1
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Schnider ST, Vigano MA, Affolter M, Aguilar G. Functionalized Protein Binders in Developmental Biology. Annu Rev Cell Dev Biol 2024; 40:119-142. [PMID: 39038471 DOI: 10.1146/annurev-cellbio-112122-025214] [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: 07/24/2024]
Abstract
Developmental biology has greatly profited from genetic and reverse genetic approaches to indirectly studying protein function. More recently, nanobodies and other protein binders derived from different synthetic scaffolds have been used to directly dissect protein function. Protein binders have been fused to functional domains, such as to lead to protein degradation, relocalization, visualization, or posttranslational modification of the target protein upon binding. The use of such functionalized protein binders has allowed the study of the proteome during development in an unprecedented manner. In the coming years, the advent of the computational design of protein binders, together with further advances in scaffold engineering and synthetic biology, will fuel the development of novel protein binder-based technologies. Studying the proteome with increased precision will contribute to a better understanding of the immense molecular complexities hidden in each step along the way to generate form and function during development.
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Affiliation(s)
| | | | | | - Gustavo Aguilar
- Current affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
- Biozentrum, Universität Basel, Basel, Switzerland;
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2
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Timalsina B, Lee S, Kaang BK. Advances in the labelling and selective manipulation of synapses. Nat Rev Neurosci 2024; 25:668-687. [PMID: 39174832 DOI: 10.1038/s41583-024-00851-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Synapses are highly specialized neuronal structures that are essential for neurotransmission, and they are dynamically regulated throughout the lifetime. Although accumulating evidence indicates that these structures are crucial for information processing and storage in the brain, their precise roles beyond neurotransmission are yet to be fully appreciated. Genetically encoded fluorescent tools have deepened our understanding of synaptic structure and function, but developing an ideal methodology to selectively visualize, label and manipulate synapses remains challenging. Here, we provide an overview of currently available synapse labelling techniques and describe their extension to enable synapse manipulation. We categorize these approaches on the basis of their conceptual bases and target molecules, compare their advantages and limitations and propose potential modifications to improve their effectiveness. These methods have broad utility, particularly for investigating mechanisms of synaptic function and synaptopathy.
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Affiliation(s)
- Binod Timalsina
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Sangkyu Lee
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Bong-Kiun Kaang
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea.
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3
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Vicidomini R, Choudhury SD, Han TH, Nguyen TH, Nguyen P, Opazo F, Serpe M. Versatile nanobody-based approach to image, track and reconstitute functional Neurexin-1 in vivo. Nat Commun 2024; 15:6068. [PMID: 39025931 PMCID: PMC11258300 DOI: 10.1038/s41467-024-50462-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
Neurexins are key adhesion proteins that coordinate extracellular and intracellular synaptic components. Nonetheless, the low abundance of these multidomain proteins has complicated any localization and structure-function studies. Here we combine an ALFA tag (AT)/nanobody (NbALFA) tool with classic genetics, cell biology and electrophysiology to examine the distribution and function of the Drosophila Nrx-1 in vivo. We generate full-length and ΔPDZ ALFA-tagged Nrx-1 variants and find that the PDZ binding motif is key to Nrx-1 surface expression. A PDZ binding motif provided in trans, via genetically encoded cytosolic NbALFA-PDZ chimera, fully restores the synaptic localization and function of NrxΔPDZ-AT. Using cytosolic NbALFA-mScarlet intrabody, we achieve compartment-specific detection of endogenous Nrx-1, track live Nrx-1 transport along the motor neuron axons, and demonstrate that Nrx-1 co-migrates with Rab2-positive vesicles. Our findings illustrate the versatility of the ALFA system and pave the way towards dissecting functional domains of complex proteins in vivo.
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Affiliation(s)
- Rosario Vicidomini
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Saumitra Dey Choudhury
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
- Centralized Core Research Facility-Microscopy, All India Institute of Medical Sciences, New Delhi, Delhi, India
| | - Tae Hee Han
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Tho Huu Nguyen
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Peter Nguyen
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Felipe Opazo
- Department of Neuro and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- NanoTag Biotechnologies GmbH, Göttingen, Germany
| | - Mihaela Serpe
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
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4
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Endo M, Tomizawa S, Kuang Q, Ozawa T. Optical control of nanobody-mediated protein activity modulation with a photocleavable fluorescent protein. Analyst 2024; 149:3865-3870. [PMID: 38916284 DOI: 10.1039/d4an00433g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Antibodies are crucial in various biological applications due to their specific binding to target molecules, altering protein function and structure. The advent of single-chain antibodies such as nanobodies has paved the way for broader applicability in both research and therapies due to their small size and efficient tissue penetration. Recently, several approaches have been reported to optically control the antigen-binding affinity of nanobodies. Here, we show an alternative strategy for creating photo-activatable nanobodies. By fusing the photocleavable protein PhoCl with the N-terminus of the nanobody (named optoNb60), we successfully demonstrated light-dependent restoration of the antigen-binding ability and the following modulation of the activity of a target protein, the beta-2 adrenergic receptor. Moreover, the activation of optoNb60 was monitored by the fluorescence changes upon photoconversion. The compatibility of the uncaging design with the previously reported optogenetic molecules using nanobodies will contribute to the further optimization of the response capabilities of existing optogenetic tools, thereby expanding their applicability.
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Affiliation(s)
- Mizuki Endo
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Saki Tomizawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Qiaoyue Kuang
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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5
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Eden T, Schaffrath AZ, Wesolowski J, Stähler T, Tode N, Richter N, Schäfer W, Hambach J, Hermans-Borgmeyer I, Woens J, Le Gall CM, Wendler S, Linke-Winnebeck C, Stobbe M, Budnicki I, Wanney A, Heitz Y, Schimmelpfennig L, Schweitzer L, Zimmer D, Stahl E, Seyfried F, Gebhardt AJ, Dieckow L, Riecken K, Fehse B, Bannas P, Magnus T, Verdoes M, Figdor CG, Hartlepp KF, Schleer H, Füner J, Tomas NM, Haag F, Rissiek B, Mann AM, Menzel S, Koch-Nolte F. Generation of nanobodies from transgenic 'LamaMice' lacking an endogenous immunoglobulin repertoire. Nat Commun 2024; 15:4728. [PMID: 38830864 PMCID: PMC11148044 DOI: 10.1038/s41467-024-48735-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/02/2024] [Indexed: 06/05/2024] Open
Abstract
Due to their exceptional solubility and stability, nanobodies have emerged as powerful building blocks for research tools and therapeutics. However, their generation in llamas is cumbersome and costly. Here, by inserting an engineered llama immunoglobulin heavy chain (IgH) locus into IgH-deficient mice, we generate a transgenic mouse line, which we refer to as 'LamaMouse'. We demonstrate that LamaMice solely express llama IgH molecules without association to Igκ or λ light chains. Immunization of LamaMice with AAV8, the receptor-binding domain of the SARS-CoV-2 spike protein, IgE, IgG2c, and CLEC9A enabled us to readily select respective target-specific nanobodies using classical hybridoma and phage display technologies, single B cell screening, and direct cloning of the nanobody-repertoire into a mammalian expression vector. Our work shows that the LamaMouse represents a flexible and broadly applicable platform for a facilitated selection of target-specific nanobodies.
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Affiliation(s)
- Thomas Eden
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alessa Z Schaffrath
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Janusz Wesolowski
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias Stähler
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Natalie Tode
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nathalie Richter
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Waldemar Schäfer
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Hambach
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Irm Hermans-Borgmeyer
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jannis Woens
- Research Department Cell and Gene Therapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Camille M Le Gall
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sabrina Wendler
- ChromoTek GmbH, Martinsried, Germany - A part of Proteintech Group, Martinsried, Germany
| | | | - Martina Stobbe
- ChromoTek GmbH, Martinsried, Germany - A part of Proteintech Group, Martinsried, Germany
| | | | | | | | | | | | | | | | - Fabienne Seyfried
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna J Gebhardt
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lynn Dieckow
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Bannas
- Department of Radiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tim Magnus
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martijn Verdoes
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carl G Figdor
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Klaus F Hartlepp
- ChromoTek GmbH, Martinsried, Germany - A part of Proteintech Group, Martinsried, Germany
| | | | | | - Nicola M Tomas
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Björn Rissiek
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna M Mann
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Menzel
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Core Facility Nanobodies, University of Bonn, Bonn, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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6
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Advedissian T, Frémont S, Echard A. Cytokinetic abscission requires actin-dependent microtubule severing. Nat Commun 2024; 15:1949. [PMID: 38431632 PMCID: PMC10908825 DOI: 10.1038/s41467-024-46062-9] [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: 05/22/2023] [Accepted: 02/09/2024] [Indexed: 03/05/2024] Open
Abstract
Cell division is completed by the abscission of the intercellular bridge connecting the daughter cells. Abscission requires the polymerization of an ESCRT-III cone close to the midbody to both recruit the microtubule severing enzyme spastin and scission the plasma membrane. Here, we found that the microtubule and the membrane cuts are two separate events that are regulated differently. Using HeLa cells, we uncovered that the F-actin disassembling protein Cofilin-1 controls the disappearance of a transient pool of branched F-actin which is precisely assembled at the tip of the ESCRT-III cone shortly before the microtubule cut. Functionally, Cofilin-1 and Arp2/3-mediated branched F-actin favor abscission by promoting local severing of the microtubules but do not participate later in the membrane scission event. Mechanistically, we propose that branched F-actin functions as a physical barrier that limits ESCRT-III cone elongation and thereby favors stable spastin recruitment. Our work thus reveals that F-actin controls the timely and local disassembly of microtubules required for cytokinetic abscission.
