1
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Sun M, Meng J, Bao W, Liu M, Li X, Wang Z, Ma Z, Wang X, Tian Z. Composite Mesoporous Silica Nanoparticles with Dual-color Afterglow for Cross-correlation-based Living Cell Imaging. Chemphyschem 2023; 24:e202200716. [PMID: 36404675 DOI: 10.1002/cphc.202200716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022]
Abstract
Room temperature phosphorescence (RTP) materials are characterized with emission after removing the excitation source. Such long-lived emission feature possesses great potential in biological fluorescence imaging because it enables a way regarding temporal dimension for separating the interference of autofluorescence and common noises typically encountered in conventional fluorescence imaging. Herein, we constructed a new type of mesoporous silica nanoparticles (MSNs)-based composite nanoparticles (NPs) with dual-color long-lived emission, namely millisecond-level green phosphorescence and sub-millisecond-level delayed red fluorescence by encapsulating a typical RTP dye and Rhodamine dye in the cavities of the MSNs with the former acting as energy donor (D) while the latter as acceptor (A). Benefiting from the close D-A proximity, energy match between the donor and the acceptor and the optimized D/A ratio in the composite NPs, efficient triplet-to-singlet Förster resonance energy transfer (TS-FRET) in the NPs occurred upon exciting the donor, which enabled dual-color long-lived emission. The preliminary results of dual-color correlation imaging of live cells based on such emission feature unequivocally verified the unique ability of such NPs for distinguishing the false positive generated by common emitters with single-color emission feature.
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Affiliation(s)
- Mingqi Sun
- School of Chemical Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jiaqi Meng
- School of Chemical Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Weier Bao
- School of Chemical Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ming Liu
- School of Chemical Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Xiaojuan Li
- School of Chemical Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Zicheng Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Zhecheng Ma
- School of Chemical Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Xuefei Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Zhiyuan Tian
- School of Chemical Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
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2
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Kikuchi K, Adair LD, Lin J, New EJ, Kaur A. Photochemical Mechanisms of Fluorophores Employed in Single-Molecule Localization Microscopy. Angew Chem Int Ed Engl 2023; 62:e202204745. [PMID: 36177530 PMCID: PMC10100239 DOI: 10.1002/anie.202204745] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 02/02/2023]
Abstract
Decoding cellular processes requires visualization of the spatial distribution and dynamic interactions of biomolecules. It is therefore not surprising that innovations in imaging technologies have facilitated advances in biomedical research. The advent of super-resolution imaging technologies has empowered biomedical researchers with the ability to answer long-standing questions about cellular processes at an entirely new level. Fluorescent probes greatly enhance the specificity and resolution of super-resolution imaging experiments. Here, we introduce key super-resolution imaging technologies, with a brief discussion on single-molecule localization microscopy (SMLM). We evaluate the chemistry and photochemical mechanisms of fluorescent probes employed in SMLM. This Review provides guidance on the identification and adoption of fluorescent probes in single molecule localization microscopy to inspire the design of next-generation fluorescent probes amenable to single-molecule imaging.
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Affiliation(s)
- Kai Kikuchi
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liam D Adair
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jiarun Lin
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Elizabeth J New
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Amandeep Kaur
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
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3
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Reille‐Seroussi M, Meyer‐Ahrens P, Aust A, Feldberg A, Mootz HD. Genetic Encoding and Enzymatic Deprotection of a Latent Thiol Side Chain to Enable New Protein Bioconjugation Applications. Angew Chem Int Ed Engl 2021; 60:15972-15979. [PMID: 33844389 PMCID: PMC8361980 DOI: 10.1002/anie.202102343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/09/2021] [Indexed: 12/11/2022]
Abstract
The thiol group of the cysteine side chain is arguably the most versatile chemical handle in proteins. To expand the scope of established and commercially available thiol bioconjugation reagents, we genetically encoded a second such functional moiety in form of a latent thiol group that can be unmasked under mild physiological conditions. Phenylacetamidomethyl (Phacm) protected homocysteine (HcP) was incorporated and its latent thiol group unmasked on purified proteins using penicillin G acylase (PGA). The enzymatic deprotection depends on steric accessibility, but can occur efficiently within minutes on exposed positions in flexible sequences. The freshly liberated thiol group does not require treatment with reducing agents. We demonstrate the potential of this approach for protein modification with conceptually new schemes for regioselective dual labeling, thiol bioconjugation in presence of a preserved disulfide bond and formation of a novel intramolecular thioether crosslink.
