1
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Fang Y, Hillman AS, Fox JM. Advances in the Synthesis of Bioorthogonal Reagents: s-Tetrazines, 1,2,4-Triazines, Cyclooctynes, Heterocycloheptynes, and trans-Cyclooctenes. Top Curr Chem (Cham) 2024; 382:15. [PMID: 38703255 DOI: 10.1007/s41061-024-00455-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/01/2024] [Indexed: 05/06/2024]
Abstract
Aligned with the increasing importance of bioorthogonal chemistry has been an increasing demand for more potent, affordable, multifunctional, and programmable bioorthogonal reagents. More advanced synthetic chemistry techniques, including transition-metal-catalyzed cross-coupling reactions, C-H activation, photoinduced chemistry, and continuous flow chemistry, have been employed in synthesizing novel bioorthogonal reagents for universal purposes. We discuss herein recent developments regarding the synthesis of popular bioorthogonal reagents, with a focus on s-tetrazines, 1,2,4-triazines, trans-cyclooctenes, cyclooctynes, hetero-cycloheptynes, and -trans-cycloheptenes. This review aims to summarize and discuss the most representative synthetic approaches of these reagents and their derivatives that are useful in bioorthogonal chemistry. The preparation of these molecules and their derivatives utilizes both classical approaches as well as the latest organic chemistry methodologies.
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Affiliation(s)
- Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
| | - Ashlyn S Hillman
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
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2
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Gregor C, Grimm F, Rehman J, Wurm CA, Egner A. Click Chemistry with Cell-Permeable Fluorophores Expands the Choice of Bioorthogonal Markers for Two-Color Live-Cell STED Nanoscopy. Cells 2024; 13:683. [PMID: 38667298 PMCID: PMC11049381 DOI: 10.3390/cells13080683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/17/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
STED nanoscopy allows for the direct observation of dynamic processes in living cells and tissues with diffraction-unlimited resolution. Although fluorescent proteins can be used for STED imaging, these labels are often outperformed in photostability by organic fluorescent dyes. This feature is especially crucial for time-lapse imaging. Unlike fluorescent proteins, organic fluorophores cannot be genetically fused to a target protein but require different labeling strategies. To achieve simultaneous imaging of more than one protein in the interior of the cell with organic fluorophores, bioorthogonal labeling techniques and cell-permeable dyes are needed. In addition, the fluorophores should preferentially emit in the red spectral range to reduce the potential phototoxic effects that can be induced by the STED light, which further restricts the choice of suitable markers. In this work, we selected five different cell-permeable organic dyes that fulfill all of the above requirements and applied them for SPIEDAC click labeling inside living cells. By combining click-chemistry-based protein labeling with other orthogonal and highly specific labeling methods, we demonstrate two-color STED imaging of different target structures in living specimens using different dye pairs. The excellent photostability of the dyes enables STED imaging for up to 60 frames, allowing the observation of dynamic processes in living cells over extended time periods at super-resolution.
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Affiliation(s)
- Carola Gregor
- Department of Optical Nanoscopy, Institut für Nanophotonik Göttingen e.V., 37077 Göttingen, Germany;
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Florian Grimm
- Abberior GmbH, Hans-Adolf-Krebs Weg 1, 37077 Göttingen, Germany; (F.G.); (J.R.)
| | - Jasmin Rehman
- Abberior GmbH, Hans-Adolf-Krebs Weg 1, 37077 Göttingen, Germany; (F.G.); (J.R.)
| | - Christian A. Wurm
- Abberior GmbH, Hans-Adolf-Krebs Weg 1, 37077 Göttingen, Germany; (F.G.); (J.R.)
| | - Alexander Egner
- Department of Optical Nanoscopy, Institut für Nanophotonik Göttingen e.V., 37077 Göttingen, Germany;
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
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3
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Kozma E, Kele P. Bioorthogonal Reactions in Bioimaging. Top Curr Chem (Cham) 2024; 382:7. [PMID: 38400853 PMCID: PMC10894152 DOI: 10.1007/s41061-024-00452-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/22/2024] [Indexed: 02/26/2024]
Abstract
Visualization of biomolecules in their native environment or imaging-aided understanding of more complex biomolecular processes are one of the focus areas of chemical biology research, which requires selective, often site-specific labeling of targets. This challenging task is effectively addressed by bioorthogonal chemistry tools in combination with advanced synthetic biology methods. Today, the smart combination of the elements of the bioorthogonal toolbox allows selective installation of multiple markers to selected targets, enabling multicolor or multimodal imaging of biomolecules. Furthermore, recent developments in bioorthogonally applicable probe design that meet the growing demands of superresolution microscopy enable more complex questions to be addressed. These novel, advanced probes enable highly sensitive, low-background, single- or multiphoton imaging of biological species and events in live organisms at resolutions comparable to the size of the biomolecule of interest. Herein, the latest developments in bioorthogonal fluorescent probe design and labeling schemes will be discussed in the context of in cellulo/in vivo (multicolor and/or superresolved) imaging schemes. The second part focuses on the importance of genetically engineered minimal bioorthogonal tags, with a particular interest in site-specific protein tagging applications to answer biological questions.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group, Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, Budapest, 1117, Hungary
| | - Péter Kele
- Chemical Biology Research Group, Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, Budapest, 1117, Hungary.
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4
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Gifford LB, Melikyan GB. HIV-1 Capsid Uncoating Is a Multistep Process That Proceeds through Defect Formation Followed by Disassembly of the Capsid Lattice. ACS NANO 2024; 18:2928-2947. [PMID: 38241476 PMCID: PMC10832047 DOI: 10.1021/acsnano.3c07678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/21/2024]
Abstract
The HIV-1 core consists of a cone-shaped capsid shell made of capsid protein (CA) hexamers and pentamers encapsulating the viral genome. HIV-1 capsid disassembly, referred to as uncoating, is important for productive infection; however, the location, timing, and regulation of uncoating remain controversial. Here, we employ amber codon suppression to directly label CA. In addition, a fluid phase fluorescent probe is incorporated into the viral core to detect small defects in the capsid lattice. This double-labeling strategy enables the visualization of uncoating of single cores in vitro and in living cells, which we found to always proceed through at least two distinct steps─the formation of a defect in the capsid lattice that initiates gradual loss of CA below a detectable level. Importantly, intact cores containing the fluid phase and CA fluorescent markers enter and uncoat in the nucleus, as evidenced by a sequential loss of both markers, prior to establishing productive infection. This two-step uncoating process is observed in different cells, including a macrophage line. Notably, the lag between the release of fluid phase marker and terminal loss of CA appears to be independent of the cell type or reverse transcription and is much longer (>5-fold) for nuclear capsids compared to cell-free cores or cores in the cytosol, suggesting that the capsid lattice is stabilized by capsid-binding nuclear factors. Our results imply that intact HIV-1 cores enter the cell nucleus and that uncoating is initiated through a localized defect in the capsid lattice prior to a global loss of CA.
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Affiliation(s)
- Levi B. Gifford
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
| | - Gregory B. Melikyan
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
- Children’s
Healthcare of Atlanta, Atlanta, Georgia 30322, United States
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5
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Sterrenberg VT, Stalling D, Knaack JIH, Soh TK, Bosse JB, Meier C. A TriPPPro-Nucleotide Reporter with Optimized Cell-Permeable Dyes for Metabolic Labeling of Cellular and Viral DNA in Living Cells. Angew Chem Int Ed Engl 2023; 62:e202308271. [PMID: 37435767 DOI: 10.1002/anie.202308271] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
The metabolic labeling of nucleic acids in living cells is highly desirable to track the dynamics of nucleic acid metabolism in real-time and has the potential to provide novel insights into cellular biology as well as pathogen-host interactions. Catalyst-free inverse electron demand Diels-Alder reactions (iEDDA) with nucleosides carrying highly reactive moieties such as axial 2-trans-cyclooctene (2TCOa) would be an ideal tool to allow intracellular labeling of DNA. However, cellular kinase phosphorylation of the modified nucleosides is needed after cellular uptake as triphosphates are not membrane permeable. Unfortunately, the narrow substrate window of most endogenous kinases limits the use of highly reactive moieties. Here, we apply our TriPPPro (triphosphate pronucleotide) approach to directly deliver a highly reactive 2TCOa-modified 2'-deoxycytidine triphosphate reporter into living cells. We show that this nucleoside triphosphate is metabolically incorporated into de novo synthesized cellular and viral DNA and can be labeled with highly reactive and cell-permeable fluorescent dye-tetrazine conjugates via iEDDA to visualize DNA in living cells directly. Thus, we present the first comprehensive method for live-cell imaging of cellular and viral nucleic acids using a two-step labeling approach.
