent products inside cells was combined with super-resolution imaging as a tool for use in biomedicine and life science.
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Affiliation(s)
- Taukeer A. Khan
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077 Göttingen, Germany (V.N.B.)
| | - Stefan Stoldt
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077 Göttingen, Germany (V.N.B.)
| | - Mariano L. Bossi
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research (MPI-MR), Jahnstrasse 29, 69120 Heidelberg, Germany;
| | - Vladimir N. Belov
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077 Göttingen, Germany (V.N.B.)
| | - Stefan W. Hell
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences (MPI-NAT), Am Fassberg 11, 37077 Göttingen, Germany (V.N.B.)
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research (MPI-MR), Jahnstrasse 29, 69120 Heidelberg, Germany;
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2
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Liu D, Pan L, Zhai H, Qiu HJ, Sun Y. Virus tracking technologies and their applications in viral life cycle: research advances and future perspectives. Front Immunol 2023; 14:1204730. [PMID: 37334362 PMCID: PMC10272434 DOI: 10.3389/fimmu.2023.1204730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
Viruses are simple yet highly pathogenic microorganisms that parasitize within cells and pose serious threats to the health, economic development, and social stability of both humans and animals. Therefore, it is crucial to understand the dynamic mechanism of virus infection in hosts. One effective way to achieve this is through virus tracking technology, which utilizes fluorescence imaging to track the life processes of virus particles in living cells in real-time, providing a comprehensively and detailed spatiotemporal dynamic process and mechanism of virus infection. This paper provides a broad overview of virus tracking technology, including the selection of fluorescent labels and virus labeling components, the development of imaging microscopes, and its applications in various virus studies. Additionally, we discuss the possibilities and challenges of its future development, offering theoretical guidance and technical support for effective prevention and control of the viral disease outbreaks and epidemics.
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Affiliation(s)
| | | | | | - Hua-Ji Qiu
- *Correspondence: Hua-Ji Qiu, ; Yuan Sun,
| | - Yuan Sun
- *Correspondence: Hua-Ji Qiu, ; Yuan Sun,
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3
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Choosing the Probe for Single-Molecule Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms232314949. [PMID: 36499276 PMCID: PMC9735909 DOI: 10.3390/ijms232314949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
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4
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Rémond E, Fehrentz J, Liénart L, Clément S, Banères J, Cavelier F. Fluorescent P‐Hydroxyphosphole for Peptide Labeling through P‐N Bond Formation. Chemistry 2022; 28:e202201526. [DOI: 10.1002/chem.202201526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Emmanuelle Rémond
- Institut des Biomolécules Max Mousseronm IBMM, UMR 5247 Pôle Chimie Balard 1919, route de Mende 34093 Montpellier cedex 5 France
| | - Jean‐Alain Fehrentz
- Institut des Biomolécules Max Mousseronm IBMM, UMR 5247 Pôle Chimie Balard 1919, route de Mende 34093 Montpellier cedex 5 France
| | - Laure Liénart
- Institut des Biomolécules Max Mousseronm IBMM, UMR 5247 Pôle Chimie Balard 1919, route de Mende 34093 Montpellier cedex 5 France
| | - Sébastien Clément
- Institut Charles Gerhardt Montpellier, ICGM, UMR 5253 Pôle Chimie Balard 1919, route de Mende 34093 Montpellier cedex 5 France
| | - Jean‐Louis Banères
- Institut des Biomolécules Max Mousseronm IBMM, UMR 5247 Pôle Chimie Balard 1919, route de Mende 34093 Montpellier cedex 5 France
| | - Florine Cavelier
- Institut des Biomolécules Max Mousseronm IBMM, UMR 5247 Pôle Chimie Balard 1919, route de Mende 34093 Montpellier cedex 5 France
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5
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Reddi RN, Rogel A, Resnick E, Gabizon R, Prasad PK, Gurwicz N, Barr H, Shulman Z, London N. Site-Specific Labeling of Endogenous Proteins Using CoLDR Chemistry. J Am Chem Soc 2021; 143:20095-20108. [PMID: 34817989 PMCID: PMC8662641 DOI: 10.1021/jacs.1c06167] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
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Chemical modifications
of native proteins can affect their stability,
activity, interactions, localization, and more. However, there are
few nongenetic methods for the installation of chemical modifications
at a specific protein site in cells. Here we report a covalent ligand
directed release (CoLDR) site-specific labeling strategy, which enables
the installation of a variety of functional tags on a target protein
while releasing the directing ligand. Using this approach, we were
able to label various proteins such as BTK, K-RasG12C,
and SARS-CoV-2 PLpro with different tags. For BTK we have
shown selective labeling in cells of both alkyne and fluorophores
tags. Protein labeling by traditional affinity methods often inhibits
protein activity since the directing ligand permanently occupies the
target binding pocket. We have shown that using CoLDR chemistry, modification
of BTK by these probes in cells preserves its activity. We demonstrated
several applications for this approach including determining the half-life
of BTK in its native environment with minimal perturbation, as well
as quantification of BTK degradation by a noncovalent proteolysis
targeting chimera (PROTAC) by in-gel fluorescence. Using an environment-sensitive
“turn-on” fluorescent probe, we were able to monitor
ligand binding to the active site of BTK. Finally, we have demonstrated
efficient CoLDR-based BTK PROTACs (DC50 < 100 nM), which
installed a CRBN binder onto BTK. This approach joins very few available
labeling strategies that maintain the target protein activity and
thus makes an important addition to the toolbox of chemical biology.
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Affiliation(s)
- Rambabu N Reddi
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Efrat Resnick
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Pragati Kishore Prasad
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Neta Gurwicz
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Barr
- Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ziv Shulman
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
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6
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Martynov VI, Pakhomov AA. BODIPY derivatives as fluorescent reporters of molecular activities in living cells. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Abstract
Fluorescent compounds have become indispensable tools for imaging molecular activities in the living cell. 4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) is currently one of the most popular fluorescent reporters due to its unique photophysical properties. This review provides a general survey and presents a summary of recent advances in the development of new BODIPY-based cellular biomarkers and biosensors. The review starts with the consideration of the properties of BODIPY derivatives required for their application as cellular reporters. Then review provides examples of the design of sensors for different biologically important molecules, ions, membrane potential, temperature and viscosity defining the live cell status. Special attention is payed to BODPY-based phototransformable reporters.
The bibliography includes 339 references.
