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Joest EF, Tampé R. Design principles for engineering light-controlled antibodies. Trends Biotechnol 2023; 41:1501-1517. [PMID: 37507295 DOI: 10.1016/j.tibtech.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023]
Abstract
Engineered antibodies are essential tools for research and advanced pharmacy. In the development of therapeutics, antibodies are excellent candidates as they offer both target recognition and modulation. Thanks to the latest advances in biotechnology, light-activated antibody fragments can be constructed to control spontaneous antigen interaction with high spatiotemporal precision. To implement conditional antigen binding, several optogenetic and optochemical engineering concepts have recently been developed. Here, we highlight the various strategies and discuss the features of opto-conditional antibodies. Each concept offers intrinsic advantages beneficial to different applications. In summary, the novel design approaches constitute a complementary toolset to promote current and upcoming antibody technologies with ultimate precision.
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Affiliation(s)
- Eike F Joest
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany.
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany.
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2
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Yang X, Zhao L, Wang Y, Ji Y, Su XC, Ma JA, Xuan W. Constructing Photoactivatable Protein with Genetically Encoded Photocaged Glutamic Acid. Angew Chem Int Ed Engl 2023; 62:e202308472. [PMID: 37587083 DOI: 10.1002/anie.202308472] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/28/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023]
Abstract
Genetically replacing an essential residue with the corresponding photocaged analogues via genetic code expansion (GCE) constitutes a useful and unique strategy to directly and effectively generate photoactivatable proteins. However, the application of this strategy is severely hampered by the limited number of encoded photocaged proteinogenic amino acids. Herein, we report the genetic incorporation of photocaged glutamic acid analogues in E. coli and mammalian cells and demonstrate their use in constructing photoactivatable variants of various fluorescent proteins and SpyCatcher. We believe genetically encoded photocaged Glu would significantly promote the design and application of photoactivatable proteins in many areas.
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Affiliation(s)
- Xiaochen Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Lei Zhao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Ying Wang
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Yanli Ji
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Jun-An Ma
- Department of Chemistry, Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
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3
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Pham PN, Zahradník J, Kolářová L, Schneider B, Fuertes G. Regulation of IL-24/IL-20R2 complex formation using photocaged tyrosines and UV light. Front Mol Biosci 2023; 10:1214235. [PMID: 37484532 PMCID: PMC10361524 DOI: 10.3389/fmolb.2023.1214235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023] Open
Abstract
Human interleukin 24 (IL-24) is a multifunctional cytokine that represents an important target for autoimmune diseases and cancer. Since the biological functions of IL-24 depend on interactions with membrane receptors, on-demand regulation of the affinity between IL-24 and its cognate partners offers exciting possibilities in basic research and may have applications in therapy. As a proof-of-concept, we developed a strategy based on recombinant soluble protein variants and genetic code expansion technology to photocontrol the binding between IL-24 and one of its receptors, IL-20R2. Screening of non-canonical ortho-nitrobenzyl-tyrosine (NBY) residues introduced at several positions in both partners was done by a combination of biophysical and cell signaling assays. We identified one position for installing NBY, tyrosine70 of IL-20R2, which results in clear impairment of heterocomplex assembly in the dark. Irradiation with 365-nm light leads to decaging and reconstitutes the native tyrosine of the receptor that can then associate with IL-24. Photocaged IL-20R2 may be useful for the spatiotemporal control of the JAK/STAT phosphorylation cascade.
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Affiliation(s)
- Phuong Ngoc Pham
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
- Faculty of Science, Charles University, Prague, Czechia
| | - Jiří Zahradník
- First Faculty of Medicine, BIOCEV Center, Charles University, Prague, Czechia
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lucie Kolářová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Bohdan Schneider
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Gustavo Fuertes
- Laboratory of Biomolecular Recognition, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
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Beyond luciferase-luciferin system: Modification, improved imaging and biomedical application. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Shade O, Ryan A, Deiters A. Targeted protein degradation through light-activated E3 ligase recruitment. Methods Enzymol 2023; 681:265-286. [PMID: 36764761 DOI: 10.1016/bs.mie.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Optical control of protein function through proteasomal degradation benefits from the noninvasive nature and spatiotemporal precision of light as a trigger. In this chapter, light activation of protein degradation with an optically controlled degron, termed optoDeg, is discussed. This method utilizes genetic code expansion to insert a photocaged analog of lysine at the N-terminal position of a protein of interest for spatial and temporal control of the N-end pathway, inducing proteasomal degradation. Methods for the use of optoDeg for degradation of the fluorescent reporter EGFP and the kinase MEK1 are described. The system is fast, with complete degradation of proteins within minutes following irradiation, and highly specific, with genetically directed introduction of the light-activated degron.
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Affiliation(s)
- Olivia Shade
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Amy Ryan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States.