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Affiliation(s)
- Vincente T Sterrenberg
- Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Dörte Stalling
- CSSB Centre for Structural Systems Biology, Notkestraße 85, Building 15, 22607, Hamburg, Germany
- Institute of Virology, Hannover Medical School (MHH), 30625, Hannover, Germany
- Leibniz Institute of Virology (LIV), 20251, Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625, Hannover, Germany
| | - J Iven H Knaack
- Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Timothy K Soh
- CSSB Centre for Structural Systems Biology, Notkestraße 85, Building 15, 22607, Hamburg, Germany
- Institute of Virology, Hannover Medical School (MHH), 30625, Hannover, Germany
- Leibniz Institute of Virology (LIV), 20251, Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625, Hannover, Germany
| | - Jens B Bosse
- CSSB Centre for Structural Systems Biology, Notkestraße 85, Building 15, 22607, Hamburg, Germany
- Institute of Virology, Hannover Medical School (MHH), 30625, Hannover, Germany
- Leibniz Institute of Virology (LIV), 20251, Hamburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625, Hannover, Germany
| | - Chris Meier
- Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
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6
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Kozma E, Bojtár M, Kele P. Bioorthogonally Assisted Phototherapy: Recent Advances and Prospects. Angew Chem Int Ed Engl 2023; 62:e202303198. [PMID: 37161824 DOI: 10.1002/anie.202303198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/11/2023]
Abstract
Photoresponsive materials offer excellent spatiotemporal control over biological processes and the emerging phototherapeutic methods are expected to have significant effects on targeted cancer therapies. Recent examples show that combination of photoactivatable approaches with bioorthogonal chemistry enhances the precision of targeted phototherapies and profound implications are foreseen particularly in the treatment of disperse/diffuse tumors. The extra level of on-target selectivity and improved spatial/temporal control considerably intensified related bioorthogonally assisted phototherapy research. The anticipated growth of further developments in the field justifies the timeliness of a brief summary of the state of the art.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Márton Bojtár
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Péter Kele
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Magyar tudósok krt. 2, 1117, Budapest, Hungary
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7
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Koehler C, Sauter PF, Klasen B, Waldmann C, Pektor S, Bausbacher N, Lemke EA, Miederer M. Genetic Code Expansion for Site-Specific Labeling of Antibodies with Radioisotopes. ACS Chem Biol 2023; 18:443-448. [PMID: 36889678 PMCID: PMC10029752 DOI: 10.1021/acschembio.2c00634] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 02/27/2023] [Indexed: 03/10/2023]
Abstract
Due to their target specificity, antibody-drug conjugates─monoclonal antibodies conjugated to a cytotoxic moiety─are efficient therapeutics that can kill malignant cells overexpressing a target gene. Linking an antibody with radioisotopes (radioimmunoconjugates) enables powerful diagnostics and/or closely related therapeutic applications, depending on the isotope. To generate site-specific radioimmunoconjugates, we utilized genetic code expansion and subsequent conjugation by inverse electron-demand Diels-Alder cycloaddition reactions. We show that, using this approach, site-specific labeling of trastuzumab with either zirconium-89 (89Zr) for diagnostics or lutetium-177 (177Lu) for therapeutics yields efficient radioimmunoconjugates. Positron emission tomography imaging revealed a high accumulation of site-specifically 89Zr-labeled trastuzumab in tumors after 24 h and low accumulation in other organs. The corresponding 177Lu-trastuzumab radioimmunoconjugates were comparably distributed in vivo.
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Affiliation(s)
- Christine Koehler
- VERAXA
Biotech GmbH, Carl-Friedrich
Gauß-Ring 5, 69124 Heidelberg, Germany
- Structural
and Computational Biology Unit, European
Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Paul F. Sauter
- VERAXA
Biotech GmbH, Carl-Friedrich
Gauß-Ring 5, 69124 Heidelberg, Germany
- Structural
and Computational Biology Unit, European
Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Benedikt Klasen
- Department
of Chemistry, TRIGA site, Johannes Gutenberg
University, Fritz-Strassmann-Weg 2, 55128 Mainz, Germany
| | - Christopher Waldmann
- Department
of Nuclear Medicine, University Medical
Center, Johannes Gutenberg University Langenbeckstraße 1, 55131 Mainz, Germany
| | - Stefanie Pektor
- Department
of Nuclear Medicine, University Medical
Center, Johannes Gutenberg University Langenbeckstraße 1, 55131 Mainz, Germany
| | - Nicole Bausbacher
- Department
of Nuclear Medicine, University Medical
Center, Johannes Gutenberg University Langenbeckstraße 1, 55131 Mainz, Germany
| | - Edward A. Lemke
- BIOCENTER, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
- IMB
Institute
of Molecular Biology, gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Matthias Miederer
- Department
of Nuclear Medicine, University Medical
Center, Johannes Gutenberg University Langenbeckstraße 1, 55131 Mainz, Germany
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8
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Berkeley RF, Debelouchina GT. Chemical tools for study and modulation of biomolecular phase transitions. Chem Sci 2022; 13:14226-14245. [PMID: 36545140 PMCID: PMC9749140 DOI: 10.1039/d2sc04907d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022] Open
Abstract
Biomolecular phase transitions play an important role in organizing cellular processes in space and time. Methods and tools for studying these transitions, and the intrinsically disordered proteins (IDPs) that often drive them, are typically less developed than tools for studying their folded protein counterparts. In this perspective, we assess the current landscape of chemical tools for studying IDPs, with a specific focus on protein liquid-liquid phase separation (LLPS). We highlight methodologies that enable imaging and spectroscopic studies of these systems, including site-specific labeling with small molecules and the diverse range of capabilities offered by inteins and protein semisynthesis. We discuss strategies for introducing post-translational modifications that are central to IDP and LLPS function and regulation. We also investigate the nascent field of noncovalent small-molecule modulators of LLPS. We hope that this review of the state-of-the-art in chemical tools for interrogating IDPs and LLPS, along with an associated perspective on areas of unmet need, can serve as a valuable and timely resource for these rapidly expanding fields of study.
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Affiliation(s)
- Raymond F. Berkeley
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California San DiegoLa JollaCAUSA
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9
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Zhao G, Li Z, Zhang R, Zhou L, Zhao H, Jiang H. Tetrazine bioorthogonal chemistry derived in vivo imaging. Front Mol Biosci 2022; 9:1055823. [PMID: 36465558 PMCID: PMC9709424 DOI: 10.3389/fmolb.2022.1055823] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/26/2022] [Indexed: 09/02/2023] Open
Abstract
Bioorthogonal chemistry represents plenty of highly efficient and biocompatible reactions that proceed selectively and rapidly in biological situations without unexpected side reactions towards miscellaneous endogenous functional groups. Arise from the strict demands of physiological reactions, bioorthogonal chemical reactions are natively selective transformations that are rarely found in biological environments. Bioorthogonal chemistry has long been applied to tracking and real-time imaging of biomolecules in their physiological environments. Thereinto, tetrazine bioorthogonal reactions are particularly important and have increasing applications in these fields owing to their unique properties of easily controlled fluorescence or radiation off-on mechanism, which greatly facilitate the tracking of real signals without been disturbed by background. In this mini review, tetrazine bioorthogonal chemistry for in vivo imaging applications will be attentively appraised to raise some guidelines for prior tetrazine bioorthogonal chemical studies.
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Affiliation(s)
- Gaoxiang Zhao
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Cancer Institute, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhutie Li
- China United Test and Evaluation (Qingdao) Co. Ltd., Qingdao, China
| | - Renshuai Zhang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Cancer Institute, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Liman Zhou
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning, China
| | - Haibo Zhao
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Department of Sports Medicine, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hongfei Jiang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Cancer Institute, Affiliated Hospital of Qingdao University, Qingdao, China
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10
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Enhanced incorporation of subnanometer tags into cellular proteins for fluorescence nanoscopy via optimized genetic code expansion. Proc Natl Acad Sci U S A 2022; 119:e2201861119. [PMID: 35858298 PMCID: PMC9304028 DOI: 10.1073/pnas.2201861119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With few-nanometer resolution recently achieved by a new generation of fluorescence nanoscopes (MINFLUX and MINSTED), the size of the tags used to label proteins will increasingly limit the ability to dissect nanoscopic biological structures. Bioorthogonal (click) chemical groups are powerful tools for the specific detection of biomolecules. Through the introduction of an engineered aminoacyl–tRNA synthetase/tRNA pair (tRNA: transfer ribonucleic acid), genetic code expansion allows for the site-specific introduction of amino acids with “clickable” side chains into proteins of interest. Well-defined label positions and the subnanometer scale of the protein modification provide unique advantages over other labeling approaches for imaging at molecular-scale resolution. We report that, by pairing a new N-terminally optimized pyrrolysyl–tRNA synthetase (chPylRS
2020
) with a previously engineered orthogonal tRNA, clickable amino acids are incorporated with improved efficiency into bacteria and into mammalian cells. The resulting enhanced genetic code expansion machinery was used to label β-actin in U2OS cell filopodia for MINFLUX imaging with minimal separation of fluorophores from the protein backbone. Selected data were found to be consistent with previously reported high-resolution information from cryoelectron tomography about the cross-sectional filament bundling architecture. Our study underscores the need for further improvements to the degree of labeling with minimal-offset methods in order to fully exploit molecular-scale optical three-dimensional resolution.