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7
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Reiber T, Zavoiura O, Dose C, Yushchenko DA. Fluorophore Multimerization as an Efficient Approach towards Bright Protein Labels. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thorge Reiber
- Department of Chemical Biology Miltenyi Biotec B.V. & Co. KG Friedrich-Ebert Straße 68 51429 Bergisch Gladbach Germany
| | - Oleksandr Zavoiura
- Department of Chemical Biology Miltenyi Biotec B.V. & Co. KG Friedrich-Ebert Straße 68 51429 Bergisch Gladbach Germany
| | - Christian Dose
- Department of Chemical Biology Miltenyi Biotec B.V. & Co. KG Friedrich-Ebert Straße 68 51429 Bergisch Gladbach Germany
| | - Dmytro A. Yushchenko
- Department of Chemical Biology Miltenyi Biotec B.V. & Co. KG Friedrich-Ebert Straße 68 51429 Bergisch Gladbach Germany
- Laboratory of Chemical Biology The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo namesti 2 16610 Prague 6 Czech Republic
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8
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Wu D, Zhou J, Creyer MN, Yim W, Chen Z, Messersmith PB, Jokerst JV. Phenolic-enabled nanotechnology: versatile particle engineering for biomedicine. Chem Soc Rev 2021; 50:4432-4483. [PMID: 33595004 PMCID: PMC8106539 DOI: 10.1039/d0cs00908c] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phenolics are ubiquitous in nature and have gained immense research attention because of their unique physiochemical properties and widespread industrial use. In recent decades, their accessibility, versatile reactivity, and relative biocompatibility have catalysed research in phenolic-enabled nanotechnology (PEN) particularly for biomedical applications which have been a major benefactor of this emergence, as largely demonstrated by polydopamine and polyphenols. Therefore, it is imperative to overveiw the fundamental mechanisms and synthetic strategies of PEN for state-of-the-art biomedical applications and provide a timely and comprehensive summary. In this review, we will focus on the principles and strategies involved in PEN and summarize the use of the PEN synthetic toolkit for particle engineering and the bottom-up synthesis of nanohybrid materials. Specifically, we will discuss the attractive forces between phenolics and complementary structural motifs in confined particle systems to synthesize high-quality products with controllable size, shape, composition, as well as surface chemistry and function. Additionally, phenolic's numerous applications in biosensing, bioimaging, and disease treatment will be highlighted. This review aims to provide guidelines for new scientists in the field and serve as an up-to-date compilation of what has been achieved in this area, while offering expert perspectives on PEN's use in translational research.
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Affiliation(s)
- Di Wu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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9
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The HaloTag as a general scaffold for far-red tunable chemigenetic indicators. Nat Chem Biol 2021; 17:718-723. [PMID: 33795886 DOI: 10.1038/s41589-021-00775-w] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/19/2021] [Indexed: 12/16/2022]
Abstract
Functional imaging using fluorescent indicators has revolutionized biology, but additional sensor scaffolds are needed to access properties such as bright, far-red emission. Here, we introduce a new platform for 'chemigenetic' fluorescent indicators, utilizing the self-labeling HaloTag protein conjugated to environmentally sensitive synthetic fluorophores. We solve a crystal structure of HaloTag bound to a rhodamine dye ligand to guide engineering efforts to modulate the dye environment. We show that fusion of HaloTag with protein sensor domains that undergo conformational changes near the bound dye results in large and rapid changes in fluorescence output. This generalizable approach affords bright, far-red calcium and voltage sensors with highly tunable photophysical and chemical properties, which can reliably detect single action potentials in cultured neurons.
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10
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OwYong TC, Ding S, Wu N, Fellowes T, Chen S, White JM, Wong WWH, Hong Y. Optimising molecular rotors to AIE fluorophores for mitochondria uptake and retention. Chem Commun (Camb) 2020; 56:14853-14856. [PMID: 33174870 DOI: 10.1039/d0cc06411d] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular rotors exhibit fluorescence enhancement in a confined environment and thus have been used extensively in biological imaging. However, many molecular rotors suffer from small Stokes shift and self-aggregation caused quenching. In this work, we have synthesised a series of red emissive molecular rotors based on cationic α-cyanostilbene. Profoundly enhanced aggregation-induced emission (AIE) properties and greatly widened Stokes shifts can be achieved by molecular engineering. With specificity to stain mitochondria, we demonstrate a simple approach to achieve cell uptake and retention upon tuning the pyridinium substituent of the dyes.
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Affiliation(s)
- Tze Cin OwYong
- ARC Centre of Excellence in Exciton Science, School of Chemistry, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia. and Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
| | - Siyang Ding
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
| | - Na Wu
- ARC Centre of Excellence in Exciton Science, School of Chemistry, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Thomas Fellowes
- ARC Centre of Excellence in Exciton Science, School of Chemistry, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Sijie Chen
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong
| | - Jonathan M White
- ARC Centre of Excellence in Exciton Science, School of Chemistry, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Wallace W H Wong
- ARC Centre of Excellence in Exciton Science, School of Chemistry, Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Yuning Hong
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
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11
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Liu SL, Wang ZG, Xie HY, Liu AA, Lamb DC, Pang DW. Single-Virus Tracking: From Imaging Methodologies to Virological Applications. Chem Rev 2020; 120:1936-1979. [PMID: 31951121 PMCID: PMC7075663 DOI: 10.1021/acs.chemrev.9b00692] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Uncovering
the mechanisms of virus infection and assembly is crucial
for preventing the spread of viruses and treating viral disease. The
technique of single-virus tracking (SVT), also known as single-virus
tracing, allows one to follow individual viruses at different parts
of their life cycle and thereby provides dynamic insights into fundamental
processes of viruses occurring in live cells. SVT is typically based
on fluorescence imaging and reveals insights into previously unreported
infection mechanisms. In this review article, we provide the readers
a broad overview of the SVT technique. We first summarize recent advances
in SVT, from the choice of fluorescent labels and labeling strategies
to imaging implementation and analytical methodologies. We then describe
representative applications in detail to elucidate how SVT serves
as a valuable tool in virological research. Finally, we present our
perspectives regarding the future possibilities and challenges of
SVT.
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Affiliation(s)
- Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China.,Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , Wuhan 430074 , P. R. China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China
| | - Hai-Yan Xie
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , P. R. China
| | - An-An Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), and Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM) , Ludwig-Maximilians-Universität , München , 81377 , Germany
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China.,College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, The Institute for Advanced Studies, and Wuhan Institute of Biotechnology , Wuhan University , Wuhan 430072 , P. R. China
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12
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Single-molecule localization to study cytoskeletal structures, membrane complexes, and mechanosensors. Biophys Rev 2019; 11:745-756. [PMID: 31529362 DOI: 10.1007/s12551-019-00595-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/03/2019] [Indexed: 12/21/2022] Open
Abstract
In the last decades, a promising breakthrough in fluorescence imaging was represented by the advent of super-resolution microscopy (SRM). Super-resolution techniques recently became a popular method to study sub-cellular structures, providing a successful approach to observe cytoskeletal and focal adhesion proteins. Among the SR techniques, single-molecule localization microscopy plays a significant role due to its ability to unveil structures and molecular organizations in biological systems. Furthermore, since they provide information at the molecular level, these techniques are increasingly being used to study the stoichiometry and interaction between several membrane channel proteins and their accessory subunits. The aim of this review is to describe the single-molecule localization-based techniques and their applications relevant to cytoskeletal structures and membrane complexes in order to provide as future prospective an overall picture of their correlation with the mechanosensor channel expression and activity.
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13
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Ochtrop P, Ernst S, Itzen A, Hedberg C. Exploring the Substrate Scope of the Bacterial Phosphocholine Transferase AnkX for Versatile Protein Functionalization. Chembiochem 2019; 20:2336-2340. [PMID: 31054261 DOI: 10.1002/cbic.201900200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Indexed: 11/06/2022]
Abstract
Site-specific protein functionalization has become an indispensable tool in modern life sciences. Here, tag-based enzymatic protein functionalization techniques are among the most versatilely applicable approaches. However, many chemo-enzymatic functionalization strategies suffer from low substrate scopes of the enzymes utilized for functional labeling probes. We report on the wide substrate scope of the bacterial enzyme AnkX towards derivatized CDP-choline analogues and demonstrate that AnkX-catalyzed phosphocholination can be used for site-specific one- and two-step protein labeling with a broad array of different functionalities, displaying fast second-order transfer rates of 5×102 to 1.8×104 m-1 s-1 . Furthermore, we also present a strategy for the site-specific dual labeling of proteins of interest, based on the exploitation of AnkX and the delabeling function of the enzyme Lem3. Our results contribute to the wide field of protein functionalization, offering an attractive chemo-enzymatic tag-based modification strategy for in vitro labeling.