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Affiliation(s)
| | - Pascal Meyer‐Ahrens
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
| | - Annika Aust
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
| | - Anna‐Lena Feldberg
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
| | - Henning D. Mootz
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
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4
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Reille‐Seroussi M, Meyer‐Ahrens P, Aust A, Feldberg A, Mootz HD. Genetic Encoding and Enzymatic Deprotection of a Latent Thiol Side Chain to Enable New Protein Bioconjugation Applications. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Marie Reille‐Seroussi
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Pascal Meyer‐Ahrens
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Annika Aust
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Anna‐Lena Feldberg
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Henning D. Mootz
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
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5
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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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6
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Zhao Q, Guo G, Zhu W, Zhu L, Da Y, Han Y, Xu H, Wu S, Cheng Y, Zhou Y, Cai X, Jiang X. Suzuki Cross-Coupling Reaction with Genetically Encoded Fluorosulfates for Fluorogenic Protein Labeling. Chemistry 2020; 26:15938-15943. [PMID: 32776653 DOI: 10.1002/chem.202002037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/24/2020] [Indexed: 11/09/2022]
Abstract
A palladium-catalyzed cross-coupling reaction with aryl halide functionalities has recently emerged as a valuable tool for protein modification. Herein, a new fluorogenic modification methodology for proteins, with genetically encoded fluorosulfate-l-tyrosine, which exhibits high efficiency and biocompatibility in bacterial cells as well as in aqueous medium, is described. Furthermore, the cross-coupling of 4-cyanophenylboronic acid on green fluorescent protein was shown to possess a unique fluorogenic property, which could open up the possibility of a responsive "off/on" switch with great potential to enable spectroscopic imaging of proteins with minimal background noise. Taken together, a convenient and efficient catalytic system has been developed that may provide broad utilities in protein visualization and live-cell imaging.
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Affiliation(s)
- Qian Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Guoying Guo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Weiwei Zhu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Liping Zhu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, P.R. China
| | - Yifan Da
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Ying Han
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Hongjiao Xu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Shuohan Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Yaping Cheng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Yani Zhou
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, P.R. China
| | - Xiaoqing Cai
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
| | - Xianxing Jiang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P.R. China
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7
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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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8
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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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9
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Mideksa YG, Fottner M, Braus S, Weiß CAM, Nguyen TA, Meier S, Lang K, Feige MJ. Site-Specific Protein Labeling with Fluorophores as a Tool To Monitor Protein Turnover. Chembiochem 2020; 21:1861-1867. [PMID: 32011787 PMCID: PMC7383901 DOI: 10.1002/cbic.201900651] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 01/28/2020] [Indexed: 12/30/2022]
Abstract
Proteins that terminally fail to acquire their native structure are detected and degraded by cellular quality control systems. Insights into cellular protein quality control are key to a better understanding of how cells establish and maintain the integrity of their proteome and of how failures in these processes cause human disease. Here we have used genetic code expansion and fast bio‐orthogonal reactions to monitor protein turnover in mammalian cells through a fluorescence‐based assay. We have used immune signaling molecules (interleukins) as model substrates and shown that our approach preserves normal cellular quality control, assembly processes, and protein functionality and works for different proteins and fluorophores. We have further extended our approach to a pulse‐chase type of assay that can provide kinetic insights into cellular protein behavior. Taken together, this study establishes a minimally invasive method to investigate protein turnover in cells as a key determinant of cellular homeostasis.
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Affiliation(s)
- Yonatan G Mideksa
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Maximilian Fottner
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Sebastian Braus
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.,Current address: Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland
| | - Caroline A M Weiß
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Tuan-Anh Nguyen
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Susanne Meier
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.,Institute for Advanced Study, Technical University of Munich, Lichtenbergstr.2a, 85748, Garching, Germany
| | - Matthias J Feige
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.,Institute for Advanced Study, Technical University of Munich, Lichtenbergstr.2a, 85748, Garching, Germany
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10
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Chen Z, Chen M, Cheng Y, Kowada T, Xie J, Zheng X, Rao J. Exploring the Condensation Reaction between Aromatic Nitriles and Amino Thiols To Optimize In Situ Nanoparticle Formation for the Imaging of Proteases and Glycosidases in Cells. Angew Chem Int Ed Engl 2020; 59:3272-3279. [PMID: 31828913 DOI: 10.1002/anie.201913314] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Indexed: 12/31/2022]
Abstract
The condensation reaction between 6-hydroxy-2-cyanobenzothiazole (CBT) and cysteine has been shown for various applications such as site-specific protein labelling and in vivo cancer imaging. This report further expands the substrate scope of this reaction by varying the substituents on aromatic nitriles and amino thiols and testing their reactivity and ability to form nanoparticles for cell imaging. The structure-activity relationship study leads to the identification of the minimum structural requirement for the macrocyclization and assembly process in forming nanoparticles. One of the scaffolds made of 2-pyrimidinecarbonitrile and cysteine joined by a benzyl linker was applied to design fluorescent probes for imaging caspase-3/7 and β-galactosidase activity in live cells. These results demonstrate the generality of this system for imaging hydrolytic enzymes.