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Affiliation(s)
- Tamara Advedissian
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 25-28 rue du Dr Roux, F-75015, Paris, France
| | - Stéphane Frémont
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 25-28 rue du Dr Roux, F-75015, Paris, France
| | - Arnaud Echard
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Membrane Traffic and Cell Division Unit, 25-28 rue du Dr Roux, F-75015, Paris, France.
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7
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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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8
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Jiang Z, Kuo YH, Arkin MR. Autophagy Receptor-Inspired Antibody-Fusion Proteins for Targeted Intracellular Degradation. J Am Chem Soc 2023; 145:23939-23947. [PMID: 37748140 PMCID: PMC10636752 DOI: 10.1021/jacs.3c05199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Indexed: 09/27/2023]
Abstract
Autophagy is responsible for the degradation of large intracellular contents, such as unwanted protein aggregates and organelles. Impaired autophagy can therefore lead to the accumulation of pathological aggregates, correlating with aging and neurodegenerative diseases. However, a broadly applicable methodology is not available for the targeted degradation of protein aggregates or organelles in mammalian cells. Herein, we developed a series of autophagy receptor-inspired targeting chimeras (AceTACs) that can induce the targeted degradation of aggregation-prone proteins and protein aggregates (e.g., huntingtin, TDP-43, and FUS mutants), as well as organelles (e.g., mitochondria, peroxisomes, and endoplasmic reticulum). These antibody-fusion-based AceTAC degraders were designed to mimic the function of autophagy receptors, simultaneously binding with the cellular targets and the LC3 proteins on the autophagosomal membrane, eventually transporting the target to the autophagy-lysosomal process for degradation. The AceTAC degradation system provides design principles for antibody-based degradation through autophagy, largely expanding the scope of intracellular targeted degradation technologies.
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Affiliation(s)
- Ziwen Jiang
- Department
of Pharmaceutical Chemistry, and Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Yu-Hsuan Kuo
- Department
of Pharmaceutical Chemistry, and Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry, and Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
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9
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Yu G, Wang J, Zhang Y, Wu H, Wang Y, Cui Y, Yang Y, Tang X, Zhang Q, Wang J, Sun J, Chen R, Wang Y, Li P. Anti-Idiotypic Nanobody Alkaline Phosphatase Fusion Protein-Triggered On-Off-On Fluorescence Immunosensor for Aflatoxin in Cereals. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37917663 DOI: 10.1021/acs.jafc.3c05376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Nanobodies (Nbs) are widely used in immunoassays with the advantages of small size and high stability. Here, the nanobody employed as the surrogate of aflatoxin antigen and the recognition mechanism of antiaflatoxin mAb with nanobody was studied by molecular modeling, which verified the feasibility of Nbs as antigen substitutes. On this basis, a nanobody-alkaline phosphatase fusion protein (Nb-AP) was constructed, and a highly sensitive "on-off-on" fluorescent immunosensor (OFO-FL immunosensor) based on the calcein/Ce3+ system was developed for aflatoxin quantification. Briefly, calcein serves as a signal transducer, and its fluorescence can be quenched after it is bound with Ce3+. In the presence of Nb-AP, AP catalyzed p-nitrophenyl phosphate to generate orthophosphate, which competes in binding with Ce3+, leading to fluorescence recovery. The method has a linearity range of 0.005-100 ng/mL, and the IC50 of the OFO-FL immunosensor was 0.063 ng/mL, which was 18-fold lower than that of conventional enzyme-linked immunosorbent assay. The assay was successfully applied in food samples with a recovery of 88-121%.
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Affiliation(s)
- Gege Yu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiamin Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yao Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haofen Wu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yueqi Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yan Cui
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuefan Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoqian Tang
- , Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Qi Zhang
- , Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jianlong Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Sun
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
| | - Ran Chen
- Sinograin Hubei Branch Quality Inspection Center Co, LTD., Wuhan 430062, China
| | - Yanru Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peiwu Li
- , Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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10
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Broch F, El Hajji L, Pietrancosta N, Gautier A. Engineering of Tunable Allosteric-like Fluorogenic Protein Sensors. ACS Sens 2023; 8:3933-3942. [PMID: 37830919 DOI: 10.1021/acssensors.3c01536] [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: 10/14/2023]
Abstract
Optical protein sensors that enable detection of relevant biomolecules of interest play central roles in biological research. Coupling fluorescent reporters with protein sensing units has enabled the development of a wide range of biosensors that recognize analytes with high selectivity. In these sensors, analyte recognition induces a conformational change in the protein sensing unit that can modulate the optical signal of the fluorescent reporter. Here, we explore various designs for the creation of tunable allosteric-like fluorogenic protein sensors through incorporation of sensing protein units within the chemogenetic fluorescence-activating and absorption-shifting tag (FAST) that selectively binds and stabilizes the fluorescent state of 4-hydroxybenzylidene rhodanine (HBR) analogs. Conformational coupling allowed us to design analyte-responsive optical protein sensors through allosteric-like modulation of fluorogen binding.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Lina El Hajji
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Nicolas Pietrancosta
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Neuroscience Paris Seine-Institut de Biologie Paris Seine (NPS-IBPS) INSERM, CNRS, Sorbonne Université, 75005 Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Institut Universitaire de France, 75231 Paris, France
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11
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Li Z, Zhang W, Zhang Q, Li P, Tang X. Self-Assembly Multivalent Fluorescence-Nanobody Coupled Multifunctional Nanomaterial with Colorimetric Fluorescence and Photothermal to Enhance Immunochromatographic Assay. ACS NANO 2023; 17:19359-19371. [PMID: 37782130 DOI: 10.1021/acsnano.3c06930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The multimodal lateral flow immunoassay (LFIA) has provided accurate and reliable results for fast and immediate detection. Nonetheless, multimodal LFIA remains challenging to develop biosensors with high sensitivity and tolerance to matrix interference in agro-food. In this study, we developed a self-assembled multivalent fluorescence-nanobody (Nb26-EGFP-H6) with 16.5-fold and 30-fold higher affinity and sensitivity than a monovalent nanobody (Nb26). Based on the Nb26-EGFP-H6, we synthesized enhanced immune-probes Zn-CN@Nb26-EGFP-H6 by pyrolyzing and oxidizing an imidazolating zeolite framework-8 (ZIF-8) to obtain photothermal metal-carbon nanomaterials (Zn-CN) for immobilizing Nb26-EGFP-H6. The rough and porous structure of Zn-CN with a large surface area facilitates the enrichment and immobilization of antibodies. A trimodal lateral flow immunoassay (tLFIA) with colorimetric, fluorescent, and photothermal triple signal outputs was constructed for the detection of aflatoxin B1 (AFB1) in maize. Attractively, the Zn-CN-based tLFIA's multiplex guarantees accurate and sensitive detection of AFB1, with triple signal detection limits of 0.0012 ng/mL (colorimetric signals), 0.0094 ng/mL (fluorescent signals), and 0.252 ng/mL (photothermal signals). The sensitivity of the trimode immunosensor was 628-fold and 42-fold higher than that of the original Nb26-based ELISA (IC50) and the unimodal LFIA (LOD). This work provides an idea for constructing a sensitive, tolerant matrix and efficient and accurate analytical platform for rapidly detecting AFB1 in food.
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Affiliation(s)
- Zhiqiang Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs; Laboratory of Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs; Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs; Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Wen Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs; Laboratory of Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs; Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs; Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Qi Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs; Laboratory of Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs; Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs; Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Food Safety Research Institute, HuBei University, Wuhan 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Peiwu Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs; Laboratory of Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs; Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs; Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Food Safety Research Institute, HuBei University, Wuhan 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- Xianghu Laboratory, Hangzhou, 311231, China
| | - Xiaoqian Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs; Laboratory of Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs; Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs; Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Food Safety Research Institute, HuBei University, Wuhan 430062, China
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12
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Shui S, Buckley S, Scheller L, Correia BE. Rational design of small-molecule responsive protein switches. Protein Sci 2023; 32:e4774. [PMID: 37656809 PMCID: PMC10510469 DOI: 10.1002/pro.4774] [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: 04/18/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Small-molecule responsive protein switches are powerful tools for controlling cellular processes. These switches are designed to respond rapidly and specifically to their inducer. They have been used in numerous applications, including the regulation of gene expression, post-translational protein modification, and signal transduction. Typically, small-molecule responsive protein switches consist of two proteins that interact with each other in the presence or absence of a small molecule. Recent advances in computational protein design already contributed to the development of protein switches with an expanded range of small-molecule inducers and increasingly sophisticated switch mechanisms. Further progress in the engineering of small-molecule responsive switches is fueled by cutting-edge computational design approaches, which will enable more complex and precise control over cellular processes and advance synthetic biology applications in biotechnology and medicine. Here, we discuss recent milestones and how technological advances are impacting the development of chemical switches.