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Affiliation(s)
- Philipp Ochtrop
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
| | - Stefan Ernst
- Department of Biochemistry and Signal Transduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246, Hamburg, Germany
| | - Aymelt Itzen
- Department of Biochemistry and Signal Transduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246, Hamburg, Germany
| | - Christian Hedberg
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
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14
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Bräuer M, Zich MT, Önder K, Müller N. The influence of commonly used tags on structural propensities and internal dynamics of peptides. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-019-02401-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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15
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Brown ZP, Takagi J. Advances in domain and subunit localization technology for electron microscopy. Biophys Rev 2019; 11:149-155. [PMID: 30834502 DOI: 10.1007/s12551-019-00513-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 02/20/2019] [Indexed: 12/26/2022] Open
Abstract
The award of the 2017 Nobel Prize in chemistry, 'for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution', was recognition that this method, and electron microscopy more generally, represent powerful techniques in the scientific armamentarium for atomic level structural assessment. Technical advances in equipment, software, and sample preparation, have allowed for high-resolution structural determination of a range of complex biological machinery such that the position of individual atoms within these mega-structures can be determined. However, not all targets are amenable to attaining such high-resolution structures and some may only be resolved at so-called intermediate resolutions. In these cases, other tools are needed to correctly characterize the domain or subunit orientation and architecture. In this review, we will outline various methods that can provide additional information to help understand the macro-level organization of proteins/biomolecular complexes when high-resolution structural description is not available. In particular, we will discuss the recent development and use of a novel protein purification approach, known as the the PA tag/NZ-1 antibody system, which provides numberous beneficial properties, when used in electron microscopy experimentation.
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Affiliation(s)
- Zuben P Brown
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan
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16
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Gruβmayer KS, Yserentant K, Herten DP. Photons in - numbers out: perspectives in quantitative fluorescence microscopy for in situ protein counting. Methods Appl Fluoresc 2019; 7:012003. [DOI: 10.1088/2050-6120/aaf2eb] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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17
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Yu S, Du Z, Dong C, Ren J. In situ study of RSK2 kinase activity in a single living cell by combining single molecule spectroscopy with activity-based probes. Analyst 2019; 144:3756-3764. [DOI: 10.1039/c9an00178f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
FCS with the ABP strategy is a very promising method for studying endogenous protein kinases in living cells.
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Affiliation(s)
- Shengrong Yu
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Zhixue Du
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
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18
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Lee E, Min K, Chang YT, Kwon Y. Efficient and wash-free labeling of membrane proteins using engineered Npu DnaE split-inteins. Protein Sci 2018; 27:1568-1574. [PMID: 30151847 DOI: 10.1002/pro.3455] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
An efficient and wash-free method to conjugate a fluorescent tag to a target membrane protein is developed, using engineered Npu DnaE split-inteins. This approach allowed fast labeling while avoiding the strenuous synthesis of a long polypeptide. Two different modes of labeling, namely specific binding and covalent conjugation, are observed. The covalent labeling was monitored within 5 min, without background staining.
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Affiliation(s)
- Euiyeon Lee
- Department of Biomedical Engineering, Dongguk University, Seoul, 04620, South Korea
| | - Kyoungmi Min
- Department of Biomedical Engineering, Dongguk University, Seoul, 04620, South Korea
| | - Young-Tae Chang
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, South Korea.,Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Youngeun Kwon
- Department of Biomedical Engineering, Dongguk University, Seoul, 04620, South Korea
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19
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Billerbeck S. Small Functional Peptides and Their Application in Superfunctionalizing Proteins. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Sonja Billerbeck
- Columbia University; Department of Chemistry; 550 West 120th Street New York NY 10027 USA
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20
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Baalmann M, Best M, Wombacher R. Site-Specific Protein Labeling Utilizing Lipoic Acid Ligase (LplA) and Bioorthogonal Inverse Electron Demand Diels-Alder Reaction. Methods Mol Biol 2018; 1728:365-387. [PMID: 29405010 DOI: 10.1007/978-1-4939-7574-7_23] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Here, we describe a two-step protocol for selective protein labeling based on enzyme-mediated peptide labeling utilizing lipoic acid ligase (LplA) and bioorthogonal chemistry. The method can be applied to purified proteins, protein in cell lysates, as well as living cells. In a first step a W37V mutant of the lipoic acid ligase (LplAW37V) from Escherichia coli is utilized to ligate a synthetic chemical handle site-specifically to a lysine residue in a 13 amino acid peptide motif-a short sequence that can be genetically expressed as a fusion with any protein of interest. In a second step, a molecular probe can be attached to the chemical handle in a bioorthogonal Diels-Alder reaction with inverse electron demand (DAinv). This method is a complementary approach to protein labeling using genetic code expansion and circumvents larger protein tags while maintaining label specificity, providing experimental flexibility and straightforwardness.
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Affiliation(s)
- Mathis Baalmann
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Marcel Best
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany.
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21
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Klementieva NV, Bozhanova NG, Zagaynova EV, Lukyanov KA, Mishin AS. Fluorophores for single-molecule localization microscopy. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017030074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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22
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Chang JB, Chen F, Yoon YG, Jung EE, Babcock H, Kang JS, Asano S, Suk HJ, Pak N, Tillberg PW, Wassie A, Cai D, Boyden ES. Iterative expansion microscopy. Nat Methods 2017; 14:593-599. [PMID: 28417997 PMCID: PMC5560071 DOI: 10.1038/nmeth.4261] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 03/20/2017] [Indexed: 12/24/2022]
Abstract
We recently developed a method called expansion microscopy, in which preserved biological specimens are physically magnified by embedding them in a densely crosslinked polyelectrolyte gel, anchoring key labels or biomolecules to the gel, mechanically homogenizing the specimen, and then swelling the gel-specimen composite by ∼4.5× in linear dimension. Here we describe iterative expansion microscopy (iExM), in which a sample is expanded ∼20×. After preliminary expansion a second swellable polymer mesh is formed in the space newly opened up by the first expansion, and the sample is expanded again. iExM expands biological specimens ∼4.5 × 4.5, or ∼20×, and enables ∼25-nm-resolution imaging of cells and tissues on conventional microscopes. We used iExM to visualize synaptic proteins, as well as the detailed architecture of dendritic spines, in mouse brain circuitry.