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11
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Clark ET, Sievers EE, Debelouchina GT. A Chemical Biology Primer for NMR Spectroscopists. JOURNAL OF MAGNETIC RESONANCE OPEN 2022; 10-11:100044. [PMID: 35494416 PMCID: PMC9053072 DOI: 10.1016/j.jmro.2022.100044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Among structural biology techniques, NMR spectroscopy offers unique capabilities that enable the atomic resolution studies of dynamic and heterogeneous biological systems under physiological and native conditions. Complex biological systems, however, often challenge NMR spectroscopists with their low sensitivity, crowded spectra or large linewidths that reflect their intricate interaction patterns and dynamics. While some of these challenges can be overcome with the development of new spectroscopic approaches, chemical biology can also offer elegant and efficient solutions at the sample preparation stage. In this tutorial, we aim to present several chemical biology tools that enable the preparation of selectively and segmentally labeled protein samples, as well as the introduction of site-specific spectroscopic probes and post-translational modifications. The four tools covered here, namely cysteine chemistry, inteins, native chemical ligation, and unnatural amino acid incorporation, have been developed and optimized in recent years to be more efficient and applicable to a wider range of proteins than ever before. We briefly introduce each tool, describe its advantages and disadvantages in the context of NMR experiments, and offer practical advice for sample preparation and analysis. We hope that this tutorial will introduce beginning researchers in the field to the possibilities chemical biology can offer to NMR spectroscopists, and that it will inspire new and exciting applications in the quest to understand protein function in health and disease.
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Affiliation(s)
- Evan T. Clark
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Elanor E. Sievers
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, Division of Physical Sciences, University of California, San Diego, La Jolla, CA 92093, U.S.A
- Corresponding author: Galia Debelouchina, University of California, San Diego, Natural Sciences Building 4322, 9500 Gilman Dr., La Jolla, CA 92093, 858-534-3038,
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12
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Schultz M, Müller R, Ermakova Y, Hoffmann JE, Schultz C. Membrane-Permeant, Bioactivatable Coumarin Derivatives for In-Cell Labelling. Chembiochem 2022; 23:e202100699. [PMID: 35199435 PMCID: PMC9305936 DOI: 10.1002/cbic.202100699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/21/2022] [Indexed: 11/29/2022]
Abstract
The delivery of small molecule fluorophores with minimal compartmentalization is currently one of the most critical technical problems in intracellular labelling. Here we introduce sulfonated and phosphonated coumarin dyes, demonstrate rapid cell entry via a prodrug approach, and show a lack of interaction with membranes, organelles, or other compartments. The dyes show no specific localization and are evenly distributed in the cells. Our fluorogenic, clickable phosphonate derivatives successfully tagged model targets in intact cells and the increase in brightness upon click reaction was around 60‐fold.
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Affiliation(s)
- Madeleine Schultz
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, Germany
| | - Rainer Müller
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, Germany
| | - Yulia Ermakova
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, Germany
| | - Jan-Erik Hoffmann
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, Germany
| | - Carsten Schultz
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg, Germany.,Dept. of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
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13
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Arsić A, Hagemann C, Stajković N, Schubert T, Nikić-Spiegel I. Minimal genetically encoded tags for fluorescent protein labeling in living neurons. Nat Commun 2022; 13:314. [PMID: 35031604 PMCID: PMC8760255 DOI: 10.1038/s41467-022-27956-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 12/22/2021] [Indexed: 12/25/2022] Open
Abstract
Modern light microscopy, including super-resolution techniques, has brought about a demand for small labeling tags that bring the fluorophore closer to the target. This challenge can be addressed by labeling unnatural amino acids (UAAs) with bioorthogonal click chemistry. The minimal size of the UAA and the possibility to couple the fluorophores directly to the protein of interest with single-residue precision in living cells make click labeling unique. Here, we establish click labeling in living primary neurons and use it for fixed-cell, live-cell, dual-color pulse-chase, and super-resolution microscopy of neurofilament light chain (NFL). We also show that click labeling can be combined with CRISPR/Cas9 genome engineering for tagging endogenous NFL. Due to its versatile nature and compatibility with advanced multicolor microscopy techniques, we anticipate that click labeling will contribute to novel discoveries in the neurobiology field.
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Affiliation(s)
- Aleksandra Arsić
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076, Tübingen, Germany
- Graduate Training Centre of Neuroscience, International Max Planck Research School, University of Tübingen, Otfried-Müller-Straße 27, 72076, Tübingen, Germany
| | - Cathleen Hagemann
- Graduate Training Centre of Neuroscience, International Max Planck Research School, University of Tübingen, Otfried-Müller-Straße 27, 72076, Tübingen, Germany
| | - Nevena Stajković
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076, Tübingen, Germany
- Graduate Training Centre of Neuroscience, International Max Planck Research School, University of Tübingen, Otfried-Müller-Straße 27, 72076, Tübingen, Germany
| | - Timm Schubert
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076, Tübingen, Germany
- Institute for Ophthalmic Research, University of Tübingen, Elfriede-Aulhorn-Straße 7, 72076, Tübingen, Germany
| | - Ivana Nikić-Spiegel
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Otfried-Müller-Straße 25, 72076, Tübingen, Germany.
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14
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Kumar GS, Racioppi S, Zurek E, Lin Q. Superfast Tetrazole-BCN Cycloaddition Reaction for Bioorthogonal Protein Labeling on Live Cells. J Am Chem Soc 2022; 144:57-62. [PMID: 34964645 PMCID: PMC8982153 DOI: 10.1021/jacs.1c10354] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Here we report the design of a superfast bioorthogonal ligation reactant pair comprising a sterically shielded, sulfonated tetrazole and bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN). The design involves placing a pair of water-soluble N-sulfonylpyrrole substituents at the C-phenyl ring of diphenyltetrazoles to favor the photoinduced cycloaddition reaction over the competing nucleophilic additions. First-principles computations provide vital insights into the origin of the tetrazole-BCN cycloaddition's superior kinetics compared to the tetrazole-spirohexene cycloaddition. The tetrazole-BCN cycloaddition also enabled rapid bioorthogonal labeling of glucagon receptors on live cells in as little as 15 s.
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Affiliation(s)
- Gangam Srikanth Kumar
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Stefano Racioppi
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Eva Zurek
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
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15
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Tian Y, Fang M, Lin Q. Intracellular bioorthogonal labeling of glucagon receptor via tetrazine ligation. Bioorg Med Chem 2021; 43:116256. [PMID: 34153838 DOI: 10.1016/j.bmc.2021.116256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 01/21/2023]
Abstract
The third intracellular loop (ICL3) in the cytosolic face of glucagon receptor (GCGR) experiences significant conformational transition during receptor activation. It thus offers an attractive site for the introduction of organic fluorophores in our efforts to construct fluorescence-based GPCR biosensors. Herein, we report our confocal microscopic study of intracellular fluorescent labeling of ICL3 using a bioorthogonal chemistry strategy. Our approach involves the site-specific introduction of a strained alkene amino acid into the ICL3 through genetic code expansion, followed by a highly specific inverse electron-demand Diels-Alder reaction with the fluorescent tetrazine probes. Among the three strained alkene amino acids examined, both SphK and 2'-aTCOK offered successful fluorescent labeling of GCGR ICL3 with the appropriate tetrazine probes. At the same time, 4'-TCOK gave high background fluorescence due to its intracellular retention. The fluorescent tetrazine probes were designed following a computational model for background-free intracellular fluorescent labeling; however, their performance varied significantly in live-cell imaging as the strong non-specific signals interfered with the specific ones. Among all GCGR ICL3 mutants bearing a strained alkene, the H339SphK/2'-aTCOK mutants provided the best reaction partners for the BODIPY-Tz1/4 reagents in the bioorthogonal labeling reactions. The results from this study highlight the challenges in identifying bioorthogonal reactant pairs suitable for intracellular labeling of low-abundance receptors in live-cell imaging studies.
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Affiliation(s)
- Yulin Tian
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, United States; Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ming Fang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, United States.
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16
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Kim DM, Park JS, Jung SW, Yeom J, Yoo SM. Biosensing Applications Using Nanostructure-Based Localized Surface Plasmon Resonance Sensors. SENSORS (BASEL, SWITZERLAND) 2021; 21:3191. [PMID: 34064431 PMCID: PMC8125509 DOI: 10.3390/s21093191] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 01/06/2023]
Abstract
Localized surface plasmon resonance (LSPR)-based biosensors have recently garnered increasing attention due to their potential to allow label-free, portable, low-cost, and real-time monitoring of diverse analytes. Recent developments in this technology have focused on biochemical markers in clinical and environmental settings coupled with advances in nanostructure technology. Therefore, this review focuses on the recent advances in LSPR-based biosensor technology for the detection of diverse chemicals and biomolecules. Moreover, we also provide recent examples of sensing strategies based on diverse nanostructure platforms, in addition to their advantages and limitations. Finally, this review discusses potential strategies for the development of biosensors with enhanced sensing performance.
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Affiliation(s)
- Dong Min Kim
- Center for Applied Life Science, Hanbat National University, Daejeon 34158, Korea;
| | - Jong Seong Park
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (J.S.P.); (S.-W.J.); (J.Y.)
| | - Seung-Woon Jung
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (J.S.P.); (S.-W.J.); (J.Y.)
| | - Jinho Yeom
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (J.S.P.); (S.-W.J.); (J.Y.)
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (J.S.P.); (S.-W.J.); (J.Y.)