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Affiliation(s)
- Sailan Shui
- Laboratory of Protein Design and Immunoengineering (LPDI)STI, EPFLLausanneSwitzerland
- Swiss Institute of Bioinformatics (SIB)LausanneSwitzerland
| | - Stephen Buckley
- Laboratory of Protein Design and Immunoengineering (LPDI)STI, EPFLLausanneSwitzerland
- Swiss Institute of Bioinformatics (SIB)LausanneSwitzerland
| | - Leo Scheller
- Laboratory of Protein Design and Immunoengineering (LPDI)STI, EPFLLausanneSwitzerland
- Swiss Institute of Bioinformatics (SIB)LausanneSwitzerland
| | - Bruno E. Correia
- Laboratory of Protein Design and Immunoengineering (LPDI)STI, EPFLLausanneSwitzerland
- Swiss Institute of Bioinformatics (SIB)LausanneSwitzerland
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13
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Ma Z, Sun Z, Lv X, Chen H, Geng Y, Geng Z. Sensitivity-enhanced nanoplasmonic biosensor using direct immobilization of two engineered nanobodies for SARS-CoV-2 spike receptor-binding domain detection. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 383:133575. [PMID: 36873859 PMCID: PMC9957344 DOI: 10.1016/j.snb.2023.133575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Sensitive, rapid, and easy-to-implement biosensors are critical in responding to highly contagious and fast-spreading severe acute respiratory syndrome coronavirus (SARS-CoV-2) mutations, enabling early infection screening for appropriate isolation and treatment measures to prevent the spread of the virus. Based on the sensing principle of localized surface plasmon resonance (LSPR) and nanobody immunological techniques, an enhanced sensitivity nanoplasmonic biosensor was developed to quantify the SARS-CoV-2 spike receptor-binding domain (RBD) in serum within 30 min. The lowest concentration in the linear range can be detected down to 0.01 ng/mL by direct immobilization of two engineered nanobodies. Both the sensor fabrication process and immune strategy are facile and inexpensive, with the potential for large-scale application. The designed nanoplasmonic biosensor achieved excellent specificity and sensitivity for SARS-CoV-2 spike RBD, providing a potential option for accurate early screening of the novel coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Zhengtai Ma
- State Key Laboratory for Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Zengchao Sun
- The Chinese Academy of Sciences Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoqing Lv
- State Key Laboratory for Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, China
| | - Hongda Chen
- State Key Laboratory for Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, China
| | - Yong Geng
- The Chinese Academy of Sciences Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhaoxin Geng
- School of Information Engineering, Minzu University of China, Beijing, China
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14
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Sun X, Zhou C, Xia S, Chen X. Small molecule-nanobody conjugate induced proximity controls intracellular processes and modulates endogenous unligandable targets. Nat Commun 2023; 14:1635. [PMID: 36964170 PMCID: PMC10039045 DOI: 10.1038/s41467-023-37237-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 03/08/2023] [Indexed: 03/26/2023] Open
Abstract
Chemically induced proximity (CIP) is a powerful tool to study cellular functions. However with current CIP inducers it is difficult to directly modulate unligandable and endogenous targets, and therapeutic translational potential is also restricted. Herein, we combine CIP and chemical nanobody engineering and create cell-permeable small molecule-nanobody conjugate inducers of proximity (SNACIPs). The SNACIP inducer cRGT carrying a cyclic cell-penetrating peptide rapidly enters live cells and dimerizes eDHFR and GFP-variants. cRGT enables minute-scale, reversible, no-wash and dose-dependent control of cellular processes including signaling cascade, cargo transport and ferroptosis. Small-molecule motifs can also be installed via post-translational modifications. Therefore, latent-type SNACIPs including cRTC are designed that are functionally assembled inside living cells. cRTC contains a nanobody against an intrinsically disordered protein TPX2, a microtubule nucleation factor overexpressed in various cancers. Cancer cell proliferation is inhibited and tumor growth is suppressed in vivo. Hence, SNACIPs are valuable proximity inducers for regulating cellular functions.
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Affiliation(s)
- Xiaofeng Sun
- Laboratory of Chemical Biology & Frontier Biotechnologies, The HIT Center for Life Sciences (HCLS), Harbin Institute of Technology (HIT), Harbin, 150001, PR China
- School of Life Science and Technology, HIT, Harbin, 150001, PR China
| | - Chengjian Zhou
- Laboratory of Chemical Biology & Frontier Biotechnologies, The HIT Center for Life Sciences (HCLS), Harbin Institute of Technology (HIT), Harbin, 150001, PR China
- School of Life Science and Technology, HIT, Harbin, 150001, PR China
| | - Simin Xia
- Laboratory of Chemical Biology & Frontier Biotechnologies, The HIT Center for Life Sciences (HCLS), Harbin Institute of Technology (HIT), Harbin, 150001, PR China
| | - Xi Chen
- Laboratory of Chemical Biology & Frontier Biotechnologies, The HIT Center for Life Sciences (HCLS), Harbin Institute of Technology (HIT), Harbin, 150001, PR China.
- School of Life Science and Technology, HIT, Harbin, 150001, PR China.
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15
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Targeting galectin-driven regulatory circuits in cancer and fibrosis. Nat Rev Drug Discov 2023; 22:295-316. [PMID: 36759557 DOI: 10.1038/s41573-023-00636-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2022] [Indexed: 02/11/2023]
Abstract
Galectins are a family of endogenous glycan-binding proteins that have crucial roles in a broad range of physiological and pathological processes. As a group, these proteins use both extracellular and intracellular mechanisms as well as glycan-dependent and independent pathways to reprogramme the fate and function of numerous cell types. Given their multifunctional roles in both tissue fibrosis and cancer, galectins have been identified as potential therapeutic targets for these disorders. Here, we focus on the therapeutic relevance of galectins, particularly galectin 1 (GAL1), GAL3 and GAL9 to tumour progression and fibrotic diseases. We consider an array of galectin-targeted strategies, including small-molecule carbohydrate inhibitors, natural polysaccharides and their derivatives, peptides, peptidomimetics and biological agents (notably, neutralizing monoclonal antibodies and truncated galectins) and discuss their mechanisms of action, selectivity and therapeutic potential in preclinical models of fibrosis and cancer. We also review the results of clinical trials that aim to evaluate the efficacy of galectin inhibitors in patients with idiopathic pulmonary fibrosis, nonalcoholic steatohepatitis and cancer. The rapid pace of glycobiology research, combined with the acute need for drugs to alleviate fibrotic inflammation and overcome resistance to anticancer therapies, will accelerate the translation of anti-galectin therapeutics into clinical practice.
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16
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Shen J, Geng L, Li X, Emery C, Kroning K, Shingles G, Lee K, Heyden M, Li P, Wang W. A general method for chemogenetic control of peptide function. Nat Methods 2023; 20:112-122. [PMID: 36481965 PMCID: PMC10069916 DOI: 10.1038/s41592-022-01697-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 10/21/2022] [Indexed: 12/13/2022]
Abstract
Natural or engineered peptides serve important biological functions. A general approach to achieve chemical-dependent activation of short peptides will be valuable for spatial and temporal control of cellular processes. Here we present a pair of chemically activated protein domains (CAPs) for controlling the accessibility of both the N- and C-terminal portion of a peptide. CAPs were developed through directed evolution of an FK506-binding protein. By fusing a peptide to one or both CAPs, the function of the peptide is blocked until a small molecule displaces them from the FK506-binding protein ligand-binding site. We demonstrate that CAPs are generally applicable to a range of short peptides, including a protease cleavage site, a dimerization-inducing heptapeptide, a nuclear localization signal peptide, and an opioid peptide, with a chemical dependence up to 156-fold. We show that the CAPs system can be utilized in cell cultures and multiple organs in living animals.
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Affiliation(s)
- Jiaqi Shen
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Lequn Geng
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Xingyu Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Catherine Emery
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Kayla Kroning
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Gwendolyn Shingles
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Kerry Lee
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Peng Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI, USA.
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA.
| | - Wenjing Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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17
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Otsuka S, Tempkin JOB, Zhang W, Politi AZ, Rybina A, Hossain MJ, Kueblbeck M, Callegari A, Koch B, Morero NR, Sali A, Ellenberg J. A quantitative map of nuclear pore assembly reveals two distinct mechanisms. Nature 2023; 613:575-581. [PMID: 36599981 PMCID: PMC9849139 DOI: 10.1038/s41586-022-05528-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/04/2022] [Indexed: 01/05/2023]
Abstract
Understanding how the nuclear pore complex (NPC) is assembled is of fundamental importance to grasp the mechanisms behind its essential function and understand its role during the evolution of eukaryotes1-4. There are at least two NPC assembly pathways-one during the exit from mitosis and one during nuclear growth in interphase-but we currently lack a quantitative map of these events. Here we use fluorescence correlation spectroscopy calibrated live imaging of endogenously fluorescently tagged nucleoporins to map the changes in the composition and stoichiometry of seven major modules of the human NPC during its assembly in single dividing cells. This systematic quantitative map reveals that the two assembly pathways have distinct molecular mechanisms, in which the order of addition of two large structural components, the central ring complex and nuclear filaments are inverted. The dynamic stoichiometry data was integrated to create a spatiotemporal model of the NPC assembly pathway and predict the structures of postmitotic NPC assembly intermediates.