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Affiliation(s)
- Zixin Chen
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Min Chen
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yunfeng Cheng
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Toshiyuki Kowada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Jinghang Xie
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Xianchuang Zheng
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jianghong Rao
- Departments of Radiology and Chemistry, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA, 94305, USA
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11
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Chen Z, Chen M, Cheng Y, Kowada T, Xie J, Zheng X, Rao J. Exploring the Condensation Reaction between Aromatic Nitriles and Amino Thiols To Optimize In Situ Nanoparticle Formation for the Imaging of Proteases and Glycosidases in Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913314] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zixin Chen
- Departments of Radiology and Chemistry Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA 94305 USA
| | - Min Chen
- Departments of Radiology and Chemistry Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA 94305 USA
| | - Yunfeng Cheng
- Departments of Radiology and Chemistry Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA 94305 USA
| | - Toshiyuki Kowada
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University 2-1-1 Katahira, Aoba-ku Sendai Miyagi 980-8577 Japan
| | - Jinghang Xie
- Departments of Radiology and Chemistry Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA 94305 USA
| | - Xianchuang Zheng
- Departments of Radiology and Chemistry Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA 94305 USA
| | - Jianghong Rao
- Departments of Radiology and Chemistry Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA 94305 USA
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12
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Kugele A, Silkenath B, Langer J, Wittmann V, Drescher M. Protein Spin Labeling with a Photocaged Nitroxide Using Diels-Alder Chemistry. Chembiochem 2019; 20:2479-2484. [PMID: 31090999 PMCID: PMC6790680 DOI: 10.1002/cbic.201900318] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 12/31/2022]
Abstract
EPR spectroscopy of diamagnetic bio-macromolecules is based on site-directed spin labeling (SDSL). Herein, a novel labeling strategy for proteins is presented. A nitroxide-based spin label has been developed and synthesized that can be ligated to proteins by an inverse-electron-demand Diels-Alder (DAinv ) cycloaddition to genetically encoded noncanonical amino acids. The nitroxide moiety is shielded by a photoremovable protecting group with an attached tetra(ethylene glycol) unit to achieve water solubility. SDSL is demonstrated on two model proteins with the photoactivatable nitroxide for DAinv reaction (PaNDA) label. The strategy features high reaction rates, combined with high selectivity, and the possibility to deprotect the nitroxide in Escherichia coli lysate.
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Affiliation(s)
- Anandi Kugele
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Bjarne Silkenath
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Jakob Langer
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Valentin Wittmann
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Malte Drescher
- Department of Chemistry andKonstanz Research School Chemical Biology (KoRS-CB)University of KonstanzUniversitätsstrasse 1078457KonstanzGermany
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13
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Mayer SV, Murnauer A, Wrisberg M, Jokisch M, Lang K. Photo‐induced and Rapid Labeling of Tetrazine‐Bearing Proteins via Cyclopropenone‐Caged Bicyclononynes. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908209] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Susanne V. Mayer
- Center for Integrated Protein Science Munich (CIPSM) Department of Chemistry, Group of Synthetic Biochemistry Technical University of Munich Institute for Advanced Study Lichtenbergstr. 4 85748 Garching Germany
| | - Anton Murnauer
- Center for Integrated Protein Science Munich (CIPSM) Department of Chemistry, Group of Synthetic Biochemistry Technical University of Munich Institute for Advanced Study Lichtenbergstr. 4 85748 Garching Germany
| | - Marie‐Kristin Wrisberg
- Center for Integrated Protein Science Munich (CIPSM) Department of Chemistry, Group of Synthetic Biochemistry Technical University of Munich Institute for Advanced Study Lichtenbergstr. 4 85748 Garching Germany
| | - Marie‐Lena Jokisch
- Center for Integrated Protein Science Munich (CIPSM) Department of Chemistry, Group of Synthetic Biochemistry Technical University of Munich Institute for Advanced Study Lichtenbergstr. 4 85748 Garching Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM) Department of Chemistry, Group of Synthetic Biochemistry Technical University of Munich Institute for Advanced Study Lichtenbergstr. 4 85748 Garching Germany
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14
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Mayer SV, Murnauer A, von Wrisberg MK, Jokisch ML, Lang K. Photo-induced and Rapid Labeling of Tetrazine-Bearing Proteins via Cyclopropenone-Caged Bicyclononynes. Angew Chem Int Ed Engl 2019; 58:15876-15882. [PMID: 31476269 PMCID: PMC6856800 DOI: 10.1002/anie.201908209] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/21/2019] [Indexed: 12/22/2022]
Abstract
Inverse electron‐demand Diels–Alder cycloadditions (iEDDAC) between tetrazines and strained alkenes/alkynes have emerged as essential tools for studying and manipulating biomolecules. A light‐triggered version of iEDDAC (photo‐iEDDAC) is presented that confers spatio‐temporal control to bioorthogonal labeling in vitro and in cellulo. A cyclopropenone‐caged dibenzoannulated bicyclo[6.1.0]nonyne probe (photo‐DMBO) was designed that is unreactive towards tetrazines before light‐activation, but engages in iEDDAC after irradiation at 365 nm. Aminoacyl tRNA synthetase/tRNA pairs were discovered for efficient site‐specific incorporation of tetrazine‐containing amino acids into proteins in living cells. In situ light activation of photo‐DMBO conjugates allows labeling of tetrazine‐modified proteins in living E. coli. This allows proteins in living cells to be modified in a spatio‐temporally controlled manner and may be extended to photo‐induced and site‐specific protein labeling in animals.