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17
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Gao Z, Li Y, Liu Z, Zhang Y, Chen F, An P, Lu W, Hu J, You C, Xu J, Zhang X, Sun B. Small-Molecule-Selective Organosilica Nanoreactors for Copper-Catalyzed Azide-Alkyne Cycloaddition Reactions in Cellular and Living Systems. NANO LETTERS 2021; 21:3401-3409. [PMID: 33843242 DOI: 10.1021/acs.nanolett.0c04930] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We reported the synthesis of a tris(triazolylmethyl)amine (TTA)-bridged organosilane, functioning as Cu(I)-stabilizing ligands, and the installation of this building block into the backbone of mesoporous organosilica nanoparticles (TTASi) by a sol-gel way. Upon coordinating with Cu(I), the mesoporous CuI-TTASi, with a restricted metal active center inside the pore, functions as a molecular-sieve-typed nanoreactor to efficiently perform Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reactions on small-molecule substrates but fails to work on macromolecules larger than the pore diameter. As a proof of concept, we witnessed the advantages of selective nanoreactors in screening protein substrates for small molecules. Also, the robust CuI-TTASi could be implanted into the body of animal models including zebrafish and mice as biorthogonal catalysts without apparent toxicity, extending its utilization in vivo ranging from fluorescent labeling to in situ drug synthesis.
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Affiliation(s)
- Zhiguo Gao
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Yaojia Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Zhikun Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Yu Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Fanghui Chen
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Peijing An
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Wenjun Lu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Jinzhong Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
| | - Chaoqun You
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Jun Xu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Baiwang Sun
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210089, PR China
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18
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Reinkemeier CD, Koehler C, Sauter PF, Shymanska NV, Echalier C, Rutkowska A, Will DW, Schultz C, Lemke EA. Synthesis and Evaluation of Novel Ring-Strained Noncanonical Amino Acids for Residue-Specific Bioorthogonal Reactions in Living Cells. Chemistry 2021; 27:6094-6099. [PMID: 33577120 PMCID: PMC8049044 DOI: 10.1002/chem.202100322] [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: 01/26/2021] [Indexed: 12/13/2022]
Abstract
Bioorthogonal reactions are ideally suited to selectively modify proteins in complex environments, even in vivo. Kinetics and product stability of these reactions are crucial parameters to evaluate their usefulness for specific applications. Strain promoted inverse electron demand Diels–Alder cycloadditions (SPIEDAC) between tetrazines and strained alkenes or alkynes are particularly popular, as they allow ultrafast labeling inside cells. In combination with genetic code expansion (GCE)‐a method that allows to incorporate noncanonical amino acids (ncAAs) site‐specifically into proteins in vivo. These reactions enable residue‐specific fluorophore attachment to proteins in living mammalian cells. Several SPIEDAC capable ncAAs have been presented and studied under diverse conditions, revealing different instabilities ranging from educt decomposition to product loss due to β‐elimination. To identify which compounds yield the best labeling inside living mammalian cells has frequently been difficult. In this study we present a) the synthesis of four new SPIEDAC reactive ncAAs that cannot undergo β‐elimination and b) a fluorescence flow cytometry based FRET‐assay to measure reaction kinetics inside living cells. Our results, which at first sight can be seen conflicting with some other studies, capture GCE‐specific experimental conditions, such as long‐term exposure of the ring‐strained ncAA to living cells, that are not taken into account in other assays.
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Affiliation(s)
- Christopher D. Reinkemeier
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- Biocentre, Departments of Biology and Chemistry JohannesGutenberg-University MainzHanns-Dieter-Hüsch-Weg 1755128MainzGermany
- Institute of Molecular BiologyAckermannweg 455128MainzGermany
| | - Christine Koehler
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- Biocentre, Departments of Biology and Chemistry JohannesGutenberg-University MainzHanns-Dieter-Hüsch-Weg 1755128MainzGermany
- Institute of Molecular BiologyAckermannweg 455128MainzGermany
- ARAXA Biosciences GmbHMeyerhofstraße 169117HeidelbergGermany
| | - Paul F. Sauter
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- ARAXA Biosciences GmbHMeyerhofstraße 169117HeidelbergGermany
| | | | - Cecile Echalier
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
| | - Anna Rutkowska
- Cellzome GmbHGlaxoSmithKlineMeyerhofstrasse 169117HeidelbergGermany
| | - David W. Will
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
| | - Carsten Schultz
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- Department of Chemical Physiology and BiochemistryOregon Health & Science University (OHSU)PortlandOregon97239-3098USA
| | - Edward A. Lemke
- European Molecular Biology LaboratoryMeyerhofstr.169117HeidelbergGermany
- Biocentre, Departments of Biology and Chemistry JohannesGutenberg-University MainzHanns-Dieter-Hüsch-Weg 1755128MainzGermany
- Institute of Molecular BiologyAckermannweg 455128MainzGermany
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19
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Deb T, Tu J, Franzini RM. Mechanisms and Substituent Effects of Metal-Free Bioorthogonal Reactions. Chem Rev 2021; 121:6850-6914. [DOI: 10.1021/acs.chemrev.0c01013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Titas Deb
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Julian Tu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M. Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
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20
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Abstract
Genetic code expansion is one of the most powerful technologies in protein engineering. In addition to the 20 canonical amino acids, the expanded genetic code is supplemented by unnatural amino acids, which have artificial side chains that can be introduced into target proteins in vitro and in vivo. A wide range of chemical groups have been incorporated co-translationally into proteins in single cells and multicellular organisms by using genetic code expansion. Incorporated unnatural amino acids have been used for novel structure-function relationship studies, bioorthogonal labelling of proteins in cellulo for microscopy and in vivo for tissue-specific proteomics, the introduction of post-translational modifications and optical control of protein function, to name a few examples. In this Minireview, the development of genetic code expansion technology is briefly introduced, then its applications in neurobiology are discussed, with a focus on studies using mammalian cells and mice as model organisms.
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Affiliation(s)
- Ivana Nikić‐Spiegel
- Werner Reichardt Centre for Integrative NeuroscienceUniversity of TübingenOtfried-Müller-Strasse 2572076TübingenGermany
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21
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Baalmann M, Neises L, Bitsch S, Schneider H, Deweid L, Werther P, Ilkenhans N, Wolfring M, Ziegler MJ, Wilhelm J, Kolmar H, Wombacher R. A Bioorthogonal Click Chemistry Toolbox for Targeted Synthesis of Branched and Well-Defined Protein-Protein Conjugates. Angew Chem Int Ed Engl 2020; 59:12885-12893. [PMID: 32342666 PMCID: PMC7496671 DOI: 10.1002/anie.201915079] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/23/2020] [Indexed: 01/19/2023]
Abstract
Bioorthogonal chemistry holds great potential to generate difficult-to-access protein-protein conjugate architectures. Current applications are hampered by challenging protein expression systems, slow conjugation chemistry, use of undesirable catalysts, or often do not result in quantitative product formation. Here we present a highly efficient technology for protein functionalization with commonly used bioorthogonal motifs for Diels-Alder cycloaddition with inverse electron demand (DAinv ). With the aim of precisely generating branched protein chimeras, we systematically assessed the reactivity, stability and side product formation of various bioorthogonal chemistries directly at the protein level. We demonstrate the efficiency and versatility of our conjugation platform using different functional proteins and the therapeutic antibody trastuzumab. This technology enables fast and routine access to tailored and hitherto inaccessible protein chimeras useful for a variety of scientific disciplines. We expect our work to substantially enhance antibody applications such as immunodetection and protein toxin-based targeted cancer therapies.
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Affiliation(s)
- Mathis Baalmann
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Laura Neises
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Sebastian Bitsch
- Institute for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiss-Straße 464287DarmstadtGermany
| | - Hendrik Schneider
- Institute for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiss-Straße 464287DarmstadtGermany
| | - Lukas Deweid
- Institute for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiss-Straße 464287DarmstadtGermany
| | - Philipp Werther
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Nadja Ilkenhans
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Martin Wolfring
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Michael J. Ziegler
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Jonas Wilhelm
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Harald Kolmar
- Institute for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiss-Straße 464287DarmstadtGermany
| | - Richard Wombacher
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
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22
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Müller D, Trucks S, Schwalbe H, Hengesbach M. Genetic Code Expansion Facilitates Position-Selective Modification of Nucleic Acids and Proteins. Chempluschem 2020; 85:1233-1243. [PMID: 32515171 DOI: 10.1002/cplu.202000150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/11/2020] [Indexed: 12/12/2022]
Abstract
Transcription and translation obey to the genetic code of four nucleobases and 21 amino acids evolved over billions of years. Both these processes have been engineered to facilitate the use of non-natural building blocks in both nucleic acids and proteins, enabling researchers with a decent toolbox for structural and functional analyses. Here, we review the most common approaches for how labeling of both nucleic acids as well as proteins in a site-selective fashion with either modifiable building blocks or spectroscopic probes can be facilitated by genetic code expansion. We emphasize methodological approaches and how these can be adapted for specific modifications, both during as well as after biomolecule synthesis. These modifications can facilitate, for example, a number of different spectroscopic analysis techniques and can under specific circumstances even be used in combination.