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Affiliation(s)
- Shotaro Otsuka
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Max Perutz Labs, University of Vienna and the Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
| | - Jeremy O B Tempkin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Wanlu Zhang
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antonio Z Politi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Arina Rybina
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - M Julius Hossain
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Moritz Kueblbeck
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andrea Callegari
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Birgit Koch
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Natalia Rosalia Morero
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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18
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Akhuli D, Dhar A, Viji AS, Bhojappa B, Palani S. ALIBY: ALFA Nanobody-Based Toolkit for Imaging and Biochemistry in Yeast. mSphere 2022; 7:e0033322. [PMID: 36190134 PMCID: PMC9599267 DOI: 10.1128/msphere.00333-22] [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: 07/08/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022] Open
Abstract
Specialized epitope tags continue to be integral components of various biochemical and cell biological applications such as fluorescence microscopy, immunoblotting, immunoprecipitation, and protein purification. However, until recently, no single tag could offer this complete set of functionalities on its own. Here, we present a plasmid-based toolkit named ALIBY (ALFA toolkit for imaging and biochemistry in yeast) that provides a universal workflow to adopt the versatile ALFA tag/NbALFA system within the well-established model organism Saccharomyces cerevisiae. The kit comprises tagging plasmids for labeling a protein of interest with the ALFA tag and detection plasmids encoding fluorescent-protein-tagged NbALFA for live-cell imaging purposes. We demonstrate the suitability of ALIBY for visualizing the spatiotemporal localization of yeast proteins (i.e., the cytoskeleton, nucleus, centrosome, mitochondria, vacuole, endoplasmic reticulum, exocyst, and divisome) in live cells. Our approach has yielded an excellent signal-to-noise ratio without off-target effects or any effect on cell growth. In summary, our yeast-specific toolkit aims to simplify and further advance the live-cell imaging of differentially abundant yeast proteins while also being suitable for biochemical applications. IMPORTANCE In yeast research, conventional fluorescent protein tags and small epitope tags are widely used to study the spatiotemporal dynamics and activity of proteins. Although proven to be efficient, these tags lack the versatility for use across different cell biological and biochemical studies of a given protein of interest. Therefore, there is an urgent need for a unified platform for visualization and biochemical and functional analyses of proteins of interest in yeast. Here, we have engineered ALIBY, a plasmid-based toolkit that expands the benefits of the recently developed ALFA tag/NbALFA system to studies in the well-established model organism Saccharomyces cerevisiae. We demonstrate that ALIBY provides a simple and versatile strain construction workflow for long-duration live-cell imaging and biochemical applications in yeast.
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Affiliation(s)
- Dipayan Akhuli
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Anubhav Dhar
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Aileen Sara Viji
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Bindu Bhojappa
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Saravanan Palani
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
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19
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Willig KI. In vivo super-resolution of the brain - How to visualize the hidden nanoplasticity? iScience 2022; 25:104961. [PMID: 36093060 PMCID: PMC9449647 DOI: 10.1016/j.isci.2022.104961] [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] [Indexed: 11/15/2022] Open
Abstract
Super-resolution fluorescence microscopy has entered most biological laboratories worldwide and its benefit is undisputable. Its application to brain imaging, for example in living mice, enables the study of sub-cellular structural plasticity and brain function directly in a living mammal. The demands of brain imaging on the different super-resolution microscopy techniques (STED, RESOLFT, SIM, ISM) and labeling strategies are discussed here as well as the challenges of the required cranial window preparation. Applications of super-resolution in the anesthetized mouse brain enlighten the stability and plasticity of synaptic nanostructures. These studies show the potential of in vivo super-resolution imaging and justify its application more widely in vivo to investigate the role of nanostructures in memory and learning.
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Affiliation(s)
- Katrin I Willig
- Group of Optical Nanoscopy in Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
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20
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Francis CR, Kincross H, Kushner EJ. Rab35 governs apicobasal polarity through regulation of actin dynamics during sprouting angiogenesis. Nat Commun 2022; 13:5276. [PMID: 36075898 PMCID: PMC9458672 DOI: 10.1038/s41467-022-32853-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/17/2022] [Indexed: 12/01/2022] Open
Abstract
In early blood vessel development, trafficking programs, such as those using Rab GTPases, are tasked with delivering vesicular cargo with high spatiotemporal accuracy. However, the function of many Rab trafficking proteins remain ill-defined in endothelial tissue; therefore, their relevance to blood vessel development is unknown. Rab35 has been shown to play an enigmatic role in cellular behaviors which differs greatly between tissue-type and organism. Importantly, Rab35 has never been characterized for its potential contribution in sprouting angiogenesis; thus, our goal was to map Rab35’s primary function in angiogenesis. Our results demonstrate that Rab35 is critical for sprout formation; in its absence, apicobasal polarity is entirely lost in vitro and in vivo. To determine mechanism, we systematically explored established Rab35 effectors and show that none are operative in endothelial cells. However, we find that Rab35 partners with DENNd1c, an evolutionarily divergent guanine exchange factor, to localize to actin. Here, Rab35 regulates actin polymerization through limiting Rac1 and RhoA activity, which is required to set up proper apicobasal polarity during sprout formation. Our findings establish that Rab35 is a potent brake of actin remodeling during blood vessel development. The promiscuous GTPase Rab35 has been shown to be involved in many important cellular functions. In this article, Francis et al. illustrate how Rab35 acts as a critical brake to actin remodeling during sprouting angiogenesis and how it is necessary for proper blood vessel development.
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Affiliation(s)
- Caitlin R Francis
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Hayle Kincross
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Erich J Kushner
- Department of Biological Sciences, University of Denver, Denver, CO, USA.
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21
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Mo J, Chen J, Shi Y, Sun J, Wu Y, Liu T, Zhang J, Zheng Y, Li Y, Chen Z. Third-Generation Covalent TMP-Tag for Fast Labeling and Multiplexed Imaging of Cellular Proteins. Angew Chem Int Ed Engl 2022; 61:e202207905. [PMID: 35816052 DOI: 10.1002/anie.202207905] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Indexed: 11/10/2022]
Abstract
Self-labeling protein tags can introduce advanced molecular motifs to specific cellular proteins. Here we introduce the third-generation covalent TMP-tag (TMP-tag3) and showcase its comparison with HaloTag and SNAP-tag. TMP-tag3 is based on a proximity-induced covalent Michael addition between an engineered Cys of E. coli dihydrofolate reductase (eDHFR) and optimized trimethoprim (TMP)-acrylamide conjugates with minimal linkers. Compared to previous versions, the TMP-tag3 features an enhanced permeability when conjugated to fluorogenic spirocyclic rhodamines. As a small protein, the 18-kD eDHFR is advantageous in tagging selected mitochondrial proteins which are less compatible with bulkier HaloTag fusions. The proximal N-C termini of eDHFR also enable facile insertion into various protein loops. TMP-tag3, HaloTag, and SNAP-tag are orthogonal to each other, collectively forming a toolbox for multiplexed live-cell imaging of cellular proteins under fluorescence nanoscopy.
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Affiliation(s)
- Jiaming Mo
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Jingting Chen
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Yabo Shi
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Jingfu Sun
- PKU-Nanjing Institute of Translational Medicine, Nanjing, 211800, Jiangsu, China
| | - Yunxiang Wu
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Tianyan Liu
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, Yiheyuan Road No.5, Beijing, 100871, China
| | - Junwei Zhang
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Yu Zheng
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, Yiheyuan Road No.5, Beijing, 100871, China.,State Key Laboratory of Membrane Biology, PKU-IDG/McGovern Institute for Brain Research, School of Life Science, Peking University, Yiheyuan Road No.5, Beijing, 100871, China
| | - Yulong Li
- Peking-Tsinghua Center for Life Science, Peking University, Beijing, Yiheyuan Road No.5, Beijing, 100871, China.,State Key Laboratory of Membrane Biology, PKU-IDG/McGovern Institute for Brain Research, School of Life Science, Peking University, Yiheyuan Road No.5, Beijing, 100871, China.,Chinese Institute for Brain Research, Beijing, 102206, China
| | - Zhixing Chen
- National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Yiheyuan Road No.5, Beijing, 100871, China.,PKU-Nanjing Institute of Translational Medicine, Nanjing, 211800, Jiangsu, China.,Peking-Tsinghua Center for Life Science, Peking University, Beijing, Yiheyuan Road No.5, Beijing, 100871, China
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22
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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 Sciences, University of Edinburgh, Hugh Robson Building George Square, Edinburgh, EH8 9XD, UK
| | - Angeliki Goutou
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building George Square, Edinburgh, EH8 9XD, UK
| | - Jack Brydon
- MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital Crewe Road South, Edinburgh, EH4 2XR, UK
| | - Cyrus R Sethna
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building George Square, Edinburgh, EH8 9XD, UK
| | - Christopher W Wood
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Roger Land Building King's Buildings, Edinburgh, EH9 3JQ, UK
| | - Sebastian Greiss
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building George Square, Edinburgh, EH8 9XD, UK
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23
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Karami S, Doroodmand MM, Mootabi-Alavi A. In Vivo Chemogenetic Biocompatibility of Mercury as a Specific Hypercalcemia Actuator in Snail's Spinal Cord Cell Manipulation: An Extracellular Field Potential Biosensor. ACS APPLIED BIO MATERIALS 2022; 5:3649-3657. [PMID: 35830462 DOI: 10.1021/acsabm.1c01064] [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: 11/29/2022]
Abstract
The in vivo chemogenetic property of mercuric ions (Hg2+) was investigated as a specific hypercalcemia actuator in snail's spinal cord cell manipulation by extracellular field potential biosensing analysis. For this purpose, a three-microelectrode system with working, counter, and pseudo reference electrodes was blindly implanted into the snail's spinal cord to electrically stimulate (triggering) the action potential with a staircase electrical voltage at a very low frequency level, along with measurement of the electrical current, as a detection system. Under optimum conditions, using the one-factor-at-a-time method, a wide linear range between 1.0 × 10-14 and 1.0 × 10-1 mol L-1 with correlation coefficients (R2) >0.98 and a response time (t90) of maximum 10.0 s were approximated. Percentages of relative standard deviation were estimated to be 3.08 (reproducibility, n = 50) and 7.31 (repeatability, n = 15). The detection limit was estimated to be sub 2.1 × 10-16 mol L-1 based on the Xb- + 3Sb definition. The reliability of this phenomenon was evidenced by the estimation of recovery percentages (between 95 and 107%) during spiking Hg2+ standard solutions. The probable mechanism behind this process could be attributed to the following: (i) the neuronal ephaptic coupling during electrical synchronization by a specific brain-triggered wave as a neuronal motor toolkit and (ii) chemical synchronization using a Hg2+ hypercalcemia actuator (biosensor). Linear correlation has been evidenced during interactions between Hg2+ and a calcium ionic channel's protein with a gram molecular weight of 66.2 ± 0.3 KCU. This process, therefore, caused an opening of the Ca2+ channel gates and majorly released the Ca2+ (hypercalcemia) that was detected as the main source of the measured electrical current. At this condition, ultratrace levels of Hg2+ ions not only were considered as nontoxic reagents but also had chemically regulating effects as ephaptic synchronizers to the neuron cells. This report may pave the way for using mercury ions at an ultratrace level for clinical controlling purposes during neuronal spinal cord cell manipulation.
