51
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Wolf P, Gavins G, Beck‐Sickinger AG, Seitz O. Strategies for Site-Specific Labeling of Receptor Proteins on the Surfaces of Living Cells by Using Genetically Encoded Peptide Tags. Chembiochem 2021; 22:1717-1732. [PMID: 33428317 PMCID: PMC8248378 DOI: 10.1002/cbic.202000797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Fluorescence microscopy imaging enables receptor proteins to be investigated within their biological context. A key challenge is to site-specifically incorporate reporter moieties into proteins without interfering with biological functions or cellular networks. Small peptide tags offer the opportunity to combine inducible labeling with small tag sizes that avoid receptor perturbation. Herein, we review the current state of live-cell labeling of peptide-tagged cell-surface proteins. Considering their importance as targets in medicinal chemistry, we focus on membrane receptors such as G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). We discuss peptide tags that i) are subject to enzyme-mediated modification reactions, ii) guide the complementation of reporter proteins, iii) form coiled-coil complexes, and iv) interact with metal complexes. Given our own contributions in the field, we place emphasis on peptide-templated labeling chemistry.
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Affiliation(s)
- Philipp Wolf
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Georgina Gavins
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
| | - Annette G. Beck‐Sickinger
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Oliver Seitz
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
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52
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Tuang S, Dieppa-Matos D, Zhang C, Shugrue CR, Dai P, Loas A, Pentelute BL. A reactive peptide interface for site-selective cysteine bioconjugation. Chem Commun (Camb) 2021; 57:3227-3230. [PMID: 33645592 PMCID: PMC8048384 DOI: 10.1039/d1cc00095k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report aqueous, site-selective modification of proteins using a reactive peptide interface comprising a nine-residue sequence. This interface is the fastest (second-order rate constant of 152 M-1 s-1) catalyst-free, cysteine-based method for modifying proteins available to date, and enables near-quantitative labeling of antibodies in cell lysate.
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Affiliation(s)
- Suan Tuang
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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53
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Laxman P, Ansari S, Gaus K, Goyette J. The Benefits of Unnatural Amino Acid Incorporation as Protein Labels for Single Molecule Localization Microscopy. Front Chem 2021; 9:641355. [PMID: 33842432 PMCID: PMC8027105 DOI: 10.3389/fchem.2021.641355] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/26/2021] [Indexed: 01/07/2023] Open
Abstract
Single Molecule Localization Microscopy (SMLM) is an imaging method that allows for the visualization of structures smaller than the diffraction limit of light (~200 nm). This is achieved through techniques such as stochastic optical reconstruction microscopy (STORM) and photoactivated localization microscopy (PALM). A large part of obtaining ideal imaging of single molecules is the choice of the right fluorescent label. An upcoming field of protein labeling is incorporating unnatural amino acids (UAAs) with an attached fluorescent dye for precise localization and visualization of individual molecules. For this technique, fluorescent probes are conjugated to UAAs and are introduced into the protein of interest (POI) as a label. Here we contrast this labeling method with other commonly used protein-based labeling methods such as fluorescent proteins (FPs) or self-labeling tags such as Halotag, SNAP-tags, and CLIP-tags, and highlight the benefits and shortcomings of the site-specific incorporation of UAAs coupled with fluorescent dyes in SMLM.
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Affiliation(s)
| | | | | | - Jesse Goyette
- European Molecular Biology Laboratory (EMBL) Australia Node in Single Molecule Sciences, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
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54
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Abreu N, Levitz J. Optogenetic Techniques for Manipulating and Sensing G Protein-Coupled Receptor Signaling. Methods Mol Biol 2021; 2173:21-51. [PMID: 32651908 DOI: 10.1007/978-1-0716-0755-8_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
G protein-coupled receptors (GPCRs) form the largest class of membrane receptors in the mammalian genome with nearly 800 human genes encoding for unique subtypes. Accordingly, GPCR signaling is implicated in nearly all physiological processes. However, GPCRs have been difficult to study due in part to the complexity of their function which can lead to a plethora of converging or diverging downstream effects over different time and length scales. Classic techniques such as pharmacological control, genetic knockout and biochemical assays often lack the precision required to probe the functions of specific GPCR subtypes. Here we describe the rapidly growing set of optogenetic tools, ranging from methods for optical control of the receptor itself to optical sensing and manipulation of downstream effectors. These tools permit the quantitative measurements of GPCRs and their downstream signaling with high specificity and spatiotemporal precision.
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Affiliation(s)
- Nohely Abreu
- Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Joshua Levitz
- Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA.
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55
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Gutzeit VA, Acosta-Ruiz A, Munguba H, Häfner S, Landra-Willm A, Mathes B, Mony J, Yarotski D, Börjesson K, Liston C, Sandoz G, Levitz J, Broichhagen J. A fine-tuned azobenzene for enhanced photopharmacology in vivo. Cell Chem Biol 2021; 28:1648-1663.e16. [PMID: 33735619 DOI: 10.1016/j.chembiol.2021.02.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/23/2020] [Accepted: 02/23/2021] [Indexed: 12/15/2022]
Abstract
Despite the power of photopharmacology for interrogating signaling proteins, many photopharmacological systems are limited by their efficiency, speed, or spectral properties. Here, we screen a library of azobenzene photoswitches and identify a urea-substituted "azobenzene-400" core that offers bistable switching between cis and trans with improved kinetics, light sensitivity, and a red-shift. We then focus on the metabotropic glutamate receptors (mGluRs), neuromodulatory receptors that are major pharmacological targets. Synthesis of "BGAG12,400," a photoswitchable orthogonal, remotely tethered ligand (PORTL), enables highly efficient, rapid optical agonism following conjugation to SNAP-tagged mGluR2 and permits robust optical control of mGluR1 and mGluR5 signaling. We then produce fluorophore-conjugated branched PORTLs to enable dual imaging and manipulation of mGluRs and highlight their power in ex vivo slice and in vivo behavioral experiments in the mouse prefrontal cortex. Finally, we demonstrate the generalizability of our strategy by developing an improved soluble, photoswitchable pore blocker for potassium channels.
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Affiliation(s)
- Vanessa A Gutzeit
- Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Amanda Acosta-Ruiz
- Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Hermany Munguba
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Stephanie Häfner
- Université Cote d'Azur, CNRS, INSERM, iBV, Nice, France; Laboratories of Excellence, Ion Channel Science and Therapeutics, Nice, France
| | - Arnaud Landra-Willm
- Université Cote d'Azur, CNRS, INSERM, iBV, Nice, France; Laboratories of Excellence, Ion Channel Science and Therapeutics, Nice, France
| | - Bettina Mathes
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Jürgen Mony
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Dzianis Yarotski
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Karl Börjesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Conor Liston
- Department of Psychiatry and Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
| | - Guillaume Sandoz
- Université Cote d'Azur, CNRS, INSERM, iBV, Nice, France; Laboratories of Excellence, Ion Channel Science and Therapeutics, Nice, France
| | - Joshua Levitz
- Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY 10065, USA; Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY 10065, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Johannes Broichhagen
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany; Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany.
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56
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Miller MA, Sletten EM. Perfluorocarbons in Chemical Biology. Chembiochem 2020; 21:3451-3462. [PMID: 32628804 PMCID: PMC7736518 DOI: 10.1002/cbic.202000297] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/03/2020] [Indexed: 01/10/2023]
Abstract
Perfluorocarbons, saturated carbon chains in which all the hydrogen atoms are replaced with fluorine, form a separate phase from both organic and aqueous solutions. Though perfluorinated compounds are not found in living systems, they can be used to modify biomolecules to confer orthogonal behavior within natural systems, such as improved stability, engineered assembly, and cell-permeability. Perfluorinated groups also provide handles for purification, mass spectrometry, and 19 F NMR studies in complex environments. Herein, we describe how the unique properties of perfluorocarbons have been employed to understand and manipulate biological systems.
