1
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Dunkelmann DL, Chin JW. Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming. Chem Rev 2024. [PMID: 39235427 DOI: 10.1021/acs.chemrev.4c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Over the past 16 years, genetic code expansion and reprogramming in living organisms has been transformed by advances that leverage the unique properties of pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs. Here we summarize the discovery of the pyrrolysine system and describe the unique properties of PylRS/tRNAPyl pairs that provide a foundation for their transformational role in genetic code expansion and reprogramming. We describe the development of genetic code expansion, from E. coli to all domains of life, using PylRS/tRNAPyl pairs, and the development of systems that biosynthesize and incorporate ncAAs using pyl systems. We review applications that have been uniquely enabled by the development of PylRS/tRNAPyl pairs for incorporating new noncanonical amino acids (ncAAs), and strategies for engineering PylRS/tRNAPyl pairs to add noncanonical monomers, beyond α-L-amino acids, to the genetic code of living organisms. We review rapid progress in the discovery and scalable generation of mutually orthogonal PylRS/tRNAPyl pairs that can be directed to incorporate diverse ncAAs in response to diverse codons, and we review strategies for incorporating multiple distinct ncAAs into proteins using mutually orthogonal PylRS/tRNAPyl pairs. Finally, we review recent advances in the encoded cellular synthesis of noncanonical polymers and macrocycles and discuss future developments for PylRS/tRNAPyl pairs.
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Affiliation(s)
- Daniel L Dunkelmann
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
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2
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Guo QR, Cao YJ. Applications of genetic code expansion technology in eukaryotes. Protein Cell 2024; 15:331-363. [PMID: 37847216 PMCID: PMC11074999 DOI: 10.1093/procel/pwad051] [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: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
Unnatural amino acids (UAAs) have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins. In eukaryotes, genetic code expansion (GCE) enables the incorporation of UAAs and facilitates posttranscriptional modification (PTM), which is not feasible in prokaryotic systems. GCE is also a powerful tool for cell or animal imaging, the monitoring of protein interactions in target cells, drug development, and switch regulation. Therefore, there is keen interest in utilizing GCE in eukaryotic systems. This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.
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Affiliation(s)
- Qiao-ru Guo
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yu J Cao
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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3
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Ao Y, Grover JR, Gifford L, Han Y, Zhong G, Katte R, Li W, Bhattacharjee R, Zhang B, Sauve S, Qin W, Ghimire D, Haque MA, Arthos J, Moradi M, Mothes W, Lemke EA, Kwong PD, Melikyan GB, Lu M. Bioorthogonal click labeling of an amber-free HIV-1 provirus for in-virus single molecule imaging. Cell Chem Biol 2024; 31:487-501.e7. [PMID: 38232732 PMCID: PMC10960674 DOI: 10.1016/j.chembiol.2023.12.017] [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: 03/27/2023] [Revised: 10/13/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
Structural dynamics of human immunodeficiency virus 1 (HIV-1) envelope (Env) glycoprotein mediate cell entry and facilitate immune evasion. Single-molecule FRET using peptides for Env labeling revealed structural dynamics of Env, but peptide use risks potential effects on structural integrity/dynamics. While incorporating noncanonical amino acids (ncAAs) into Env by amber stop-codon suppression, followed by click chemistry, offers a minimally invasive approach, this has proved to be technically challenging for HIV-1. Here, we develope an intact amber-free HIV-1 system that overcomes hurdles of preexisting viral amber codons. We achieved dual-ncAA incorporation into Env on amber-free virions, enabling single-molecule Förster resonance energy transfer (smFRET) studies of click-labeled Env that validated the previous peptide-based labeling approaches by confirming the intrinsic propensity of Env to dynamically sample multiple conformational states. Amber-free click-labeled Env also enabled real-time tracking of single virion internalization and trafficking in cells. Our system thus permits in-virus bioorthogonal labeling of proteins, compatible with studies of virus entry, trafficking, and egress from cells.
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Affiliation(s)
- Yuanyun Ao
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Jonathan R Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Levi Gifford
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yang Han
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Guohua Zhong
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Revansiddha Katte
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Rajanya Bhattacharjee
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; International PhD Program of the Institute of Molecular Biology, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephanie Sauve
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Wenyi Qin
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Dibya Ghimire
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - Md Anzarul Haque
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Edward A Lemke
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gregory B Melikyan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Maolin Lu
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA.
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4
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Ao Y, Grover JR, Han Y, Zhong G, Qin W, Ghimire D, Haque A, Bhattacharjee R, Zhang B, Arthos J, Lemke EA, Kwong PD, Lu M. An intact amber-free HIV-1 system for in-virus protein bioorthogonal click labeling that delineates envelope conformational dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530526. [PMID: 36909529 PMCID: PMC10002649 DOI: 10.1101/2023.02.28.530526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
The HIV-1 envelope (Env) glycoprotein is conformationally dynamic and mediates membrane fusion required for cell entry. Single-molecule fluorescence resonance energy transfer (smFRET) of Env using peptide tags has provided mechanistic insights into the dynamics of Env conformations. Nevertheless, using peptide tags risks potential effects on structural integrity. Here, we aim to establish minimally invasive smFRET systems of Env on the virus by combining genetic code expansion and bioorthogonal click chemistry. Amber stop-codon suppression allows site-specifically incorporating noncanonical/unnatural amino acids (ncAAs) at introduced amber sites into proteins. However, ncAA incorporation into Env (or other HIV-1 proteins) in the virus context has been challenging due to low copies of Env on virions and incomplete amber suppression in mammalian cells. Here, we developed an intact amber-free virus system that overcomes impediments from preexisting ambers in HIV-1. Using this system, we successfully incorporated dual ncAAs at amber-introduced sites into Env on intact virions. Dual-ncAA incorporated Env retained similar neutralization sensitivities to neutralizing antibodies as wildtype. smFRET of click-labeled Env on intact amber-free virions recapitulated conformational profiles of Env. The amber-free HIV-1 infectious system also permits in-virus protein bioorthogonal labeling, compatible with various advanced microscopic studies of virus entry, trafficking, and egress in living cells. Amber-free HIV-1 infectious systems actualized minimal invasive Env tagging for smFRET, versatile for in-virus bioorthogonal click labeling in advanced microscopic studies of virus-host interactions.
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5
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Direct Capsid Labeling of Infectious HIV-1 by Genetic Code Expansion Allows Detection of Largely Complete Nuclear Capsids and Suggests Nuclear Entry of HIV-1 Complexes via Common Routes. mBio 2022; 13:e0195922. [PMID: 35972146 PMCID: PMC9600849 DOI: 10.1128/mbio.01959-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The cone-shaped mature HIV-1 capsid is the main orchestrator of early viral replication. After cytosolic entry, it transports the viral replication complex along microtubules toward the nucleus. While it was initially believed that the reverse transcribed genome is released from the capsid in the cytosol, recent observations indicate that a high amount of capsid protein (CA) remains associated with subviral complexes during import through the nuclear pore complex (NPC). Observation of postentry events via microscopic detection of HIV-1 CA is challenging, since epitope shielding limits immunodetection and the genetic fragility of CA hampers direct labeling approaches. Here, we present a minimally invasive strategy based on genetic code expansion and click chemistry that allows for site-directed fluorescent labeling of HIV-1 CA, while retaining virus morphology and infectivity. Thereby, we could directly visualize virions and subviral complexes using advanced microscopy, including nanoscopy and correlative imaging. Quantification of signal intensities of subviral complexes revealed an amount of CA associated with nuclear complexes in HeLa-derived cells and primary T cells consistent with a complete capsid and showed that treatment with the small molecule inhibitor PF74 did not result in capsid dissociation from nuclear complexes. Cone-shaped objects detected in the nucleus by electron tomography were clearly identified as capsid-derived structures by correlative microscopy. High-resolution imaging revealed dose-dependent clustering of nuclear capsids, suggesting that incoming particles may follow common entry routes.
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Meineke B, Heimgärtner J, Craig AJ, Landreh M, Moodie LWK, Elsässer SJ. A Genetically Encoded Picolyl Azide for Improved Live Cell Copper Click Labeling. Front Chem 2021; 9:768535. [PMID: 34858945 PMCID: PMC8632528 DOI: 10.3389/fchem.2021.768535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
Bioorthogonal chemistry allows rapid and highly selective reactivity in biological environments. The copper-catalyzed azide–alkyne cycloaddition (CuAAC) is a classic bioorthogonal reaction routinely used to modify azides or alkynes that have been introduced into biomolecules. Amber suppression is an efficient method for incorporating such chemical handles into proteins on the ribosome, in which noncanonical amino acids (ncAAs) are site specifically introduced into the polypeptide in response to an amber (UAG) stop codon. A variety of ncAA structures containing azides or alkynes have been proven useful for performing CuAAC chemistry on proteins. To improve CuAAC efficiency, biologically incorporated alkyne groups can be reacted with azide substrates that contain copper-chelating groups. However, the direct incorporation of copper-chelating azides into proteins has not been explored. To remedy this, we prepared the ncAA paz-lysine (PazK), which contains a picolyl azide motif. We show that PazK is efficiently incorporated into proteins by amber suppression in mammalian cells. Furthermore, PazK-labeled proteins show improved reactivity with alkyne reagents in CuAAC.