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Affiliation(s)
- Sajedeh Karami
- Department of Chemistry, Shiraz University, Shiraz 71454, Iran
| | | | - Amir Mootabi-Alavi
- Physiological Division of Department of Basic Science, School of Veterinary Medicine, Shiraz University, Shiraz 71454, Iran
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Mo J, Chen J, Shi Y, Sun J, Wu Y, Liu T, Zhang J, Zheng Y, Li Y, Chen Z. Third‐Generation Covalent TMP‐Tag for Fast Labeling and Multiplexed Imaging of Cellular Proteins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jiaming Mo
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Jingting Chen
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Yabo Shi
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Jingfu Sun
- PKU-Nanjing Institute of translational medicine n/a CHINA
| | - Yunxiang Wu
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Tianyan Liu
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Junwei Zhang
- Peking University College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center CHINA
| | - Yu Zheng
- Peking University School of life science CHINA
| | - Yulong Li
- Peking University School of life science CHINA
| | - Zhixing Chen
- Peking University College of Future Technology 5 Yiheyuan Rd. 100871 Beijing CHINA
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25
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Heiss TK, Dorn RS, Ferreira AJ, Love AC, Prescher JA. Fluorogenic Cyclopropenones for Multicomponent, Real-Time Imaging. J Am Chem Soc 2022; 144:7871-7880. [PMID: 35442034 PMCID: PMC9377832 DOI: 10.1021/jacs.2c02058] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fluorogenic bioorthogonal reactions enable biomolecule visualization in real time. These reactions comprise reporters that "light up" upon reaction with complementary partners. While the spectrum of fluorogenic chemistries is expanding, few transformations are compatible with live cells due to cross-reactivities or insufficient signal turn-on. To address the need for more suitable chemistries for cellular imaging, we developed a fluorogenic reaction featuring cyclopropenone reporters and phosphines. The transformation involves regioselective activation and cyclization of cyclopropenones to form coumarin products. With optimal probes, the reaction provides >1600-fold signal turn-on, one of the highest fluorescence enhancements reported to date. The bioorthogonal motifs were evaluated in vitro and in cells. The reaction was also found to be compatible with other common fluorogenic transformations, enabling multicomponent, real-time imaging. Collectively, these data suggest that the cyclopropenone-phosphine reaction will bolster efforts to track biomolecule targets in their native settings.
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Affiliation(s)
- Tyler K Heiss
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Robert S Dorn
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Andrew J Ferreira
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Anna C Love
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, California 92697, United States.,Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States.,Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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26
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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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27
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Barakat S, Berksöz M, Zahedimaram P, Piepoli S, Erman B. Nanobodies as molecular imaging probes. Free Radic Biol Med 2022; 182:260-275. [PMID: 35240292 DOI: 10.1016/j.freeradbiomed.2022.02.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 12/12/2022]
Abstract
Camelidae derived single-domain antibodies (sdAbs), commonly known as nanobodies (Nbs), are the smallest antibody fragments with full antigen-binding capacity. Owing to their desirable properties such as small size, high specificity, strong affinity, excellent stability, and modularity, nanobodies are on their way to overtake conventional antibodies in terms of popularity. To date, a broad range of nanobodies have been generated against different molecular targets with applications spanning basic research, diagnostics, and therapeutics. In the field of molecular imaging, nanobody-based probes have emerged as a powerful tool. Radioactive or fluorescently labeled nanobodies are now used to detect and track many targets in different biological systems using imaging techniques. In this review, we provide an overview of the use of nanobodies as molecular probes. Additionally, we discuss current techniques for the generation, conjugation, and intracellular delivery of nanobodies.
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Affiliation(s)
- Sarah Barakat
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.
| | - Melike Berksöz
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.
| | - Pegah Zahedimaram
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.
| | - Sofia Piepoli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, 34342, Bebek, Istanbul, Turkey.
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, 34342, Bebek, Istanbul, Turkey.
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28
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Ji F, Ren J, Vincke C, Jia L, Muyldermans S. Nanobodies: From Serendipitous Discovery of Heavy Chain-Only Antibodies in Camelids to a Wide Range of Useful Applications. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2446:3-17. [PMID: 35157266 DOI: 10.1007/978-1-0716-2075-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The presence of unique heavy chain-only antibodies (HCAbs) in camelids was discovered at Vrije Universiteit Brussel (VUB, Brussels, Belgium) at a time when many researchers were exploring the cloning and expression of smaller antigen-binding fragments (Fv and Fab) from hybridoma-derived antibodies. The potential importance of this discovery was anticipated, and efforts were immediately undertaken to understand the emergence and ontogeny of these HCAbs as well as to investigate the applications of the single-domain antigen-binding variable domains of HCAbs (nanobodies). Nanobodies were demonstrated to possess multiple biochemical and biophysical advantages over other antigen-binding antibody fragments and alternative scaffolds. Today, nanobodies have a significant and growing impact on research, biotechnology, and medicine.
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Affiliation(s)
- Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Cécile Vincke
- Cellular and Molecular Immunology Laboratory, Vrije Universiteit Brussel, Brussels, Belgium.,Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels, Belgium
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Serge Muyldermans
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China. .,Cellular and Molecular Immunology Laboratory, Vrije Universiteit Brussel, Brussels, Belgium.
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29
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Shen Y, Luchetti A, Fernandes G, Do Heo W, Silva AJ. The emergence of molecular systems neuroscience. Mol Brain 2022; 15:7. [PMID: 34983613 PMCID: PMC8728933 DOI: 10.1186/s13041-021-00885-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
Systems neuroscience is focused on how ensemble properties in the brain, such as the activity of neuronal circuits, gives rise to internal brain states and behavior. Many of the studies in this field have traditionally involved electrophysiological recordings and computational approaches that attempt to decode how the brain transforms inputs into functional outputs. More recently, systems neuroscience has received an infusion of approaches and techniques that allow the manipulation (e.g., optogenetics, chemogenetics) and imaging (e.g., two-photon imaging, head mounted fluorescent microscopes) of neurons, neurocircuits, their inputs and outputs. Here, we will review novel approaches that allow the manipulation and imaging of specific molecular mechanisms in specific cells (not just neurons), cell ensembles and brain regions. These molecular approaches, with the specificity and temporal resolution appropriate for systems studies, promise to infuse the field with novel ideas, emphases and directions, and are motivating the emergence of a molecularly oriented systems neuroscience, a new discipline that studies how the spatial and temporal patterns of molecular systems modulate circuits and brain networks, and consequently shape the properties of brain states and behavior.
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Affiliation(s)
- Yang Shen
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Alessandro Luchetti
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Giselle Fernandes
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Alcino J Silva
- Departments of Neurobiology, Psychiatry and Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, and Brain Research Institute, UCLA, Los Angeles, CA, USA.
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30
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Ziegler MJ, Yserentant K, Dunsing V, Middel V, Gralak AJ, Pakari K, Bargstedt J, Kern C, Petrich A, Chiantia S, Strähle U, Herten DP, Wombacher R. Mandipropamid as a chemical inducer of proximity for in vivo applications. Nat Chem Biol 2022; 18:64-69. [PMID: 34934192 PMCID: PMC8709788 DOI: 10.1038/s41589-021-00922-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/13/2021] [Indexed: 11/26/2022]
Abstract
Direct control of protein interactions by chemically induced protein proximity holds great potential for both cell and synthetic biology as well as therapeutic applications. Low toxicity, orthogonality and excellent cell permeability are important criteria for chemical inducers of proximity (CIPs), in particular for in vivo applications. Here, we present the use of the agrochemical mandipropamid (Mandi) as a highly efficient CIP in cell culture systems and living organisms. Mandi specifically induces complex formation between a sixfold mutant of the plant hormone receptor pyrabactin resistance 1 (PYR1) and abscisic acid insensitive (ABI). It is orthogonal to other plant hormone-based CIPs and rapamycin-based CIP systems. We demonstrate the applicability of the Mandi system for rapid and efficient protein translocation in mammalian cells and zebrafish embryos, protein network shuttling and manipulation of endogenous proteins.