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Affiliation(s)
- Margeaux A Miller
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E Young Dr E, Los Angeles, CA, 90095, USA
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E Young Dr E, Los Angeles, CA, 90095, USA
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57
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Ando T, Takamori Y, Yokoyama T, Yamamoto M, Kawakami T. Directed evolution of dibenzocyclooctyne-reactive peptide tags for protein labeling. Biochem Biophys Res Commun 2020; 534:27-33. [PMID: 33310184 DOI: 10.1016/j.bbrc.2020.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/03/2020] [Indexed: 01/02/2023]
Abstract
Protein labeling with a functional molecule is a technique widely used for protein research. The covalent reaction of self-labeling peptide tags with synthetic probe-modified small molecules enables tag-fused protein labeling with chemically diverse molecules, including fluorescent probes. We report the discovery, by in vitro directed evolution, of a novel 23-mer dibenzocyclooctyne (DBCO)-reactive peptide (DRP) tag using Systematic Evolution of Ligands by EXponential enrichment (SELEX) with a combination of a reconstituted cell-free translation system (PURE system) and cDNA display. The N- and C-terminal DRP truncations created a shorter 16-mer DBCO-reactive peptide (sDRP) tag without significant reactivity reduction. By fusing the sDRP tag to a model protein, we showed the chemical labeling and in-gel fluorescence imaging of the sDRP-fused protein using a fluorescent DBCO probe. Results showed that sDRP tag-mediated protein labeling has potential for use as a basic molecular tool in a variety of applications for protein research.
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Affiliation(s)
- Takehiro Ando
- Department of Life and Environmental Sciences, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Yukio Takamori
- Department of Life and Environmental Sciences, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Takumi Yokoyama
- Department of Life and Environmental Sciences, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Mizuki Yamamoto
- Department of Integrated Applied Life Science, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Takashi Kawakami
- Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan; JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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58
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Jia F, Wang J, Zhao Y, Zhang Y, Luo Q, Qi L, Hou Y, Du J, Wang F. In Situ Visualization of Proteins in Single Cells by Time-of-Flight-Secondary Ion Mass Spectrometry Coupled with Genetically Encoded Chemical Tags. Anal Chem 2020; 92:15517-15525. [PMID: 33203209 DOI: 10.1021/acs.analchem.0c03448] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In situ visualization of proteins of interest in single cells is attractive in cell biology, molecular biology, and biomedicine fields. Time-of-flight-secondary ion mass spectrometry (ToF-SIMS) is a powerful tool for imaging small organic molecules in single cells, yet difficult to image biomacromolecules such as proteins and DNA. Herein, a universal strategy is reported to image specific proteins in single cells by ToF-SIMS following genetic incorporation of fluorine-containing unnatural amino acids as a chemical tag into the proteins via a genetic code expansion technique. The method was developed and validated by imaging a green fluorescence protein (GFP) in Escherichia coli (E. coli) and human HeLa cancer cells and then utilized to visualize the characteristic polar distribution of chemotaxis protein CheA in E. coli cells and the interaction between high-mobility group box 1 protein and cisplatin-damaged DNA in HeLa cells. The present work highlights the power of ToF-SIMS imaging combined with genetically encoded chemical tags for in situ visualization of specific proteins as well as the interactions between proteins and drugs or drug-damaged DNA in single cells.
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Affiliation(s)
- Feifei Jia
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Jie Wang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,College of Chemistry and Materials Science, Key Laboratory of Functional Molecular Solids, the Ministry of Education, Anhui Laboratory of Molecular-Based Materials, Anhui Normal University, Wuhu, Anhui 241000, People's Republic of China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Yanyan Zhang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Luyu Qi
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yinzhu Hou
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jun Du
- College of Chemistry and Materials Science, Key Laboratory of Functional Molecular Solids, the Ministry of Education, Anhui Laboratory of Molecular-Based Materials, Anhui Normal University, Wuhu, Anhui 241000, People's Republic of China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.,Basic Medical College, Shandong University of Chinese Traditional Medicine, Jinan 250355, People's Republic of China
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59
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Bachollet SPJT, Addi C, Pietrancosta N, Mallet JM, Dumat B. Fluorogenic Protein Probes with Red and Near-Infrared Emission for Genetically Targeted Imaging*. Chemistry 2020; 26:14467-14473. [PMID: 32691883 DOI: 10.1002/chem.202002911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Indexed: 11/09/2022]
Abstract
Fluorogenic probes are important tools to image proteins with high contrast and no wash protocols. In this work, we rationally designed and synthesized a small set of four protein fluorogens with red or near-infrared emission. The fluorophores were characterized in the presence of albumin as a model protein environment and exhibited good fluorogenicity and brightness (fluorescence quantum yield up to 36 %). Once conjugated to a haloalkane ligand, the probes reacted with the protein self-labeling tag HaloTag with a high fluorescence enhancement (up to 156-fold). The spectroscopic properties of the fluorogens and their reaction with HaloTag were investigated experimentally in vitro and with the help of molecular dynamics. The two most promising probes, one in the red and one in the near-infrared range, were finally applied to image the nucleus or actin in live-cell and in wash-free conditions using fluorogenic and chemogenetic targeting of HaloTag fusion proteins.
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Affiliation(s)
- Sylvestre P J T Bachollet
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Cyril Addi
- Membrane Traffic and Cell Division Lab, Cell Biology and Infection Department, Institut Pasteur, CNRS UMR3691, Sorbonne Université, 75005, Paris, France
| | - Nicolas Pietrancosta
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.,Neuroscience Paris Seine-Institut de Biologie Paris Seine (NPS-IBPS) INSERM, CNRS, Sorbonne Université, Paris, France
| | - Jean-Maurice Mallet
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Blaise Dumat
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
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60
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Macias‐Contreras M, Zhu L. The Collective Power of Genetically Encoded Protein/Peptide Tags and Bioorthogonal Chemistry in Biological Fluorescence Imaging. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Miguel Macias‐Contreras
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
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61
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Ye F, Huang W, Li C, Li G, Yang W, Liu SH, Yin J, Sun Y, Yang G. Near‐Infrared Fluorescence/Photoacoustic Agent with an Intensifying Optical Performance for Imaging‐Guided Effective Photothermal Therapy. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.202000170] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Fengying Ye
- Key Laboratory of Pesticide and Chemical Biology (Ministry of Education); Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis; International Joint Research Center for Intelligent Biosensing Technology and Health; College of Chemistry Central China Normal University Wuhan 430079 P. R. China
| | - Weijing Huang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences Wuhan University Wuhan 430072 P. R. China
| | - Chonglu Li
- Key Laboratory of Pesticide and Chemical Biology (Ministry of Education); Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis; International Joint Research Center for Intelligent Biosensing Technology and Health; College of Chemistry Central China Normal University Wuhan 430079 P. R. China
| | - Guangjin Li
- Key Laboratory of Pesticide and Chemical Biology (Ministry of Education); Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis; International Joint Research Center for Intelligent Biosensing Technology and Health; College of Chemistry Central China Normal University Wuhan 430079 P. R. China
| | - Wen‐Chao Yang
- Key Laboratory of Pesticide and Chemical Biology (Ministry of Education); Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis; International Joint Research Center for Intelligent Biosensing Technology and Health; College of Chemistry Central China Normal University Wuhan 430079 P. R. China
| | - Sheng Hua Liu
- Key Laboratory of Pesticide and Chemical Biology (Ministry of Education); Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis; International Joint Research Center for Intelligent Biosensing Technology and Health; College of Chemistry Central China Normal University Wuhan 430079 P. R. China
| | - Jun Yin
- Key Laboratory of Pesticide and Chemical Biology (Ministry of Education); Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis; International Joint Research Center for Intelligent Biosensing Technology and Health; College of Chemistry Central China Normal University Wuhan 430079 P. R. China
| | - Yao Sun
- Key Laboratory of Pesticide and Chemical Biology (Ministry of Education); Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis; International Joint Research Center for Intelligent Biosensing Technology and Health; College of Chemistry Central China Normal University Wuhan 430079 P. R. China
| | - Guang‐Fu Yang
- Key Laboratory of Pesticide and Chemical Biology (Ministry of Education); Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis; International Joint Research Center for Intelligent Biosensing Technology and Health; College of Chemistry Central China Normal University Wuhan 430079 P. R. China
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62
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63
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Cleveland JD, Tucker CL. Photo-SNAP-tag, a Light-Regulated Chemical Labeling System. ACS Chem Biol 2020; 15:2212-2220. [PMID: 32623878 DOI: 10.1021/acschembio.0c00412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methods that allow labeling and tracking of proteins have been instrumental for understanding their function. Traditional methods for labeling proteins include fusion to fluorescent proteins or self-labeling chemical tagging systems such as SNAP-tag or Halo-tag. These latter approaches allow bright fluorophores or other chemical moieties to be attached to a protein of interest through a small fusion tag. In this work, we sought to improve the versatility of self-labeling chemical-tagging systems by regulating their activity with light. We used light-inducible dimerizers to reconstitute a split SNAP-tag (modified human O6-alkylguanine-DNA-alkyltransferase, hAGT) protein, allowing tight light-dependent control of chemical labeling. In addition, we generated a small split SNAP-tag fragment that can efficiently self-assemble with its complement fragment, allowing high labeling efficacy with a small tag. We envision these tools will extend the versatility and utility of the SNAP-tag chemical system for protein labeling applications.