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Affiliation(s)
- Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
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23
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Baalmann M, Neises L, Bitsch S, Schneider H, Deweid L, Werther P, Ilkenhans N, Wolfring M, Ziegler MJ, Wilhelm J, Kolmar H, Wombacher R. A Bioorthogonal Click Chemistry Toolbox for Targeted Synthesis of Branched and Well‐Defined Protein–Protein Conjugates. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mathis Baalmann
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Laura Neises
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Sebastian Bitsch
- Institute for Organic Chemistry and Biochemistry Technische Universität Darmstadt Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Hendrik Schneider
- Institute for Organic Chemistry and Biochemistry Technische Universität Darmstadt Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Lukas Deweid
- Institute for Organic Chemistry and Biochemistry Technische Universität Darmstadt Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Philipp Werther
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Nadja Ilkenhans
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Martin Wolfring
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Michael J. Ziegler
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Jonas Wilhelm
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry Technische Universität Darmstadt Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
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24
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Lim BJ, Ackermann BE, Debelouchina GT. Targetable Tetrazine-Based Dynamic Nuclear Polarization Agents for Biological Systems. Chembiochem 2020; 21:1315-1319. [PMID: 31746101 PMCID: PMC7445144 DOI: 10.1002/cbic.201900609] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Indexed: 12/13/2022]
Abstract
Dynamic nuclear polarization (DNP) has shown great promise as a tool to enhance the nuclear magnetic resonance signals of proteins in the cellular environment. As sensitivity increases, the ability to select and efficiently polarize a specific macromolecule over the cellular background has become desirable. Herein, we address this need and present a tetrazine-based DNP agent that can be targeted selectively to proteins containing the unnatural amino acid (UAA) norbornene-lysine. This UAA can be introduced efficiently into the cellular milieu by genetic means. Our approach is bio-orthogonal and easily adaptable to any protein of interest. We illustrate the scope of our methodology and investigate the DNP transfer mechanisms in several biological systems. Our results shed light on the complex polarization-transfer pathways in targeted DNP and ultimately pave the way to selective DNP-enhanced NMR spectroscopy in both bacterial and mammalian cells.
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Affiliation(s)
- Byung Joon Lim
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bryce E. Ackermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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25
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Németh E, Knorr G, Németh K, Kele P. A Bioorthogonally Applicable, Fluorogenic, Large Stokes-Shift Probe for Intracellular Super-Resolution Imaging of Proteins. Biomolecules 2020; 10:biom10030397. [PMID: 32143419 PMCID: PMC7175155 DOI: 10.3390/biom10030397] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/28/2020] [Accepted: 03/01/2020] [Indexed: 01/02/2023] Open
Abstract
Herein, we present the synthesis and application of a fluorogenic, large Stokes-shift (>100 nm), bioorthogonally conjugatable, membrane-permeable tetrazine probe, which can be excited at common laser line 488 nm and detected at around 600 nm. The applied design enabled improved fluorogenicity in the orange/red emission range, thus efficient suppression of background and autofluorescence upon imaging biological samples. Moreover, unlike our previous advanced probes, it does not require the presence of special target platforms or microenvironments to achieve similar fluorogenicity and can be generally applied, e.g., on translationally bioorthogonalized proteins. Live-cell labeling schemes revealed that the fluorogenic probe is suitable for specific labeling of intracellular proteins, site-specifically modified with a cyclooctynylated, non-canonical amino acid, even under no-wash conditions. Furthermore, the probe was found to be applicable in stimulated emission depletion (STED) super-resolution microscopy imaging using a 660 nm depletion laser. Probably the most salient feature of this new probe is that the large Stokes-shift allows dual-color labeling schemes of cellular structures using distinct excitation and the same detection wavelengths for the combined probes, which circumvents chromatic aberration related problems.
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26
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Pigga JE, Fox JM. Flow Photochemical Syntheses of trans-Cyclooctenes and trans-Cycloheptenes Driven by Metal Complexation. Isr J Chem 2020; 60:207-218. [PMID: 34108738 PMCID: PMC8186252 DOI: 10.1002/ijch.201900085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Indexed: 12/19/2022]
Abstract
trans-Cyclooctenes and trans-cycloheptenes have long been the subject of physical organic study, but the broader application had been limited by synthetic accessibility. This account describes the development of a general, flow photochemical method for the preparative synthesis of trans-cycloalkene derivatives. Here, photoisom erization takes place in a closed-loop flow reactor where the reaction mixture is continuously cycled through Ag(I) on silica gel. Selective complexation of the trans-isomer by Ag(I) during flow drives an otherwise unfavorable isomeric ratio toward the trans-isomer. Analogous photoreactions under batch-conditions are low yielding, and flow chemistry is necessary in order to obtain trans-cycloalkenes in preparatively useful yields. The applications of the method to bioorthogonal chemistry and stereospecific transannulation chemistry are described.
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Affiliation(s)
- Jessica E Pigga
- Department of Chemistry and Biochemistry University of Delaware, Newark DE 19716
| | - Joseph M Fox
- Department of Chemistry and Biochemistry University of Delaware, Newark DE 19716
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27
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Abstract
The split inteins from the DnaE cyanobacterial family are efficient and versatile tools for protein engineering and chemical biology applications. Their ultrafast splicing kinetics allow for the efficient production of native proteins from two separate polypeptides both in vitro and in cells. They can also be used to generate proteins with C-terminal thioesters for downstream applications. In this chapter, we describe a method based on a genetically fused version of the DnaE intein Npu for the preparation of doubly modified proteins through recombinant expression. In particular, we provide protocols for the recombinant production of modified ubiquitin through amber suppression where fused Npu is used (1) as a traceless purification tag or (2) as a protein engineering tool to introduce C-terminal modifications for subsequent attachment to other proteins of interest. Our purification protocol allows for quick and facile separation of truncated products and eliminates the need for engineering protease cleavage sites. Our approach can be easily adapted to different proteins and applications where the simultaneous presence of internal and C-terminal modifications is desirable.
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28
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Lambert WD, Fang Y, Mahapatra S, Huang Z, Am Ende CW, Fox JM. Installation of Minimal Tetrazines through Silver-Mediated Liebeskind-Srogl Coupling with Arylboronic Acids. J Am Chem Soc 2019; 141:17068-17074. [PMID: 31603679 DOI: 10.1021/jacs.9b08677] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Described is a general method for the installation of a minimal 6-methyltetrazin-3-yl group via the first example of a Ag-mediated Liebeskind-Srogl cross-coupling. The attachment of bioorthogonal tetrazines on complex molecules typically relies on linkers that can negatively impact the physiochemical properties of conjugates. Cross-coupling with arylboronic acids and a new reagent, 3-((p-biphenyl-4-ylmethyl)thio)-6-methyltetrazine (b-Tz), proceeds under mild, PdCl2(dppf)-catalyzed conditions to introduce minimal, linker-free tetrazine functionality. Safety considerations guided our design of b-Tz which can be prepared on decagram scale without handling hydrazine and without forming volatile, high-nitrogen tetrazine byproducts. Replacing conventional Cu(I) salts used in Liebeskind-Srogl cross-coupling with a Ag2O mediator resulted in higher yields across a broad library of aryl and heteroaryl boronic acids and provides improved access to a fluorogenic tetrazine-BODIPY conjugate. A covalent probe for MAGL incorporating 6-methyltetrazinyl functionality was synthesized in high yield and labeled endogenous MAGL in live cells. This new Ag-mediated cross-coupling method using b-Tz is anticipated to find additional applications for directly introducing the tetrazine subunit to complex substrates.
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Affiliation(s)
- William D Lambert
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Yinzhi Fang
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Subham Mahapatra
- Pfizer Worldwide Research and Development , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Zhen Huang
- Pfizer Worldwide Research and Development , 1 Portland Street , Cambridge , Massachusetts 02139 , United States
| | - Christopher W Am Ende
- Pfizer Worldwide Research and Development , Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Joseph M Fox
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
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29
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Beliu G, Kurz AJ, Kuhlemann AC, Behringer-Pliess L, Meub M, Wolf N, Seibel J, Shi ZD, Schnermann M, Grimm JB, Lavis LD, Doose S, Sauer M. Bioorthogonal labeling with tetrazine-dyes for super-resolution microscopy. Commun Biol 2019; 2:261. [PMID: 31341960 PMCID: PMC6642216 DOI: 10.1038/s42003-019-0518-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/27/2019] [Indexed: 12/28/2022] Open
Abstract
Genetic code expansion (GCE) technology allows the specific incorporation of functionalized noncanonical amino acids (ncAAs) into proteins. Here, we investigated the Diels-Alder reaction between trans-cyclooct-2-ene (TCO)-modified ncAAs, and 22 known and novel 1,2,4,5-tetrazine-dye conjugates spanning the entire visible wavelength range. A hallmark of this reaction is its fluorogenicity - the tetrazine moiety can elicit substantial quenching of the dye. We discovered that photoinduced electron transfer (PET) from the excited dye to tetrazine is the main quenching mechanism in red-absorbing oxazine and rhodamine derivatives. Upon reaction with dienophiles quenching interactions are reduced resulting in a considerable increase in fluorescence intensity. Efficient and specific labeling of all tetrazine-dyes investigated permits super-resolution microscopy with high signal-to-noise ratio even at the single-molecule level. The different cell permeability of tetrazine-dyes can be used advantageously for specific intra- and extracellular labeling of proteins and highly sensitive fluorescence imaging experiments in fixed and living cells.