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Affiliation(s)
- Susanne V Mayer
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Anton Murnauer
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Marie-Kristin von Wrisberg
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Marie-Lena Jokisch
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
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15
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16
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Chen Y, Tsao K, Acton SL, Keillor JW. A Green BODIPY-Based, Super-Fluorogenic, Protein-Specific Labelling Agent. Angew Chem Int Ed Engl 2018; 57:12390-12394. [DOI: 10.1002/anie.201805482] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/02/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Yingche Chen
- Department of Chemistry; University of Ottawa; 10 Marie-Curie Ottawa ON K1N 6N5 Canada
| | - Kelvin Tsao
- Department of Chemistry; University of Ottawa; 10 Marie-Curie Ottawa ON K1N 6N5 Canada
| | - Sydney L. Acton
- Department of Chemistry; University of Ottawa; 10 Marie-Curie Ottawa ON K1N 6N5 Canada
| | - Jeffrey W. Keillor
- Department of Chemistry; University of Ottawa; 10 Marie-Curie Ottawa ON K1N 6N5 Canada
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17
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Eising S, Xin BT, Kleinpenning F, Heming JJA, Florea BI, Overkleeft HS, Bonger KM. Coordination-Assisted Bioorthogonal Chemistry: Orthogonal Tetrazine Ligation with Vinylboronic Acid and a Strained Alkene. Chembiochem 2018; 19:1648-1652. [DOI: 10.1002/cbic.201800275] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Selma Eising
- Department of Biomolecular Chemistry; Institute for Molecules and Materials; Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Bo-Tao Xin
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Fleur Kleinpenning
- Department of Biomolecular Chemistry; Institute for Molecules and Materials; Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Jurriaan J. A. Heming
- Department of Biomolecular Chemistry; Institute for Molecules and Materials; Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Bogdan I. Florea
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Kimberly M. Bonger
- Department of Biomolecular Chemistry; Institute for Molecules and Materials; Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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18
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Gatterdam K, Joest EF, Gatterdam V, Tampé R. The Scaffold Design of Trivalent Chelator Heads Dictates Affinity and Stability for Labeling His-tagged Proteins in vitro and in Cells. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Karl Gatterdam
- Institute of Biochemistry; Biocenter; Goethe University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Eike F. Joest
- Institute of Biochemistry; Biocenter; Goethe University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Volker Gatterdam
- Institute of Biochemistry; Biocenter; Goethe University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Robert Tampé
- Institute of Biochemistry; Biocenter; Goethe University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
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19
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Gatterdam K, Joest EF, Gatterdam V, Tampé R. The Scaffold Design of Trivalent Chelator Heads Dictates Affinity and Stability for Labeling His-tagged Proteins in vitro and in Cells. Angew Chem Int Ed Engl 2018; 57:12395-12399. [PMID: 29845721 DOI: 10.1002/anie.201802746] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/01/2018] [Indexed: 11/08/2022]
Abstract
Small chemical/biological interaction pairs are at the forefront in tracing protein function and interaction at high signal-to-background ratios in cellular pathways. However, the optimal design of scaffold, linker, and chelator head still deserve systematic investigation to achieve the highest affinity and kinetic stability for in vitro and especially cellular applications. We report on a library of N-nitrilotriacetic acid (NTA)-based multivalent chelator heads (MCHs) built on linear, cyclic, and dendritic scaffolds and compare these with regard to their binding affinity and stability for the labeling of cellular His-tagged proteins. Furthermore, we describe a new approach for tracing cellular target proteins at picomolar probe concentrations in cells. Finally, we outline fundamental differences between the MCH scaffolds and define a cyclic trisNTA chelator that displays the highest affinity and kinetic stability of all reported reversible, low-molecular-weight interaction pairs.
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Affiliation(s)
- Karl Gatterdam
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Eike F Joest
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Volker Gatterdam
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
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20
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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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21
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Gatterdam K, Joest EF, Dietz MS, Heilemann M, Tampé R. Super-Chelators for Advanced Protein Labeling in Living Cells. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800827] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Karl Gatterdam
- Institute of Biochemistry; Biocenter; Goethe-University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Eike F. Joest
- Institute of Biochemistry; Biocenter; Goethe-University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Marina S. Dietz
- Institute of Physical and Theoretical Chemistry; Goethe-University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry; Goethe-University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
| | - Robert Tampé
- Institute of Biochemistry; Biocenter; Goethe-University Frankfurt; Max-von-Laue-Str. 9 60438 Frankfurt/M Germany
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22
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Gatterdam K, Joest EF, Dietz MS, Heilemann M, Tampé R. Super-Chelators for Advanced Protein Labeling in Living Cells. Angew Chem Int Ed Engl 2018; 57:5620-5625. [PMID: 29464841 DOI: 10.1002/anie.201800827] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/17/2018] [Indexed: 12/17/2022]
Abstract
Live-cell labeling, super-resolution microscopy, single-molecule applications, protein localization, or chemically induced assembly are emerging approaches, which require specific and very small interaction pairs. The minimal disturbance of protein function is essential to derive unbiased insights into cellular processes. Herein, we define a new class of hexavalent N-nitrilotriacetic acid (hexaNTA) chelators, displaying the highest affinity and stability of all NTA-based small interaction pairs described so far. Coupled to bright organic fluorophores with fine-tuned photophysical properties, the super-chelator probes were delivered into human cells by chemically gated nanopores. These super-chelators permit kinetic profiling, multiplexed labeling of His6 - and His12 -tagged proteins as well as single-molecule-based super-resolution imaging.
