1
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Ballard E, Sakurai M, Yu L, Liu L, Oura S, Huang J, Wu J. Incompatibility in cell adhesion constitutes a barrier to interspecies chimerism. Cell Stem Cell 2024; 31:1419-1426.e7. [PMID: 39181131 DOI: 10.1016/j.stem.2024.07.010] [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: 01/05/2024] [Revised: 06/05/2024] [Accepted: 07/30/2024] [Indexed: 08/27/2024]
Abstract
Interspecies blastocyst complementation holds great potential to address the global shortage of transplantable organs by growing human organs in animals. However, a major challenge in this approach is the limited chimerism of human cells in evolutionarily distant animal hosts due to various xenogeneic barriers. Here, we reveal that human pluripotent stem cells (PSCs) struggle to adhere to animal PSCs. To overcome this barrier, we developed a synthetic biology strategy that leverages nanobody-antigen interactions to enhance interspecies cell adhesion. We engineered cells to express nanobodies and their corresponding antigens on their outer membranes, significantly improving adhesion between different species' PSCs during in vitro assays and increasing the chimerism of human PSCs in mouse embryos. Studying and manipulating interspecies pluripotent cell adhesion will provide valuable insights into cell interaction dynamics during chimera formation and early embryogenesis.
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Affiliation(s)
- Emily Ballard
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Masahiro Sakurai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lizhong Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Seiya Oura
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jia Huang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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2
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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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3
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Alfadhli A, Bates TA, Barklis RL, Romanaggi C, Tafesse FG, Barklis E. A nanobody interaction with SARS-COV-2 Spike allows the versatile targeting of lentivirus vectors. J Virol 2024; 98:e0079524. [PMID: 39207135 PMCID: PMC11406891 DOI: 10.1128/jvi.00795-24] [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: 05/06/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
While investigating methods to target gene delivery vectors to specific cell types, we examined the potential of using a nanobody against the SARS-CoV-2 Spike protein receptor-binding domain to direct lentivirus infection of Spike-expressing cells. Using four different approaches, we found that lentiviruses with surface-exposed nanobody domains selectively infect Spike-expressing cells. Targeting is dependent on the fusion function of the Spike protein, and conforms to a model in which nanobody binding to the Spike protein triggers the Spike fusion machinery. The nanobody-Spike interaction also is capable of directing cell-cell fusion and the selective infection of nanobody-expressing cells by Spike-pseudotyped lentivirus vectors. Significantly, cells infected with SARS-CoV-2 are efficiently and selectively infected by lentivirus vectors pseudotyped with a chimeric nanobody protein. Our results suggest that cells infected by any virus that forms syncytia may be targeted for gene delivery by using an appropriate nanobody or virus receptor mimic. Vectors modified in this fashion may prove useful in the delivery of immunomodulators to infected foci to mitigate the effects of viral infections.IMPORTANCEWe have discovered that lentiviruses decorated on their surfaces with a nanobody against the SARS-CoV-2 Spike protein selectively infect Spike-expressing cells. Infection is dependent on the specificity of the nanobody and the fusion function of the Spike protein and conforms to a reverse fusion model, in which nanobody binding to Spike triggers the Spike fusion machinery. The nanobody-Spike interaction also can drive cell-cell fusion and infection of nanobody-expressing cells with viruses carrying the Spike protein. Importantly, cells infected with SARS-CoV-2 are selectively infected with nanobody-decorated lentiviruses. These results suggest that cells infected by any virus that expresses an active receptor-binding fusion protein may be targeted by vectors for delivery of cargoes to mitigate infections.
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Affiliation(s)
- Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Timothy A Bates
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Robin Lid Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - CeAnn Romanaggi
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, USA
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4
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Weng D, Yang L, Xie Y. Engineering and characterization of GFP-targeting nanobody: Expression, purification, and post-translational modification analysis. Protein Expr Purif 2024; 221:106501. [PMID: 38782081 DOI: 10.1016/j.pep.2024.106501] [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: 02/21/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Nanobodies are single-variable domain antibodies with excellent properties, which are evolving as versatile tools to guide cognate antigens in vitro and in vivo for biological research, diagnosis, and treatment. Given their simple structure, nanobodies are readily produced in multiple systems. However, selecting an appropriate expression system is crucial because different conditions might cause proteins to produce different folds or post-translational modifications (PTMs), and these differences often result in different functions. At present, the strategies of PTMs are rarely reported. The GFP nanobody can specifically target the GFP protein. Here, we engineered a GFP nanobody fused with 6 × His tag and Fc tag, respectively, and expressed in bacteria and mammalian cells. The 6 × His-GFP-nanobody was produced from Escherichia coli at high yields and the pull-down assay indicated that it can precipitate the GFP protein. Meanwhile, the Fc-GFP-nanobody can be expressed in HEK293T cells, and the co-immunoprecipitation experiment can trace and target the GFP-tagged protein in vivo. Furthermore, some different PTMs in antigen-binding regions have been identified after using mass spectrometry (MS) to analyze the GFP nanobodies, which are expressed in prokaryotes and eukaryotes. In this study, a GFP nanobody was designed, and its binding ability was verified by using the eukaryotic and prokaryotic protein expression systems. In addition, this GFP nanobody was transformed into a useful instrument for more in-depth functional investigations of GFP fusion proteins. MS was further used to explore the reason for the difference in binding ability, providing a novel perspective for the study of GFP nanobodies and protein expression purification.