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Affiliation(s)
- Gerti Beliu
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Andreas J. Kurz
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Alexander C. Kuhlemann
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lisa Behringer-Pliess
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Mara Meub
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Natalia Wolf
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jürgen Seibel
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Zhen-Dan Shi
- Imaging Probe Development Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD 20850 USA
| | - Martin Schnermann
- Center for Cancer Research, Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702 USA
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147 USA
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147 USA
| | - Sören Doose
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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30
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Nödling AR, Spear LA, Williams TL, Luk LYP, Tsai YH. Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells. Essays Biochem 2019; 63:237-266. [PMID: 31092687 PMCID: PMC6610526 DOI: 10.1042/ebc20180042] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Genetic code expansion allows unnatural (non-canonical) amino acid incorporation into proteins of interest by repurposing the cellular translation machinery. The development of this technique has enabled site-specific incorporation of many structurally and chemically diverse amino acids, facilitating a plethora of applications, including protein imaging, engineering, mechanistic and structural investigations, and functional regulation. Particularly, genetic code expansion provides great tools to study mammalian proteins, of which dysregulations often have important implications in health. In recent years, a series of methods has been developed to modulate protein function through genetically incorporated unnatural amino acids. In this review, we will first discuss the basic concept of genetic code expansion and give an up-to-date list of amino acids that can be incorporated into proteins in mammalian cells. We then focus on the use of unnatural amino acids to activate, inhibit, or reversibly modulate protein function by translational, optical or chemical control. The features of each approach will also be highlighted.
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Affiliation(s)
| | - Luke A Spear
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Thomas L Williams
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
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31
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Reille-Seroussi M, Mayer SV, Dörner W, Lang K, Mootz HD. Expanding the genetic code with a lysine derivative bearing an enzymatically removable phenylacetyl group. Chem Commun (Camb) 2019; 55:4793-4796. [PMID: 30945708 DOI: 10.1039/c9cc00475k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We report the genetically encoded incorporation of phenylacetyl protected lysine (PacK) into proteins in Escherichia coli. This unnatural side-chain modification can be enzymatically removed using either penicillin G acylase (PGA) or, surprisingly, the sirtuin SrtN from Bacillus subtilis. Our approach expands the toolbox to reversibly control protein structure and function under very mild and non-denaturing conditions, as demonstrated by triggering the activity of the nonribosomal peptide synthetase GrsA.
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Affiliation(s)
- Marie Reille-Seroussi
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany.
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32
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Devaraj NK. The Future of Bioorthogonal Chemistry. ACS CENTRAL SCIENCE 2018; 4:952-959. [PMID: 30159392 PMCID: PMC6107859 DOI: 10.1021/acscentsci.8b00251] [Citation(s) in RCA: 320] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Indexed: 05/18/2023]
Abstract
Bioorthogonal reactions have found widespread use in applications ranging from glycan engineering to in vivo imaging. Researchers have devised numerous reactions that can be predictably performed in a biological setting. Depending on the requirements of the intended application, one or more reactions from the available toolkit can be readily deployed. As an increasing number of investigators explore and apply chemical reactions in living systems, it is clear that there are a myriad of ways in which the field may advance. This article presents an outlook on the future of bioorthogonal chemistry. I discuss currently emerging opportunities and speculate on how bioorthogonal reactions might be applied in research and translational settings. I also outline hurdles that must be cleared if progress toward these goals is to be made. Given the incredible past successes of bioorthogonal chemistry and the rapid pace of innovations in the field, the future is undoubtedly very bright.
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33
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Hoffmann JE, Dziuba D, Stein F, Schultz C. A Bifunctional Noncanonical Amino Acid: Synthesis, Expression, and Residue-Specific Proteome-wide Incorporation. Biochemistry 2018; 57:4747-4752. [PMID: 29932646 DOI: 10.1021/acs.biochem.8b00397] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mapping of weak and hence transient interactions between low-abundance interacting molecules is still a major challenge in systems biology and protein biochemistry. Therefore, additional system-wide acting tools are needed to determine protein interactomics. Most important are reagents that can be applied at any kind of protein interface and the possibility to enrich cross-linked fragments with high efficiency. In this study, we report the synthesis of a novel noncanonical amino acid that features a diazirine group for ultraviolet cross-linking as well as an alkyne group for labeling by click chemistry. This bifunctional amino acid, called PrDiAzK, may be inserted into almost any protein interface with minimal structural perturbation using genetic code expansion. We demonstrate that PrDiAzK can be site-selectively incorporated into proteins in both bacterial and mammalian cell cultures, and we show that PrDiAzK allows protein labeling as well as cross-linking. In addition, we tested PrDiAzK for proteome-wide incorporation via stochastic orthogonal recoding of translation, implying potential applications in system-wide mapping of protein-protein interactions in the future.
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Affiliation(s)
- Jan-Erik Hoffmann
- Department of Physiology & Pharmacology , Oregon Health & Science University , L334, 3181 Southwest Sam Jackson Park Road , Portland , Oregon 97239-3098 , United States
| | - Dmytro Dziuba
- European Molecular Biology Laboratory , Cell Biology & Biophysics Unit , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
| | - Frank Stein
- European Molecular Biology Laboratory , Cell Biology & Biophysics Unit , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
| | - Carsten Schultz
- Department of Physiology & Pharmacology , Oregon Health & Science University , L334, 3181 Southwest Sam Jackson Park Road , Portland , Oregon 97239-3098 , United States.,European Molecular Biology Laboratory , Cell Biology & Biophysics Unit , Meyerhofstrasse 1 , 69117 Heidelberg , Germany
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34
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Kormos A, Koehler C, Fodor EA, Rutkai ZR, Martin ME, Mező G, Lemke EA, Kele P. Bistetrazine-Cyanines as Double-Clicking Fluorogenic Two-Point Binder or Crosslinker Probes. Chemistry 2018; 24:8841-8847. [PMID: 29676491 DOI: 10.1002/chem.201800910] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Indexed: 12/20/2022]
Abstract
Fluorogenic probes can be used to minimize the background fluorescence of unreacted and nonspecifically adsorbed reagents. The preceding years have brought substantial developments in the design and synthesis of bioorthogonally applicable fluorogenic systems mainly based on the quenching effects of azide and tetrazine moieties. The modulation power exerted by these bioorthogonal motifs typically becomes less efficient on more conjugated systems; that is, on probes with redshifted emission wavelength. To reach efficient quenching, that is, fluorogenicity, even in the red range of the spectrum, we present the synthesis, fluorogenic, and conjugation characterization of bistetrazine-cyanine probes with emission maxima between 600 and 620 nm. The probes can bind to genetically altered proteins harboring an 11-amino acid peptide tag with two appending cyclooctyne motifs. Moreover, we also demonstrate the use of these bistetrazines as fluorogenic, covalent cross-linkers between monocyclooctynylated proteins.
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Affiliation(s)
- Attila Kormos
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., 1117, Budapest, Hungary
| | - Christine Koehler
- Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University Mainz, Johannes-von-Mullerweg 6, 55128, Mainz, Germany.,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Eszter A Fodor
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., 1117, Budapest, Hungary
| | - Zsófia R Rutkai
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., 1117, Budapest, Hungary
| | - Madison E Martin
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., 1117, Budapest, Hungary
| | - Gábor Mező
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Pázmány Péter sétány 1a, 1117, Budapest, Hungary
| | - Edward A Lemke
- Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University Mainz, Johannes-von-Mullerweg 6, 55128, Mainz, Germany.,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Péter Kele
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., 1117, Budapest, Hungary
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35
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Oliveira BL, Guo Z, Bernardes GJL. Inverse electron demand Diels-Alder reactions in chemical biology. Chem Soc Rev 2018; 46:4895-4950. [PMID: 28660957 DOI: 10.1039/c7cs00184c] [Citation(s) in RCA: 628] [Impact Index Per Article: 104.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emerging inverse electron demand Diels-Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility. With the recent discovery of novel dienophiles and optimal tetrazine coupling partners, attention has now been turned to the use of IEDDA approaches in basic biology, imaging and therapeutics. Here we review this bioorthogonal reaction and its promising applications for live cell and animal studies. We first discuss the key factors that contribute to the fast IEDDA kinetics and describe the most recent advances in the synthesis of tetrazine and dienophile coupling partners. Both coupling partners have been incorporated into proteins for tracking and imaging by use of fluorogenic tetrazines that become strongly fluorescent upon reaction. Selected notable examples of such applications are presented. The exceptional fast kinetics of this catalyst-free reaction, even using low concentrations of coupling partners, make it amenable for in vivo radiolabelling using pretargeting methodologies, which are also discussed. Finally, IEDDA reactions have recently found use in bioorthogonal decaging to activate proteins or drugs in gain-of-function strategies. We conclude by showing applications of the IEDDA reaction in the construction of biomaterials that are used for drug delivery and multimodal imaging, among others. The use and utility of the IEDDA reaction is interdisciplinary and promises to revolutionize chemical biology, radiochemistry and materials science.
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Affiliation(s)
- B L Oliveira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Z Guo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - G J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. and Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, Lisboa, 1649-028, Portugal.