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Affiliation(s)
- Birthe Meineke
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden
| | - Johannes Heimgärtner
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden
| | - Alexander J Craig
- Drug Design and Discovery, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Lindon W K Moodie
- Drug Design and Discovery, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Uppsala, Sweden.,Uppsala Antibiotic Centre, Uppsala University, Uppsala, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden
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7
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Heisler IA, Meech SR. Altered relaxation dynamics of excited state reactions by confinement in reverse micelles probed by ultrafast fluorescence up-conversion. Chem Soc Rev 2021; 50:11486-11502. [PMID: 34661209 DOI: 10.1039/d1cs00516b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Chemical reactions in confined environments are important in areas as diverse as heterogenous catalysis, environmental chemistry and biochemistry, yet they are much less well understood than the equivalent reactions in either the gas phase or in free solution. The understanding of chemical reactions in solution was greatly enhanced by real time studies of model reactions, through ultrafast spectroscopy (especially when supported by molecular dynamics simulation). Here we review some of the efforts that have been made to adapt this approach to the investigation of reactions in confined media. Specifically, we review the application of ultrafast fluorescence spectroscopy to measure reaction dynamics in the nanoconfined water phase of reverse micelles, as a function of the droplet radius and the charge on the interface. Methods of measurement and modelling of the reactions are outlined. In all of the cases studied (which are focused on ultrafast intramolecular reactions) the effect of confinement was to suppress the reaction. Even in the largest micelles the result in the bulk aqueous phase was not usually recovered, suggesting an important role for specific interactions between reactant and environment, for example at the interface. There was no simple one-to-one correspondence with direct measures of the dynamics of the confined phase. Thus, understanding the effect of confinement on reaction rate appears to require not only knowledge of the dynamics of the reaction in solutions and the effect of confinement on the medium, but also of the interaction between reactant and confining medium.
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Affiliation(s)
- Ismael A Heisler
- Departamento de Física, Universidade Federal do Paraná, Curitiba, Paraná, CEP 81531-980, Brazil
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK.
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8
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Zagotta WN, Sim BS, Nhim AK, Raza MM, Evans EG, Venkatesh Y, Jones CM, Mehl RA, Petersson EJ, Gordon SE. An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET. eLife 2021; 10:e70236. [PMID: 34623258 PMCID: PMC8500717 DOI: 10.7554/elife.70236] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022] Open
Abstract
With the recent explosion in high-resolution protein structures, one of the next frontiers in biology is elucidating the mechanisms by which conformational rearrangements in proteins are regulated to meet the needs of cells under changing conditions. Rigorously measuring protein energetics and dynamics requires the development of new methods that can resolve structural heterogeneity and conformational distributions. We have previously developed steady-state transition metal ion fluorescence resonance energy transfer (tmFRET) approaches using a fluorescent noncanonical amino acid donor (Anap) and transition metal ion acceptor to probe conformational rearrangements in soluble and membrane proteins. Here, we show that the fluorescent noncanonical amino acid Acd has superior photophysical properties that extend its utility as a donor for tmFRET. Using maltose-binding protein (MBP) expressed in mammalian cells as a model system, we show that Acd is comparable to Anap in steady-state tmFRET experiments and that its long, single-exponential lifetime is better suited for probing conformational distributions using time-resolved FRET. These experiments reveal differences in heterogeneity in the apo and holo conformational states of MBP and produce accurate quantification of the distributions among apo and holo conformational states at subsaturating maltose concentrations. Our new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.
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Affiliation(s)
- William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Brandon S Sim
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Anthony K Nhim
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Marium M Raza
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Eric Gb Evans
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Chloe M Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
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9
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Bartels K, Lasitza‐Male T, Hofmann H, Löw C. Single-Molecule FRET of Membrane Transport Proteins. Chembiochem 2021; 22:2657-2671. [PMID: 33945656 PMCID: PMC8453700 DOI: 10.1002/cbic.202100106] [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: 03/08/2021] [Revised: 05/03/2021] [Indexed: 12/31/2022]
Abstract
Uncovering the structure and function of biomolecules is a fundamental goal in structural biology. Membrane-embedded transport proteins are ubiquitous in all kingdoms of life. Despite structural flexibility, their mechanisms are typically studied by ensemble biochemical methods or by static high-resolution structures, which complicate a detailed understanding of their dynamics. Here, we review the recent progress of single molecule Förster Resonance Energy Transfer (smFRET) in determining mechanisms and timescales of substrate transport across membranes. These studies do not only demonstrate the versatility and suitability of state-of-the-art smFRET tools for studying membrane transport proteins but they also highlight the importance of membrane mimicking environments in preserving the function of these proteins. The current achievements advance our understanding of transport mechanisms and have the potential to facilitate future progress in drug design.
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Affiliation(s)
- Kim Bartels
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| | - Tanya Lasitza‐Male
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Hagen Hofmann
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
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10
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Quast RB, Margeat E. Single-molecule FRET on its way to structural biology in live cells. Nat Methods 2021; 18:344-345. [PMID: 33686302 DOI: 10.1038/s41592-021-01084-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Robert B Quast
- Centre de Biologie Structurale (CBS), CNRS, INSERM, University Montpellier, Montpellier, France
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, University Montpellier, Montpellier, France.
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11
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Nasir I, Bentley EP, Deniz AA. Ratiometric Single-Molecule FRET Measurements to Probe Conformational Subpopulations of Intrinsically Disordered Proteins. ACTA ACUST UNITED AC 2021; 12:e80. [PMID: 32159932 PMCID: PMC7508418 DOI: 10.1002/cpch.80] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past few decades, numerous examples have demonstrated that intrinsic disorder in proteins lies at the heart of many vital processes, including transcriptional regulation, stress response, cellular signaling, and most recently protein liquid-liquid phase separation. The so-called intrinsically disordered proteins (IDPs) involved in these processes have presented a challenge to the classic protein "structure-function paradigm," as their functions do not necessarily involve well-defined structures. Understanding the mechanisms of IDP function is likewise challenging because traditional structure determination methods often fail with such proteins or provide little information about the diverse array of structures that can be related to different functions of a single IDP. Single-molecule fluorescence methods can overcome this ensemble-average masking, allowing the resolution of subpopulations and dynamics and thus providing invaluable insights into IDPs and their function. In this protocol, we describe a ratiometric single-molecule Förster resonance energy transfer (smFRET) routine that permits the investigation of IDP conformational subpopulations and dynamics. We note that this is a basic protocol, and we provide brief information and references for more complex analysis schemes available for in-depth characterization. This protocol covers optical setup preparation and protein handling and provides insights into experimental design and outcomes, together with background information about theory and a brief discussion of troubleshooting. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Ratiometric smFRET detection and analysis of IDPs Support Protocol 1: Fluorophore labeling of a protein through maleimide chemistry Support Protocol 2: Sample chamber preparation Support Protocol 3: Determination of direct excitation of acceptor by donor excitation and leakage of donor emission to acceptor emission channel.
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Affiliation(s)
- Irem Nasir
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California.,Department of Biology and Biological Engineering, Division of Chemical Biology, Chalmers Institute of Technology, Gothenburg, Sweden
| | - Emily P Bentley
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
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12
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Site-Specific Incorporation of Two ncAAs for Two-Color Bioorthogonal Labeling and Crosslinking of Proteins on Live Mammalian Cells. Cell Rep 2021; 31:107811. [PMID: 32579937 DOI: 10.1016/j.celrep.2020.107811] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/17/2020] [Accepted: 06/03/2020] [Indexed: 11/22/2022] Open
Abstract
The pyrrolysyl-tRNA/pyrrolysyl-tRNA synthetase (PylT/RS) pair from the archaeon Methanosarcina mazei (Mma) is widely used in protein engineering to site-specifically introduce noncanonical amino acids (ncAAs) through nonsense codon suppression. Here, we engineer the PylT/RS pair encoded by Methanogenic archaeon ISO4-G1 (G1) to be orthogonal to Mma PylT/RS and alter the G1 PylRS active site to accept a complementary ncAA spectrum. We combine the resulting mutual orthogonal pairs for site-specific dual ncAA incorporation of two lysine analogs with high selectivity and efficiency. Demonstrating the robustness of the system, we incorporate two ncAAs with compatible bioorthogonal reactivity into a Notch receptor, as well as a G protein-coupled receptor. We show that selective and site-specific incorporation of two ncAAs allows for two-color bioorthogonal labeling as well as chemical-controlled crosslinking of surface proteins on live mammalian cells.
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13
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Sappakhaw K, Jantarug K, Slavoff SA, Israsena N, Uttamapinant C. A Genetic Code Expansion-Derived Molecular Beacon for the Detection of Intracellular Amyloid-β Peptide Generation. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:3980-3985. [PMID: 38504667 PMCID: PMC10946459 DOI: 10.1002/ange.202010703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/19/2020] [Indexed: 11/09/2022]
Abstract
Polypeptides generated from proteolytic processing of protein precursors, or proteolytic proteoforms, play an important role in diverse biological functions and diseases. However, their often-small size and intricate post-translational biogenesis preclude the use of simple genetic tagging in their cellular studies. Herein, we develop a labeling strategy for this class of proteoforms, based on residue-specific genetic code expansion labeling with a molecular beacon design. We demonstrate the utility of such a design by creating a molecular beacon reporter to detect amyloid-β peptides, known to be involved in the pathogenesis of Alzheimer's disease, as they are produced from amyloid precursor protein (APP) along the endocytic pathway of living cells.