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Affiliation(s)
- Jae-Byum Chang
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Biomedical Engineering, Sungkyunkwan University, Seoul, Korea
| | - Fei Chen
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Young-Gyu Yoon
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Erica E. Jung
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Hazen Babcock
- Harvard Center for Advanced Imaging, Harvard University, Cambridge, MA, USA
| | | | - Shoh Asano
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Ho-Jun Suk
- Health Sciences and Technology, MIT, Cambridge, MA, USA
| | - Nikita Pak
- Department of Mechanical Engineering, MIT, Cambridge, MA, USA
| | - Paul W. Tillberg
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Asmamaw Wassie
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Dawen Cai
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Edward S. Boyden
- Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- McGovern Institute, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
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23
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Wieczorek A, Werther P, Euchner J, Wombacher R. Green- to far-red-emitting fluorogenic tetrazine probes - synthetic access and no-wash protein imaging inside living cells. Chem Sci 2017; 8:1506-1510. [PMID: 28572909 PMCID: PMC5452268 DOI: 10.1039/c6sc03879d] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/19/2016] [Indexed: 12/23/2022] Open
Abstract
Fluorogenic probes for bioorthogonal labeling chemistry are highly beneficial to reduce background signal in fluorescence microscopy imaging. 1,2,4,5-Tetrazines are known substrates for the bioorthogonal inverse electron demand Diels-Alder reaction (DAinv) and tetrazine substituted fluorophores can exhibit fluorogenic properties. Herein, we report the synthesis of a palette of novel fluorogenic tetrazine dyes derived from widely-used fluorophores that cover the entire emission range from green to far-red. We demonstrate the power of the new fluorogenic probes in fixed and live cell labeling experiments and present the first example of intracellular live cell protein imaging using tetrazine-based probes under no-wash conditions.
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Affiliation(s)
- Achim Wieczorek
- Institut für Pharmazie und Molekulare Biotechnologie , Ruprecht-Karls-Universität Heidelberg , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany .
| | - Philipp Werther
- Institut für Pharmazie und Molekulare Biotechnologie , Ruprecht-Karls-Universität Heidelberg , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany .
| | - Jonas Euchner
- Institut für Pharmazie und Molekulare Biotechnologie , Ruprecht-Karls-Universität Heidelberg , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany .
| | - Richard Wombacher
- Institut für Pharmazie und Molekulare Biotechnologie , Ruprecht-Karls-Universität Heidelberg , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany .
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24
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Del Secco B, Malachin G, Milli L, Zanna N, Papini E, Cornia A, Tavano R, Tomasini C. Form Matters: Stable Helical Foldamers Preferentially Target Human Monocytes and Granulocytes. ChemMedChem 2017; 12:337-345. [DOI: 10.1002/cmdc.201600597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Benedetta Del Secco
- Dipartimento di Chimica Ciamician; Alma Mater Studiorum Università di Bologna; Via Selmi 2 40126 Bologna Italy
| | - Giulia Malachin
- Dipartimento di Scienze Biomediche; Università di Padova; Viale G. Colombo 3 35121 Padova Italy
| | - Lorenzo Milli
- Dipartimento di Chimica Ciamician; Alma Mater Studiorum Università di Bologna; Via Selmi 2 40126 Bologna Italy
| | - Nicola Zanna
- Dipartimento di Chimica Ciamician; Alma Mater Studiorum Università di Bologna; Via Selmi 2 40126 Bologna Italy
| | - Emanuele Papini
- Dipartimento di Scienze Biomediche; Università di Padova; Viale G. Colombo 3 35121 Padova Italy
| | - Andrea Cornia
- Dipartimento di Scienze Chimiche e Geologiche; Università di Modena e Reggio Emilia & INSTM; Via G. Campi 103 41125 Modena Italy
| | - Regina Tavano
- Dipartimento di Scienze Biomediche; Università di Padova; Viale G. Colombo 3 35121 Padova Italy
| | - Claudia Tomasini
- Dipartimento di Chimica Ciamician; Alma Mater Studiorum Università di Bologna; Via Selmi 2 40126 Bologna Italy
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25
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Hauke S, von Appen A, Quidwai T, Ries J, Wombacher R. Specific protein labeling with caged fluorophores for dual-color imaging and super-resolution microscopy in living cells. Chem Sci 2017; 8:559-566. [PMID: 28451202 PMCID: PMC5351804 DOI: 10.1039/c6sc02088g] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/01/2016] [Indexed: 01/10/2023] Open
Abstract
We present new fluorophore-conjugates for dual-color photoactivation and super-resolution imaging inside live mammalian cells. These custom-designed, photo-caged Q-rhodamines and fluoresceins are cell-permeable, bright and localize specifically to intracellular targets. We utilized established orthogonal protein labeling strategies to precisely attach the photoactivatable fluorophores to proteins with subsequent activation of fluorescence by irradiation with UV light. That way, diffusive cytosolic proteins, histone proteins as well as filigree mitochondrial networks and focal adhesion proteins were visualized inside living cells. We applied the new photoactivatable probes in inverse fluorescence recovery after photo-bleaching (iFRAP) experiments, gaining real-time access to protein dynamics from live biological settings with resolution in space and time. Finally, we used the caged Q-rhodamine for photo-activated localization microscopy (PALM) on both fixed and live mammalian cells, where the superior molecular brightness and photo-stability directly resulted in improved localization precisions for different protein targets.
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Affiliation(s)
- Sebastian Hauke
- Institute of Pharmacy and Molecular Biotechnology , Ruprecht-Karls-University Heidelberg , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany . ; ; Tel: +49 6221 544879
| | - Alexander von Appen
- Institute of Pharmacy and Molecular Biotechnology , Ruprecht-Karls-University Heidelberg , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany . ; ; Tel: +49 6221 544879
| | - Tooba Quidwai
- European Molecular Biology Laboratory , Meyerhofstraße 1 , 69117 Heidelberg , Germany
| | - Jonas Ries
- European Molecular Biology Laboratory , Meyerhofstraße 1 , 69117 Heidelberg , Germany
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology , Ruprecht-Karls-University Heidelberg , Im Neuenheimer Feld 364 , 69120 Heidelberg , Germany . ; ; Tel: +49 6221 544879
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26
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De Clercq DJH, Tavernier J, Lievens S, Van Calenbergh S. Chemical Dimerizers in Three-Hybrid Systems for Small Molecule-Target Protein Profiling. ACS Chem Biol 2016; 11:2075-90. [PMID: 27267544 DOI: 10.1021/acschembio.5b00811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The identification of the molecular targets and mechanisms underpinning the beneficial or detrimental effects of small-molecule leads and drugs constitutes a crucial aspect of current drug discovery. Over the last two decades, three-hybrid (3H) systems have progressively taken an important position in the armamentarium of small molecule-target protein profiling technologies. Yet, a prerequisite for successful 3H analysis is the availability of appropriate chemical inducers of dimerization. Herein, we present a comprehensive and critical overview of the chemical dimerizers specifically applied in both yeast and mammalian three-hybrid systems for small molecule-target protein profiling within the broader scope of target deconvolution and drug discovery. Furthermore, examples and alternative suggestions for typical components of chemical dimerizers for 3H systems are discussed. As illustrated, more tools have become available that increase the sensitivity and efficiency of 3H-based screening platforms. Hence, it is anticipated that the great potential of 3H systems will further materialize in important contributions to drug discovery.
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Affiliation(s)
- Dries J. H. De Clercq
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Jan Tavernier
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sam Lievens
- Department
of Medical Protein Research, Vlaams Instituut voor Biotechnologie, 9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Serge Van Calenbergh
- Laboratory
for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
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27
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Chen X, Li F, Wu YW. Chemical labeling of intracellular proteins via affinity conjugation and strain-promoted cycloadditions in live cells. Chem Commun (Camb) 2016; 51:16537-40. [PMID: 26421329 DOI: 10.1039/c5cc05208d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A versatile chemical labeling approach was developed, where intracellular proteins were first incorporated with a bioorthogonal group via affinity conjugation, and subsequently labeled via strain-promoted cycloaddition reactions in live cells.