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Affiliation(s)
- Joseph D. Cleveland
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Chandra L. Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
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64
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Sharma A, Sun J, Singaram I, Ralko A, Lee D, Cho W. Photostable and Orthogonal Solvatochromic Fluorophores for Simultaneous In Situ Quantification of Multiple Cellular Signaling Molecules. ACS Chem Biol 2020; 15:1913-1920. [PMID: 32525312 PMCID: PMC7909721 DOI: 10.1021/acschembio.0c00241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Ratiometric fluorescence sensors are powerful tools for direct quantification of diverse biological analytes. To overcome a shortage of solvatochromic fluorophores crucial for in situ ratiometric imaging of biological targets, we prepared and characterized a small library of modular fluorophores with diverse spectral properties. Among them, WCB and WCR showed excellent spectral properties, including high photostability, brightness, and solvatochromism, and are ideally suited for dual ratiometric imaging due to their spectral orthogonality. By conjugating WCB and WCR with protein-based lipid sensors, we were able to achieve robust simultaneous in situ quantitative imaging of two metabolically linked signaling lipids, phosphatidylinositol-4,5-bisphosphate and phosphatidylinositol-3,4,5-trisphosphate in live cells. This study shows that any combination of signaling molecules can be simultaneously quantified in a spatiotemporally resolved manner by ratiometric imaging with finely tuned solvatochromic fluorophores.
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Affiliation(s)
| | | | - Indira Singaram
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, 60607, United States
| | - Arthur Ralko
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, 60607, United States
| | - Daesung Lee
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, 60607, United States
| | - Wonhwa Cho
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, 60607, United States
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65
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Poc P, Gutzeit VA, Ast J, Lee J, Jones BJ, D'Este E, Mathes B, Lehmann M, Hodson DJ, Levitz J, Broichhagen J. Interrogating surface versus intracellular transmembrane receptor populations using cell-impermeable SNAP-tag substrates. Chem Sci 2020; 11:7871-7883. [PMID: 34123074 PMCID: PMC8163392 DOI: 10.1039/d0sc02794d] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/02/2020] [Indexed: 01/13/2023] Open
Abstract
Employing self-labelling protein tags for the attachment of fluorescent dyes has become a routine and powerful technique in optical microscopy to visualize and track fused proteins. However, membrane permeability of the dyes and the associated background signals can interfere with the analysis of extracellular labelling sites. Here we describe a novel approach to improve extracellular labelling by functionalizing the SNAP-tag substrate benzyl guanine ("BG") with a charged sulfonate ("SBG"). This chemical manipulation can be applied to any SNAP-tag substrate, improves solubility, reduces non-specific staining and renders the bioconjugation handle impermeable while leaving its cargo untouched. We report SBG-conjugated fluorophores across the visible spectrum, which cleanly label SNAP-fused proteins in the plasma membrane of living cells. We demonstrate the utility of SBG-conjugated fluorophores to interrogate class A, B and C G protein-coupled receptors (GPCRs) using a range of imaging approaches including nanoscopic superresolution imaging, analysis of GPCR trafficking from intra- and extracellular pools, in vivo labelling in mouse brain and analysis of receptor stoichiometry using single molecule pull down.
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Affiliation(s)
- Pascal Poc
- Max Planck Institute for Medical Research, Department of Chemical Biology Jahnstr. 29 69120 Heidelberg Germany
| | - Vanessa A Gutzeit
- Neuroscience Graduate Program, Weill Cornell Medicine New York NY 10065 USA
| | - Julia Ast
- Institute of Metabolism and Systems Research (IMSR), Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham Birmingham UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners Birmingham UK
| | - Joon Lee
- Department of Biochemistry, Weill Cornell Medicine New York NY 10065 USA
| | - Ben J Jones
- Section of Investigative Medicine, Imperial College London London W12 0NN UK
| | - Elisa D'Este
- Optical Microscopy Facility, Max Planck Institute for Medical Research Heidelberg Germany
| | - Bettina Mathes
- Max Planck Institute for Medical Research, Department of Chemical Biology Jahnstr. 29 69120 Heidelberg Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Pharmacology and Cell Biology Robert-Rössle-Str. 10 13125 Berlin Germany
| | - David J Hodson
- Institute of Metabolism and Systems Research (IMSR), Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham Birmingham UK
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners Birmingham UK
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine New York NY 10065 USA
- Tri-Institutional PhD Program in Chemical Biology New York NY 10065 USA
| | - Johannes Broichhagen
- Max Planck Institute for Medical Research, Department of Chemical Biology Jahnstr. 29 69120 Heidelberg Germany
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Chemical Biology Robert-Rössle-Str. 10 13125 Berlin Germany
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66
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Simultaneous Live Imaging of Multiple Endogenous Proteins Reveals a Mechanism for Alzheimer's-Related Plasticity Impairment. Cell Rep 2020; 27:658-665.e4. [PMID: 30995464 DOI: 10.1016/j.celrep.2019.03.041] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/17/2018] [Accepted: 03/11/2019] [Indexed: 12/15/2022] Open
Abstract
CaMKIIα is a central mediator of bidirectional synaptic plasticity, including long-term potentiation (LTP) and long-term depression (LTD). To study how CaMKIIα movement during plasticity is affected by soluble amyloid-β peptide oligomers (Aβ), we used FingR intrabodies to simultaneously image endogenous CaMKIIα and markers for excitatory versus inhibitory synapses in live neurons. Aβ blocks LTP-stimulus-induced CaMKIIα accumulation at excitatory synapses. This block requires CaMKII activity, is dose and time dependent, and also occurs at synapses without detectable Aβ; it is specific to LTP, as CaMKIIα accumulation at inhibitory synapses during LTD is not reduced. As CaMKII movement to excitatory synapses is required for normal LTP, its impairment can mechanistically explain Aβ-induced impairment of LTP. CaMKII movement during LTP requires binding to the NMDA receptor, and Aβ induces internalization of NMDA receptors. However, surprisingly, this internalization does not cause the block in CaMKIIα movement and is observed for extrasynaptic, but not synaptic, NMDA receptors.
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67
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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68
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Zhang Y, Raymo FM. Photoactivatable fluorophores for single-molecule localization microscopy of live cells. Methods Appl Fluoresc 2020; 8:032002. [PMID: 32325443 DOI: 10.1088/2050-6120/ab8c5c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Photochemical reactions can be designed to convert either irreversibly or reversibly a nonemissive reactant into an emissive product. The irreversible disconnection of a photocleavable group from an emissive chromophore or the reversible interconversion of a photochromic component is generally exploited to implement these operating principles for fluorescence switching. In both instances, the interplay of activating radiation, to convert the nonemissive state into the emissive species, and exciting radiation, to produce fluorescence from the latter, can be exploited to switch fluorescence on in a given area of interest at a precise interval of time. Such a level of spatiotemporal control provides the opportunity to reconstruct sub-diffraction images with resolution at the nanometer level. Indeed, closely-spaced emitters can be switched on under photochemical control at distinct intervals of time and localized independently at the single-molecule level. In combination with appropriate intracellular targeting strategies, some of these photoactivatable fluorophores can be switched and localized inside live cells to permit the visualization of sub-cellular structures with a spatial resolution that would be impossible to achieve with conventional fluorophores. As a result, photoactivatable fluorophores can become invaluable probes for the implementation of super-resolution imaging schemes aimed at the elucidation of the fundamental factors controlling cellular functions at the molecular level.
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Affiliation(s)
- Yang Zhang
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, Coral Gables, FL, United States of America
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69
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Macias-Contreras M, Little KN, Zhu L. Expanding the substrate selectivity of SNAP/CLIP-tagging of intracellular targets. Methods Enzymol 2020; 638:233-257. [PMID: 32416915 DOI: 10.1016/bs.mie.2020.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
SNAP-tag belongs to a class of genetic tools of protein labeling that complements fluorescent proteins. This single-turnover enzyme is a mutant of human DNA repair protein O6-alkylguanine-DNA alkyltransferase (hAGT). It accepts, in most cases, label-carrying O6-benzylguanines or benzyl-2-chloro-6-aminopyrimidines as suitable substrates. In this article, strategies and methods to expand the scope of the labels for intracellular proteins of live cells via the actions of SNAP-tag are presented. CLIP-tag is another mutant of the hAGT that was engineered to have mutually exclusive substrate specificity from SNAP-tag. The use of complementary bioorthogonal chemical reactions in conjunction with orthogonal enzymatic SNAP/CLIP-tags for the purpose of dual-color intracellular labeling is also described.