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Affiliation(s)
- Dunchu Weng
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Lin Yang
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yajun Xie
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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5
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Gelová Z, Ingles-Prieto A, Bohstedt T, Frommelt F, Chi G, Chang YN, Garcia J, Wolf G, Azzollini L, Tremolada S, Scacioc A, Hansen JS, Serrano I, Droce A, Bernal JC, Burgess-Brown NA, Carpenter EP, Dürr KL, Kristensen P, Geertsma ER, Štefanić S, Scarabottolo L, Wiedmer T, Puetter V, Sauer DB, Superti-Furga G. Protein Binder Toolbox for Studies of Solute Carrier Transporters. J Mol Biol 2024; 436:168665. [PMID: 38878854 DOI: 10.1016/j.jmb.2024.168665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/01/2024]
Abstract
Transporters of the solute carrier superfamily (SLCs) are responsible for the transmembrane traffic of the majority of chemical substances in cells and tissues and are therefore of fundamental biological importance. As is often the case with membrane proteins that can be heavily glycosylated, a lack of reliable high-affinity binders hinders their functional analysis. Purifying and reconstituting transmembrane proteins in their lipidic environments remains challenging and standard approaches to generate binders for multi-transmembrane proteins, such as SLCs, channels or G protein-coupled receptors (GPCRs) are lacking. While generating protein binders to 27 SLCs, we produced full length protein or cell lines as input material for binder generation by selected binder generation platforms. As a result, we obtained 525 binders for 22 SLCs. We validated the binders with a cell-based validation workflow using immunofluorescent and immunoprecipitation methods to process all obtained binders. Finally, we demonstrated the potential applications of the binders that passed our validation pipeline in structural, biochemical, and biological applications using the exemplary protein SLC12A6, an ion transporter relevant in human disease. With this work, we were able to generate easily renewable and highly specific binders against SLCs, which will greatly facilitate the study of this neglected protein family. We hope that the process will serve as blueprint for the generation of binders against the entire superfamily of SLC transporters.
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Affiliation(s)
- Zuzana Gelová
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tina Bohstedt
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Julio Garcia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | - Andreea Scacioc
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jesper S Hansen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Iciar Serrano
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Aida Droce
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elisabeth P Carpenter
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Katharina L Dürr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Eric R Geertsma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Saša Štefanić
- Nanobody Service Facility, University of Zurich, AgroVet-Strickhof, Eschikon, Switzerland
| | | | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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6
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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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7
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Wu J, Fu J. Toward developing human organs via embryo models and chimeras. Cell 2024; 187:3194-3219. [PMID: 38906095 PMCID: PMC11239105 DOI: 10.1016/j.cell.2024.05.027] [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: 05/30/2023] [Revised: 02/02/2024] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
Developing functional organs from stem cells remains a challenging goal in regenerative medicine. Existing methodologies, such as tissue engineering, bioprinting, and organoids, only offer partial solutions. This perspective focuses on two promising approaches emerging for engineering human organs from stem cells: stem cell-based embryo models and interspecies organogenesis. Both approaches exploit the premise of guiding stem cells to mimic natural development. We begin by summarizing what is known about early human development as a blueprint for recapitulating organogenesis in both embryo models and interspecies chimeras. The latest advances in both fields are discussed before highlighting the technological and knowledge gaps to be addressed before the goal of developing human organs could be achieved using the two approaches. We conclude by discussing challenges facing embryo modeling and interspecies organogenesis and outlining future prospects for advancing both fields toward the generation of human tissues and organs for basic research and translational applications.
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Affiliation(s)
- Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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8
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Alfadhli A, Bates TA, Barklis RL, Romanaggi C, Tafesse FG, Barklis E. A Nanobody Interaction with SARS-CoV-2 Spike Allows the Versatile Targeting of Lentivirus Vectors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597774. [PMID: 38895228 PMCID: PMC11185593 DOI: 10.1101/2024.06.06.597774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
While investigating methods to target gene delivery vectors to specific cell types, we examined the potential of using a nanobody against the SARS-CoV-2 Spike protein receptor binding domain to direct lentivirus infection of Spike-expressing cells. Using three different approaches, we found that lentiviruses with surface-exposed nanobody domains selectively infect Spike-expressing cells. The targeting is dependent on the fusion function of Spike, and conforms to a model in which nanobody binding to the Spike protein triggers the Spike fusion machinery. The nanobody-Spike interaction also is capable of directing cell-cell fusion, and the selective infection of nanobody-expressing cells by Spike-pseudotyped lentivirus vectors. Significantly, cells infected with SARS-CoV-2 are efficiently and selectively infected by lentivirus vectors pseudotyped with a chimeric nanobody protein. Our results suggest that cells infected by any virus that forms syncytia may be targeted for gene delivery using an appropriate nanobody or virus receptor mimic. Vectors modified in this fashion may prove useful in the delivery of immunomodulators to infected foci to mitigate the effects of viral infections. IMPORTANCE We have discovered that lentiviruses decorated on their surfaces with a nanobody against the SARS-CoV-2 Spike protein selectively infect Spike-expressing cells. Infection is dependent on the specificity of the nanobody and the fusion function of the Spike protein, and conforms to a reverse fusion model, in which nanobody binding to Spike triggers the Spike fusion machinery. The nanobody-Spike interaction also can drive cell-cell fusion, and infection of nanobody-expressing cells with viruses carrying the Spike protein. Importantly, cells infected with SARS-CoV-2 are selectively infected with nanobody-decorated lentiviruses. These results suggest that cells infected by any virus that expresses an active receptor-binding fusion protein may be targeted by vectors for delivery of cargoes to mitigate infections.