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Affiliation(s)
- Khomkrit Sappakhaw
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Krittapas Jantarug
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
| | - Sarah A Slavoff
- Department of Chemistry Yale University New Haven CT 06520 USA
| | - Nipan Israsena
- Stem Cell and Cell Therapy Research Unit and Department of Pharmacology Faculty of Medicine Chulalongkorn University Bangkok 10330 Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong 21210 Thailand
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14
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Sappakhaw K, Jantarug K, Slavoff SA, Israsena N, Uttamapinant C. A Genetic Code Expansion-Derived Molecular Beacon for the Detection of Intracellular Amyloid-β Peptide Generation. Angew Chem Int Ed Engl 2021; 60:3934-3939. [PMID: 33063327 PMCID: PMC7898502 DOI: 10.1002/anie.202010703] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/19/2020] [Indexed: 12/01/2022]
Abstract
Polypeptides generated from proteolytic processing of protein precursors, or proteolytic proteoforms, play an important role in diverse biological functions and diseases. However, their often-small size and intricate post-translational biogenesis preclude the use of simple genetic tagging in their cellular studies. Herein, we develop a labeling strategy for this class of proteoforms, based on residue-specific genetic code expansion labeling with a molecular beacon design. We demonstrate the utility of such a design by creating a molecular beacon reporter to detect amyloid-β peptides, known to be involved in the pathogenesis of Alzheimer's disease, as they are produced from amyloid precursor protein (APP) along the endocytic pathway of living cells.
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Affiliation(s)
- Khomkrit Sappakhaw
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Rayong21210Thailand
| | - Krittapas Jantarug
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Rayong21210Thailand
| | | | - Nipan Israsena
- Stem Cell and Cell Therapy Research Unit and Department of PharmacologyFaculty of MedicineChulalongkorn UniversityBangkok10330Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Rayong21210Thailand
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15
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Hadar D, Gelkop S, Vaserman L, Amiram M. Efficient Incorporation of Clickable Unnatural Amino Acids Enables Rapid and Biocompatible Labeling of Proteins in Vitro and in Bacteria. Chembiochem 2021; 22:1379-1384. [PMID: 33350556 DOI: 10.1002/cbic.202000663] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/22/2020] [Indexed: 11/09/2022]
Abstract
Site-specific incorporation of unnatural amino acids (uAAs) bearing a bioorthogonal group has enabled the attachment - typically at a single site or at a few sites per protein - of chemical groups at precise locations for protein and biomaterial labeling, conjugation, and functionalization. Herein, we report the evolution of chromosomal Methanocaldococcus jannaschii tyrosyl-tRNA synthetase (aaRS) for the alkyne-bearing uAA, 4-propargyloxy-l-phenylalanine (pPR), with ∼30-fold increased production of green fluorescent protein containing three instances of pPR compared with a previously described M. jannaschii-derived aaRS for pPR, when expressed from a single chromosomal copy. We show that when expressed from multicopy plasmids, the evolved aaRSs enable the production - using a genomically recoded Escherichia coli and the non-recoded BL21 E. coli strain - of elastin-like polypeptides (ELPs) containing multiple pPR residues in high yields. We further show that the multisite incorporation of pPR in ELPs facilitates the rapid, robust, and nontoxic fluorescent labeling of these proteins in bacteria. The evolved variants described in this work can be used to produce a variety of protein and biomaterial conjugates and to create efficient minimal tags for protein labeling.
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Affiliation(s)
- Dagan Hadar
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Sigal Gelkop
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Livne Vaserman
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
| | - Miriam Amiram
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva, 8410501, Israel
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16
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Xie Y, Fang Y, Huang Z, Tallon AM, am Ende CW, Fox JM. Divergent Synthesis of Monosubstituted and Unsymmetrical 3,6‐Disubstituted Tetrazines from Carboxylic Ester Precursors. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yixin Xie
- Department of Chemistry and Biochemistry University of Delaware Newark DE 19716 USA
| | - Yinzhi Fang
- Department of Chemistry and Biochemistry University of Delaware Newark DE 19716 USA
| | - Zhen Huang
- Pfizer Worldwide Research and Development 1 Portland Street Cambridge MA 02139 USA
| | - Amanda M. Tallon
- Department of Chemistry and Biochemistry University of Delaware Newark DE 19716 USA
| | | | - Joseph M. Fox
- Department of Chemistry and Biochemistry University of Delaware Newark DE 19716 USA
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17
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Xie Y, Fang Y, Huang Z, Tallon AM, Am Ende CW, Fox JM. Divergent Synthesis of Monosubstituted and Unsymmetrical 3,6-Disubstituted Tetrazines from Carboxylic Ester Precursors. Angew Chem Int Ed Engl 2020; 59:16967-16973. [PMID: 32559350 PMCID: PMC7733736 DOI: 10.1002/anie.202005569] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/02/2020] [Indexed: 11/06/2022]
Abstract
Since tetrazines are important tools to the field of bioorthogonal chemistry, there is a need for new approaches to synthesize unsymmetrical and 3-monosubstituted tetrazines. Described here is a general, one-pot method for converting (3-methyloxetan-3-yl)methyl carboxylic esters into 3-thiomethyltetrazines. These versatile intermediates were applied to the synthesis of unsymmetrical tetrazines through Pd-catalyzed cross-coupling and in the first catalytic thioether reduction to access monosubstituted tetrazines. This method enables the development of new tetrazine compounds possessing a favorable combination of kinetics, small size, and hydrophilicity. It was applied to a broad range of aliphatic and aromatic ester precursors and to the synthesis of heterocycles including BODIPY fluorophores and biotin. In addition, a series of tetrazine probes for monoacylglycerol lipase (MAGL) were synthesized and the most reactive one was applied to the labeling of endogenous MAGL in live cells.
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Affiliation(s)
- Yixin Xie
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Zhen Huang
- Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, MA, 02139, USA
| | - Amanda M Tallon
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Christopher W Am Ende
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT, 06340, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
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18
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Elia N. Using unnatural amino acids to selectively label proteins for cellular imaging: a cell biologist viewpoint. FEBS J 2020; 288:1107-1117. [PMID: 32640070 PMCID: PMC7983921 DOI: 10.1111/febs.15477] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/16/2020] [Accepted: 07/03/2020] [Indexed: 12/12/2022]
Abstract
Twenty-five years ago, GFP revolutionized the field of cell biology by enabling scientists to visualize, for the first time, proteins in living cells. However, when it comes to current, state-of-the-art imaging technologies, fluorescent proteins (such as GFP) have several limitations that result from their size and photophysics. Over the past decade, an elegant, alternative approach, which is based on the direct labeling of proteins with fluorescent dyes and is compatible with live-cell and super-resolution imaging applications, has been introduced. In this approach, an unnatural amino acid that can covalently bind a fluorescent dye is incorporated into the coding sequence of a protein. The protein of interest is thereby site-specifically fluorescently labeled inside the cell, eliminating the need for protein- or peptide-labeling tags. Whether this labeling approach will change cell biology research is currently unclear, but it clearly has the potential to do so. In this short review, a general overview of this approach is provided, focusing on the imaging of site-specifically labeled proteins in mammalian tissue culture cells, and highlighting its advantages and limitations for cellular imaging.
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Affiliation(s)
- Natalie Elia
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Beer Sheva, Israel
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19
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König AI, Sorkin R, Alon A, Nachmias D, Dhara K, Brand G, Yifrach O, Arbely E, Roichman Y, Elia N. Live cell single molecule tracking and localization microscopy of bioorthogonally labeled plasma membrane proteins. NANOSCALE 2020; 12:3236-3248. [PMID: 31970355 DOI: 10.1039/c9nr08594g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Tracking the localization and mobility of individual proteins in live cells is key for understanding how they mediate their function. Such information can be obtained from single molecule imaging techniques including as Single Particle Tracking (SPT) and Single Molecule Localization Microscopy (SMLM). Genetic code expansion (GCE) combined with bioorthogonal chemistry offers an elegant approach for direct labeling of proteins with fluorescent dyes, holding great potential for improving protein labeling in single molecule applications. Here we calibrated conditions for performing SPT and live-SMLM of bioorthogonally labeled plasma membrane proteins in live mammalian cells. Using SPT, the diffusion of bioorthogonally labeled EGF receptor and the prototypical Shaker voltage-activated potassium channel (Kv) was measured and characterized. Applying live-SMLM to bioorthogonally labeled Shaker Kv channels enabled visualizing the plasma membrane distribution of the channel over time with ∼30 nm accuracy. Finally, by competitive labeling with two Fl-dyes, SPT and live-SMLM were performed in a single cell and both the density and dynamics of the EGF receptor were measured at single molecule resolution in subregions of the cell. We conclude that GCE and bioorthogonal chemistry is a highly suitable, flexible approach for protein labeling in quantitative single molecule applications that outperforms current protein live-cell labeling approaches.