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Affiliation(s)
- Karl Gatterdam
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Eike F Joest
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Marina S Dietz
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M, Germany
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23
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Werther P, Möhler JS, Wombacher R. A Bifunctional Fluorogenic Rhodamine Probe for Proximity-Induced Bioorthogonal Chemistry. Chemistry 2017; 23:18216-18224. [DOI: 10.1002/chem.201703607] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Philipp Werther
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Jasper S. Möhler
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Richard Wombacher
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
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24
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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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25
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Virdee S. 2016 EMBO Chemical Biology Conference. Chembiochem 2016; 18:66-71. [PMID: 27862792 DOI: 10.1002/cbic.201600597] [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: 11/08/2016] [Indexed: 11/07/2022]
Abstract
The full breadth of the field: The 2016 EMBO Chemical Biology Conference, covering topics from tool development to biological applications and from computational drug design to synthetic chemistry, took place in Heidelberg from 31st August to 3rd September.
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Affiliation(s)
- Satpal Virdee
- University of Dundee, MRC Protein Phosphorylation and Ubiquitylation Unit, Dow Street, Dundee, DD1 5EH, UK
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26
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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: 110] [Impact Index Per Article: 13.8] [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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27
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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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28
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Fan X, Ge Y, Lin F, Yang Y, Zhang G, Ngai WSC, Lin Z, Zheng S, Wang J, Zhao J, Li J, Chen PR. Optimized Tetrazine Derivatives for Rapid Bioorthogonal Decaging in Living Cells. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xinyuan Fan
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - Yun Ge
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Feng Lin
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Yi Yang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Gong Zhang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - William Shu Ching Ngai
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Zhi Lin
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Siqi Zheng
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Jie Wang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - Jingyi Zhao
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - Jie Li
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Peng R. Chen
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
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29
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Fan X, Ge Y, Lin F, Yang Y, Zhang G, Ngai WSC, Lin Z, Zheng S, Wang J, Zhao J, Li J, Chen PR. Optimized Tetrazine Derivatives for Rapid Bioorthogonal Decaging in Living Cells. Angew Chem Int Ed Engl 2016; 55:14046-14050. [DOI: 10.1002/anie.201608009] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Xinyuan Fan
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - Yun Ge
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Feng Lin
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Yi Yang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Gong Zhang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - William Shu Ching Ngai
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Zhi Lin
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Siqi Zheng
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Jie Wang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - Jingyi Zhao
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
| | - Jie Li
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Peng R. Chen
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences; Beijing 100871 China
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30
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Kozma E, Nikić I, Varga BR, Aramburu IV, Kang JH, Fackler OT, Lemke EA, Kele P. Hydrophilic trans-Cyclooctenylated Noncanonical Amino Acids for Fast Intracellular Protein Labeling. Chembiochem 2016; 17:1518-24. [PMID: 27223658 DOI: 10.1002/cbic.201600284] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Indexed: 01/02/2023]
Abstract
Introduction of bioorthogonal functionalities (e.g., trans-cyclooctene-TCO) into a protein of interest by site-specific genetic encoding of non-canonical amino acids (ncAAs) creates uniquely targetable platforms for fluorescent labeling schemes in combination with tetrazine-functionalized dyes. However, fluorescent labeling of an intracellular protein is usually compromised by high background, arising from the hydrophobicity of ncAAs; this is typically compensated for by hours-long washout to remove excess ncAAs from the cellular interior. To overcome these problems, we designed, synthesized, and tested new, hydrophilic TCO-ncAAs. One derivative, DOTCO-lysine was genetically incorporated into proteins with good yield. The increased hydrophilicity shortened the excess ncAA washout time from hours to minutes, thus permitting rapid labeling and subsequent fluorescence microscopy.
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Affiliation(s)
- Eszter Kozma
- Hungarian Academy of Sciences, Research Centre for Natural Sciences, Institute of Organic Chemistry, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Ivana Nikić
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Balázs R Varga
- Hungarian Academy of Sciences, Research Centre for Natural Sciences, Institute of Organic Chemistry, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Iker Valle Aramburu
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jun Hee Kang
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Oliver T Fackler
- Center of Infectious Diseases, Integrative Virology, University of Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
| | - Péter Kele
- Hungarian Academy of Sciences, Research Centre for Natural Sciences, Institute of Organic Chemistry, Magyar tudósok krt. 2, 1117, Budapest, Hungary.
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31
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Knorr G, Kozma E, Herner A, Lemke EA, Kele P. New Red-Emitting Tetrazine-Phenoxazine Fluorogenic Labels for Live-Cell Intracellular Bioorthogonal Labeling Schemes. Chemistry 2016; 22:8972-9. [PMID: 27218228 DOI: 10.1002/chem.201600590] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Indexed: 11/09/2022]
Abstract
The synthesis of a set of tetrazine-bearing fluorogenic dyes suitable for intracellular labeling of proteins in live cells is presented. The red excitability and emission properties ensure minimal autofluorescence, while through-bond energy-transfer-based fluorogenicity reduces nonspecific background fluorescence of unreacted dyes. The tetrazine motif efficiently quenches fluorescence of the phenoxazine core, which can be selectively turned on chemically upon bioorthogonal inverse-electron-demand Diels-Alder reaction with proteins modified genetically with strained trans-cyclooctenes.