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Affiliation(s)
- Michael J Ziegler
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Klaus Yserentant
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Institute of Cardiovascular Sciences & School of Chemistry, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Valentin Dunsing
- Institute of Biology and Biochemistry, University of Potsdam, Potsdam, Germany
| | - Volker Middel
- Institute of Biological and Chemical Systems (IBCS)-Biological Information Processing (BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Antoni J Gralak
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Kaisa Pakari
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Jörn Bargstedt
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Christoph Kern
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Annett Petrich
- Institute of Biology and Biochemistry, University of Potsdam, Potsdam, Germany
| | - Salvatore Chiantia
- Institute of Biology and Biochemistry, University of Potsdam, Potsdam, Germany
| | - Uwe Strähle
- Institute of Biological and Chemical Systems (IBCS)-Biological Information Processing (BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Dirk-Peter Herten
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
- Institute of Cardiovascular Sciences & School of Chemistry, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
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31
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Wagner TR, Rothbauer U. Nanobodies - Little helpers unravelling intracellular signaling. Free Radic Biol Med 2021; 176:46-61. [PMID: 34536541 DOI: 10.1016/j.freeradbiomed.2021.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/26/2021] [Accepted: 09/08/2021] [Indexed: 11/21/2022]
Abstract
The identification of diagnostic and therapeutic targets requires a comprehensive understanding of cellular processes, for which advanced technologies in biomedical research are needed. The emergence of nanobodies (Nbs) derived from antibody fragments of camelid heavy chain-only antibodies as intracellular research tools offers new possibilities to study and modulate target antigens in living cells. Here we summarize this rapidly changing field, beginning with a brief introduction of Nbs, followed by an overview of how target-specific Nbs can be generated, and introduce the selection of intrabodies as research tools. Intrabodies, by definition, are intracellular functional Nbs that target ectopic or endogenous intracellular antigens within living cells. Such binders can be applied in various formats, e.g. as chromobodies for live cell microscopy or as biosensors to decipher complex intracellular signaling pathways. In addition, protein knockouts can be achieved by target-specific Nbs, while modulating Nbs have the potential as future therapeutics. The development of fine-tunable and switchable Nb-based systems that simultaneously provide spatial and temporal control has recently taken the application of these binders to the next level.
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Affiliation(s)
- Teresa R Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany.
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32
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Writing and erasing O-GlcNAc from target proteins in cells. Biochem Soc Trans 2021; 49:2891-2901. [PMID: 34783346 DOI: 10.1042/bst20210865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/15/2022]
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) is a widespread reversible modification on nucleocytoplasmic proteins that plays an important role in many biochemical processes and is highly relevant to numerous human diseases. The O-GlcNAc modification has diverse functional impacts on individual proteins and glycosites, and methods for editing this modification on substrates are essential to decipher these functions. Herein, we review recent progress in developing methods for O-GlcNAc regulation, with a focus on methods for editing O-GlcNAc with protein- and site-selectivity in cells. The applications, advantages, and limitations of currently available strategies for writing and erasing O-GlcNAc and future directions are also discussed. These emerging approaches to manipulate O-GlcNAc on a target protein in cells will greatly accelerate the development of functional studies and enable therapeutic interventions in the O-GlcNAc field.
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33
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Kolesov DV, Sokolinskaya EL, Lukyanov KA, Bogdanov AM. Molecular Tools for Targeted Control of Nerve Cell Electrical Activity. Part II. Acta Naturae 2021; 13:17-32. [PMID: 35127143 PMCID: PMC8807539 DOI: 10.32607/actanaturae.11415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/14/2021] [Indexed: 01/01/2023] Open
Abstract
In modern life sciences, the issue of a specific, exogenously directed manipulation of a cell's biochemistry is a highly topical one. In the case of electrically excitable cells, the aim of the manipulation is to control the cells' electrical activity, with the result being either excitation with subsequent generation of an action potential or inhibition and suppression of the excitatory currents. The techniques of electrical activity stimulation are of particular significance in tackling the most challenging basic problem: figuring out how the nervous system of higher multicellular organisms functions. At this juncture, when neuroscience is gradually abandoning the reductionist approach in favor of the direct investigation of complex neuronal systems, minimally invasive methods for brain tissue stimulation are becoming the basic element in the toolbox of those involved in the field. In this review, we describe three approaches that are based on the delivery of exogenous, genetically encoded molecules sensitive to external stimuli into the nervous tissue. These approaches include optogenetics (overviewed in Part I), as well as chemogenetics and thermogenetics (described here, in Part II), which is significantly different not only in the nature of the stimuli and structure of the appropriate effector proteins, but also in the details of experimental applications. The latter circumstance is an indication that these are rather complementary than competing techniques.
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Affiliation(s)
- D. V. Kolesov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - E. L. Sokolinskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - K. A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - A. M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
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34
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Woloschuk RM, Reed PMM, Jaikaran ASI, Demmans KZ, Youn J, Kanelis V, Uppalapati M, Woolley GA. Structure-based design of a photoswitchable affibody scaffold. Protein Sci 2021; 30:2359-2372. [PMID: 34590762 DOI: 10.1002/pro.4196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022]
Abstract
Photo-control of affinity reagents offers a general approach for high-resolution spatiotemporal control of diverse molecular processes. In an effort to develop general design principles for a photo-controlled affinity reagent, we took a structure-based approach to the design of a photoswitchable Z-domain, among the simplest of affinity reagent scaffolds. A chimera, designated Z-PYP, of photoactive yellow protein (PYP) and the Z-domain, was designed based on the concept of mutually exclusive folding. NMR analysis indicated that, in the dark, the PYP domain of the chimera was folded, and the Z-domain was unfolded. Blue light caused loss of structure in PYP and a two- to sixfold change in the apparent affinity of Z-PYP for its target as determined using size exclusion chromatography, UV-Vis based assays, and enyzme-linked immunosorbent assay (ELISA). A thermodynamic model indicated that mutations to decrease Z-domain folding energy would alter target affinity without loss of switching. This prediction was confirmed experimentally with a double alanine mutant in helix 3 of the Z-domain of the chimera (Z-PYP-AA) showing >30-fold lower dark-state binding and no loss in switching. The effect of decreased dark-state binding affinity was tested in a two-hybrid transcriptional control format and enabled pronounced light/dark differences in yeast growth in vivo. Finally, the design was transferable to the αZ-Taq affibody enabling tunable light-dependent binding both in vitro and in vivo to the Z-Taq target. This system thus provides a framework for the focused development of light switchable affibodies for a range of targets.
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Affiliation(s)
- Ryan M Woloschuk
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Anna S I Jaikaran
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Karl Z Demmans
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey Youn
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Voula Kanelis
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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35
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Tsai YH, Doura T, Kiyonaka S. Tethering-based chemogenetic approaches for the modulation of protein function in live cells. Chem Soc Rev 2021; 50:7909-7923. [PMID: 34114579 DOI: 10.1039/d1cs00059d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Proteins are the workhorse molecules performing various tasks to sustain life. To investigate the roles of a protein under physiological conditions, the rapid modulation of the protein with high specificity in a living system would be ideal, but achieving this is often challenging. To address this challenge, researchers have developed chemogenetic strategies for the rapid and selective modulation of protein function in live cells. Here, the target protein is modified genetically to become sensitive to a designer molecule that otherwise has no effect on other cellular biomolecules. One powerful chemogenetic strategy is to introduce a tethering point into the target protein, allowing covalent or non-covalent attachment of the designer molecule. In this tutorial review, we focus on tethering-based chemogenetic approaches for modulating protein function in live cells. We first describe genetic, optogenetic and chemical means to study protein function. These means lay the basis for the chemogenetic concept, which is explained in detail. The next section gives an overview, including advantages and limitations, of tethering tactics that have been employed for modulating cellular protein function. The third section provides examples of the modulation of cell-surface proteins using tethering-based chemogenetics through non-covalent tethering and covalent tethering for irreversible modulation or functional switching. The fourth section presents intracellular examples. The last section summarizes key considerations in implementing tethering-based chemogenetics and shows perspectives highlighting future directions and other applications of this burgeoning research field.
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Affiliation(s)
- Yu-Hsuan Tsai
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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36
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Lucchi R, Bentanachs J, Oller-Salvia B. The Masking Game: Design of Activatable Antibodies and Mimetics for Selective Therapeutics and Cell Control. ACS CENTRAL SCIENCE 2021; 7:724-738. [PMID: 34079893 PMCID: PMC8161478 DOI: 10.1021/acscentsci.0c01448] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Indexed: 05/04/2023]
Abstract
The high selectivity and affinity of antibody binding have made antibodies all-pervasive tools in therapy, diagnosis, and basic science. A plethora of chemogenetic approaches has been devised to make antibodies responsive to stimuli ranging from light to enzymatic activity, temperature, pH, ions, and effector molecules. Within a single decade, the field of activatable antibodies has yielded marketed therapeutics capable of engaging antigens that could not be targeted with traditional antibodies, as well as new tools to control intracellular protein location and investigate biological processes. Many opportunities remain untapped, waiting for more efficient and generally applicable masking strategies to be developed at the interface between chemistry and biotechnology.
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Affiliation(s)
- Roberta Lucchi
- Grup d’Enginyeria
de Materials, Institut Químic de
Sarrià (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
| | - Jordi Bentanachs
- Grup d’Enginyeria
de Materials, Institut Químic de
Sarrià (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
| | - Benjamí Oller-Salvia
- Grup d’Enginyeria
de Materials, Institut Químic de
Sarrià (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
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37
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Ramirez DH, Ge Y, Woo CM. O-GlcNAc Engineering on a Target Protein in Cells with Nanobody-OGT and Nanobody-splitOGA. Curr Protoc 2021; 1:e117. [PMID: 33950562 PMCID: PMC8162732 DOI: 10.1002/cpz1.117] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The monosaccharide O-linked N-acetyl glucosamine (O-GlcNAc) is an essential and dynamic post-translational modification (PTM) that decorates thousands of nucleocytoplasmic proteins. Interrogating the role of O-GlcNAc on a target protein is crucial yet challenging to perform in cells. We recently reported a pair of methods to selectively install or remove O-GlcNAc on a target protein in cells using an engineered O-GlcNAc transferase (OGT) or split O-GlcNAcase (OGA) fused to a nanobody. Target protein O-GlcNAcylation and de-O-GlcNAcylation complements methods to interrogate the role of O-GlcNAc on a global scale or at individual glycosites. Herein, we describe a protocol for utilizing the nanobody-OGT and nanobody-splitOGA systems to screen for O-GlcNAc functionality on a target protein. We additionally include associated protocols for the detection of O-GlcNAc and cloning procedures to adapt the method for the user's target protein of interest. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Target protein O-GlcNAcylation of JunB using nanobody-OGT Basic Protocol 2: Target protein deglycosylation of Nup62 using nanobody-splitOGA Alternate Protocol: Verification of the O-GlcNAc state of a tagged target protein through chemoenzymatic labeling Support Protocol: Cloning of new nanobody-OGT/nanobody-splitOGA and target protein pairs.