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Affiliation(s)
- Xi Chen
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund, Germany. and Max-Planck Institute for Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Fu Li
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund, Germany. and Max-Planck Institute for Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund, Germany. and Max-Planck Institute for Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
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28
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Baranczak A, Connelly S, Liu Y, Choi S, Grimster NP, Powers ET, Wilson IA, Kelly JW. Fluorogenic small molecules requiring reaction with a specific protein to create a fluorescent conjugate for biological imaging--what we know and what we need to learn. Biopolymers 2016; 101:484-95. [PMID: 24105107 DOI: 10.1002/bip.22407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/03/2013] [Indexed: 01/03/2023]
Abstract
We seek fluorogenic small molecules that generate a fluorescent conjugate signal if and only if they react with a given protein-of-interest (i.e., small molecules for which noncovalent binding to the protein-of-interest is insufficient to generate fluorescence). Consequently, it is the new chemical entity afforded by the generally irreversible reaction between the small molecule and the protein-of-interest that enables the energy of an electron occupying the lowest unoccupied molecular orbital (LUMO) of the chromophore to be given off as a photon instead of being dissipated by nonradiative mechanisms in complex biological environments. This category of fluorogenic small molecules is created by starting with environmentally sensitive fluorophores that are modified by an essential functional group that efficiently quenches the fluorescence until a chemoselective reaction between that functional group and the protein-of-interest occurs, yielding the fluorescent conjugate. Fluorogenic small molecules are envisioned to be useful for a wide variety of applications, including live cell imaging without the requirement for washing steps and pulse-chase kinetic analyses of protein synthesis, trafficking, degradation, etc.
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Affiliation(s)
- Aleksandra Baranczak
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, 92037
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29
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Specific cell surface labeling of GPCRs using split GFP. Sci Rep 2016; 6:20568. [PMID: 26857153 PMCID: PMC4746647 DOI: 10.1038/srep20568] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/07/2016] [Indexed: 01/13/2023] Open
Abstract
Specific cell surface labeling is essential for visualizing the internalization processes of G-protein coupled receptors (GPCRs) and for gaining mechanistic insight of GPCR functions. Here we present a rapid, specific, and versatile labeling scheme for GPCRs at living-cell membrane with the use of a split green fluorescent protein (GFP). Demonstrated with two GPCRs, GPR17 and CysLT2R, we show that two β-stands (β-stands 10 and 11) derived from a superfolder GFP (sfGFP) can be engineered to one of the three extracellular loop of a GPCR. The complementary fragment of sfGFP has nine β-strands (β-stands 1-9) that carries the mature fluorophore, and can be proteolytically derived from the full-length sfGFP. Separately the GFP fragments are non-fluorescent, but become fluorescent upon assembly, thus allowing specific labeling of the target proteins. The two GFP fragments rapidly assemble and the resulting complex is extremely tight under non-denaturing conditions, which allows real-time and quantitative assessment of the internalized GPCRs. We envision that this labeling scheme will be of great use for labeling other membrane proteins in various biological and pharmacological applications.
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30
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Schmidt TT, Hombauer H. Visualization of mismatch repair complexes using fluorescence microscopy. DNA Repair (Amst) 2016; 38:58-67. [DOI: 10.1016/j.dnarep.2015.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/30/2015] [Accepted: 11/30/2015] [Indexed: 11/15/2022]
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31
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Söveges B, Imre T, Szende T, Póti ÁL, Cserép GB, Hegedűs T, Kele P, Németh K. A systematic study of protein labeling by fluorogenic probes using cysteine targeting vinyl sulfone-cyclooctyne tags. Org Biomol Chem 2016; 14:6071-8. [DOI: 10.1039/c6ob00810k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Protein labeling by cycloocytynylated vinyl sulfone linkers is fast and thiol-selective, and subsequent click reaction with fluorogenic azides generates intensive fluorescence.
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Affiliation(s)
- B. Söveges
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Organic Chemistry
- Chemical Biology Research Group
- Hungary
| | - T. Imre
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Organic Chemistry
- MS Metabolomics Research Group
- Hungary
| | - T. Szende
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Organic Chemistry
- Chemical Biology Research Group
- Hungary
| | - Á. L. Póti
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Enzymology
- Protein Research Group
- Hungary
| | - G. B. Cserép
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Organic Chemistry
- Chemical Biology Research Group
- Hungary
| | - T. Hegedűs
- MTA-SE Molecular Biophysics Research Group
- Department of Biophysics and Radiation Biology
- Semmelweis University
- Tuzolto u. 37-47
- H-1094 Budapest
| | - P. Kele
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Organic Chemistry
- Chemical Biology Research Group
- Hungary
| | - K. Németh
- Research Centre for Natural Sciences of Hungarian Academy of Sciences
- Institute of Organic Chemistry
- Chemical Biology Research Group
- Hungary
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32
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Todorovski T, Suñol D, Riera A, Macias MJ. Addition of HOBt improves the conversion of thioester-Amine chemical ligation. Biopolymers 2015; 104:693-702. [PMID: 26396113 DOI: 10.1002/bip.22745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/10/2015] [Accepted: 09/18/2015] [Indexed: 11/07/2022]
Abstract
The syntheses of large peptides and of those containing non-natural amino acids can be facilitated by the application of convergent approaches, dissecting the native sequence into segments connected through a ligation reaction. We describe an improvement of the ligation protocol used to prepare peptides and proteins without cysteine residues at the ligation junction. We have found that the addition of HOBt to the ligation, improves the conversion of the ligation reaction without affecting the epimerization rate or chemoselectivity, and it can be efficiently used with peptides containing phosphorylated amino acids.
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Affiliation(s)
- Toni Todorovski
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - David Suñol
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.,Departament de Química Orgànica, University of Barcelona, Martí i Franquès, 1, Barcelona, 08028, Spain
| | - Maria J Macias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys, Barcelona, 23 08010, Spain
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33
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Uno SN, Tiwari DK, Kamiya M, Arai Y, Nagai T, Urano Y. A guide to use photocontrollable fluorescent proteins and synthetic smart fluorophores for nanoscopy. Microscopy (Oxf) 2015; 64:263-77. [PMID: 26152215 DOI: 10.1093/jmicro/dfv037] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/12/2015] [Indexed: 12/28/2022] Open
Abstract
Recent advances in nanoscopy, which breaks the diffraction barrier and can visualize structures smaller than the diffraction limit in cells, have encouraged biologists to investigate cellular processes at molecular resolution. Since nanoscopy depends not only on special optics but also on 'smart' photophysical properties of photocontrollable fluorescent probes, including photoactivatability, photoswitchability and repeated blinking, it is important for biologists to understand the advantages and disadvantages of fluorescent probes and to choose appropriate ones for their specific requirements. Here, we summarize the characteristics of currently available fluorescent probes based on both proteins and synthetic compounds applicable to nanoscopy and provide a guideline for selecting optimal probes for specific applications.