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Liang X, Zhang Y, Zhou J, Bu Z, Liu J, Zhang K. Tumor microenvironment-triggered intratumoral in situ construction of theranostic supramolecular self-assembly. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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7
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O'Shea JM, Goutou A, Brydon J, Sethna CR, Wood CW, Greiss S. Generation of Photocaged Nanobodies for Intracellular Applications in an Animal Using Genetic Code Expansion and Computationally Guided Protein Engineering. Chembiochem 2022; 23:e202200321. [PMID: 35731601 PMCID: PMC9542635 DOI: 10.1002/cbic.202200321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 11/12/2022]
Abstract
Nanobodies are becoming increasingly popular as tools for manipulating and visualising proteins in vivo. The ability to control nanobody/antigen interactions using light could provide precise spatiotemporal control over protein function. We develop a general approach to engineer photo-activatable nanobodies using photocaged amino acids that are introduced into the target binding interface by genetic code expansion. Guided by computational alanine scanning and molecular dynamics simulations, we tune nanobody/target binding affinity to eliminate binding before uncaging. Upon photo-activation using 365 nm light, binding is restored. We use this approach to generate improved photocaged variants of two anti-GFP nanobodies that function robustly when directly expressed in a complex intracellular environment together with their antigen. We apply them to control subcellular protein localisation in the nematode worm Caenorhabditis elegans. Our approach applies predictions derived from computational modelling directly in a living animal and demonstrates the importance of accounting for in vivo effects on protein-protein interactions.
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Affiliation(s)
- Jack M. O'Shea
- Centre for Discovery Brain SciencesUniversity of Edinburgh, Hugh Robson Building George SquareEdinburghEH8 9XDUK
| | - Angeliki Goutou
- Centre for Discovery Brain SciencesUniversity of Edinburgh, Hugh Robson Building George SquareEdinburghEH8 9XDUK
| | - Jack Brydon
- MRC Institute of Genetics & Molecular MedicineUniversity of Edinburgh, Western General Hospital Crewe Road SouthEdinburghEH4 2XRUK
| | - Cyrus R. Sethna
- Centre for Discovery Brain SciencesUniversity of Edinburgh, Hugh Robson Building George SquareEdinburghEH8 9XDUK
| | - Christopher W. Wood
- Institute of Quantitative Biology, Biochemistry and BiotechnologyUniversity of Edinburgh, Roger Land Building King's BuildingsEdinburghEH9 3JQUK
| | - Sebastian Greiss
- Centre for Discovery Brain SciencesUniversity of Edinburgh, Hugh Robson Building George SquareEdinburghEH8 9XDUK
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Joest EF, Winter C, Wesalo JS, Deiters A, Tampé R. Efficient Amber Suppression via Ribosomal Skipping for In Situ Synthesis of Photoconditional Nanobodies. ACS Synth Biol 2022; 11:1466-1476. [PMID: 35060375 PMCID: PMC9157392 DOI: 10.1021/acssynbio.1c00471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetic code expansion is a versatile method for in situ synthesis of modified proteins. During mRNA translation, amber stop codons are suppressed to site-specifically incorporate non-canonical amino acids. Thus, nanobodies can be equipped with photocaged amino acids to control target binding on demand. The efficiency of amber suppression and protein synthesis can vary with unpredictable background expression, and the reasons are hardly understood. Here, we identified a substantial limitation that prevented synthesis of nanobodies with N-terminal modifications for light control. After systematic analyses, we hypothesized that nanobody synthesis was severely affected by ribosomal inaccuracy during the early phases of translation. To circumvent a background-causing read-through of a premature stop codon, we designed a new suppression concept based on ribosomal skipping. As an example, we generated intrabodies with photoactivated target binding in mammalian cells. The findings provide valuable insights into the genetic code expansion and describe a versatile synthesis route for the generation of modified nanobodies that opens up new perspectives for efficient site-specific integration of chemical tools. In the area of photopharmacology, our flexible intrabody concept builds an ideal platform to modulate target protein function and interaction.
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Affiliation(s)
- Eike F Joest
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M, Germany
| | - Christian Winter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M, Germany
| | - Joshua S Wesalo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M, Germany
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Jedlitzke B, Mootz HD. A light-activatable photocaged variant of the ultra-high affinity ALFA-tag nanobody. Chembiochem 2022; 23:e202200079. [PMID: 35411584 PMCID: PMC9324849 DOI: 10.1002/cbic.202200079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/18/2022] [Indexed: 11/25/2022]
Abstract
Nanobodies against short linear peptide‐epitopes are widely used to detect and bind proteins of interest (POI) in fusion constructs. Engineered nanobodies that can be controlled by light have found very recent attention for various extra‐ and intracellular applications. We here report the design of a photocaged variant of the ultra‐high affinity ALFA‐tag nanobody, also termed ALFA‐tag photobody. ortho‐Nitrobenzyl tyrosine was incorporated into the paratope region of the nanobody by genetic code expansion technology and resulted in a ≥9,200 to 100,000‐fold impairment of the binding affinity. Irradiation with light (365 nm) leads to decaging and reconstitutes the native nanobody. We show the light‐dependent binding of the ALFA‐tag photobody to HeLa cells presenting the ALFA‐tag. The generation of the first photobody directed against a short peptide epitope underlines the generality of our photobody design concept. We envision that this photobody will be useful for the spatiotemporal control of proteins in many applications using cultured cells.