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Affiliation(s)
| | - Yun Ge
- 12 Oxford St, Cambridge MA 02138
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38
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Ge Y, Ramirez DH, Yang B, D'Souza AK, Aonbangkhen C, Wong S, Woo CM. Target protein deglycosylation in living cells by a nanobody-fused split O-GlcNAcase. Nat Chem Biol 2021; 17:593-600. [PMID: 33686291 PMCID: PMC8085020 DOI: 10.1038/s41589-021-00757-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 01/07/2021] [Accepted: 01/28/2021] [Indexed: 01/31/2023]
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) is an essential and dynamic post-translational modification that is presented on thousands of nucleocytoplasmic proteins. Interrogating the role of O-GlcNAc on a single target protein is crucial, yet challenging to perform in cells. Herein, we developed a nanobody-fused split O-GlcNAcase (OGA) as an O-GlcNAc eraser for selective deglycosylation of a target protein in cells. After systematic cellular optimization, we identified a split OGA with reduced inherent deglycosidase activity that selectively removed O-GlcNAc from the desired target protein when directed by a nanobody. We demonstrate the generality of the nanobody-fused split OGA using four nanobodies against five target proteins and use the system to study the impact of O-GlcNAc on the transcription factors c-Jun and c-Fos. The nanobody-directed O-GlcNAc eraser provides a new strategy for the functional evaluation and engineering of O-GlcNAc via the selective removal of O-GlcNAc from individual proteins directly in cells.
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Affiliation(s)
- Yun Ge
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Daniel H Ramirez
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Bo Yang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Alexandria K D'Souza
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Chanat Aonbangkhen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Stephanie Wong
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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39
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Winkler J, De Meyer A, Mylle E, Storme V, Grones P, Van Damme D. Nanobody-Dependent Delocalization of Endocytic Machinery in Arabidopsis Root Cells Dampens Their Internalization Capacity. FRONTIERS IN PLANT SCIENCE 2021; 12:538580. [PMID: 33815429 PMCID: PMC8018273 DOI: 10.3389/fpls.2021.538580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/23/2021] [Indexed: 05/08/2023]
Abstract
Plant cells perceive and adapt to an ever-changing environment by modifying their plasma membrane (PM) proteome. Whereas secretion deposits new integral membrane proteins, internalization by endocytosis removes membrane proteins and associated ligands, largely with the aid of adaptor protein (AP) complexes and the scaffolding molecule clathrin. Two AP complexes function in clathrin-mediated endocytosis at the PM in plant cells, the heterotetrameric AP-2 complex and the hetero-octameric TPLATE complex (TPC). Whereas single subunit mutants in AP-2 develop into viable plants, genetic mutation of a single TPC subunit causes fully penetrant male sterility and silencing single subunits leads to seedling lethality. To address TPC function in somatic root cells, while minimizing indirect effects on plant growth, we employed nanobody-dependent delocalization of a functional, GFP-tagged TPC subunit, TML, in its respective homozygous genetic mutant background. In order to decrease the amount of functional TPC at the PM, we targeted our nanobody construct to the mitochondria and fused it to TagBFP2 to visualize it independently of its bait. We furthermore limited the effect of our delocalization to those tissues that are easily accessible for live-cell imaging by expressing it from the PIN2 promoter, which is active in root epidermal and cortex cells. With this approach, we successfully delocalized TML from the PM. Moreover, we also show co-recruitment of TML-GFP and AP2A1-TagRFP to the mitochondria, suggesting that our approach delocalized complexes, rather than individual adaptor complex subunits. In line with the specific expression domain, we only observed minor effects on root growth, yet realized a clear reduction of endocytic flux in epidermal root cells. Nanobody-dependent delocalization in plants, here exemplified using a TPC subunit, has the potential to be widely applicable to achieve specific loss-of-function analysis of otherwise lethal mutants.
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Affiliation(s)
- Joanna Winkler
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Andreas De Meyer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Veronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Peter Grones
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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40
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Vigano MA, Ell CM, Kustermann MMM, Aguilar G, Matsuda S, Zhao N, Stasevich TJ, Affolter M, Pyrowolakis G. Protein manipulation using single copies of short peptide tags in cultured cells and in Drosophila melanogaster. Development 2021; 148:dev191700. [PMID: 33593816 PMCID: PMC7990863 DOI: 10.1242/dev.191700] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 02/09/2021] [Indexed: 01/01/2023]
Abstract
Cellular development and function rely on highly dynamic molecular interactions among proteins distributed in all cell compartments. Analysis of these interactions has been one of the main topics in cellular and developmental research, and has been mostly achieved by the manipulation of proteins of interest (POIs) at the genetic level. Although genetic strategies have significantly contributed to our current understanding, targeting specific interactions of POIs in a time- and space-controlled manner or analysing the role of POIs in dynamic cellular processes, such as cell migration or cell division, would benefit from more-direct approaches. The recent development of specific protein binders, which can be expressed and function intracellularly, along with advancement in synthetic biology, have contributed to the creation of a new toolbox for direct protein manipulations. Here, we have selected a number of short-tag epitopes for which protein binders from different scaffolds have been generated and showed that single copies of these tags allowed efficient POI binding and manipulation in living cells. Using Drosophila, we also find that single short tags can be used for POI manipulation in vivo.
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Affiliation(s)
- M Alessandra Vigano
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Clara-Maria Ell
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
- Institute for Biology I, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Manuela M M Kustermann
- Institute for Biology I, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Gustavo Aguilar
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Shinya Matsuda
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Markus Affolter
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - George Pyrowolakis
- Institute for Biology I, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
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41
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Abstract
Allosteric regulation in proteins is fundamental to many important biological processes. Allostery has been employed to control protein functions by regulating protein activity. Engineered allosteric regulation allows controlling protein activity in subsecond time scale and has a broad range of applications, from dissecting spatiotemporal dynamics in biochemical cascades to applications in biotechnology and medicine. Here, we review the concept of allostery in proteins and various approaches to identify allosteric sites and pathways. We then provide an overview of strategies and tools used in allosteric protein regulation and their utility in biological applications. We highlight various classes of proteins, where regulation is achieved through allostery. Finally, we analyze the current problems, critical challenges, and future prospective in achieving allosteric regulation in proteins.
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Affiliation(s)
| | - Jiaxing Chen
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
- Departments of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033-0850, United States
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
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42
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He L, Tan P, Huang Y, Zhou Y. Design of Smart Antibody Mimetics with Photosensitive Switches. Adv Biol (Weinh) 2021; 5:e2000541. [PMID: 34028213 DOI: 10.1002/adbi.202000541] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/11/2021] [Indexed: 11/10/2022]
Abstract
As two prominent examples of intracellular single-domain antibodies or antibody mimetics derived from synthetic protein scaffolds, monobodies and nanobodies are gaining wide applications in cell biology, structural biology, synthetic immunology, and theranostics. Herein, a generally applicable method to engineer light-controllable monobodies and nanobodies, designated as moonbody and sunbody, respectively, is introduced. These engineered antibody-like modular domains enable rapid and reversible antibody-antigen recognition by utilizing light. By the paralleled insertion of two light-oxygen-voltage domain 2 modules into a single sunbody and the use of bivalent sunbodies, the range of dynamic changes of photoswitchable sunbodies is substantially enhanced. Furthermore, the use of moonbodies or sunbodies to precisely control protein degradation, gene transcription, and base editing by harnessing the power of light is demonstrated.
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Affiliation(s)
- Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Peng Tan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
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43
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Schneider F, Sych T, Eggeling C, Sezgin E. Influence of nanobody binding on fluorescence emission, mobility, and organization of GFP-tagged proteins. iScience 2021; 24:101891. [PMID: 33364580 PMCID: PMC7753935 DOI: 10.1016/j.isci.2020.101891] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/02/2020] [Accepted: 12/01/2020] [Indexed: 12/22/2022] Open
Abstract
Advanced fluorescence microscopy studies require specific and monovalent molecular labeling with bright and photostable fluorophores. This necessity led to the widespread use of fluorescently labeled nanobodies against commonly employed fluorescent proteins (FPs). However, very little is known how these nanobodies influence their target molecules. Here, we tested commercially available nanobodies and observed clear changes of the fluorescence properties, mobility and organization of green fluorescent protein (GFP) tagged proteins after labeling with the anti-GFP nanobody. Intriguingly, we did not observe any co-diffusion of fluorescently labeled nanobodies with the GFP-labeled proteins. Our results suggest significant binding of the nanobodies to a non-emissive, likely oligomerized, form of the FPs, promoting disassembly into monomeric form after binding. Our findings have significant implications on the application of nanobodies and GFP labeling for studying dynamic and quantitative protein organization in the plasma membrane of living cells using advanced imaging techniques.