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Affiliation(s)
- Shin-Nosuke Uno
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Dhermendra K Tiwari
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Yoshiyuki Arai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Takeharu Nagai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Yasuteru Urano
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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34
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Halpern AR, Howard MD, Vaughan JC. Point by Point: An Introductory Guide to Sample Preparation for Single-Molecule, Super-Resolution Fluorescence Microscopy. ACTA ACUST UNITED AC 2015; 7:103-20. [DOI: 10.1002/9780470559277.ch140241] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Aaron R. Halpern
- Department of Chemistry, University of Washington; Seattle Washington
| | - Marco D. Howard
- Department of Chemistry, University of Washington; Seattle Washington
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington; Seattle Washington
- Department of Physiology and Biophysics, University of Washington; Seattle Washington
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35
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Best M, Degen A, Baalmann M, Schmidt TT, Wombacher R. Two-step protein labeling by using lipoic acid ligase with norbornene substrates and subsequent inverse-electron demand Diels-Alder reaction. Chembiochem 2015; 16:1158-62. [PMID: 25900689 DOI: 10.1002/cbic.201500042] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 12/24/2022]
Abstract
Inverse-electron-demand Diels-Alder cycloaddition (DAinv ) between strained alkenes and tetrazines is a highly bio-orthogonal reaction that has been applied in the specific labeling of biomolecules. In this work we present a two-step labeling protocol for the site-specific labeling of proteins based on attachment of a highly stable norbornene derivative to a specific peptide sequence by using a mutant of the enzyme lipoic acid ligase A (LplA(W37V) ), followed by the covalent attachment of tetrazine-modified fluorophores to the norbornene moiety through the bio-orthogonal DAinv . We investigated 15 different norbornene derivatives for their selective enzymatic attachment to a 13-residue lipoic acid acceptor peptide (LAP) by using a standardized HPLC protocol. Finally, we used this two-step labeling strategy to label proteins in cell lysates in a site-specific manner and performed cell-surface labeling on living cells.
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Affiliation(s)
- Marcel Best
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany)
| | - Anna Degen
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany)
| | - Mathis Baalmann
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany)
| | - Tobias T Schmidt
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany)
| | - Richard Wombacher
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg (Germany).
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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Marchetti L, Luin S, Bonsignore F, de Nadai T, Beltram F, Cattaneo A. Ligand-induced dynamics of neurotrophin receptors investigated by single-molecule imaging approaches. Int J Mol Sci 2015; 16:1949-79. [PMID: 25603178 PMCID: PMC4307343 DOI: 10.3390/ijms16011949] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 01/05/2015] [Indexed: 01/14/2023] Open
Abstract
Neurotrophins are secreted proteins that regulate neuronal development and survival, as well as maintenance and plasticity of the adult nervous system. The biological activity of neurotrophins stems from their binding to two membrane receptor types, the tropomyosin receptor kinase and the p75 neurotrophin receptors (NRs). The intracellular signalling cascades thereby activated have been extensively investigated. Nevertheless, a comprehensive description of the ligand-induced nanoscale details of NRs dynamics and interactions spanning from the initial lateral movements triggered at the plasma membrane to the internalization and transport processes is still missing. Recent advances in high spatio-temporal resolution imaging techniques have yielded new insight on the dynamics of NRs upon ligand binding. Here we discuss requirements, potential and practical implementation of these novel approaches for the study of neurotrophin trafficking and signalling, in the framework of current knowledge available also for other ligand-receptor systems. We shall especially highlight the correlation between the receptor dynamics activated by different neurotrophins and the respective signalling outcome, as recently revealed by single-molecule tracking of NRs in living neuronal cells.
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Affiliation(s)
- Laura Marchetti
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Stefano Luin
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Fulvio Bonsignore
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Teresa de Nadai
- Biology Laboratory (BioSNS), Scuola Normale Superiore and Istituto di Neuroscienze-CNR, via Moruzzi 1, Pisa I-56100, Italy.
| | - Fabio Beltram
- National Enterprise for nanoScience and nanoTechnology (NEST) Laboratory, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa I-56127, Italy.
| | - Antonino Cattaneo
- Biology Laboratory (BioSNS), Scuola Normale Superiore and Istituto di Neuroscienze-CNR, via Moruzzi 1, Pisa I-56100, Italy.
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Marchetti L, De Nadai T, Bonsignore F, Calvello M, Signore G, Viegi A, Beltram F, Luin S, Cattaneo A. Site-specific labeling of neurotrophins and their receptors via short and versatile peptide tags. PLoS One 2014; 9:e113708. [PMID: 25426999 PMCID: PMC4245215 DOI: 10.1371/journal.pone.0113708] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/28/2014] [Indexed: 01/29/2023] Open
Abstract
We present a toolbox for the study of molecular interactions occurring between NGF and its receptors. By means of a suitable insertional mutagenesis method we show the insertion of an 8 amino acid tag (A4) into the sequence of NGF and of 12 amino acid tags (A1 and S6) into the sequence of TrkA and P75NTR NGF-receptors. These tags are shortened versions of the acyl and peptidyl carrier proteins; they are here covalently conjugated to the biotin-substituted arm of a coenzyme A (coA) substrate by phosphopantetheinyl transferase enzymes (PPTases). We demonstrate site-specific biotinylation of the purified recombinant tagged neurotrophin, in both the immature proNGF and mature NGF forms. The resulting tagged NGF is fully functional: it can signal and promote PC12 cells differentiation similarly to recombinant wild-type NGF. Furthermore, we show that the insertion of A1 and S6 tags into human TrkA and P75NTR sequences leads to the site-specific biotinylation of these receptors at the cell surface of living cells. Crucially, the two tags are labeled selectively by two different PPTases: this is exploited to reach orthogonal fluorolabeling of the two receptors co-expressed at low density in living cells. We describe the protocols to obtain the enzymatic, site-specific biotinylation of neurotrophins and their receptors as an alternative to their chemical, nonspecific biotinylation. The present strategy has three main advantages: i) it yields precise control of stoichiometry and site of biotin conjugation; ii) the tags used can be functionalized with virtually any small probe that can be carried by coA substrates, besides (and in addition to) biotin; iii) above all it makes possible to image and track interacting molecules at the single-molecule level in living systems.