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Affiliation(s)
- Miguel Macias-Contreras
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States
| | - Kevin N Little
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States
| | - Lei Zhu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States.
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70
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Song Y, Xiong F, Peng J, Fung YME, Huang Y, Li X. Introducing aldehyde functionality to proteins using ligand-directed affinity labeling. Chem Commun (Camb) 2020; 56:6134-6137. [PMID: 32364188 DOI: 10.1039/d0cc01982h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Aldehyde is a versatile chemical handle for protein modification. Although many methods have been developed to label proteins with aldehyde, target-specific methods amenable to endogenous proteins are limited. Here, we report a simple affinity probe strategy to introduce aldehydes to native proteins. Notably, the probe contains a latent aldehyde functionality that is only exposed upon target binding, thereby enabling a one-pot labeling procedure.
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Affiliation(s)
- Yinan Song
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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71
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Leippe P, Broichhagen J, Cailliau K, Mougel A, Morel M, Dissous C, Trauner D, Vicogne J. Transformation of Receptor Tyrosine Kinases into Glutamate Receptors and Photoreceptors. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Philipp Leippe
- Department of ChemistryLudwig-Maximilians-Universität München and Munich Center for Integrated Protein Science Butenandtstrasse 5–13 81377 München Germany
- Present address: Department of Chemical BiologyMax Planck Institute for Medical Research Jahnstr. 29 69120 Heidelberg Germany
| | - Johannes Broichhagen
- Department of ChemistryLudwig-Maximilians-Universität München and Munich Center for Integrated Protein Science Butenandtstrasse 5–13 81377 München Germany
- Present address: Department of Chemical BiologyForschungsinstitut für Molekulare Pharmakologie Robert-Rössle Str. 10 13125 Berlin Germany
| | - Katia Cailliau
- CNRS UMR 8576University of Lille Villeneuve d'Asq France
| | - Alexandra Mougel
- Univ. LilleCNRSInserm, CHU LilleInstitut Pasteur de LilleU1019—UMR 8204, Center for Infection and Immunity of Lille (CIIL) 59000 Lille France
| | - Marion Morel
- Department of Biochemistry and Molecular BiologyBoonshoft School of MedicineWright State University Dayton OH 45435 USA
| | - Colette Dissous
- Univ. LilleCNRSInserm, CHU LilleInstitut Pasteur de LilleU1019—UMR 8204, Center for Infection and Immunity of Lille (CIIL) 59000 Lille France
| | - Dirk Trauner
- Department of ChemistryLudwig-Maximilians-Universität München and Munich Center for Integrated Protein Science Butenandtstrasse 5–13 81377 München Germany
- Department of ChemistrySilver Center for Arts and ScienceNew York University 100 Washington Square East New York NY 10003 USA
| | - Jérôme Vicogne
- Univ. LilleCNRSInserm, CHU LilleInstitut Pasteur de LilleU1019—UMR 8204, Center for Infection and Immunity of Lille (CIIL) 59000 Lille France
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72
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Zhang Y, Raymo FM. Live-Cell Imaging at the Nanoscale with Bioconjugatable and Photoactivatable Fluorophores. Bioconjug Chem 2020; 31:1052-1062. [PMID: 32150390 DOI: 10.1021/acs.bioconjchem.0c00073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Optical diffraction fundamentally limits the spatial resolution of conventional fluorescence images to length scales that are, at least, 2 orders of magnitude longer than the dimensions of individual molecules. As a result, the development of innovative probes and imaging schemes to overcome diffraction is very much needed to enable the investigation of the fundamental factors regulating cellular functions at the molecular level. In this context, the chemical synthesis of molecular constructs with photoactivatable fluorescence and the ability to label subcellular components of live cells can have transformative implications. Indeed, the fluorescence of the resulting assemblies can be activated with spatiotemporal control, even in the intracellular environment, to permit the sequential localization of individual emissive labels with precision at the nanometer level and the gradual reconstruction of images with subdiffraction resolution. The implementation of these operating principles for subdiffraction imaging, however, is only possible if demanding photochemical and photophysical requirements to enable photoactivation and localization as well as stringent structural requisites to allow the covalent labeling of intracellular targets in live cells are satisfied. Because of these complications, only a few synthetic photoactivatable fluorophores with appropriate performance for live-cell imaging at the nanoscale have been developed so far. Significant synthetic efforts in conjunction with spectroscopic analyses are still very much needed to advance this promising research area further and turn photoactivatable fluorophores into the imaging probes of choice for the investigation of live cells.
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Affiliation(s)
- Yang Zhang
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, Coral Gables, Florida 33146-0431, United States
| | - Françisco M Raymo
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, Coral Gables, Florida 33146-0431, United States
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73
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Kumar N, Hori Y, Nishiura M, Kikuchi K. Rapid no-wash labeling of PYP-tag proteins with reactive fluorogenic ligands affords stable fluorescent protein conjugates for long-term cell imaging studies. Chem Sci 2020; 11:3694-3701. [PMID: 34094058 PMCID: PMC8152630 DOI: 10.1039/d0sc00499e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Covalent labeling systems that employ protein-tags or chemical probes to convert proteins into fluorescent conjugates are powerful tools for carrying out real time imaging and pulse-chase tracking studies that enable the spatiotemporal role of proteins in complex biological systems to be investigated. In this study, we have covalently modified a specific nucleophilic cysteine residue of the PYP-tag protein with weakly fluorescent α,β-unsaturated ketone (conjugate addition) and α-halomethyl ketone (SN2 reaction) acceptors to afford highly fluorescent PYP-tag-dimethylaminocoumarin (DMAC) conjugates, whose ligands are covalently bound to the PYP-protein through stable thioether linkers. A chloromethylketone derived DMAC-CMK reagent was found to afford the best kinetic and stability profile for labeling the PYP-tag in cellular systems, with in vitro studies demonstrating that PYP-DMAC-CMK conjugates exhibit excellent photostability and cellular stability profiles which enables them to be used for long-term protein imaging studies in cellular systems. The potential of using this no wash fluorescent labeling PYP-tag-DMAC system to visualise dividing cells undergoing mitosis and for imaging a PYP-tag fused telomere binding protein bound to chromatin in cell nuclei has been demonstrated.