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Affiliation(s)
- Andres I König
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
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20
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Alex A, Piano V, Polley S, Stuiver M, Voss S, Ciossani G, Overlack K, Voss B, Wohlgemuth S, Petrovic A, Wu Y, Selenko P, Musacchio A, Maffini S. Electroporated recombinant proteins as tools for in vivo functional complementation, imaging and chemical biology. eLife 2019; 8:48287. [PMID: 31310234 PMCID: PMC6656429 DOI: 10.7554/elife.48287] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/12/2019] [Indexed: 02/06/2023] Open
Abstract
Delivery of native or chemically modified recombinant proteins into mammalian cells shows promise for functional investigations and various technological applications, but concerns that sub-cellular localization and functional integrity of delivered proteins may be affected remain high. Here, we surveyed batch electroporation as a delivery tool for single polypeptides and multi-subunit protein assemblies of the kinetochore, a spatially confined and well-studied subcellular structure. After electroporation into human cells, recombinant fluorescent Ndc80 and Mis12 multi-subunit complexes exhibited native localization, physically interacted with endogenous binding partners, and functionally complemented depleted endogenous counterparts to promote mitotic checkpoint signaling and chromosome segregation. Farnesylation is required for kinetochore localization of the Dynein adaptor Spindly. In cells with chronically inhibited farnesyl transferase activity, in vitro farnesylation and electroporation of recombinant Spindly faithfully resulted in robust kinetochore localization. Our data show that electroporation is well-suited to deliver synthetic and chemically modified versions of functional proteins, and, therefore, constitutes a promising tool for applications in chemical and synthetic biology.
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Affiliation(s)
- Amal Alex
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Valentina Piano
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Soumitra Polley
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Marchel Stuiver
- In-Cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Berlin, Germany
| | - Stephanie Voss
- Chemical Genomics Centre, Max Planck Society, Dortmund, Germany
| | - Giuseppe Ciossani
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Katharina Overlack
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Beate Voss
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sabine Wohlgemuth
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Arsen Petrovic
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Yaowen Wu
- Chemical Genomics Centre, Max Planck Society, Dortmund, Germany.,Department of Chemistry, Umeå University, Umeå, Sweden
| | - Philipp Selenko
- In-Cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Berlin, Germany.,Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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21
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Orré T, Rossier O, Giannone G. The inner life of integrin adhesion sites: From single molecules to functional macromolecular complexes. Exp Cell Res 2019; 379:235-244. [DOI: 10.1016/j.yexcr.2019.03.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/07/2019] [Accepted: 03/27/2019] [Indexed: 12/31/2022]
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22
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Jakob L, Gust A, Grohmann D. Evaluation and optimisation of unnatural amino acid incorporation and bioorthogonal bioconjugation for site-specific fluorescent labelling of proteins expressed in mammalian cells. Biochem Biophys Rep 2019; 17:1-9. [PMID: 30450427 PMCID: PMC6226565 DOI: 10.1016/j.bbrep.2018.10.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/08/2018] [Accepted: 10/18/2018] [Indexed: 11/21/2022] Open
Abstract
Many biophysical techniques that are available to study the structure, function and dynamics of cellular constituents require modification of the target molecules. Site-specific labelling of a protein is of particular interest for fluorescence-based single-molecule measurements including single-molecule FRET or super-resolution microscopy. The labelling procedure should be highly specific but minimally invasive to preserve sensitive biomolecules. The modern molecular engineering toolkit provides elegant solutions to achieve the site-specific modification of a protein of interest often necessitating the incorporation of an unnatural amino acid to introduce a unique reactive moiety. The Amber suppression strategy allows the site-specific incorporation of unnatural amino acids into a protein of interest. Recently, this approach has been transferred to the mammalian expression system. Here, we demonstrate how the combination of unnatural amino acid incorporation paired with current bioorthogonal labelling strategies allow the site-specific engineering of fluorescent dyes into proteins produced in the cellular environment of a human cell. We describe in detail which parameters are important to ensure efficient incorporation of unnatural amino acids into a target protein in human expression systems. We furthermore outline purification and bioorthogonal labelling strategies that allow fast protein preparation and labelling of the modified protein. This way, the complete eukaryotic proteome becomes available for single-molecule fluorescence assays.
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Affiliation(s)
| | | | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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23
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Müller TG, Sakin V, Müller B. A Spotlight on Viruses-Application of Click Chemistry to Visualize Virus-Cell Interactions. Molecules 2019; 24:molecules24030481. [PMID: 30700005 PMCID: PMC6385038 DOI: 10.3390/molecules24030481] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/18/2019] [Accepted: 01/19/2019] [Indexed: 01/03/2023] Open
Abstract
The replication of a virus within its host cell involves numerous interactions between viral and cellular factors, which have to be tightly controlled in space and time. The intricate interplay between viral exploitation of cellular pathways and the intrinsic host defense mechanisms is difficult to unravel by traditional bulk approaches. In recent years, novel fluorescence microscopy techniques and single virus tracking have transformed the investigation of dynamic virus-host interactions. A prerequisite for the application of these imaging-based methods is the attachment of a fluorescent label to the structure of interest. However, their small size, limited coding capacity and multifunctional proteins render viruses particularly challenging targets for fluorescent labeling approaches. Click chemistry in conjunction with genetic code expansion provides virologists with a novel toolbox for site-specific, minimally invasive labeling of virion components, whose potential has just recently begun to be exploited. Here, we summarize recent achievements, current developments and future challenges for the labeling of viral nucleic acids, proteins, glycoproteins or lipids using click chemistry in order to study dynamic processes in virus-cell interactions.
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Affiliation(s)
- Thorsten G Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Volkan Sakin
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
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24
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Structure and Synthesis of Antifungal Disulfide β-Strand Proteins from Filamentous Fungi. Microorganisms 2018; 7:microorganisms7010005. [PMID: 30591636 PMCID: PMC6352176 DOI: 10.3390/microorganisms7010005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/24/2018] [Accepted: 12/24/2018] [Indexed: 02/03/2023] Open
Abstract
The discovery and understanding of the mode of action of new antimicrobial agents is extremely urgent, since fungal infections cause 1.5 million deaths annually. Antifungal peptides and proteins represent a significant group of compounds that are able to kill pathogenic fungi. Based on phylogenetic analyses the ascomycetous, cysteine-rich antifungal proteins can be divided into three different groups: Penicillium chrysogenum antifungal protein (PAF), Neosartorya fischeri antifungal protein 2 (NFAP2) and “bubble-proteins” (BP) produced, for example, by P. brevicompactum. They all dominantly have β-strand secondary structures that are stabilized by several disulfide bonds. The PAF group (AFP antifungal protein from Aspergillus giganteus, PAF and PAFB from P. chrysogenum,Neosartorya fischeri antifungal protein (NFAP)) is the best characterized with their common β-barrel tertiary structure. These proteins and variants can efficiently be obtained either from fungi production or by recombinant expression. However, chemical synthesis may be a complementary aid for preparing unusual modifications, e.g., the incorporation of non-coded amino acids, fluorophores, or even unnatural disulfide bonds. Synthetic variants up to ca. 6–7 kDa can also be put to good use for corroborating structure determination. A short overview of the structural peculiarities of antifungal β-strand disulfide bridged proteins will be given. Here, we describe the structural propensities of some known antifungal proteins from filamentous fungi which can also be prepared with modern synthetic chemistry methods.
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25
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Saal KA, Richter F, Rehling P, Rizzoli SO. Combined Use of Unnatural Amino Acids Enables Dual-Color Super-Resolution Imaging of Proteins via Click Chemistry. ACS NANO 2018; 12:12247-12254. [PMID: 30525434 DOI: 10.1021/acsnano.8b06047] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent advances in optical nanoscopy have brought the imaging resolution to the size of the individual macromolecules, thereby setting stringent requirements for the fluorescent labels. Such requirements are optimally fulfilled by the incorporation of unnatural amino acids (UAAs) in the proteins of interest (POIs), followed by fluorophore conjugation via click chemistry. However, this approach has been limited to single POIs in mammalian cells. Here we solve this problem by incorporating different UAAs in different POIs, which are expressed in independent cell sets. The cells are then fused, thereby combining the different proteins and organelles, and are easily imaged by dual-color super-resolution microscopy. This procedure, which we termed Fuse2Click, is simple, requires only the well-established Amber codon, and allows the use of all previously optimized UAAs and tRNA/RS pairs. This should render it a tool of choice for multicolor click-based imaging.