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Affiliation(s)
- Falk Schneider
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65 Solna, Sweden
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
- Jena Center of Soft Matters, Friedrich-Schiller-University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65 Solna, Sweden
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44
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Winkler J, De Meyer A, Mylle E, Storme V, Grones P, Van Damme D. Nanobody-Dependent Delocalization of Endocytic Machinery in Arabidopsis Root Cells Dampens Their Internalization Capacity. FRONTIERS IN PLANT SCIENCE 2021. [PMID: 33815429 DOI: 10.1101/2020.02.27.968446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plant cells perceive and adapt to an ever-changing environment by modifying their plasma membrane (PM) proteome. Whereas secretion deposits new integral membrane proteins, internalization by endocytosis removes membrane proteins and associated ligands, largely with the aid of adaptor protein (AP) complexes and the scaffolding molecule clathrin. Two AP complexes function in clathrin-mediated endocytosis at the PM in plant cells, the heterotetrameric AP-2 complex and the hetero-octameric TPLATE complex (TPC). Whereas single subunit mutants in AP-2 develop into viable plants, genetic mutation of a single TPC subunit causes fully penetrant male sterility and silencing single subunits leads to seedling lethality. To address TPC function in somatic root cells, while minimizing indirect effects on plant growth, we employed nanobody-dependent delocalization of a functional, GFP-tagged TPC subunit, TML, in its respective homozygous genetic mutant background. In order to decrease the amount of functional TPC at the PM, we targeted our nanobody construct to the mitochondria and fused it to TagBFP2 to visualize it independently of its bait. We furthermore limited the effect of our delocalization to those tissues that are easily accessible for live-cell imaging by expressing it from the PIN2 promoter, which is active in root epidermal and cortex cells. With this approach, we successfully delocalized TML from the PM. Moreover, we also show co-recruitment of TML-GFP and AP2A1-TagRFP to the mitochondria, suggesting that our approach delocalized complexes, rather than individual adaptor complex subunits. In line with the specific expression domain, we only observed minor effects on root growth, yet realized a clear reduction of endocytic flux in epidermal root cells. Nanobody-dependent delocalization in plants, here exemplified using a TPC subunit, has the potential to be widely applicable to achieve specific loss-of-function analysis of otherwise lethal mutants.
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Affiliation(s)
- Joanna Winkler
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Andreas De Meyer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Veronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Peter Grones
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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45
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Wagner TR, Rothbauer U. Nanobodies Right in the Middle: Intrabodies as Toolbox to Visualize and Modulate Antigens in the Living Cell. Biomolecules 2020; 10:biom10121701. [PMID: 33371447 PMCID: PMC7767433 DOI: 10.3390/biom10121701] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 01/01/2023] Open
Abstract
In biomedical research, there is an ongoing demand for new technologies to elucidate disease mechanisms and develop novel therapeutics. This requires comprehensive understanding of cellular processes and their pathophysiology based on reliable information on abundance, localization, post-translational modifications and dynamic interactions of cellular components. Traceable intracellular binding molecules provide new opportunities for real-time cellular diagnostics. Most prominently, intrabodies derived from antibody fragments of heavy-chain only antibodies of camelids (nanobodies) have emerged as highly versatile and attractive probes to study and manipulate antigens within the context of living cells. In this review, we provide an overview on the selection, delivery and usage of intrabodies to visualize and monitor cellular antigens in living cells and organisms. Additionally, we summarize recent advances in the development of intrabodies as cellular biosensors and their application to manipulate disease-related cellular processes. Finally, we highlight switchable intrabodies, which open entirely new possibilities for real-time cell-based diagnostics including live-cell imaging, target validation and generation of precisely controllable binding reagents for future therapeutic applications.
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Affiliation(s)
- Teresa R. Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany;
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany;
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
- Correspondence: ; Tel.: +49-7121-5153-0415; Fax: +49-7121-5153-0816
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46
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Gettemans J, De Dobbelaer B. Transforming nanobodies into high-precision tools for protein function analysis. Am J Physiol Cell Physiol 2020; 320:C195-C215. [PMID: 33264078 DOI: 10.1152/ajpcell.00435.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Single-domain antibodies, derived from camelid heavy antibodies (nanobodies) or shark variable new antigen receptors, have attracted increasing attention in recent years due to their extremely versatile nature and the opportunities they offer for downstream modification. Discovered more than three decades ago, these 120-amino acid (∼15-kDa) antibody fragments are known to bind their target with high specificity and affinity. Key features of nanobodies that make them very attractive include their single-domain nature, small size, and affordable high-level expression in prokaryotes, and their cDNAs are routinely obtained in the process of their isolation. This facilitates and stimulates new experimental approaches. Hence, it allows researchers to formulate new answers to complex biomedical questions. Through elementary PCR-based technologies and chemical modification strategies, their primary structure can be altered almost at leisure while retaining their specificity and biological activity, transforming them into highly tailored tools that meet the increasing demands of current-day biomedical research. In this review, various aspects of camelid nanobodies are expounded, including intracellular delivery in recombinant format for manipulation of, i.e., cytoplasmic targets, their derivatization to improve nanobody orientation as a capturing device, approaches to reversibly bind their target, their potential as protein-silencing devices in cells, the development of strategies to transfer nanobodies through the blood-brain barrier and their application in CAR-T experimentation. We also discuss some of their disadvantages and conclude with future prospects.
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Affiliation(s)
- Jan Gettemans
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Brian De Dobbelaer
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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47
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Cheloha RW, Harmand TJ, Wijne C, Schwartz TU, Ploegh HL. Exploring cellular biochemistry with nanobodies. J Biol Chem 2020; 295:15307-15327. [PMID: 32868455 PMCID: PMC7650250 DOI: 10.1074/jbc.rev120.012960] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
Reagents that bind tightly and specifically to biomolecules of interest remain essential in the exploration of biology and in their ultimate application to medicine. Besides ligands for receptors of known specificity, agents commonly used for this purpose are monoclonal antibodies derived from mice, rabbits, and other animals. However, such antibodies can be expensive to produce, challenging to engineer, and are not necessarily stable in the context of the cellular cytoplasm, a reducing environment. Heavy chain-only antibodies, discovered in camelids, have been truncated to yield single-domain antibody fragments (VHHs or nanobodies) that overcome many of these shortcomings. Whereas they are known as crystallization chaperones for membrane proteins or as simple alternatives to conventional antibodies, nanobodies have been applied in settings where the use of standard antibodies or their derivatives would be impractical or impossible. We review recent examples in which the unique properties of nanobodies have been combined with complementary methods, such as chemical functionalization, to provide tools with unique and useful properties.
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Affiliation(s)
- Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte Wijne
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
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48
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de Beer MA, Giepmans BNG. Nanobody-Based Probes for Subcellular Protein Identification and Visualization. Front Cell Neurosci 2020; 14:573278. [PMID: 33240044 PMCID: PMC7667270 DOI: 10.3389/fncel.2020.573278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding how building blocks of life contribute to physiology is greatly aided by protein identification and cellular localization. The two main labeling approaches developed over the past decades are labeling with antibodies such as immunoglobulin G (IgGs) or use of genetically encoded tags such as fluorescent proteins. However, IgGs are large proteins (150 kDa), which limits penetration depth and uncertainty of target position caused by up to ∼25 nm distance of the label created by the chosen targeting approach. Additionally, IgGs cannot be easily recombinantly modulated and engineered as part of fusion proteins because they consist of multiple independent translated chains. In the last decade single domain antigen binding proteins are being explored in bioscience as a tool in revealing molecular identity and localization to overcome limitations by IgGs. These nanobodies have several potential benefits over routine applications. Because of their small size (15 kDa), nanobodies better penetrate during labeling procedures and improve resolution. Moreover, nanobodies cDNA can easily be fused with other cDNA. Multidomain proteins can thus be easily engineered consisting of domains for targeting (nanobodies) and visualization by fluorescence microscopy (fluorescent proteins) or electron microscopy (based on certain enzymes). Additional modules for e.g., purification are also easily added. These nanobody-based probes can be applied in cells for live-cell endogenous protein detection or may be purified prior to use on molecules, cells or tissues. Here, we present the current state of nanobody-based probes and their implementation in microscopy, including pitfalls and potential future opportunities.
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Affiliation(s)
- Marit A de Beer
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ben N G Giepmans
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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Jedlitzke B, Mootz HD. Photocaged Nanobodies Delivered into Cells for Light Activation of Biological Processes. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Benedikt Jedlitzke
- Institute of Biochemistry Department of Chemistry and Pharmacy University of Muenster Correns-Str. 36 48149 Münster Germany
| | - Henning D. Mootz
- Institute of Biochemistry Department of Chemistry and Pharmacy University of Muenster Correns-Str. 36 48149 Münster Germany
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Muyldermans S. A guide to: generation and design of nanobodies. FEBS J 2020; 288:2084-2102. [PMID: 32780549 PMCID: PMC8048825 DOI: 10.1111/febs.15515] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/03/2020] [Accepted: 08/07/2020] [Indexed: 01/09/2023]
Abstract
A nanobody (Nb) is a registered trademark of Ablynx, referring to the single antigen-binding domain of heavy chain-only antibodies (HCAbs) that are circulating in Camelidae. Nbs are produced recombinantly in micro-organisms and employed as research tools or for diagnostic and therapeutic applications. They were - and still are - also named single-domain antibodies (sdAbs) or variable domain of the heavy chain of HCAbs (VHH). A variety of methods are currently in use for the fast and efficient generation of target-specific Nbs. Such Nbs are produced at low cost and associate with high affinity to their cognate antigen. They are robust, strictly monomeric and easy to tailor into more complex entities to meet the requirements of their application. Here, we review the various sources and different strategies that have been developed to identify rapidly, target-specific Nbs. We further discuss a variety of engineering technologies that have been explored to broaden the application range of Nbs and summarise those applications where designed Nbs might offer a marked advantage over other affinity reagents.
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Affiliation(s)
- Serge Muyldermans
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, Belgium.,Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, China
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