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Affiliation(s)
- Laura Marchetti
- NEST, Scuola Normale Superiore and Istituto Nanoscienze – CNR, Pisa, Italy
- BioSNS Laboratory, Scuola Normale Superiore and Istituto di Neuroscienze - CNR, Pisa, Italy
| | - Teresa De Nadai
- BioSNS Laboratory, Scuola Normale Superiore and Istituto di Neuroscienze - CNR, Pisa, Italy
| | - Fulvio Bonsignore
- NEST, Scuola Normale Superiore and Istituto Nanoscienze – CNR, Pisa, Italy
| | | | | | - Alessandro Viegi
- BioSNS Laboratory, Scuola Normale Superiore and Istituto di Neuroscienze - CNR, Pisa, Italy
| | - Fabio Beltram
- NEST, Scuola Normale Superiore and Istituto Nanoscienze – CNR, Pisa, Italy
- IIT@NEST, Center for Nanotechnology Innovation, Pisa, Italy
| | - Stefano Luin
- NEST, Scuola Normale Superiore and Istituto Nanoscienze – CNR, Pisa, Italy
- * E-mail: (SL); (AC)
| | - Antonino Cattaneo
- BioSNS Laboratory, Scuola Normale Superiore and Istituto di Neuroscienze - CNR, Pisa, Italy
- * E-mail: (SL); (AC)
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Abstract
Gut microbes play a key role in human health and nutrition by catabolizing a wide variety of glycans via enzymatic activities that are not encoded in the human genome. The ability to recognize and process carbohydrates strongly influences the structure of the gut microbial community. While the effects of diet on the microbiota are well documented, little is known about the molecular processes driving metabolism. To provide mechanistic insight into carbohydrate catabolism in gut symbionts, we studied starch processing in real time in the model Bacteroides thetaiotaomicron starch utilization system (Sus) by single-molecule fluorescence. Although previous studies have explored Sus protein structure and function, the transient interactions, assembly, and collaboration of these outer membrane proteins have not yet been elucidated in live cells. Our live-cell superresolution imaging reveals that the polymeric starch substrate dynamically recruits Sus proteins, serving as an external scaffold for bacterial membrane assembly of the Sus complex, which may promote efficient capturing and degradation of starch. Furthermore, by simultaneously localizing multiple Sus outer membrane proteins on the B. thetaiotaomicron cell surface, we have characterized the dynamics and stoichiometry of starch-induced Sus complex assembly on the molecular scale. Finally, based on Sus protein knockout strains, we have discerned the mechanism of starch-induced Sus complex assembly in live anaerobic cells with nanometer-scale resolution. Our insights into the starch-induced outer membrane protein assembly central to this conserved nutrient uptake mechanism pave the way for the development of dietary or pharmaceutical therapies to control Bacteroidetes in the intestinal tract to enhance human health and treat disease. In this study, we used nanometer-scale superresolution imaging to reveal dynamic interactions between the proteins involved in starch processing by the prominent human gut symbiont Bacteroides thetaiotaomicron in real time in live cells. These results represent the first working model of starch utilization system (Sus) complex assembly and function during glycan catabolism and are likely to describe aspects of how other Sus-like systems function in human gut Bacteroidetes. Our results provide unique mechanistic insights into a glycan catabolism strategy that is prevalent within the human gut microbial community. Proper understanding of this conserved nutrient uptake mechanism is essential for the development of dietary or pharmaceutical therapies to control intestinal tract microbial populations, to enhance human health, and to treat disease.
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Di Maria F, Palamà IE, Baroncini M, Barbieri A, Bongini A, Bizzarri R, Gigli G, Barbarella G. Live cell cytoplasm staining and selective labeling of intracellular proteins by non-toxic cell-permeant thiophene fluorophores. Org Biomol Chem 2014; 12:1603-10. [PMID: 24469410 DOI: 10.1039/c3ob41982g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A structurally correlated series of cell-permeant thiophene fluorophores, characterized by intense green or red fluorescence inside live mouse embryonic fibroblasts, was developed. The fluorophores displayed rapid internalization, excellent retention inside the cells, and high optical stability in the cytosolic environment and did not alter cell viability and reproducibility. Depending on the molecular structure, they experienced distinct fate inside the cells: from bright and lasting staining of the cytoplasm to selective tagging of a small set of globular proteins.
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Affiliation(s)
- F Di Maria
- Laboratorio MIST.E-R, National Research Council, Via Gobetti 101, I-40129 Bologna, Italy
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41
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Wieneke R, Labòria N, Rajan M, Kollmannsperger A, Natale F, Cardoso MC, Tampé R. Live-cell targeting of his-tagged proteins by multivalent N-nitrilotriacetic acid carrier complexes. J Am Chem Soc 2014; 136:13975-8. [PMID: 25238106 DOI: 10.1021/ja5063357] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Selective and fast labeling of proteins in living cells is a major challenge. Live-cell labeling techniques require high specificity, high labeling density, and cell permeability of the tagging molecule to target the protein of interest. Here we report on the site-specific, rapid, and efficient labeling of endogenous and recombinant histidine-tagged proteins in distinct subcellular compartments using cell-penetrating multivalent chelator carrier complexes. In vivo labeling was followed in real time in living cells, demonstrating a high specificity and high degree of colocalization in the crowded cellular environment.
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Affiliation(s)
- Ralph Wieneke
- Institute of Biochemistry, Goethe-University Frankfurt , Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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42
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Hayashi-Takanaka Y, Stasevich TJ, Kurumizaka H, Nozaki N, Kimura H. Evaluation of chemical fluorescent dyes as a protein conjugation partner for live cell imaging. PLoS One 2014; 9:e106271. [PMID: 25184362 PMCID: PMC4153647 DOI: 10.1371/journal.pone.0106271] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/04/2014] [Indexed: 12/11/2022] Open
Abstract
To optimize live cell fluorescence imaging, the choice of fluorescent substrate is a critical factor. Although genetically encoded fluorescent proteins have been used widely, chemical fluorescent dyes are still useful when conjugated to proteins or ligands. However, little information is available for the suitability of different fluorescent dyes for live imaging. We here systematically analyzed the property of a number of commercial fluorescent dyes when conjugated with antigen-binding (Fab) fragments directed against specific histone modifications, in particular, phosphorylated H3S28 (H3S28ph) and acetylated H3K9 (H3K9ac). These Fab fragments were conjugated with a fluorescent dye and loaded into living HeLa cells. H3S28ph-specific Fab fragments were expected to be enriched in condensed chromosomes, as H3S28 is phosphorylated during mitosis. However, the degree of Fab fragment enrichment on mitotic chromosomes varied depending on the conjugated dye. In general, green fluorescent dyes showed higher enrichment, compared to red and far-red fluorescent dyes, even when dye∶protein conjugation ratios were similar. These differences are partly explained by an altered affinity of Fab fragment after dye-conjugation; some dyes have less effect on the affinity, while others can affect it more. Moreover, red and far-red fluorescent dyes tended to form aggregates in the cytoplasm. Similar results were observed when H3K9ac-specific Fab fragments were used, suggesting that the properties of each dye affect different Fab fragments similarly. According to our analysis, conjugation with green fluorescent dyes, like Alexa Fluor 488 and Dylight 488, has the least effect on Fab affinity and is the best for live cell imaging, although these dyes are less photostable than red fluorescent dyes. When multicolor imaging is required, we recommend the following dye combinations for optimal results: Alexa Fluor 488 (green), Cy3 (red), and Cy5 or CF640 (far-red).
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Affiliation(s)
- Yoko Hayashi-Takanaka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Timothy J. Stasevich
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | | | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
- * E-mail:
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43
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Wang TY, Friedman LJ, Gelles J, Min W, Hoskins AA, Cornish VW. The covalent trimethoprim chemical tag facilitates single molecule imaging with organic fluorophores. Biophys J 2014; 106:272-8. [PMID: 24411259 DOI: 10.1016/j.bpj.2013.11.4488] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/05/2013] [Accepted: 11/25/2013] [Indexed: 11/24/2022] Open
Abstract
Chemical tags can be used to selectively label proteins with fluorophores that have high photon outputs. By permitting straightforward single molecule (SM) detection and imaging with organic fluorophores, chemical tags have the potential to advance SM imaging as a routine experimental tool for studying biological mechanism. However, there has been little characterization of the photophysical consequences of using chemical tags with organic fluorophores. Here, we examine the effect the covalent trimethoprim chemical tag (A-TMP-tag) has on the SM imaging performance of the fluorophores, Atto655 and Alexa647, by evaluating the photophysical properties of these fluorophores and their A-TMP-tag conjugates. We measure SM photon flux, survival lifetime, and total photon output under conditions that mimic the live cell environment and demonstrate that the A-TMP-tag complements the advantageous SM imaging properties of Atto655 and Alexa647. We also measure the ensemble properties of quantum yield and photostability lifetime, revealing a correlation between SM and ensemble properties. Taken together, these findings establish a systematic method for evaluating the impact chemical tags have on fluorophores for SM imaging and demonstrate that the A-TMP-tag with Atto655 and Alexa647 are promising reagents for biological imaging.