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Affiliation(s)
- Kim-A Saal
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration , University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain , Göttingen , Germany
| | - Frank Richter
- Institute for Cellular Biochemistry , University Medical Center Göttingen , Göttingen , Germany
| | - Peter Rehling
- Institute for Cellular Biochemistry , University Medical Center Göttingen , Göttingen , Germany
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration , University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain , Göttingen , Germany
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26
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Darko A, Boyd SJ, Fox JM. Large-Scale Flow Photochemical Synthesis of Functionalized trans-Cyclooctenes Using Sulfonated Silica Gel. SYNTHESIS-STUTTGART 2018; 50:4875-4882. [PMID: 34176978 PMCID: PMC8224989 DOI: 10.1055/s-0037-1610240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Functionalized trans-cyclooctenes are useful bioorthogonal reagents that are typically prepared using a flow photoisomerization method where the product is captured by AgNO3 on silica gel. While this method is effective, the leaching of silver can be problematic when scaling up syntheses. It is shown here that Ag(I) immobilized on tosic silica gel can be used to capture trans-cyclooctene products at higher loadings without leaching. It is demonstrated that the sulfonated silica gel can be regenerated and reused with similar yields over multiple runs. Nine different trans-cyclooctenes were synthesized, including those commonly utilized in bioorthogonal chemistry as well as new amine and carboxylic acid derivatives.
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Affiliation(s)
- Ampofo Darko
- Department of Chemistry, University of Tennessee, Knoxville, TN, 37996
| | - Samantha J. Boyd
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark DE 19716
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27
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Neubert F, Beliu G, Terpitz U, Werner C, Geis C, Sauer M, Doose S. Bioorthogonal Click Chemistry Enables Site-specific Fluorescence Labeling of Functional NMDA Receptors for Super-Resolution Imaging. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Franziska Neubert
- Department of Biotechnology and Biophysics; University of Würzburg; Biocenter; Am Hubland 97074 Würzburg Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics; University of Würzburg; Biocenter; Am Hubland 97074 Würzburg Germany
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics; University of Würzburg; Biocenter; Am Hubland 97074 Würzburg Germany
| | - Christian Werner
- Department of Biotechnology and Biophysics; University of Würzburg; Biocenter; Am Hubland 97074 Würzburg Germany
| | - Christian Geis
- Hans-Berger Department of Neurology; Center for Sepsis Control and Care (CSCC); Jena University Hospital; Am Klinikum 1 07747 Jena Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics; University of Würzburg; Biocenter; Am Hubland 97074 Würzburg Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics; University of Würzburg; Biocenter; Am Hubland 97074 Würzburg Germany
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28
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Neubert F, Beliu G, Terpitz U, Werner C, Geis C, Sauer M, Doose S. Bioorthogonal Click Chemistry Enables Site-specific Fluorescence Labeling of Functional NMDA Receptors for Super-Resolution Imaging. Angew Chem Int Ed Engl 2018; 57:16364-16369. [PMID: 30347512 DOI: 10.1002/anie.201808951] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/15/2018] [Indexed: 12/20/2022]
Abstract
Super-resolution microscopy requires small fluorescent labels. We report the application of genetic code expansion in combination with bioorthogonal click chemistry to label the NR1 domain of the NMDA receptor. We generated NR1 mutants incorporating an unnatural amino acid at various positions in order to attach small organic fluorophores such as Cy5-tetrazine site-specifically to the extracellular domain of the receptor. Mutants were optimized with regard to protein expression, labeling efficiency and receptor functionality as tested by fluorescence microscopy and whole-cell patch clamp. The results show that bioorthogonal click chemistry in combination with small organic dyes is superior to available immunocytochemistry protocols for receptor labeling in live and fixed cells and enables single-molecule sensitive super-resolution microscopy experiments.
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Affiliation(s)
- Franziska Neubert
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Am Hubland, 97074, Würzburg, Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Am Hubland, 97074, Würzburg, Germany
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Am Hubland, 97074, Würzburg, Germany
| | - Christian Werner
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Am Hubland, 97074, Würzburg, Germany
| | - Christian Geis
- Hans-Berger Department of Neurology, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Am Hubland, 97074, Würzburg, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Am Hubland, 97074, Würzburg, Germany
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29
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Schmidt A, Altincekic N, Gustmann H, Wachtveitl J, Hengesbach M. The Protein Microenvironment Governs the Suitability of Labeling Sites for Single-Molecule Spectroscopy of RNP Complexes. ACS Chem Biol 2018; 13:2472-2483. [PMID: 30060648 DOI: 10.1021/acschembio.8b00348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single-molecule techniques allow unique insights into biological systems as they provide unrivaled access to structural dynamics and conformational heterogeneity. One major bottleneck for reliable single-molecule Förster resonance energy transfer (smFRET) analysis is the identification of suitable fluorophore labeling sites that neither impair the function of the biological system nor cause photophysical artifacts of the fluorophore. To address this issue, we identified the contribution of virtually all individual parameters that affect Förster resonance energy transfer between two fluorophores attached to a ribonucleoprotein complex consisting of the RNA-binding protein L7Ae and a cognate kink turn containing RNA. A non-natural amino acid was incorporated at various positions of the protein using an amber suppression system (pEVOL) to label the protein via copper(I)-catalyzed alkyne-azide cycloaddition. On the basis of simulations followed by functional, structural, and multiparameter fluorescence analysis of five different smFRET RNPs, new insights into the design of smFRET RNPs were obtained. From this, a correlation between the photophysical properties of fluorophores attached to the protein and the predictability of the corresponding smFRET construct was established. Additionally, we identify a straightforward experimental method for characterizing selected labeling sites. Overall, this protocol allows fast generation and assessment of functional RNPs for accurate single-molecule experiments.
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Affiliation(s)
- Andreas Schmidt
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Henrik Gustmann
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, 60438 Frankfurt, Germany
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30
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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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31
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Abstract
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.
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32
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Oliveira BL, Guo Z, Bernardes GJL. Inverse electron demand Diels-Alder reactions in chemical biology. Chem Soc Rev 2018; 46:4895-4950. [PMID: 28660957 DOI: 10.1039/c7cs00184c] [Citation(s) in RCA: 644] [Impact Index Per Article: 107.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emerging inverse electron demand Diels-Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility. With the recent discovery of novel dienophiles and optimal tetrazine coupling partners, attention has now been turned to the use of IEDDA approaches in basic biology, imaging and therapeutics. Here we review this bioorthogonal reaction and its promising applications for live cell and animal studies. We first discuss the key factors that contribute to the fast IEDDA kinetics and describe the most recent advances in the synthesis of tetrazine and dienophile coupling partners. Both coupling partners have been incorporated into proteins for tracking and imaging by use of fluorogenic tetrazines that become strongly fluorescent upon reaction. Selected notable examples of such applications are presented. The exceptional fast kinetics of this catalyst-free reaction, even using low concentrations of coupling partners, make it amenable for in vivo radiolabelling using pretargeting methodologies, which are also discussed. Finally, IEDDA reactions have recently found use in bioorthogonal decaging to activate proteins or drugs in gain-of-function strategies. We conclude by showing applications of the IEDDA reaction in the construction of biomaterials that are used for drug delivery and multimodal imaging, among others. The use and utility of the IEDDA reaction is interdisciplinary and promises to revolutionize chemical biology, radiochemistry and materials science.
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Affiliation(s)
- B L Oliveira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Z Guo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - G J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. and Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, Lisboa, 1649-028, Portugal.
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33
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Fang Y, Zhang H, Huang Z, Scinto SL, Yang JC, Am Ende CW, Dmitrenko O, Johnson DS, Fox JM. Photochemical syntheses, transformations, and bioorthogonal chemistry of trans-cycloheptene and sila trans-cycloheptene Ag(i) complexes. Chem Sci 2018; 9:1953-1963. [PMID: 29675242 PMCID: PMC5892336 DOI: 10.1039/c7sc04773h] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 01/05/2018] [Indexed: 11/21/2022] Open
Abstract
A photochemical synthesis of AgNO3 complexes of trans-cycloheptene (TCH) and trans-1-sila-4-cycloheptene (Si-TCH) derivatives is described. A low temperature flow photoreactor was designed to enable the synthesis of carbocyclic TCH derivatives due to their thermal sensitivity in the absence of metal coordination. Unlike the free carbocycles, TCH·AgNO3 complexes can be handled at rt and stored for weeks in the freezer (-18 °C). Si-TCH·AgNO3 complexes are especially robust, and are bench stable for days at rt, and for months in the freezer. X-ray crystallography was used to characterize a Si-TCH·AgNO3 complex for the first time. With decomplexation of AgNO3in situ, metal-free TCO and Si-TCH derivatives can engage in a range of cycloaddition reactions as well as dihydroxylation reactions. Computation was used to predict that Si-TCH would engage in bioorthogonal reactions that are more rapid than the most reactive trans-cyclooctenes. Metal-free Si-TCH derivatives were shown to display good stability in solution, and to engage in the fastest bioorthogonal reaction reported to date (k2 1.14 × 107 M-1 s-1 in 9 : 1 H2O : MeOH). Utility in bioorthogonal protein labeling in live cells is described, including labeling of GFP with an unnatural tetrazine-containing amino acid. The reactivity and specificity of the Si-TCH reagents with tetrazines in live mammalian cells was also evaluated using the HaloTag platform. The cell labeling experiments show that Si-TCH derivatives are best suited as probe molecules in the cellular environment.