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Affiliation(s)
- Gergely Knorr
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Eszter Kozma
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - András Herner
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 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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32
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Varon Silva D. ECBS & ICBS 2015 Joint Meeting: Bringing Chemistry to Life. Chembiochem 2016; 17:447-52. [PMID: 26710339 DOI: 10.1002/cbic.201500684] [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: 09/14/2015] [Indexed: 01/11/2023]
Abstract
The European Chemical Biology Society (ECBS) and the International Chemical Biology Society (ICBS) recently organized a joint meeting in Berlin. This meeting had more than 250 participants. Four keynote lectures were given by Timothy Mitchison, David Tirrell, Carolyn Bertozzi and Jason Chin; in addition there were 13 invited speakers, 20 selected oral talks and 30 talks selected from 90 posters. The meeting was divided into six topics: chemoproteomics, epigenetics, conjugates for target delivering, anti-infectives, molecular imaging and probing the structure, and function of post-translational modifications. The highlights of the meeting are presented in this report.
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Affiliation(s)
- Daniel Varon Silva
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 01, 14476, Potsdam, Germany.
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33
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Wagner JA, Mercadante D, Nikić I, Lemke EA, Gräter F. Origin of Orthogonality of Strain-Promoted Click Reactions. Chemistry 2015; 21:12431-5. [PMID: 26178299 PMCID: PMC4600239 DOI: 10.1002/chem.201501727] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Indexed: 12/31/2022]
Abstract
Site-specific labeling of biomolecules is rapidly advancing due to the discovery of novel mutually orthogonal reactions. Quantum chemistry studies have also increased our understanding of their relative rates, although these have until now been based on highly simplified reactants. Here we examine a set of strain-promoted click-type cycloaddition reactions of n-propyl azide, 3-benzyl tetrazine and 3-benzyl-6-methyl tetrazine with cyclooctenes/ynes, in which we aim to address all relevant structural details of the reactants. Our calculations have included the obligatory handles used to attach the label and biomolecule as these can critically influence the stereochemistry and electron demand of the reaction. We systematically computed orbital gaps, activation and distortion energies using density functional theory and determined experimental rates for validation. Our results challenge the current paradigm of the inverse electron demand for this class of reactions. We found that the ubiquitous handles, when next to the triple bond of cyclooctynes, can switch the Diels-Alder type ligations to normal electron demand, a class we term as SPINEDAC reactions. Electron donating substituents on tetrazine can enhance normal demand but also increase distortion penalties. The presence and isomeric configuration of handles thus determine the reaction speed and regioselectivity. Our findings can be directly utilized in engineering genuine cycloaddition click chemistries for biological labeling.
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Affiliation(s)
- Johannes A Wagner
- Heidelberg Institute for Theoretical Studies69118 Heidelberg (Germany), Fax: (+49) 6221-533-298 E-mail:
- Institute for Theoretical Physics, Heidelberg University69120 Heidelberg (Germany)
| | - Davide Mercadante
- Heidelberg Institute for Theoretical Studies69118 Heidelberg (Germany), Fax: (+49) 6221-533-298 E-mail:
- Interdisciplinary Center for Scientific Computing69120 Heidelberg (Germany)
| | - Ivana Nikić
- European Molecular Biology Laboratory69117 Heidelberg (Germany)
| | - Edward A Lemke
- European Molecular Biology Laboratory69117 Heidelberg (Germany)
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies69118 Heidelberg (Germany), Fax: (+49) 6221-533-298 E-mail:
- Interdisciplinary Center for Scientific Computing69120 Heidelberg (Germany)
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34
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Hoffmann JE, Plass T, Nikić I, Aramburu IV, Koehler C, Gillandt H, Lemke EA, Schultz C. Highly Stabletrans-Cyclooctene Amino Acids for Live-Cell Labeling. Chemistry 2015; 21:12266-70. [DOI: 10.1002/chem.201501647] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 12/17/2022]
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35
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Wieneke R, Raulf A, Kollmannsperger A, Heilemann M, Tampé R. SLAP: Small Labeling Pair for Single-Molecule Super-Resolution Imaging. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201503215] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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36
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Wieneke R, Raulf A, Kollmannsperger A, Heilemann M, Tampé R. SLAP: Small Labeling Pair for Single-Molecule Super-Resolution Imaging. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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37
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Mühlberg M, Hoesl MG, Kuehne C, Dernedde J, Budisa N, Hackenberger CPR. Orthogonal dual-modification of proteins for the engineering of multivalent protein scaffolds. Beilstein J Org Chem 2015; 11:784-791. [PMID: 26124880 PMCID: PMC4464295 DOI: 10.3762/bjoc.11.88] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/05/2015] [Indexed: 01/12/2023] Open
Abstract
To add new tools to the repertoire of protein-based multivalent scaffold design, we have developed a novel dual-labeling strategy for proteins that combines residue-specific incorporation of unnatural amino acids with chemical oxidative aldehyde formation at the N-terminus of a protein. Our approach relies on the selective introduction of two different functional moieties in a protein by mutually orthogonal copper-catalyzed azide-alkyne cycloaddition (CuAAC) and oxime ligation. This method was applied to the conjugation of biotin and β-linked galactose residues to yield an enzymatically active thermophilic lipase, which revealed specific binding to Erythrina cristagalli lectin by SPR binding studies.