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36
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Kozma E, Estrada Girona G, Paci G, Lemke EA, Kele P. Bioorthogonal double-fluorogenic siliconrhodamine probes for intracellular super-resolution microscopy. Chem Commun (Camb) 2018; 53:6696-6699. [PMID: 28530747 DOI: 10.1039/c7cc02212c] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A series of double-fluorogenic siliconrhodamine probes were synthesized. These tetrazine-functionalized, membrane-permeable labels allowed site-specific bioorthogonal tagging of genetically manipulated intracellular proteins and subsequent imaging using super-resolution microscopy.
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Affiliation(s)
- E Kozma
- "Lendület" Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary.
| | - G Estrada Girona
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, D-69117, Germany
| | - G Paci
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, D-69117, Germany
| | - E A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, D-69117, Germany
| | - P Kele
- "Lendület" Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary.
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37
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Knorr G, Kozma E, Schaart JM, Németh K, Török G, Kele P. Bioorthogonally Applicable Fluorogenic Cyanine-Tetrazines for No-Wash Super-Resolution Imaging. Bioconjug Chem 2018; 29:1312-1318. [DOI: 10.1021/acs.bioconjchem.8b00061] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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38
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Lang K. Building Peptide Bonds in Haifa: The Seventh Chemical Protein Synthesis (CPS) Meeting. Chembiochem 2018; 19:115-120. [PMID: 29251813 DOI: 10.1002/cbic.201700606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Indexed: 01/24/2023]
Abstract
The power of CPS, live! More than 90 attendees from around the world came together in Haifa to present and hear about cutting-edge science in protein chemistry, from advances in synthetic methods to applications in biology and medicine. The meeting was a powerful demonstration that chemical protein synthesis can provide otherwise unattainable insights into protein structure and function.
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Affiliation(s)
- Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstrasse 4, 85748, Garching, Germany
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39
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Abstract
Genetic code expansion is commonly used to introduce bioorthogonal reactive functional groups onto proteins for labeling. In recent years, the inverse electron demand Diels-Alder reaction between tetrazines and strained trans-cyclooctenes has increased in popularity as a bioorthogonal ligation for protein labeling due to its fast reaction rate and high in vivo stability. We provide methods for the facile synthesis of a tetrazine containing amino acid, Tet-v2.0, and the site-specific incorporation of Tet-v2.0 into proteins via genetic code expansion. Furthermore, we demonstrate that proteins containing Tet-v2.0 can be quickly and efficiently reacted with strained alkene labels at low concentrations. This chemistry has enabled the labeling of protein surfaces with fluorophores, inhibitors, or common posttranslational modifications such as glycosylation or lipidation.
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40
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Koehler C, Lemke EA. MultiBacTAG-Genetic Code Expansion Using the Baculovirus Expression System in Sf21 Cells. Methods Mol Biol 2018; 1728:297-311. [PMID: 29405006 DOI: 10.1007/978-1-4939-7574-7_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The combination of genetic code expansion (GCE) and baculovirus-based protein expression in Spodoptera frugiperda cells is a powerful tool to express multiprotein complexes with site-specifically introduced noncanonical amino acids. This protocol describes the integration of synthetase and tRNA gene indispensable for GCE into the backbone of the Bacmid, the Tn7-mediated transposition of various genes of interest, as well as the final expression of protein using the MultiBacTAG system with different noncanonical amino acids.
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Affiliation(s)
- Christine Koehler
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University, Johannes-von-Mullerweg 6, Mainz, Germany.,Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany. .,Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University, Johannes-von-Mullerweg 6, Mainz, Germany. .,Institute of Molecular Biology (IMB), 55128, Mainz, Germany.
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41
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Nikić-Spiegel I. Genetic Code Expansion- and Click Chemistry-Based Site-Specific Protein Labeling for Intracellular DNA-PAINT Imaging. Methods Mol Biol 2018; 1728:279-295. [PMID: 29405005 DOI: 10.1007/978-1-4939-7574-7_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Super-resolution microscopy allows imaging of cellular structures at nanometer resolution. This comes with a demand for small labels which can be attached directly to the structures of interest. In the context of protein labeling, one way to achieve this is by using genetic code expansion (GCE) and click chemistry. With GCE, small labeling handles in the form of noncanonical amino acids (ncAAs) are site-specifically introduced into a target protein. In a subsequent step, these amino acids can be directly labeled with small organic dyes by click chemistry reactions. Click chemistry labeling can also be combined with other methods, such as DNA-PAINT in which a "clickable" oligonucleotide is first attached to the ncAA-bearing target protein and then labeled with complementary fluorescent oligonucleotides. This protocol will cover both aspects: I describe (1) how to encode ncAAs and perform intracellular click chemistry-based labeling with an improved GCE system for eukaryotic cells and (2) how to combine click chemistry-based labeling with DNA-PAINT super-resolution imaging. As an example, I show click-PAINT imaging of vimentin and low-abundance nuclear protein, nucleoporin 153.
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Affiliation(s)
- Ivana Nikić-Spiegel
- Werner Reichardt Centre for Integrative Neuroscience, The Eberhard Karls University of Tübingen, Tübingen, Germany.
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42
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Muttach F, Muthmann N, Reichert D, Anhäuser L, Rentmeister A. A benzylic linker promotes methyltransferase catalyzed norbornene transfer for rapid bioorthogonal tetrazine ligation. Chem Sci 2017; 8:7947-7953. [PMID: 29619168 PMCID: PMC5858020 DOI: 10.1039/c7sc03631k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/09/2017] [Indexed: 01/21/2023] Open
Abstract
Site-specific alkylation of complex biomolecules is critical for late-stage product diversification as well as post-synthetic labeling and manipulation of proteins and nucleic acids. Promiscuous methyltransferases in combination with analogs of S-adenosyl-l-methionine (AdoMet) can functionalize all major classes of biomolecules. We show that benzylic moieties are transferred by Ecm1 with higher catalytic efficiency than the natural AdoMet. A relative specificity of up to 80% is achieved when a norbornene moiety is placed in para-position, enabling for the first time enzymatic norbornene transfer to specific positions in DNA and RNA- even in cell lysate. Subsequent tetrazine ligation of the stable norbornene moiety is fast, efficient, biocompatible and - in combination with an appropriate tetrazine - fluorogenic.
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Affiliation(s)
- F Muttach
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - N Muthmann
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - D Reichert
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM) , University of Münster , Germany .
| | - L Anhäuser
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
| | - A Rentmeister
- University of Münster , Department of Chemistry , Institute of Biochemistry , Wilhelm-Klemm-Str. 2 , 48149 Münster , Germany .
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM) , University of Münster , Germany .
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43
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Brabham R, Fascione MA. Pyrrolysine Amber Stop-Codon Suppression: Development and Applications. Chembiochem 2017; 18:1973-1983. [DOI: 10.1002/cbic.201700148] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/28/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Robin Brabham
- York Structural Biology Laboratory; Department of Chemistry; University of York; Heslington Road York YO10 5DD UK
| | - Martin A. Fascione
- York Structural Biology Laboratory; Department of Chemistry; University of York; Heslington Road York YO10 5DD UK
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44
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Demeter O, Kormos A, Koehler C, Mező G, Németh K, Kozma E, Takács LB, Lemke EA, Kele P. Bisazide Cyanine Dyes as Fluorogenic Probes for Bis-Cyclooctynylated Peptide Tags and as Fluorogenic Cross-Linkers of Cyclooctynylated Proteins. Bioconjug Chem 2017; 28:1552-1559. [PMID: 28441009 DOI: 10.1021/acs.bioconjchem.7b00178] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Herein we present the synthesis and fluorogenic characterization of a series of double-quenched bisazide cyanine probes with emission maxima between 565 and 580 nm that can participate in covalent, two-point binding bioorthogonal tagging schemes in combination with bis-cyclooctynylated peptides. Compared to other fluorogenic cyanines, these double-quenched systems showed remarkable fluorescence intensity increase upon formation of cyclic dye-peptide conjugates. Furthermore, we also demonstrated that these bisazides are useful fluorogenic cross-linking platforms that are able to form a covalent linkage between monocyclooctynylated proteins.