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Affiliation(s)
- Benedikt Jedlitzke
- Institute of BiochemistryDepartment of Chemistry and PharmacyUniversity of MuensterCorrensstr. 3648149MünsterGermany
| | - Henning D. Mootz
- Institute of BiochemistryDepartment of Chemistry and PharmacyUniversity of MuensterCorrensstr. 3648149MünsterGermany
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Colecraft HM, Trimmer JS. Controlling ion channel function with renewable recombinant antibodies. J Physiol 2022; 600:2023-2036. [PMID: 35238051 PMCID: PMC9058206 DOI: 10.1113/jp282403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/11/2022] [Indexed: 11/08/2022] Open
Abstract
Selective ion channel modulators play a critical role in physiology in defining the contribution of specific ion channels to physiological function and as proof of concept for novel therapeutic strategies. Antibodies are valuable research tools that have broad uses including defining the expression and localization of ion channels in native tissue, and capturing ion channel proteins for subsequent analyses. In this review, we detail how renewable and recombinant antibodies can be used to control ion channel function. We describe the different forms of renewable and recombinant antibodies that have been used and the mechanisms by which they modulate ion channel function. We highlight the use of recombinant antibodies that are expressed intracellularly (intrabodies) as genetically-encoded tools to control ion channel function. We also offer perspectives of avenues of future research that may be opened by the application of emerging technologies for engineering recombinant antibodies for enhanced utility in ion channel research. Overall, this review provides insights that may help stimulate and guide interested researchers to develop and incorporate renewable and recombinant antibodies as valuable tools to control ion channel function. Abstract figure legend Two different approaches for controlling ion channel function using renewable recombinant antibodies. On the left, an externally applied intact IgG antibody (purple) binds to an extracellular domain of an ion channel (light blue) to control ion channel function. On the right, a genetically-encoded intrabody, in this example a camelid nanobody (green) fused to an effector molecule (red) binds to an intracellular auxiliary subunit of an ion channel (dark blue) to control ion channel function. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Henry M Colecraft
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - James S Trimmer
- Department of Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA, 95616, USA
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Lepeta K, Bauer M, Aguilar G, Vigano MA, Matsuda S, Affolter M. Studying Protein Function Using Nanobodies and Other Protein Binders in Drosophila. Methods Mol Biol 2022; 2540:219-237. [PMID: 35980580 DOI: 10.1007/978-1-0716-2541-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The direct manipulation of proteins by nanobodies and other protein binders has become an additional and valuable approach to investigate development and homeostasis in Drosophila. In contrast to other techniques, that indirectly interfere with proteins via their nucleic acids (CRISPR, RNAi, etc.), protein binders permit direct and acute protein manipulation. Since the first use of a nanobody in Drosophila a decade ago, many different applications exploiting protein binders have been introduced. Most of these applications use nanobodies against GFP to regulate GFP fusion proteins. In order to exert specific protein manipulations, protein binders are linked to domains that confer them precise biochemical functions. Here, we reflect on the use of tools based on protein binders in Drosophila. We describe their key features and provide an overview of the available reagents. Finally, we briefly explore the future avenues that protein binders might open up and thus further contribute to better understand development and homeostasis of multicellular organisms.
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Affiliation(s)
| | - Milena Bauer
- Biozentrum der Universität Basel, Basel, Switzerland
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Genetically encoded intrabodies as high-precision tools to visualize and manipulate neuronal function. Semin Cell Dev Biol 2021; 126:117-124. [PMID: 34782184 DOI: 10.1016/j.semcdb.2021.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 11/24/2022]
Abstract
Basic neuroscience research employs numerous forms of antibodies as key reagents in diverse applications. While the predominant use of antibodies is as immunolabeling reagents, neuroscientists are making increased use of intracellular antibodies or intrabodies. Intrabodies are recombinant antibodies genetically encoded for expression within neurons. These can be used to target various cargo (fluorescent proteins, reporters, enzymes, etc.) to specific molecules and subcellular domains to report on and manipulate neuronal function with high precision. Intrabodies have the advantages inherent in all genetically encoded recombinant antibodies but represent a distinct subclass in that their structure allows for their expression and function within cells. The high precision afforded by the ability to direct their expression to specific cell types, and the selective binding of intrabodies to targets within these allows intrabodies to offer unique advantages for neuroscience research, given the tremendous molecular, cellular and morphological complexity of brain neurons. Intrabodies expressed within neurons have been used for a variety of purposes in basic neuroscience research. Here I provide a general background to intrabodies and their development, and examples of their emerging utility as valuable basic neuroscience research tools.
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