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Affiliation(s)
- Michaela Mühlberg
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustr. 3, 14195 Berlin, Germany
| | - Michael G Hoesl
- Technische Universität Berlin, AK Biokatalyse, Institut für Chemie, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Christian Kuehne
- Charité - Universitätsmedizin Berlin, Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Jens Dernedde
- Charité - Universitätsmedizin Berlin, Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nediljko Budisa
- Technische Universität Berlin, AK Biokatalyse, Institut für Chemie, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Christian P R Hackenberger
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany
- Humboldt Universität zu Berlin, Institut für Organische und Bioorganische Chemie, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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38
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Kennedy EJ. EMBO conference series: Chemical Biology 2014. Chembiochem 2014; 15:2783-7. [PMID: 25318996 DOI: 10.1002/cbic.201402527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Indexed: 11/07/2022]
Abstract
Around 300 people from 18 countries took part in the fourth biennial Chemical Biology conference at The European Molecular Biology Laboratory (EMBL) in Heidelberg, from August 20 to 23, 2014. Many advances in the field of chemical biology were presented in talks and poster sessions. Picture: Petra Riedinger (EMBL).
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Affiliation(s)
- Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 240 W. Green Street, Athens, GA 30602 (USA).
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39
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Chen Y, Clouthier CM, Tsao K, Strmiskova M, Lachance H, Keillor JW. Coumarin-based fluorogenic probes for no-wash protein labeling. Angew Chem Int Ed Engl 2014; 53:13785-8. [PMID: 25314130 DOI: 10.1002/anie.201408015] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Indexed: 12/25/2022]
Abstract
A fluorescent protein-labeling strategy was developed in which a protein of interest (POI) is genetically tagged with a short peptide sequence presenting two Cys residues that can selectively react with synthetic fluorogenic reagents. These fluorogens comprise a fluorophore and two maleimide groups that quench fluorescence until they both undergo thiol addition during the labeling reaction. Novel fluorogens were prepared and kinetically characterized to demonstrate the importance of a methoxy substituent on the maleimide in suppressing reactivity with glutathione, an intracellular thiol, while maintaining reactivity with the dithiol tag. This system allows the rapid and specific labeling of intracellular POIs.
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Affiliation(s)
- Yingche Chen
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5 (Canada)
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40
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Chen Y, Clouthier CM, Tsao K, Strmiskova M, Lachance H, Keillor JW. Coumarin-Based Fluorogenic Probes for No-Wash Protein Labeling. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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41
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Wang Q, Sun T, Xu J, Shen Z, Briggs SP, Zhou D, Wang L. Response and adaptation of Escherichia coli to suppression of the amber stop codon. Chembiochem 2014; 15:1744-9. [PMID: 25044429 PMCID: PMC4156322 DOI: 10.1002/cbic.201402235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Indexed: 11/08/2022]
Abstract
Some extant organisms reassign the amber stop codon to a sense codon through evolution, and suppression of the amber codon with engineered tRNAs has been exploited to expand the genetic code for incorporating non-canonical amino acids (ncAAs) in live systems. However, it is unclear how the host cells respond and adapt to such amber suppression. Herein we suppressed the amber codon in Escherichia coli with an orthogonal tRNA/synthetase pair and cultured the cells under such a pressure for about 500 generations. We discovered that E. coli quickly counteracted the suppression with transposon insertion to inactivate the orthogonal synthetase. Persistent amber suppression evading transposon inactivation led to global proteomic changes with a notable up-regulation of a previously uncharacterized protein (YdiI) for which we identified an unexpected function of expelling plasmids. These results should be valuable for understanding codon reassignment in genetic code evolution and for improving the efficiency of ncAA incorporation.
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Affiliation(s)
- Qian Wang
- Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193 (China)
| | - Tingting Sun
- Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing, 100191 (China)
| | - Jianfeng Xu
- Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Zhouxin Shen
- Section of Cell and Development Biology, University of California at San Diego, La Jolla, CA 92093 (USA)
| | - Steven P. Briggs
- Section of Cell and Development Biology, University of California at San Diego, La Jolla, CA 92093 (USA)
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing, 100191 (China)
| | - Lei Wang
- Jack H. Skirball Center for Chemical Biology & Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
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42
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Stone MB, Veatch SL. Far-red organic fluorophores contain a fluorescent impurity. Chemphyschem 2014; 15:2240-6. [PMID: 24782148 PMCID: PMC4180537 DOI: 10.1002/cphc.201402002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/06/2014] [Indexed: 11/06/2022]
Abstract
Far-red organic fluorophores commonly used in traditional and super-resolution localization microscopy are found to contain a fluorescent impurity with green excitation and near-red emission. This near-red fluorescent impurity can interfere with some multicolor stochastic optical reconstruction microscopy/photoactivated localization microscopy measurements in live cells and produce subtle artifacts in chemically fixed cells. We additionally describe alternatives to avoid artifacts in super-resolution localization microscopy.