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Affiliation(s)
- Orsolya Demeter
- "Lendület" Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Attila Kormos
- "Lendület" Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Christine Koehler
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69117, Heidelberg, Germany
| | - Gábor Mező
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences , Pázmány Péter sétány 1a, H-1117, Budapest, Hungary
| | - Krisztina Németh
- "Lendület" Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Eszter Kozma
- "Lendület" Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Levente B Takács
- "Lendület" Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory , Meyerhofstrasse 1, D-69117, Heidelberg, Germany
| | - Péter Kele
- "Lendület" Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok krt. 2, H-1117, Budapest, Hungary
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45
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Kozma E, Demeter O, Kele P. Bio-orthogonal Fluorescent Labelling of Biopolymers through Inverse-Electron-Demand Diels-Alder Reactions. Chembiochem 2017; 18:486-501. [PMID: 28070925 PMCID: PMC5363342 DOI: 10.1002/cbic.201600607] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 02/06/2023]
Abstract
Bio-orthogonal labelling schemes based on inverse-electron-demand Diels-Alder (IEDDA) cycloaddition have attracted much attention in chemical biology recently. The appealing features of this reaction, such as the fast reaction kinetics, fully bio-orthogonal nature and high selectivity, have helped chemical biologists gain deeper understanding of biochemical processes at the molecular level. Listing the components and discussing the possibilities and limitations of these reagents, we provide a recent snapshot of the field of IEDDA-based biomolecular manipulation with special focus on fluorescent modulation approaches through the use of bio-orthogonalized building blocks. At the end, we discuss challenges that need to be addressed for further developments in order to overcome recent limitations and to enable researchers to answer biomolecular questions in more detail.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research GroupInstitute of Organic ChemistryResearch Centre for Natural SciencesHungarian Academy of Sciences1117 Magyar tudósok krt. 2BudapestHungary
| | - Orsolya Demeter
- Chemical Biology Research GroupInstitute of Organic ChemistryResearch Centre for Natural SciencesHungarian Academy of Sciences1117 Magyar tudósok krt. 2BudapestHungary
| | - Péter Kele
- Chemical Biology Research GroupInstitute of Organic ChemistryResearch Centre for Natural SciencesHungarian Academy of Sciences1117 Magyar tudósok krt. 2BudapestHungary
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46
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Kipper K, Lundius EG, Ćurić V, Nikić I, Wiessler M, Lemke EA, Elf J. Application of Noncanonical Amino Acids for Protein Labeling in a Genomically Recoded Escherichia coli. ACS Synth Biol 2017; 6:233-255. [PMID: 27775882 DOI: 10.1021/acssynbio.6b00138] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small synthetic fluorophores are in many ways superior to fluorescent proteins as labels for imaging. A major challenge is to use them for a protein-specific labeling in living cells. Here, we report on our use of noncanonical amino acids that are genetically encoded via the pyrrolysyl-tRNA/pyrrolysyl-RNA synthetase pair at artificially introduced TAG codons in a recoded E. coli strain. The strain is lacking endogenous TAG codons and the TAG-specific release factor RF1. The amino acids contain bioorthogonal groups that can be clicked to externally supplied dyes, thus enabling protein-specific labeling in live cells. We find that the noncanonical amino acid incorporation into the target protein is robust for diverse amino acids and that the usefulness of the recoded E. coli strain mainly derives from the absence of release factor RF1. However, the membrane permeable dyes display high nonspecific binding in intracellular environment and the electroporation of hydrophilic nonmembrane permeable dyes severely impairs growth of the recoded strain. In contrast, proteins exposed on the outer membrane of E. coli can be labeled with hydrophilic dyes with a high specificity as demonstrated by labeling of the osmoporin OmpC. Here, labeling can be made sufficiently specific to enable single molecule studies as exemplified by OmpC single particle tracking.
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Affiliation(s)
- Kalle Kipper
- Department
of Molecular and Cell Biology, Science for Life Laboratory, Uppsala University, Se-751 24 Uppsala, Sweden
| | - Ebba G. Lundius
- Department
of Molecular and Cell Biology, Science for Life Laboratory, Uppsala University, Se-751 24 Uppsala, Sweden
| | - Vladimir Ćurić
- Department
of Molecular and Cell Biology, Science for Life Laboratory, Uppsala University, Se-751 24 Uppsala, Sweden
| | - Ivana Nikić
- Structural
and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
| | - Manfred Wiessler
- Biological
Chemistry, Deutsche Krebsforschungszentrum, Heidelberg, 69120, Germany
| | - Edward A. Lemke
- Structural
and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
| | - Johan Elf
- Department
of Molecular and Cell Biology, Science for Life Laboratory, Uppsala University, Se-751 24 Uppsala, Sweden
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47
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Nikić I, Estrada Girona G, Kang JH, Paci G, Mikhaleva S, Koehler C, Shymanska NV, Ventura Santos C, Spitz D, Lemke EA. Debugging Eukaryotic Genetic Code Expansion for Site-Specific Click-PAINT Super-Resolution Microscopy. Angew Chem Int Ed Engl 2016; 55:16172-16176. [PMID: 27804198 PMCID: PMC5215487 DOI: 10.1002/anie.201608284] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/20/2016] [Indexed: 01/29/2023]
Abstract
Super‐resolution microscopy (SRM) greatly benefits from the ability to install small photostable fluorescent labels into proteins. Genetic code expansion (GCE) technology addresses this demand, allowing the introduction of small labeling sites, in the form of uniquely reactive noncanonical amino acids (ncAAs), at any residue in a target protein. However, low incorporation efficiency of ncAAs and high background fluorescence limit its current SRM applications. Redirecting the subcellular localization of the pyrrolysine‐based GCE system for click chemistry, combined with DNA‐PAINT microscopy, enables the visualization of even low‐abundance proteins inside mammalian cells. This approach links a versatile, biocompatible, and potentially unbleachable labeling method with residue‐specific precision. Moreover, our reengineered GCE system eliminates untargeted background fluorescence and substantially boosts the expression yield, which is of general interest for enhanced protein engineering in eukaryotes using GCE.
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Affiliation(s)
- Ivana Nikić
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Present address: Werner Reichardt Centre for Integrative, Neuroscience, University of Tübingen, Tübingen, 72076, Germany
| | - Gemma Estrada Girona
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jun Hee Kang
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Giulia Paci
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Sofya Mikhaleva
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Christine Koehler
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Nataliia V Shymanska
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Camilla Ventura Santos
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Daniel Spitz
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
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48
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Nikić I, Estrada Girona G, Kang JH, Paci G, Mikhaleva S, Koehler C, Shymanska NV, Ventura Santos C, Spitz D, Lemke EA. Verbesserte Erweiterung des eukaryotischen genetischen Codes für seitenspezifische, hochauflösende Click-PAINT-Mikroskopie. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608284] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ivana Nikić
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
- Aktuelle Adresse: Werner Reichardt Zentrum für integrative Neurowissenschaften; Universität Tübingen; 72076 Tübingen Deutschland
| | - Gemma Estrada Girona
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Jun Hee Kang
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Giulia Paci
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Sofya Mikhaleva
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Christine Koehler
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Nataliia V. Shymanska
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Camilla Ventura Santos
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Daniel Spitz
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Edward A. Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
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49
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Peng T, Hang HC. Site-Specific Bioorthogonal Labeling for Fluorescence Imaging of Intracellular Proteins in Living Cells. J Am Chem Soc 2016; 138:14423-14433. [PMID: 27768298 DOI: 10.1021/jacs.6b08733] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Over the past years, fluorescent proteins (e.g., green fluorescent proteins) have been widely utilized to visualize recombinant protein expression and localization in live cells. Although powerful, fluorescent protein tags are limited by their relatively large sizes and potential perturbation to protein function. Alternatively, site-specific labeling of proteins with small-molecule organic fluorophores using bioorthogonal chemistry may provide a more precise and less perturbing method. This approach involves site-specific incorporation of unnatural amino acids (UAAs) into proteins via genetic code expansion, followed by bioorthogonal chemical labeling with small organic fluorophores in living cells. While this approach has been used to label extracellular proteins for live cell imaging studies, site-specific bioorthogonal labeling and fluorescence imaging of intracellular proteins in live cells is still challenging. Herein, we systematically evaluate site-specific incorporation of diastereomerically pure bioorthogonal UAAs bearing stained alkynes or alkenes into intracellular proteins for inverse-electron-demand Diels-Alder cycloaddition reactions with tetrazine-functionalized fluorophores for live cell labeling and imaging in mammalian cells. Our studies show that site-specific incorporation of axial diastereomer of trans-cyclooct-2-ene-lysine robustly affords highly efficient and specific bioorthogonal labeling with monosubstituted tetrazine fluorophores in live mammalian cells, which enabled us to image the intracellular localization and real-time dynamic trafficking of IFITM3, a small membrane-associated protein with only 137 amino acids, for the first time. Our optimized UAA incorporation and bioorthogonal labeling conditions also enabled efficient site-specific fluorescence labeling of other intracellular proteins for live cell imaging studies in mammalian cells.
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Affiliation(s)
- Tao Peng
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen 518055, China.,Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States
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50
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Bolbat A, Schultz C. Recent developments of genetically encoded optical sensors for cell biology. Biol Cell 2016; 109:1-23. [PMID: 27628952 DOI: 10.1111/boc.201600040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/06/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
Optical sensors are powerful tools for live cell research as they permit to follow the location, concentration changes or activities of key cellular players such as lipids, ions and enzymes. Most of the current sensor probes are based on fluorescence which provides great spatial and temporal precision provided that high-end microscopy is used and that the timescale of the event of interest fits the response time of the sensor. Many of the sensors developed in the past 20 years are genetically encoded. There is a diversity of designs leading to simple or sometimes complicated applications for the use in live cells. Genetically encoded sensors began to emerge after the discovery of fluorescent proteins, engineering of their improved optical properties and the manipulation of their structure through application of circular permutation. In this review, we will describe a variety of genetically encoded biosensor concepts, including those for intensiometric and ratiometric sensors based on single fluorescent proteins, Forster resonance energy transfer-based sensors, sensors utilising bioluminescence, sensors using self-labelling SNAP- and CLIP-tags, and finally tetracysteine-based sensors. We focus on the newer developments and discuss the current approaches and techniques for design and application. This will demonstrate the power of using optical sensors in cell biology and will help opening the field to more systematic applications in the future.
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Affiliation(s)
- Andrey Bolbat
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Heidelberg, 69117, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Heidelberg, 69117, Germany
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