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Affiliation(s)
- Naresh Kumar
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Suita Osaka 565-0871 Japan
| | - Miyako Nishiura
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Suita Osaka 565-0871 Japan
- Quantum Information and Quantum Biology Division, Osaka University Suita Osaka 565-0871 Japan
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74
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Leippe P, Broichhagen J, Cailliau K, Mougel A, Morel M, Dissous C, Trauner D, Vicogne J. Transformation of Receptor Tyrosine Kinases into Glutamate Receptors and Photoreceptors. Angew Chem Int Ed Engl 2020; 59:6720-6723. [DOI: 10.1002/anie.201915352] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Philipp Leippe
- Department of ChemistryLudwig-Maximilians-Universität München and Munich Center for Integrated Protein Science Butenandtstrasse 5–13 81377 München Germany
- Present address: Department of Chemical BiologyMax Planck Institute for Medical Research Jahnstr. 29 69120 Heidelberg Germany
| | - Johannes Broichhagen
- Department of ChemistryLudwig-Maximilians-Universität München and Munich Center for Integrated Protein Science Butenandtstrasse 5–13 81377 München Germany
- Present address: Department of Chemical BiologyForschungsinstitut für Molekulare Pharmakologie Robert-Rössle Str. 10 13125 Berlin Germany
| | - Katia Cailliau
- CNRS UMR 8576University of Lille Villeneuve d'Asq France
| | - Alexandra Mougel
- Univ. LilleCNRSInserm, CHU LilleInstitut Pasteur de LilleU1019—UMR 8204, Center for Infection and Immunity of Lille (CIIL) 59000 Lille France
| | - Marion Morel
- Department of Biochemistry and Molecular BiologyBoonshoft School of MedicineWright State University Dayton OH 45435 USA
| | - Colette Dissous
- Univ. LilleCNRSInserm, CHU LilleInstitut Pasteur de LilleU1019—UMR 8204, Center for Infection and Immunity of Lille (CIIL) 59000 Lille France
| | - Dirk Trauner
- Department of ChemistryLudwig-Maximilians-Universität München and Munich Center for Integrated Protein Science Butenandtstrasse 5–13 81377 München Germany
- Department of ChemistrySilver Center for Arts and ScienceNew York University 100 Washington Square East New York NY 10003 USA
| | - Jérôme Vicogne
- Univ. LilleCNRSInserm, CHU LilleInstitut Pasteur de LilleU1019—UMR 8204, Center for Infection and Immunity of Lille (CIIL) 59000 Lille France
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75
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Gil de Montes E, Istrate A, Navo CD, Jiménez-Moreno E, Hoyt EA, Corzana F, Robina I, Jiménez-Osés G, Moreno-Vargas AJ, Bernardes GJL. Stable Pyrrole-Linked Bioconjugates through Tetrazine-Triggered Azanorbornadiene Fragmentation. Angew Chem Int Ed Engl 2020; 59:6196-6200. [PMID: 31981460 DOI: 10.1002/anie.201914529] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/22/2020] [Indexed: 01/22/2023]
Abstract
An azanorbornadiene bromovinyl sulfone reagent for cysteine-selective bioconjugation has been developed. Subsequent reaction with dipyridyl tetrazine leads to bond cleavage and formation of a pyrrole-linked conjugate. The latter involves ligation of the tetrazine to the azanorbornadiene-tagged protein through inverse electron demand Diels-Alder cycloaddition with subsequent double retro-Diels-Alder reactions to form a stable pyrrole linkage. The sequence of site-selective bioconjugation followed by bioorthogonal bond cleavage was efficiently employed for the labelling of three different proteins. This method benefits from easy preparation of these reagents, selectivity for cysteine, and stability after reaction with a commercial tetrazine, which has potential for the routine preparation of protein conjugates for chemical biology studies.
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Affiliation(s)
- Enrique Gil de Montes
- Departamento de Química Orgánica, Facultad de Química), Universidad de Sevilla, C/ Prof. García González, 1, 41012-, Sevilla, Spain
| | - Alena Istrate
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Claudio D Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Ester Jiménez-Moreno
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Emily A Hoyt
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006, Logroño, Spain
| | - Inmaculada Robina
- Departamento de Química Orgánica, Facultad de Química), Universidad de Sevilla, C/ Prof. García González, 1, 41012-, Sevilla, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Antonio J Moreno-Vargas
- Departamento de Química Orgánica, Facultad de Química), Universidad de Sevilla, C/ Prof. García González, 1, 41012-, Sevilla, Spain
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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76
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Gil de Montes E, Istrate A, Navo CD, Jiménez‐Moreno E, Hoyt EA, Corzana F, Robina I, Jiménez‐Osés G, Moreno‐Vargas AJ, Bernardes GJL. Stable Pyrrole‐Linked Bioconjugates through Tetrazine‐Triggered Azanorbornadiene Fragmentation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Enrique Gil de Montes
- Departamento de Química OrgánicaFacultad de Química)Universidad de Sevilla C/ Prof. García González, 1 41012- Sevilla Spain
| | - Alena Istrate
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Claudio D. Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNEBasque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 801A 48160 Derio Spain
| | - Ester Jiménez‐Moreno
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Emily A. Hoyt
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Francisco Corzana
- Departamento de QuímicaCentro de Investigación en Síntesis QuímicaUniversidad de La Rioja 26006 Logroño Spain
| | - Inmaculada Robina
- Departamento de Química OrgánicaFacultad de Química)Universidad de Sevilla C/ Prof. García González, 1 41012- Sevilla Spain
| | - Gonzalo Jiménez‐Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNEBasque Research and Technology Alliance (BRTA) Bizkaia Technology Park, Building 801A 48160 Derio Spain
| | - Antonio J. Moreno‐Vargas
- Departamento de Química OrgánicaFacultad de Química)Universidad de Sevilla C/ Prof. García González, 1 41012- Sevilla Spain
| | - Gonçalo J. L. Bernardes
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
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Kojima H, Fujita Y, Takeuchi R, Ikebe Y, Ohashi N, Yamamoto K, Itoh T. Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins. Cell Chem Biol 2020; 27:334-349.e11. [PMID: 31991094 DOI: 10.1016/j.chembiol.2020.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/10/2019] [Accepted: 01/06/2020] [Indexed: 12/31/2022]
Abstract
Fluorescent molecules have contributed to basic biological research but there are currently only a limited number of probes available for the detection of non-enzymatic proteins. Here, we report turn-on fluorescent probes mediated by conjugate addition and cyclization (TCC probes). These probes react with multiple amino acids and exhibit a 36-fold greater emission intensity after reaction. We analyzed the reactions between TCC probes and nuclear receptors by electrospray ionization mass spectrometry, X-ray crystallography, spectrofluorometry, and fluorescence microscopy. In vitro analysis showed that probes consisting of a protein ligand and TCC could label vitamin D receptor and peroxisome proliferator-activated receptor γ. Moreover, we demonstrated that not only a ligand unit but also a peptide unit can label the target protein in a complex mixture.
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Affiliation(s)
- Hiroyuki Kojima
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Yuki Fujita
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Ryosuke Takeuchi
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Yuka Ikebe
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Nami Ohashi
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Keiko Yamamoto
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Toshimasa Itoh
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.
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78
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Gerasimaitė R, Seikowski J, Schimpfhauser J, Kostiuk G, Gilat T, D'Este E, Schnorrenberg S, Lukinavičius G. Efflux pump insensitive rhodamine–jasplakinolide conjugates for G- and F-actin imaging in living cells. Org Biomol Chem 2020; 18:2929-2937. [DOI: 10.1039/d0ob00369g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fluorescent actin probes made of 6′-carbopyronines and jasplakinolide are insensitive to efflux pumps and stain F- and G-actin efficiently in living cells, allowing high quality 2D and 3D nanoscopy of dynamic actin structures.
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Affiliation(s)
- Rūta Gerasimaitė
- Chromatin Labeling and Imaging Group
- Department of Nanobiophotonics
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
| | - Jan Seikowski
- Facility for Synthetic Chemistry
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
| | - Jens Schimpfhauser
- Facility for Synthetic Chemistry
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
| | - Georgij Kostiuk
- Chromatin Labeling and Imaging Group
- Department of Nanobiophotonics
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
| | - Tanja Gilat
- Department of Nanobiophotonics
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
| | - Elisa D'Este
- Optical Microscopy Facility
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
| | - Sebastian Schnorrenberg
- Department of Nanobiophotonics
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group
- Department of Nanobiophotonics
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
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79
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Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling. iScience 2019; 22:256-268. [PMID: 31786521 PMCID: PMC6906691 DOI: 10.1016/j.isci.2019.11.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/26/2019] [Accepted: 11/12/2019] [Indexed: 11/16/2022] Open
Abstract
Electron microscopy (EM) is a technology that enables visualization of single proteins at a nanometer resolution. However, current protein analysis by EM mainly relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised by large size of antibody, precluding precise detection of protein location in biological samples. Here, we develop a specific chemical labeling method for EM detection of proteins at single-molecular level. Rational design of α-helical peptide tag and probe structure provided a complementary reaction pair that enabled specific cysteine conjugation of the tag. The developed chemical labeling with gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency and detectability of high-density clusters of tag-fused G protein-coupled receptors in freeze-fracture replicas compared with immunogold labeling. Furthermore, in ultrathin sections, the spatial resolution of the chemical labeling was significantly higher than that of antibody-mediated labeling. These results demonstrate substantial advantages of the chemical labeling approach for single protein visualization by EM.
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Affiliation(s)
- Shigekazu Tabata
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan; Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Marijo Jevtic
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Nobutaka Kurashige
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Hirokazu Fuchida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Munetsugu Kido
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Kazushi Tani
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Naoki Zenmyo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Shohei Uchinomiya
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Harumi Harada
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Makoto Itakura
- Department of Biochemistry, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
| | - Ryuichi Shigemoto
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria.
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan.