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Affiliation(s)
- Matthew B. Stone
- Department of Biophysics, University of Michigan, 930 N University, Ann Arbor MI 48109
| | - Sarah L. Veatch
- Department of Biophysics, University of Michigan, 930 N University, Ann Arbor MI 48109
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43
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Rutkowska A, Plass T, Hoffmann JE, Yushchenko DA, Feng S, Schultz C. T-CrAsH: A Heterologous Chemical Crosslinker. Chembiochem 2014; 15:1765-8. [DOI: 10.1002/cbic.201402189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Indexed: 01/12/2023]
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44
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Milles S, Lemke EA. Mapping Multivalency and Differential Affinities within Large Intrinsically Disordered Protein Complexes with Segmental Motion Analysis. Angew Chem Int Ed Engl 2014; 53:7364-7. [DOI: 10.1002/anie.201403694] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Sigrid Milles
- Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg (Germany)
| | - Edward A. Lemke
- Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg (Germany)
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45
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Meimetis LG, Carlson JCT, Giedt RJ, Kohler RH, Weissleder R. Ultrafluorogenic coumarin-tetrazine probes for real-time biological imaging. Angew Chem Int Ed Engl 2014; 53:7531-4. [PMID: 24915832 DOI: 10.1002/anie.201403890] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Indexed: 01/08/2023]
Abstract
We have developed a series of new ultrafluorogenic probes in the blue-green region of the visible-light spectrum that display fluorescence enhancement exceeding 11,000-fold. These fluorogenic dyes integrate a coumarin fluorochrome with the bioorthogonal trans-cyclooctene(TCO)-tetrazine chemistry platform. By exploiting highly efficient through-bond energy transfer (TBET), these probes exhibit the highest brightness enhancements reported for any bioorthogonal fluorogenic dyes. No-wash, fluorogenic imaging of diverse targets including cell-surface receptors in cancer cells, mitochondria, and the actin cytoskeleton is possible within seconds, with minimal background signal and no appreciable nonspecific binding, opening the possibility for in vivo sensing.
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Affiliation(s)
- Labros G Meimetis
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114 (USA)
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46
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Meimetis LG, Carlson JCT, Giedt RJ, Kohler RH, Weissleder R. Ultrafluorogenic Coumarin-Tetrazine Probes for Real-Time Biological Imaging. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403890] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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47
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Milles S, Lemke EA. Detektion von Mehrbindigkeit und differenziellen Affinitäten in großen, intrinsisch ungeordneten Proteinen mithilfe von Segmentbewegungsanalyse. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403694] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sigrid Milles
- Structural and Computational Biology Unit, EMBL, Meyerhofstraße 1, 69117 Heidelberg (Deutschland)
| | - Edward A. Lemke
- Structural and Computational Biology Unit, EMBL, Meyerhofstraße 1, 69117 Heidelberg (Deutschland)
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48
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Zlitni A, Janzen N, Foster FS, Valliant JF. Catching Bubbles: Targeting Ultrasound Microbubbles Using Bioorthogonal Inverse‐Electron‐Demand Diels–Alder Reactions. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Aimen Zlitni
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St W., Hamilton, Ont., L8S 4M1 (Canada)
| | - Nancy Janzen
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St W., Hamilton, Ont., L8S 4M1 (Canada)
| | - F. Stuart Foster
- Department of Medical Biophysics, University of Toronto, Sunnybrook Hospital, Toronto, Ont. M4N S658 (Canada)
| | - John F. Valliant
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St W., Hamilton, Ont., L8S 4M1 (Canada)
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49
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Zlitni A, Janzen N, Foster FS, Valliant JF. Catching bubbles: targeting ultrasound microbubbles using bioorthogonal inverse-electron-demand Diels-Alder reactions. Angew Chem Int Ed Engl 2014; 53:6459-63. [PMID: 24829138 DOI: 10.1002/anie.201402473] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 03/18/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Aimen Zlitni
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St W., Hamilton, Ont., L8S 4M1 (Canada)
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50
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Yang Y, Lin S, Lin W, Chen PR. Ligand-assisted dual-site click labeling of EGFR on living cells. Chembiochem 2014; 15:1738-43. [PMID: 24810988 DOI: 10.1002/cbic.201400057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Indexed: 12/13/2022]
Abstract
We have developed a dual-site click labeling strategy for the simultaneous installation of a FRET donor-acceptor pair onto the extracellular domains of epidermal growth factor receptor (EGFR) on living cells. Our method integrates the genetic code expansion strategy, enzyme-mediated protein labeling, and ligand-assisted Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) into a tri-step labeling procedure. This enabled cis-membrane FRET imaging of EGFR under living conditions. This procedure might be generally applicable for dual-site labeling and cis-membrane FRET analysis of the domain-domain dynamics of important mammalian cell-surface receptors.
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Affiliation(s)
- Yi Yang
- Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, 202, Chengfu Road, Beijing 100871 (China)
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