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Affiliation(s)
- Yinzhi Fang
- Brown Laboratories , Department of Chemistry and Biochemistry , University of Delaware , Newark , DE 19716 , USA .
| | - Han Zhang
- Brown Laboratories , Department of Chemistry and Biochemistry , University of Delaware , Newark , DE 19716 , USA .
| | - Zhen Huang
- Pfizer Worldwide Research and Development , Cambridge , Massachusetts 02139 , USA
| | - Samuel L Scinto
- Brown Laboratories , Department of Chemistry and Biochemistry , University of Delaware , Newark , DE 19716 , USA .
| | - Jeffrey C Yang
- Pfizer Worldwide Research and Development , Cambridge , Massachusetts 02139 , USA
| | | | - Olga Dmitrenko
- Brown Laboratories , Department of Chemistry and Biochemistry , University of Delaware , Newark , DE 19716 , USA .
| | - Douglas S Johnson
- Pfizer Worldwide Research and Development , Cambridge , Massachusetts 02139 , USA
| | - Joseph M Fox
- Brown Laboratories , Department of Chemistry and Biochemistry , University of Delaware , Newark , DE 19716 , USA .
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34
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Lambert WD, Scinto SL, Dmitrenko O, Boyd SJ, Magboo R, Mehl RA, Chin JW, Fox JM, Wallace S. Computationally guided discovery of a reactive, hydrophilic trans-5-oxocene dienophile for bioorthogonal labeling. Org Biomol Chem 2018; 15:6640-6644. [PMID: 28752889 PMCID: PMC5708333 DOI: 10.1039/c7ob01707c] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The use of organic chemistry principles and prediction techniques has enabled the development of new bioorthogonal reactions. As this "toolbox" expands to include new reaction manifolds and orthogonal reaction pairings, the continued development of existing reactions remains an important objective. This is particularly important in cellular imaging, where non-specific background fluorescence has been linked to the hydrophobicity of the bioorthogonal moiety. Here we report that trans-5-oxocene (oxoTCO) displays enhanced reactivity and hydrophilicity compared to trans-cyclooctene (TCO) in the tetrazine ligation reaction. Aided by ab initio calculations we show that the insertion of a single oxygen atom into the trans-cyclooctene (TCO) ring system is sufficient to impart aqueous solubility and also results in significant rate acceleration by increasing angle strain. We demonstrate the rapid and quantitative cycloaddition of oxoTCO using a water-soluble tetrazine derivative and a protein substrate containing a site-specific genetically encoded tetrazine moiety both in vitro and in vivo. We anticipate that oxoTCO will find use in studies where hydrophilicity and fast bioconjugation kinetics are paramount.
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Affiliation(s)
- William D Lambert
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Samuel L Scinto
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Olga Dmitrenko
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Samantha J Boyd
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | | | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Joseph M Fox
- Brown Laboratory, Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716, USA.
| | - Stephen Wallace
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK and Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, UK
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35
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Lerner E, Cordes T, Ingargiol A, Alhadid Y, Chung S, Michalet X, Weiss S. Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science 2018; 359:eaan1133. [PMID: 29348210 PMCID: PMC6200918 DOI: 10.1126/science.aan1133] [Citation(s) in RCA: 323] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Classical structural biology can only provide static snapshots of biomacromolecules. Single-molecule Förster resonance energy transfer (smFRET) paved the way for studying dynamics in macromolecular structures under biologically relevant conditions. Since its first implementation in 1996, smFRET experiments have confirmed previously hypothesized mechanisms and provided new insights into many fundamental biological processes, such as DNA maintenance and repair, transcription, translation, and membrane transport. We review 22 years of contributions of smFRET to our understanding of basic mechanisms in biochemistry, molecular biology, and structural biology. Additionally, building on current state-of-the-art implementations of smFRET, we highlight possible future directions for smFRET in applications such as biosensing, high-throughput screening, and molecular diagnostics.
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Affiliation(s)
- Eitan Lerner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Antonino Ingargiol
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Yazan Alhadid
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - SangYoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
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36
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Voith von Voithenberg L, Lamb DC. Single Pair Förster Resonance Energy Transfer: A Versatile Tool To Investigate Protein Conformational Dynamics. Bioessays 2018; 40. [DOI: 10.1002/bies.201700078] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 12/05/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Lena Voith von Voithenberg
- Department Chemie; Center for Nanoscience (CeNS); Center for Integrated Protein Science Munich (CIPSM); Nanosystem Initiative Munich (NIM); Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
- BIOSS Centre for Signalling Studies; Schänzlestr. 18 79104 Freiburg Germany
| | - Don C. Lamb
- Department Chemie; Center for Nanoscience (CeNS); Center for Integrated Protein Science Munich (CIPSM); Nanosystem Initiative Munich (NIM); Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 München Germany
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37
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Koehler C, Lemke EA. MultiBacTAG-Genetic Code Expansion Using the Baculovirus Expression System in Sf21 Cells. Methods Mol Biol 2018; 1728:297-311. [PMID: 29405006 DOI: 10.1007/978-1-4939-7574-7_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The combination of genetic code expansion (GCE) and baculovirus-based protein expression in Spodoptera frugiperda cells is a powerful tool to express multiprotein complexes with site-specifically introduced noncanonical amino acids. This protocol describes the integration of synthetase and tRNA gene indispensable for GCE into the backbone of the Bacmid, the Tn7-mediated transposition of various genes of interest, as well as the final expression of protein using the MultiBacTAG system with different noncanonical amino acids.
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Affiliation(s)
- Christine Koehler
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University, Johannes-von-Mullerweg 6, Mainz, Germany.,Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit & Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany. .,Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University, Johannes-von-Mullerweg 6, Mainz, Germany. .,Institute of Molecular Biology (IMB), 55128, Mainz, Germany.
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38
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Wang L. Engineering the Genetic Code in Cells and Animals: Biological Considerations and Impacts. Acc Chem Res 2017; 50:2767-2775. [PMID: 28984438 DOI: 10.1021/acs.accounts.7b00376] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Expansion of the genetic code allows unnatural amino acids (Uaas) to be site-specifically incorporated into proteins in live biological systems, thus enabling novel properties selectively introduced into target proteins in vivo for basic biological studies and for engineering of novel biological functions. Orthogonal components including tRNA and aminoacyl-tRNA synthetase (aaRS) are expressed in live cells to decode a unique codon (often the amber stop codon UAG) as the desired Uaa. Initially developed in E. coli, this methodology has now been expanded in multiple eukaryotic cells and animals. In this Account, we focus on addressing various biological challenges for rewriting the genetic code, describing impacts of code expansion on cell physiology and discussing implications for fundamental studies of code evolution. Specifically, a general method using the type-3 polymerase III promoter was developed to efficiently express prokaryotic tRNAs as orthogonal tRNAs and a transfer strategy was devised to generate Uaa-specific aaRS for use in eukaryotic cells and animals. The aaRSs have been found to be highly amenable for engineering substrate specificity toward Uaas that are structurally far deviating from the native amino acid, dramatically increasing the stereochemical diversity of Uaas accessible. Preparation of the Uaa in ester or dipeptide format markedly increases the bioavailability of Uaas to cells and animals. Nonsense-mediated mRNA decay (NMD), an mRNA surveillance mechanism of eukaryotic cells, degrades mRNA containing a premature stop codon. Inhibition of NMD increases Uaa incorporation efficiency in yeast and Caenorhabditis elegans. In bacteria, release factor one (RF1) competes with the orthogonal tRNA for the amber stop codon to terminate protein translation, leading to low Uaa incorporation efficiency. Contradictory to the paradigm that RF1 is essential, it is discovered that RF1 is actually nonessential in E. coli. Knockout of RF1 dramatically increases Uaa incorporation efficiency and enables Uaa incorporation at multiple sites, making it feasible to use Uaa for directed evolution. Using these strategies, the genetic code has been effectively expanded in yeast, mammalian cells, stem cells, worms, fruit flies, zebrafish, and mice. It is also intriguing to find out that the legitimate UAG codons terminating endogenous genes are not efficiently suppressed by the orthogonal tRNA/aaRS in E. coli. Moreover, E. coli responds to amber suppression pressure promptly using transposon insertion to inactivate the introduced orthogonal aaRS. Persistent amber suppression evading transposon inactivation leads to global proteomic changes with a notable up-regulation of a previously uncharacterized protein YdiI, for which an unexpected function of expelling plasmids is discovered. Genome integration of the orthogonal tRNA/aaRS in mice results in minor changes in RNA transcripts but no significant physiological impairment. Lastly, the RF1 knockout E. coli strains afford a previously unavailable model organism for studying otherwise intractable questions on code evolution in real time in the laboratory. We expect that genetically encoding Uaas in live systems will continue to unfold new questions and directions for studying biology in vivo, investigating the code itself, and reprograming genomes for synthetic biology.
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Affiliation(s)
- Lei Wang
- Department of Pharmaceutical Chemistry
and the Cardiovascular Research Institute, University of California, San
Francisco, California 94158, United States
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39
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Pelosse M, Crocker H, Gorda B, Lemaire P, Rauch J, Berger I. MultiBac: from protein complex structures to synthetic viral nanosystems. BMC Biol 2017; 15:99. [PMID: 29084535 PMCID: PMC5661938 DOI: 10.1186/s12915-017-0447-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The MultiBac baculovirus/insect cell expression vector system was conceived as a user-friendly, modular tool-kit for producing multiprotein complexes for structural biology applications. MultiBac has allowed the structure and function of many molecular machines to be elucidated, including previously inaccessible high-value drug targets. More recently, MultiBac developments have shifted to customized baculoviral genomes that are tailored for a range of applications, including synthesizing artificial proteins by genetic code expansion. We review some of these developments, including the ongoing rewiring of the MultiBac system for mammalian applications, notably CRISPR/Cas9-mediated gene editing.