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80
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A general strategy to develop cell permeable and fluorogenic probes for multicolour nanoscopy. Nat Chem 2019; 12:165-172. [PMID: 31792385 DOI: 10.1038/s41557-019-0371-1] [Citation(s) in RCA: 193] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 10/09/2019] [Indexed: 01/19/2023]
Abstract
Live-cell fluorescence nanoscopy is a powerful tool to study cellular biology on a molecular scale, yet its use is held back by the paucity of suitable fluorescent probes. Fluorescent probes based on regular fluorophores usually suffer from a low cell permeability and an unspecific background signal. Here we report a general strategy to transform regular fluorophores into fluorogenic probes with an excellent cell permeability and a low unspecific background signal. Conversion of a carboxyl group found in rhodamines and related fluorophores into an electron-deficient amide does not affect the spectroscopic properties of the fluorophore, but allows us to rationally tune the dynamic equilibrium between two different forms: a fluorescent zwitterion and a non-fluorescent, cell-permeable spirolactam. Furthermore, the equilibrium generally shifts towards the fluorescent form when the probe binds to its cellular targets. The resulting increase in fluorescence can be up to 1,000-fold. Using this simple design principle, we created fluorogenic probes in various colours for different cellular targets for wash-free, multicolour, live-cell nanoscopy.
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81
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Branched Photoswitchable Tethered Ligands Enable Ultra-efficient Optical Control and Detection of G Protein-Coupled Receptors In Vivo. Neuron 2019; 105:446-463.e13. [PMID: 31784287 DOI: 10.1016/j.neuron.2019.10.036] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/26/2019] [Accepted: 10/27/2019] [Indexed: 01/01/2023]
Abstract
The limitations of classical drugs have spurred the development of covalently tethered photoswitchable ligands to control neuromodulatory receptors. However, a major shortcoming of tethered photopharmacology is the inability to obtain optical control with an efficacy comparable with that of the native ligand. To overcome this, we developed a family of branched photoswitchable compounds to target metabotropic glutamate receptors (mGluRs). These compounds permit photo-agonism of Gi/o-coupled group II mGluRs with near-complete efficiency relative to glutamate when attached to receptors via a range of orthogonal, multiplexable modalities. Through a chimeric approach, branched ligands also allow efficient optical control of Gq-coupled mGluR5, which we use to probe the spatiotemporal properties of receptor-induced calcium oscillations. In addition, we report branched, photoswitch-fluorophore compounds for simultaneous receptor imaging and manipulation. Finally, we demonstrate this approach in vivo in mice, where photoactivation of SNAP-mGluR2 in the medial prefrontal cortex reversibly modulates working memory in normal and disease-associated states.
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82
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Fluorescent Protein-Based Indicators for Functional Super-Resolution Imaging of Biomolecular Activities in Living Cells. Int J Mol Sci 2019; 20:ijms20225784. [PMID: 31744242 PMCID: PMC6887983 DOI: 10.3390/ijms20225784] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 11/16/2022] Open
Abstract
Super-resolution light microscopy (SRM) offers a unique opportunity for diffraction-unlimited imaging of biomolecular activities in living cells. To realize such potential, genetically encoded indicators were developed recently from fluorescent proteins (FPs) that exhibit phototransformation behaviors including photoactivation, photoconversion, and photoswitching, etc. Super-resolution observations of biomolecule interactions and biochemical activities have been demonstrated by exploiting the principles of bimolecular fluorescence complementation (BiFC), points accumulation for imaging nanoscale topography (PAINT), and fluorescence fluctuation increase by contact (FLINC), etc. To improve functional nanoscopy with the technology of genetically encoded indicators, it is essential to fully decipher the photo-induced chemistry of FPs and opt for innovative indicator designs that utilize not only fluorescence intensity but also multi-parametric readouts such as phototransformation kinetics. In parallel, technical improvements to both the microscopy optics and image analysis pipeline are promising avenues to increase the sensitivity and versatility of functional SRM.
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83
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Affiliation(s)
- Katsuya Maruyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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84
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85
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A dimerization-based fluorogenic dye-aptamer module for RNA imaging in live cells. Nat Chem Biol 2019; 16:69-76. [PMID: 31636432 PMCID: PMC6920041 DOI: 10.1038/s41589-019-0381-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 08/22/2019] [Indexed: 01/19/2023]
Abstract
Live-cell imaging of RNA has remained a challenge because of the lack of naturally fluorescent RNAs. Recently developed RNA aptamers that can light-up small fluorogenic dyes could overcome this limitation, but they still suffer from poor brightness and photostability. Here, we propose a concept of cell-permeable fluorogenic dimer of sulforhodamine B dyes (Gemini-561) and corresponding dimerized aptamer (o-Coral) that can drastically enhance performance of the current RNA imaging method. The unprecedented brightness and photostability together with high affinity of this complex allowed, for the first time, direct fluorescence imaging in live mammalian cells of RNA polymerase-III transcription products as well as messenger RNAs labelled with a single copy of the aptamer, i.e. without tag multimerization. The developed fluorogenic module enables fast and sensitive detection of RNA inside live cells, while the proposed design concept opens the route to new generation of ultrabright RNA probes.
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86
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Kumar N, Hori Y, Kikuchi K. Photoactive yellow protein and its chemical probes: an approach to protein labelling in living cells. J Biochem 2019; 166:121-127. [PMID: 31340005 DOI: 10.1093/jb/mvz051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/20/2019] [Indexed: 01/18/2023] Open
Abstract
Labelling technologies developed over the past few years have changed the way of looking at biomolecules and have made a considerable contribution to our understanding of the functions and regulation of dynamic biological processes. One of the robust technologies employed to image proteins in a cellular environment is based on the use of chemical tags and their fluorescent probes, which provides flexibility in developing probes with a wide range of synthetic fluorophores. A variety of chemical tags, ranging from short amino acid sequences to small proteins, have been employed to generate protein-labelling systems. One such chemical tag is the photoactive yellow protein (PYP)-tag, which is a small bacterial protein, developed for the selective labelling and imaging of proteins. Herein, we briefly discuss the protein-labelling system developed based on PYP-tag technology, with a focus on the design strategy for PYP-tag labelling probes and their applications in protein imaging.
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Affiliation(s)
- Naresh Kumar
- Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.,Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.,Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
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87
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Hoshi Y, Tanikawa Y, Okada E, Kawaguchi H, Nemoto M, Shimizu K, Kodama T, Watanabe M. In situ estimation of optical properties of rat and monkey brains using femtosecond time-resolved measurements. Sci Rep 2019; 9:9165. [PMID: 31235830 PMCID: PMC6591507 DOI: 10.1038/s41598-019-45736-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/14/2019] [Indexed: 01/15/2023] Open
Abstract
An accurate knowledge of tissue optical properties (absorption coefficients, μa, and reduced scattering coefficients, μs') is critical for precise modeling of light propagation in biological tissue, essential for developing diagnostic and therapeutic optical techniques that utilize diffusive photons. A great number of studies have explored the optical properties of various tissue, and these values are not known in detail due to difficulties in the experimental determination and significant variations in tissue constitution. Especially, in situ estimates of the optical properties of brain tissue, a common measurement target in optical imaging, is a challenge because of its layer structure (where the thin gray matter covers the white matter). Here, we report an approach to in situ estimates of the μa and μs' of the gray and white matter in living rat and monkey brains by using femtosecond time-resolved measurements and Monte Carlo simulation. The results demonstrate that the μa of the gray matter is larger than that of the white matter, while there was no significant difference in the μs' between the gray and white matter. The optical properties of the rat brain were very similar to those of the monkey brain except for the μa of the gray matter here.