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Affiliation(s)
- Tracy Y Wang
- Department of Chemistry, Columbia University, New York, New York
| | - Larry J Friedman
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts
| | - Wei Min
- Department of Chemistry, Columbia University, New York, New York
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin
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44
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Hauke S, Best M, Schmidt TT, Baalmann M, Krause A, Wombacher R. Two-step protein labeling utilizing lipoic acid ligase and Sonogashira cross-coupling. Bioconjug Chem 2014; 25:1632-7. [PMID: 25152073 DOI: 10.1021/bc500349h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Labeling proteins in their natural settings with fluorescent proteins or protein tags often leads to problems. Despite the high specificity, these methods influence the natural functions due to the rather large size of the proteins used. Here we present a two-step labeling procedure for the attachment of various fluorescent probes to a small peptide sequence (13 amino acids) using enzyme-mediated peptide labeling in combination with palladium-catalyzed Sonogashira cross-coupling. We identified p-iodophenyl derivatives from a small library that can be covalently attached to a lysine residue within a specific 13-amino-acid peptide sequence by Escherichia coli lipoic acid ligase A (LplA). The derivatization with p-iodophenyl subsequently served as a reactive handle for bioorthogonal transition metal-catalyzed Sonogashira cross-coupling with alkyne-functionalized fluorophores on both the peptide as well as on the protein level. Our two-step labeling strategy combines high selectivity of enzyme-mediated labeling with the chemoselectivity of palladium-catalyzed Sonogashira cross-coupling.
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Affiliation(s)
- Sebastian Hauke
- Institute for Pharmacy and Molecular Biotechnology, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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45
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Ichimura T, Jin T, Fujita H, Higuchi H, Watanabe TM. Nano-scale measurement of biomolecules by optical microscopy and semiconductor nanoparticles. Front Physiol 2014; 5:273. [PMID: 25120488 PMCID: PMC4114191 DOI: 10.3389/fphys.2014.00273] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/05/2014] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, great developments in optical microscopy have made this technology increasingly compatible with biological studies. Fluorescence microscopy has especially contributed to investigating the dynamic behaviors of live specimens and can now resolve objects with nanometer precision and resolution due to super-resolution imaging. Additionally, single particle tracking provides information on the dynamics of individual proteins at the nanometer scale both in vitro and in cells. Complementing advances in microscopy technologies has been the development of fluorescent probes. The quantum dot, a semi-conductor fluorescent nanoparticle, is particularly suitable for single particle tracking and super-resolution imaging. This article overviews the principles of single particle tracking and super resolution along with describing their application to the nanometer measurement/observation of biological systems when combined with quantum dot technologies.
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Affiliation(s)
- Taro Ichimura
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan
| | - Takashi Jin
- Laboratory for Nano-Bio Probes, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; Graduate School of Frontier Biosciences, Osaka University Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
| | - Hideaki Fujita
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
| | - Hideo Higuchi
- Department of Physics, School of Science, The University of Tokyo Bunkyo, Tokyo, Japan
| | - Tomonobu M Watanabe
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; Graduate School of Frontier Biosciences, Osaka University Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
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46
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Manikandan M, Nasser Abdelhamid H, Talib A, Wu HF. Facile synthesis of gold nanohexagons on graphene templates in Raman spectroscopy for biosensing cancer and cancer stem cells. Biosens Bioelectron 2014; 55:180-6. [DOI: 10.1016/j.bios.2013.11.037] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/08/2013] [Accepted: 11/11/2013] [Indexed: 02/07/2023]
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47
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Bücherl CA, Bader A, Westphal AH, Laptenok SP, Borst JW. FRET-FLIM applications in plant systems. PROTOPLASMA 2014; 251:383-394. [PMID: 24390247 DOI: 10.1007/s00709-013-0595-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 12/05/2013] [Indexed: 05/28/2023]
Abstract
A hallmark of cellular processes is the spatio-temporally regulated interplay of biochemical components. Assessing spatial information of molecular interactions within living cells is difficult using traditional biochemical methods. Developments in green fluorescent protein technology in combination with advances in fluorescence microscopy have revolutionised this field of research by providing the genetic tools to investigate the spatio-temporal dynamics of biomolecules in live cells. In particular, fluorescence lifetime imaging microscopy (FLIM) has become an inevitable technique for spatially resolving cellular processes and physical interactions of cellular components in real time based on the detection of Förster resonance energy transfer (FRET). In this review, we provide a theoretical background of FLIM as well as FRET-FLIM analysis. Furthermore, we show two cases in which advanced microscopy applications revealed many new insights of cellular processes in living plant cells as well as in whole plants.
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48
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Grußmayer KS, Kurz A, Herten DP. Single-Molecule Studies on the Label Number Distribution of Fluorescent Markers. Chemphyschem 2014; 15:734-42. [DOI: 10.1002/cphc.201300840] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 01/14/2014] [Indexed: 01/17/2023]
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49
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Dent KC, Hagen C, Grünewald K. Critical step-by-step approaches toward correlative fluorescence/soft X-ray cryo-microscopy of adherent mammalian cells. Methods Cell Biol 2014; 124:179-216. [PMID: 25287842 DOI: 10.1016/b978-0-12-801075-4.00009-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Soft X-ray cryo-microscopy/tomography with its extraordinary capability to map vitreous cells with high absorption contrast in their full three-dimensional extent, and at a resolution exceeding super-resolution fluorescence microscopy, is a valuable tool for integrative structural cell biology. Focusing on cell biological applications, its ongoing methodological development gained momentum by combining it with fluorescence cryo-microscopy, thus correlating highly resolved structural and specific information in situ. In this chapter, we provide a basic description of the techniques, as well as an overview of equipment and methods available to carry out correlative soft X-ray cryo-tomography experiments on frozen-hydrated cells grown on a planar support. Our aim here is to suggest ways that biologically representative data can be recorded to the highest possible resolution, while also keeping in mind the limitations of the technique during data acquisition and analysis. We have written from our perspective as electron cryo-microscopists/structural cell biologists who have experience using correlative fluorescence/cryoXM/T at synchrotron beamlines presently available for external users in Europe (HZB TXM at U41-FSGM, BESSY II, Berlin/Germany; Carl Zeiss TXMs at MISTRAL, ALBA, Barcelona/Spain, and B24, DLS, Oxfordshire, UK).
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Affiliation(s)
- Kyle C Dent
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom; Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Christoph Hagen
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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50
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da Cruz EHG, Carvalho PHPR, Corrêa JR, Silva DAC, Diogo EBT, de Souza Filho JD, Cavalcanti BC, Pessoa C, de Oliveira HCB, Guido BC, da Silva Filho DA, Neto BAD, da Silva Júnior EN. Design, synthesis and application of fluorescent 2,1,3-benzothiadiazole-triazole-linked biologically active lapachone derivatives. NEW J CHEM 2014. [DOI: 10.1039/c3nj01499a] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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