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Affiliation(s)
- Martin Pelosse
- The School of Biochemistry and Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, Tankard's Close, Bristol, BS8 1TD, UK
| | - Hannah Crocker
- The School of Biochemistry and Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, Tankard's Close, Bristol, BS8 1TD, UK
| | - Barbara Gorda
- The School of Biochemistry and Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, Tankard's Close, Bristol, BS8 1TD, UK
| | - Paul Lemaire
- Geneva Biotech SARL, Avenue de la Roseraie 64, 1205, Genève, Switzerland
| | - Jens Rauch
- Systems Biology Ireland, University College Dublin, Belfield Dublin 4, Republic of Ireland
| | - Imre Berger
- The School of Biochemistry and Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, Tankard's Close, Bristol, BS8 1TD, UK.
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40
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Abstract
Fluorescence nanoscopy uniquely combines minimally invasive optical access to the internal nanoscale structure and dynamics of cells and tissues with molecular detection specificity. While the basic physical principles of 'super-resolution' imaging were discovered in the 1990s, with initial experimental demonstrations following in 2000, the broad application of super-resolution imaging to address cell-biological questions has only more recently emerged. Nanoscopy approaches have begun to facilitate discoveries in cell biology and to add new knowledge. One current direction for method improvement is the ambition to quantitatively account for each molecule under investigation and assess true molecular colocalization patterns via multi-colour analyses. In pursuing this goal, the labelling of individual molecules to enable their visualization has emerged as a central challenge. Extending nanoscale imaging into (sliced) tissue and whole-animal contexts is a further goal. In this Review we describe the successes to date and discuss current obstacles and possibilities for further development.
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41
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Schvartz T, Aloush N, Goliand I, Segal I, Nachmias D, Arbely E, Elia N. Direct fluorescent-dye labeling of α-tubulin in mammalian cells for live cell and superresolution imaging. Mol Biol Cell 2017; 28:2747-2756. [PMID: 28835375 PMCID: PMC5638579 DOI: 10.1091/mbc.e17-03-0161] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/28/2022] Open
Abstract
This work describes an elegant approach for direct, site-specific labeling of proteins with fluorescent-dyes for live cell imaging. By integrating a noncanonical amino acid that is capable of binding a fluorescent dye into tubulin, we directly and specifically labeled tubulin with a fluorescent-dye and imaged microtubules in live mammlian cells. Genetic code expansion and bioorthogonal labeling provide for the first time a way for direct, site-specific labeling of proteins with fluorescent-dyes in live cells. Although the small size and superb photophysical parameters of fluorescent-dyes offer unique advantages for high-resolution microscopy, this approach has yet to be embraced as a tool in live cell imaging. Here we evaluated the feasibility of this approach by applying it for α-tubulin labeling. After a series of calibrations, we site-specifically labeled α-tubulin with silicon rhodamine (SiR) in live mammalian cells in an efficient and robust manner. SiR-labeled tubulin successfully incorporated into endogenous microtubules at high density, enabling video recording of microtubule dynamics in interphase and mitotic cells. Applying this labeling approach to structured illumination microscopy resulted in an increase in resolution, highlighting the advantages in using a smaller, brighter tag. Therefore, using our optimized assay, genetic code expansion provides an attractive tool for labeling proteins with a minimal, bright tag in quantitative high-resolution imaging.
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Affiliation(s)
- Tomer Schvartz
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel
| | - Noa Aloush
- The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel.,Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Inna Goliand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel
| | - Inbar Segal
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel
| | - Dikla Nachmias
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel
| | - Eyal Arbely
- The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel.,Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Natalie Elia
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel .,The National Institute for Biotechnology in the Negev, Beer Sheva 84105, Israel
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42
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Tosevski V, Ulashchik E, Trovato A, Cappella P. CyTOF Mass Cytometry for Click Proliferation Assays. ACTA ACUST UNITED AC 2017; 81:7.50.1-7.50.14. [PMID: 28678421 DOI: 10.1002/cpcy.25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Novel cell analyzers, including polychromatic flow cytometers and isotopical cytometry by time of flight (CyTOF) mass cytometers, enable simultaneous measurement of virtually bondless characteristics at the single-cell level. BrdU assays for quantifying cellular proliferation are common but have several limitations, including the need for a DNA denaturation step and inability to simultaneously resolve multiple parameters and phenotypic complexity. Click chemistry reactions have become popular in the past decade, as they can resolve these issues. This protocol introduces a novel assay able to bridge flow cytometry and CyTOF analysis for active S-phase determination in cell cycle applications, combining well-established click chemistry with a novel iodo-deoxyuridine (IdU) azide derivative and a cross-reactive anti-IdU antibody for detecting incorporated EdU during DNA synthesis. This method is preferred over traditional BrdU-based assays for complex and multiparametric experiments. It provides a feasible cost-effective approach for detecting ethynyl-labeled nucleotides, with the advantage of combining flow and mass cytometry analyses. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Vinko Tosevski
- Mass Cytometry Facility, University of Zurich, Zurich, Switzerland
| | - Egor Ulashchik
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus.,Primetech ALC, Minsk, Belarus
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43
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Sakin V, Hanne J, Dunder J, Anders-Össwein M, Laketa V, Nikić I, Kräusslich HG, Lemke EA, Müller B. A Versatile Tool for Live-Cell Imaging and Super-Resolution Nanoscopy Studies of HIV-1 Env Distribution and Mobility. Cell Chem Biol 2017; 24:635-645.e5. [PMID: 28457706 DOI: 10.1016/j.chembiol.2017.04.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/12/2017] [Accepted: 04/06/2017] [Indexed: 12/27/2022]
Abstract
The envelope glycoproteins (Env) of HIV-1 mediate cell entry through fusion of the viral envelope with a target cell membrane. Intramembrane mobility and clustering of Env trimers at the viral budding site are essential for its function. Previous live-cell and super-resolution microscopy studies were limited by lack of a functional fluorescent Env derivative, requiring antibody labeling for detection. Introduction of a bio-orthogonal amino acid by genetic code expansion, combined with click chemistry, offers novel possibilities for site-specific, minimally invasive labeling. Using this approach, we established efficient incorporation of non-canonical amino acids within HIV-1 Env in mammalian cells. The engineered protein retained plasma membrane localization, glycosylation, virion incorporation, and fusogenic activity, and could be rapidly and specifically labeled with synthetic dyes. This strategy allowed us to revisit Env dynamics and nanoscale distribution at the plasma membrane close to its native state, applying fluorescence recovery after photo bleaching and STED nanoscopy, respectively.
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Affiliation(s)
- Volkan Sakin
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Janina Hanne
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany; Optical Nanoscopy Division, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Jessica Dunder
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Maria Anders-Össwein
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Vibor Laketa
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany; German Center for Infection Research, Partner Site Heidelberg, 69120 Heidelberg, Germany
| | - Ivana Nikić
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, 69117 Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany; German Center for Infection Research, Partner Site Heidelberg, 69120 Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, 69117 Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.
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44
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Schumacher D, Lemke O, Helma J, Gerszonowicz L, Waller V, Stoschek T, Durkin PM, Budisa N, Leonhardt H, Keller BG, Hackenberger CPR. Broad substrate tolerance of tubulin tyrosine ligase enables one-step site-specific enzymatic protein labeling. Chem Sci 2017; 8:3471-3478. [PMID: 28507719 PMCID: PMC5418632 DOI: 10.1039/c7sc00574a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/18/2017] [Indexed: 12/31/2022] Open
Abstract
The broad substrate tolerance of tubulin tyrosine ligase enables its wide applicability for protein functionalization.
The broad substrate tolerance of tubulin tyrosine ligase is the basic rationale behind its wide applicability for chemoenzymatic protein functionalization. In this context, we report that the wild-type enzyme enables ligation of various unnatural amino acids that are substantially bigger than and structurally unrelated to the natural substrate, tyrosine, without the need for extensive protein engineering. This unusual substrate flexibility is due to the fact that the enzyme's catalytic pocket forms an extended cavity during ligation, as confirmed by docking experiments and all-atom molecular dynamics simulations. This feature enabled one-step C-terminal biotinylation and fluorescent coumarin labeling of various functional proteins as demonstrated with ubiquitin, an antigen binding nanobody, and the apoptosis marker Annexin V. Its broad substrate tolerance establishes tubulin tyrosine ligase as a powerful tool for in vitro enzyme-mediated protein modification with single functional amino acids in a specific structural context.