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Affiliation(s)
- Yoko Hoshi
- Department of Biomedical Optics, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Japan.
| | - Yukari Tanikawa
- Human Informatics Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Eiji Okada
- Department of Electronics and Electrical Engineering, Keio University, Yokohama, Japan
| | - Hiroshi Kawaguchi
- Human Informatics Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | | | - Kosuke Shimizu
- Department of Molecular Imaging, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tohru Kodama
- Sleep Disorders Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masataka Watanabe
- Sleep Disorders Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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88
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Orré T, Rossier O, Giannone G. The inner life of integrin adhesion sites: From single molecules to functional macromolecular complexes. Exp Cell Res 2019; 379:235-244. [DOI: 10.1016/j.yexcr.2019.03.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/07/2019] [Accepted: 03/27/2019] [Indexed: 12/31/2022]
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89
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MacNevin CJ, Watanabe T, Weitzman M, Gulyani A, Fuehrer S, Pinkin NK, Tian X, Liu F, Jin J, Hahn KM. Membrane-Permeant, Environment-Sensitive Dyes Generate Biosensors within Living Cells. J Am Chem Soc 2019; 141:7275-7282. [PMID: 30994345 DOI: 10.1021/jacs.8b09841] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Dyes with environment-sensitive fluorescence have proven useful to study the spatiotemporal dynamics of protein activity in living cells. When attached to proteins, their fluorescence can reflect protein conformational changes, post-translational modifications, or protein interactions. However, the utility of such dye-protein conjugates has been limited because it is difficult to load them into cells. They usually must be introduced using techniques that perturb cell physiology, limit throughput, or generate fluorescent vesicles (e.g., electroporation, microinjection, or membrane transduction peptides). Here we circumvent these problems by modifying a proven, environment-sensitive biosensor fluorophore so that it can pass through cell membranes without staining intracellular compartments and can be attached to proteins within living cells using unnatural amino acid (UAA) mutagenesis. Reactive groups were incorporated for attachment to UAAs or small molecules (mero166, azide; mero167, alkyne; mero76, carboxylic acid). These dyes are bright and fluoresce at long wavelengths (reaching ε = 100 000 M-1 cm-1, ϕ = 0.24, with excitation 565 nm and emission 594 nm). The utility of mero166 was demonstrated by in-cell labeling of a UAA to generate a biosensor for the small GTPase Cdc42. In addition, conjugation of mero166 to a small molecule produced a membrane-permeable probe that reported the localization of the DNA methyltransferase G9a in cells. This approach provides a strategy to access biosensors for many targets and to more practically harness the varied environmental sensitivities of synthetic dyes.
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Affiliation(s)
- Christopher J MacNevin
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Takashi Watanabe
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Matthew Weitzman
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Akash Gulyani
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Sheryl Fuehrer
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Nicholas K Pinkin
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Xu Tian
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Feng Liu
- Center for Integrative Chemical Biology and Drug Discovery, School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Jian Jin
- Center for Integrative Chemical Biology and Drug Discovery, School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Klaus M Hahn
- Department of Pharmacology, School of Medicine , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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90
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Erdmann RS, Baguley SW, Richens JH, Wissner RF, Xi Z, Allgeyer ES, Zhong S, Thompson AD, Lowe N, Butler R, Bewersdorf J, Rothman JE, St Johnston D, Schepartz A, Toomre D. Labeling Strategies Matter for Super-Resolution Microscopy: A Comparison between HaloTags and SNAP-tags. Cell Chem Biol 2019; 26:584-592.e6. [PMID: 30745239 PMCID: PMC6474801 DOI: 10.1016/j.chembiol.2019.01.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 07/13/2018] [Accepted: 01/07/2019] [Indexed: 12/22/2022]
Abstract
Super-resolution microscopy requires that subcellular structures are labeled with bright and photostable fluorophores, especially for live-cell imaging. Organic fluorophores may help here as they can yield more photons-by orders of magnitude-than fluorescent proteins. To achieve molecular specificity with organic fluorophores in live cells, self-labeling proteins are often used, with HaloTags and SNAP-tags being the most common. However, how these two different tagging systems compare with each other is unclear, especially for stimulated emission depletion (STED) microscopy, which is limited to a small repertoire of fluorophores in living cells. Herein, we compare the two labeling approaches in confocal and STED imaging using various proteins and two model systems. Strikingly, we find that the fluorescent signal can be up to 9-fold higher with HaloTags than with SNAP-tags when using far-red rhodamine derivatives. This result demonstrates that the labeling strategy matters and can greatly influence the duration of super-resolution imaging.
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Affiliation(s)
- Roman S. Erdmann
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, USA
| | - Stephanie Wood Baguley
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Jennifer H. Richens
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Rebecca F. Wissner
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, USA
| | - Zhiqun Xi
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Edward S. Allgeyer
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Sheng Zhong
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | | | - Nicholas Lowe
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Richard Butler
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA,Department of Biomedical Engineering, Yale University, 55 Prospect Street, New Haven, CT, USA
| | - James E. Rothman
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA
| | - Daniel St Johnston
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Alanna Schepartz
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, USA
| | - Derek Toomre
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, USA.
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91
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Matos MJ, Navo CD, Hakala T, Ferhati X, Guerreiro A, Hartmann D, Bernardim B, Saar KL, Compañón I, Corzana F, Knowles TPJ, Jiménez‐Osés G, Bernardes GJL. Quaternization of Vinyl/Alkynyl Pyridine Enables Ultrafast Cysteine‐Selective Protein Modification and Charge Modulation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901405] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Maria J. Matos
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Claudio D. Navo
- Departamento de QuímicaUniversidad de La RiojaCentro de Investigación en Síntesis Química 26006 Logroño Spain
- CIC bioGUNEBizkaia Technology Park Building 801A 48170 Derio Spain
| | - Tuuli Hakala
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Xhenti Ferhati
- Departamento de QuímicaUniversidad de La RiojaCentro de Investigación en Síntesis Química 26006 Logroño Spain
| | - Ana Guerreiro
- Instituto de Medicina Molecular, Faculdade de MedicinaUniversidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - David Hartmann
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Barbara Bernardim
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Kadi L. Saar
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Ismael Compañón
- Departamento de QuímicaUniversidad de La RiojaCentro de Investigación en Síntesis Química 26006 Logroño Spain
| | - Francisco Corzana
- Departamento de QuímicaUniversidad de La RiojaCentro de Investigación en Síntesis Química 26006 Logroño Spain
| | - Tuomas P. J. Knowles
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Gonzalo Jiménez‐Osés
- Departamento de QuímicaUniversidad de La RiojaCentro de Investigación en Síntesis Química 26006 Logroño Spain
- CIC bioGUNEBizkaia Technology Park Building 801A 48170 Derio Spain
| | - Gonçalo J. L. Bernardes
- Department of ChemistryUniversity of Cambridge Lensfield Road CB2 1EW Cambridge UK
- Instituto de Medicina Molecular, Faculdade de MedicinaUniversidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
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92
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Matos MJ, Navo CD, Hakala T, Ferhati X, Guerreiro A, Hartmann D, Bernardim B, Saar KL, Compañón I, Corzana F, Knowles TPJ, Jiménez-Osés G, Bernardes GJL. Quaternization of Vinyl/Alkynyl Pyridine Enables Ultrafast Cysteine-Selective Protein Modification and Charge Modulation. Angew Chem Int Ed Engl 2019; 58:6640-6644. [PMID: 30897271 PMCID: PMC6618083 DOI: 10.1002/anie.201901405] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/11/2019] [Indexed: 12/31/2022]
Abstract
Quaternized vinyl‐ and alkynyl‐pyridine reagents were shown to react in an ultrafast and selective manner with several cysteine‐tagged proteins at near‐stoichiometric quantities. We have demonstrated that this method can effectively create a homogenous antibody–drug conjugate that features a precise drug‐to‐antibody ratio of 2, which was stable in human plasma and retained its specificity towards Her2+ cells. Finally, the developed warhead introduces a +1 charge to the overall net charge of the protein, which enabled us to show that the electrophoretic mobility of the protein may be tuned through the simple attachment of a quaternized vinyl pyridinium reagent at the cysteine residues. We anticipate the generalized use of quaternized vinyl‐ and alkynyl‐pyridine reagents not only for bioconjugation, but also as warheads for covalent inhibition and as tools to profile cysteine reactivity.
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Affiliation(s)
- Maria J Matos
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Claudio D Navo
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006, Logroño, Spain.,CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170, Derio, Spain
| | - Tuuli Hakala
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Xhenti Ferhati
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006, Logroño, Spain
| | - Ana Guerreiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - David Hartmann
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Barbara Bernardim
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Kadi L Saar
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Ismael Compañón
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006, Logroño, Spain
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006, Logroño, Spain
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Gonzalo Jiménez-Osés
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006, Logroño, Spain.,CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170, Derio, Spain
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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93
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Zhang C, Vinogradova EV, Spokoyny AM, Buchwald SL, Pentelute BL. Arylation Chemistry for Bioconjugation. Angew Chem Int Ed Engl 2019; 58:4810-4839. [PMID: 30399206 PMCID: PMC6433541 DOI: 10.1002/anie.201806009] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Indexed: 12/20/2022]
Abstract
Bioconjugation chemistry has been used to prepare modified biomolecules with functions beyond what nature intended. Central to these techniques is the development of highly efficient and selective bioconjugation reactions that operate under mild, biomolecule compatible conditions. Methods that form a nucleophile-sp2 carbon bond show promise for creating bioconjugates with new modifications, sometimes resulting in molecules with unparalleled functions. Here we outline and review sulfur, nitrogen, selenium, oxygen, and carbon arylative bioconjugation strategies and their applications to modify peptides, proteins, sugars, and nucleic acids.
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Affiliation(s)
- Chi Zhang
- Dr. C. Zhang, Dr. E. V. Vinogradova, Prof. Dr. A. M. Spokoyny, Prof. Dr. S. L. Buchwald, Prof. Dr. B. L. Pentelute, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA, ,
| | - Ekaterina V. Vinogradova
- Dr. C. Zhang, Dr. E. V. Vinogradova, Prof. Dr. A. M. Spokoyny, Prof. Dr. S. L. Buchwald, Prof. Dr. B. L. Pentelute, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA, ,
- Dr. E. V. Vinogradova, The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alexander M. Spokoyny
- Dr. C. Zhang, Dr. E. V. Vinogradova, Prof. Dr. A. M. Spokoyny, Prof. Dr. S. L. Buchwald, Prof. Dr. B. L. Pentelute, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA, ,
- Prof. Dr. A. M. Spokoyny, Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Stephen L. Buchwald
- Dr. C. Zhang, Dr. E. V. Vinogradova, Prof. Dr. A. M. Spokoyny, Prof. Dr. S. L. Buchwald, Prof. Dr. B. L. Pentelute, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA, ,
| | - Bradley L. Pentelute
- Dr. C. Zhang, Dr. E. V. Vinogradova, Prof. Dr. A. M. Spokoyny, Prof. Dr. S. L. Buchwald, Prof. Dr. B. L. Pentelute, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA, ,
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94
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Szymczak LC, Mrksich M. Using Peptide Arrays To Discover the Sequence-Specific Acetylation of the Histidine-Tyrosine Dyad. Biochemistry 2019; 58:1810-1817. [PMID: 30817132 DOI: 10.1021/acs.biochem.9b00022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reactions that can selectively modify amino acid sequences within peptides and proteins are important for preparing protein reagents, immobilizing proteins, and making antibody-drug conjugates. The development of new reactions often begins with known chemistries and optimizes yields using a small set of peptide reactants. This article describes the use of peptide arrays and self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI-MS) to discover and characterize unanticipated sequence-selective reactions of peptides. This work reports the selective acetylation of HY (histidine-tyrosine) and YH (tyrosine-histidine) dyads when treated with acetic anhydride in aqueous conditions. More broadly, this example illustrates the benefits of using peptide arrays and a label-free analysis method to discover peptide-modifying reactions and gain mechanistic insight into their sequence specificity.
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Affiliation(s)
- Lindsey C Szymczak
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Milan Mrksich
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States.,Department of Biomedical Engineering , Northwestern University , Evanston , Illinois 60208 , United States
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95
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Sakamoto S, Kiyonaka S, Hamachi I. Construction of ligand assay systems by protein-based semisynthetic biosensors. Curr Opin Chem Biol 2019; 50:10-18. [PMID: 30875618 DOI: 10.1016/j.cbpa.2019.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 01/14/2023]
Abstract
Proteins as causative agents of diseases such as cancers, diabetes and neurological disorders are attractive drug targets. For developing chemicals selectively acting on key disease-causing proteins, one useful concept is the direct conversion of such target proteins into biosensors. This approach provides ligand-binding assay systems based on protein-based biosensors, which can quantitatively evaluate interactions between the protein and a specific ligand in many environments. Site-specific chemical modifications are used widely for the creation of protein-based semisynthetic biosensors in vitro. Notably, a few bio-orthogonal approaches capable of selectively modifying drug-targets have been developed, allowing conversion of specific target proteins into semisynthetic biosensors in live cells. These biosensors can be used for quantitative drug binding analyses in native environments. In this review, we discuss recent efforts for the construction of ligand assay systems using semisynthetic protein-based biosensors and their application to quantitative analysis and high-throughput screening of small molecules for drug discovery.
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Affiliation(s)
- Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shigeki Kiyonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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96
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Jung KH, Kim SF, Liu Y, Zhang X. A Fluorogenic
AggTag
Method Based on Halo‐ and SNAP‐Tags to Simultaneously Detect Aggregation of Two Proteins in Live Cells. Chembiochem 2019; 20:1078-1087. [DOI: 10.1002/cbic.201800782] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Kwan Ho Jung
- Department of ChemistryThe Pennsylvania State University University Park PA 16802 USA
| | - Sojung F. Kim
- Department of ChemistryThe Pennsylvania State University University Park PA 16802 USA
| | - Yu Liu
- Department of ChemistryThe Pennsylvania State University University Park PA 16802 USA
| | - Xin Zhang
- Department of ChemistryThe Pennsylvania State University University Park PA 16802 USA
- Department of Biochemistry and Molecular BiologyThe Pennsylvania State University University Park PA 16802 USA
- The Huck Institutes of the Life SciencesThe Pennsylvania State University University Park PA 16802 USA
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97
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Zhang C, Vinogradova EV, Spokoyny AM, Buchwald SL, Pentelute BL. Arylierungschemie für die Biokonjugation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806009] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Chi Zhang
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Ekaterina V. Vinogradova
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
- The Skaggs Institute for Chemical Biology and Department of Molecular MedicineThe Scripps Research Institute La Jolla CA 92037 USA
| | - Alexander M. Spokoyny
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
- Department of Chemistry and BiochemistryUniversity of California, Los Angeles 607 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Stephen L. Buchwald
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Bradley L. Pentelute
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
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98
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Jung KH, Fares M, Grainger LS, Wolstenholme CH, Hou A, Liu Y, Zhang X. A SNAP-tag fluorogenic probe mimicking the chromophore of the red fluorescent protein Kaede. Org Biomol Chem 2019; 17:1906-1915. [PMID: 30265264 DOI: 10.1039/c8ob01483c] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Self-labelling protein tags with fluorogenic probes serve as great fluorescence imaging tools to understand key questions of protein dynamics and functions in living cells. In the present study, we report a SNAP-tag fluorogenic probe 4c mimicking the chromophore of the red fluorescent protein Kaede. The molecular rotor properties of 4c were utilized as a fluorogenic probe for SNAP-tag, such that conjugation with SNAPf protein leads to inhibition of twisted intramolecular charge transfer, triggering fluorogenecity. Upon conjugation with SNAPf, 4c exhibited approximately a 90-fold enhancement in fluorescence intensity with fast labelling kinetics (k2 = 15 000 M-1 s-1). Biochemical and spectroscopic studies confirmed that fluorescence requires formation of folded SNAPf·4c covalent conjugate between Cys 145 and 4c. Confocal microscopy and flow cytometry showed that 4c is capable of detecting SNAPf proteins or SNAPf fused with a protein of interest in living cells. This work provides a framework to develop the large family of FP chromophores into fluorogenic probes for self-labelling protein tags.
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Affiliation(s)
- Kwan Ho Jung
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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99
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Wang L, Frei MS, Salim A, Johnsson K. Small-Molecule Fluorescent Probes for Live-Cell Super-Resolution Microscopy. J Am Chem Soc 2019; 141:2770-2781. [PMID: 30550714 DOI: 10.1021/jacs.8b11134] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Super-resolution fluorescence microscopy is a powerful tool to visualize biomolecules and cellular structures at the nanometer scale. Employing these techniques in living cells has opened up the possibility to study dynamic processes with unprecedented spatial and temporal resolution. Different physical approaches to super-resolution microscopy have been introduced over the last years. A bottleneck to apply these approaches for live-cell imaging has become the availability of appropriate fluorescent probes that can be specifically attached to biomolecules. In this Perspective, we discuss the role of small-molecule fluorescent probes for live-cell super-resolution microscopy and the challenges that need to be overcome for their generation. Recent trends in the development of labeling strategies are reviewed together with the required chemical and spectroscopic properties of the probes. Finally, selected examples of the use of small-molecule fluorescent probes in live-cell super-resolution microscopy are given.
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Affiliation(s)
- Lu Wang
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
| | - Michelle S Frei
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany.,Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Aleksandar Salim
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany.,Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Kai Johnsson
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany.,Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
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100
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Affiliation(s)
- Seiji SAKAMOTO
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
| | - Itaru HAMACHI
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
- ERATO Innovative Molecular Technology for Neuroscience Project, Japan Science and Technology Agency (JST)
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