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Affiliation(s)
- Dominik Schumacher
- Department of Chemical-Biology , Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Str. 10 , 13125 Berlin , Germany . .,Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
| | - Oliver Lemke
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustr. 3 , 14195 Berlin , Germany .
| | - Jonas Helma
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Lena Gerszonowicz
- Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
| | - Verena Waller
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Tina Stoschek
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Patrick M Durkin
- Department of Chemistry , TU Berlin , Müller-Breslau-Str. 10 , 10623 Berlin , Germany
| | - Nediljko Budisa
- Department of Chemistry , TU Berlin , Müller-Breslau-Str. 10 , 10623 Berlin , Germany
| | - Heinrich Leonhardt
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustr. 3 , 14195 Berlin , Germany .
| | - Christian P R Hackenberger
- Department of Chemical-Biology , Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Str. 10 , 13125 Berlin , Germany . .,Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
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45
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Kums J, Nelke J, Rüth B, Schäfer V, Siegmund D, Wajant H. Quantitative analysis of cell surface antigen-antibody interaction using Gaussia princeps luciferase antibody fusion proteins. MAbs 2017; 9:506-520. [PMID: 28095113 DOI: 10.1080/19420862.2016.1274844] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Cell surface antigen-specific antibodies are of substantial diagnostic and therapeutic importance. The binding properties of such antibodies are usually evaluated by cell-free assays, in particular surface plasmon resonance (SPR) analysis, or flow cytometry. SPR analyses allow the detailed quantitative and dynamic evaluation of the binding properties of antibodies, but need purified, typically recombinantly produced antigens. It can, however, be difficult to produce the required antigen. Furthermore, cellular factors influencing the antigen-antibody interaction are not considered by this method. Flow cytometry-based analyses do not have these limitations, but require elaborated calibration controls for absolute quantification of bound molecules. To overcome the limitations of SRP and flow cytometry in the characterization of cell surface antigen-specific antibodies, we developed Fn14-specific antibody 18D1 as an example of an antibody fusion protein format that includes the luciferase of Gaussia princeps (GpL), which enables very simple and highly sensitive cellular binding studies. We found that GpL-tagging of the C-terminus of the antibody light chain does not affect the interaction of 18D1-IgG1 with its antigen and Fc-gamma receptors (FcγRs). In accordance with this, the GpL(LC-CT)-18D1-IgG1 antibody fusion protein showed basically the same FcγR-dependent agonistic properties as the parental 18D1 antibody. Similar results were obtained with isotype switch variants of 18D1 and antibodies specific for CD95, LTβR and CD40. In sum, we demonstrate that antibody GpL fusion proteins are easily manageable and versatile tools for the characterization of cell surface antigen-antibody interactions that have the potential to considerably extend the instrumentarium for the evaluation of antibodies.
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Affiliation(s)
- Juliane Kums
- a Division of Molecular Internal Medicine, Department of Internal Medicine II , University Hospital Würzburg , Würzburg , Germany
| | - Johannes Nelke
- a Division of Molecular Internal Medicine, Department of Internal Medicine II , University Hospital Würzburg , Würzburg , Germany
| | - Benedikt Rüth
- a Division of Molecular Internal Medicine, Department of Internal Medicine II , University Hospital Würzburg , Würzburg , Germany
| | - Viktoria Schäfer
- a Division of Molecular Internal Medicine, Department of Internal Medicine II , University Hospital Würzburg , Würzburg , Germany
| | - Daniela Siegmund
- a Division of Molecular Internal Medicine, Department of Internal Medicine II , University Hospital Würzburg , Würzburg , Germany
| | - Harald Wajant
- a Division of Molecular Internal Medicine, Department of Internal Medicine II , University Hospital Würzburg , Würzburg , Germany
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46
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Gan Q, Lehman BP, Bobik TA, Fan C. Expanding the genetic code of Salmonella with non-canonical amino acids. Sci Rep 2016; 6:39920. [PMID: 28008993 PMCID: PMC5180212 DOI: 10.1038/srep39920] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/29/2016] [Indexed: 12/21/2022] Open
Abstract
The diversity of non-canonical amino acids (ncAAs) endows proteins with new features for a variety of biological studies and biotechnological applications. The genetic code expansion strategy, which co-translationally incorporates ncAAs into specific sites of target proteins, has been applied in many organisms. However, there have been only few studies on pathogens using genetic code expansion. Here, we introduce this technique into the human pathogen Salmonella by incorporating p-azido-phenylalanine, benzoyl-phenylalanine, acetyl-lysine, and phosphoserine into selected Salmonella proteins including a microcompartment shell protein (PduA), a type III secretion effector protein (SteA), and a metabolic enzyme (malate dehydrogenase), and demonstrate practical applications of genetic code expansion in protein labeling, photocrosslinking, and post-translational modification studies in Salmonella. This work will provide powerful tools for a wide range of studies on Salmonella.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Brent P Lehman
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
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47
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Peng T, Hang HC. Site-Specific Bioorthogonal Labeling for Fluorescence Imaging of Intracellular Proteins in Living Cells. J Am Chem Soc 2016; 138:14423-14433. [PMID: 27768298 DOI: 10.1021/jacs.6b08733] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Over the past years, fluorescent proteins (e.g., green fluorescent proteins) have been widely utilized to visualize recombinant protein expression and localization in live cells. Although powerful, fluorescent protein tags are limited by their relatively large sizes and potential perturbation to protein function. Alternatively, site-specific labeling of proteins with small-molecule organic fluorophores using bioorthogonal chemistry may provide a more precise and less perturbing method. This approach involves site-specific incorporation of unnatural amino acids (UAAs) into proteins via genetic code expansion, followed by bioorthogonal chemical labeling with small organic fluorophores in living cells. While this approach has been used to label extracellular proteins for live cell imaging studies, site-specific bioorthogonal labeling and fluorescence imaging of intracellular proteins in live cells is still challenging. Herein, we systematically evaluate site-specific incorporation of diastereomerically pure bioorthogonal UAAs bearing stained alkynes or alkenes into intracellular proteins for inverse-electron-demand Diels-Alder cycloaddition reactions with tetrazine-functionalized fluorophores for live cell labeling and imaging in mammalian cells. Our studies show that site-specific incorporation of axial diastereomer of trans-cyclooct-2-ene-lysine robustly affords highly efficient and specific bioorthogonal labeling with monosubstituted tetrazine fluorophores in live mammalian cells, which enabled us to image the intracellular localization and real-time dynamic trafficking of IFITM3, a small membrane-associated protein with only 137 amino acids, for the first time. Our optimized UAA incorporation and bioorthogonal labeling conditions also enabled efficient site-specific fluorescence labeling of other intracellular proteins for live cell imaging studies in mammalian cells.
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Affiliation(s)
- Tao Peng
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen 518055, China.,Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University , New York, New York 10065, United States
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48
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Komar AA. The "periodic table" of the genetic code: A new way to look at the code and the decoding process. ACTA ACUST UNITED AC 2016; 4:e1234431. [PMID: 28090420 DOI: 10.1080/21690731.2016.1234431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/05/2016] [Indexed: 01/18/2023]
Abstract
Henri Grosjean and Eric Westhof recently presented an information-rich, alternative view of the genetic code, which takes into account current knowledge of the decoding process, including the complex nature of interactions between mRNA, tRNA and rRNA that take place during protein synthesis on the ribosome, and it also better reflects the evolution of the code. The new asymmetrical circular genetic code has a number of advantages over the traditional codon table and the previous circular diagrams (with a symmetrical/clockwise arrangement of the U, C, A, G bases). Most importantly, all sequence co-variances can be visualized and explained based on the internal logic of the thermodynamics of codon-anticodon interactions.
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Affiliation(s)
- Anton A Komar
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA; Department of Biochemistry and Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
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49
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Eising S, Lelivelt F, Bonger KM. Vinylboronic Acids as Fast Reacting, Synthetically Accessible, and Stable Bioorthogonal Reactants in the Carboni-Lindsey Reaction. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605271] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Selma Eising
- Department of Biomolecular Chemistry; Institute for Molecules and Materials; Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Francis Lelivelt
- Department of Biomolecular Chemistry; Institute for Molecules and Materials; Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen 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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50
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Eising S, Lelivelt F, Bonger KM. Vinylboronic Acids as Fast Reacting, Synthetically Accessible, and Stable Bioorthogonal Reactants in the Carboni-Lindsey Reaction. Angew Chem Int Ed Engl 2016; 55:12243-7. [PMID: 27605057 PMCID: PMC5113785 DOI: 10.1002/anie.201605271] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/10/2016] [Indexed: 11/09/2022]
Abstract
Bioorthogonal reactions are widely used for the chemical modification of biomolecules. The application of vinylboronic acids (VBAs) as non‐strained, synthetically accessible and water‐soluble reaction partners in a bioorthogonal inverse electron‐demand Diels–Alder (iEDDA) reaction with 3,6‐dipyridyl‐s‐tetrazines is described. Depending on the substituents, VBA derivatives give second‐order rate constants up to 27 m−1 s−1 in aqueous environments at room temperature, which is suitable for biological labeling applications. The VBAs are shown to be biocompatible, non‐toxic, and highly stable in aqueous media and cell lysate. Furthermore, VBAs can be used orthogonally to the strain‐promoted alkyne–azide cycloaddition for protein modification, making them attractive complements to the bioorthogonal molecular toolbox.
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Affiliation(s)
- Selma Eising
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Francis Lelivelt
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, 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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