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9
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Joubbi S, Micheli A, Milazzo P, Maccari G, Ciano G, Cardamone D, Medini D. Antibody design using deep learning: from sequence and structure design to affinity maturation. Brief Bioinform 2024; 25:bbae307. [PMID: 38960409 PMCID: PMC11221890 DOI: 10.1093/bib/bbae307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/20/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024] Open
Abstract
Deep learning has achieved impressive results in various fields such as computer vision and natural language processing, making it a powerful tool in biology. Its applications now encompass cellular image classification, genomic studies and drug discovery. While drug development traditionally focused deep learning applications on small molecules, recent innovations have incorporated it in the discovery and development of biological molecules, particularly antibodies. Researchers have devised novel techniques to streamline antibody development, combining in vitro and in silico methods. In particular, computational power expedites lead candidate generation, scaling and potential antibody development against complex antigens. This survey highlights significant advancements in protein design and optimization, specifically focusing on antibodies. This includes various aspects such as design, folding, antibody-antigen interactions docking and affinity maturation.
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Affiliation(s)
- Sara Joubbi
- Department of Computer Science, University of Pisa, Largo B. Pontecorvo, 3, 56127, Pisa, Italy
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Via Fiorentina, 1, 53100, Siena, Italy
| | - Alessio Micheli
- Department of Computer Science, University of Pisa, Largo B. Pontecorvo, 3, 56127, Pisa, Italy
| | - Paolo Milazzo
- Department of Computer Science, University of Pisa, Largo B. Pontecorvo, 3, 56127, Pisa, Italy
| | - Giuseppe Maccari
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Via Fiorentina, 1, 53100, Siena, Italy
| | - Giorgio Ciano
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Via Fiorentina, 1, 53100, Siena, Italy
| | - Dario Cardamone
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Via Fiorentina, 1, 53100, Siena, Italy
| | - Duccio Medini
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Via Fiorentina, 1, 53100, Siena, Italy
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10
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Douglas CM, Bird JE, Kopinke D, Esser KA. An optimized approach to study nanoscale sarcomere structure utilizing super-resolution microscopy with nanobodies. PLoS One 2024; 19:e0300348. [PMID: 38687705 PMCID: PMC11060602 DOI: 10.1371/journal.pone.0300348] [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: 11/06/2023] [Accepted: 02/23/2024] [Indexed: 05/02/2024] Open
Abstract
The sarcomere is the fundamental contractile unit in skeletal muscle, and the regularity of its structure is critical for function. Emerging data demonstrates that nanoscale changes to the regularity of sarcomere structure can affect the overall function of the protein dense ~2μm sarcomere. Further, sarcomere structure is implicated in many clinical conditions of muscle weakness. However, our understanding of how sarcomere structure changes in disease, especially at the nanoscale, has been limited in part due to the inability to robustly detect and measure at sub-sarcomere resolution. We optimized several methodological steps and developed a robust pipeline to analyze sarcomere structure using structured illumination super-resolution microscopy in conjunction with commercially-available and fluorescently-conjugated Variable Heavy-Chain only fragment secondary antibodies (nanobodies), and achieved a significant increase in resolution of z-disc width (353nm vs. 62nm) compared to confocal microscopy. The combination of these methods provides a unique approach to probe sarcomere protein localization at the nanoscale and may prove advantageous for analysis of other cellular structures.
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Affiliation(s)
- Collin M. Douglas
- Department of Physiology and Aging, University of Florida, Gainesville, Florida, United States of America
| | - Jonathan E. Bird
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, Florida, United States of America
| | - Daniel Kopinke
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, Florida, United States of America
| | - Karyn A. Esser
- Department of Physiology and Aging, University of Florida, Gainesville, Florida, United States of America
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11
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Pandey RK, Mehrotra S. Engineering high affinity antigen-binders: Beyond conventional antibodies. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 140:37-57. [PMID: 38762275 DOI: 10.1016/bs.apcsb.2023.12.014] [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: 05/20/2024]
Abstract
For decades, antibodies have remained the archetypal binding proteins that can be rapidly produced with high affinity and specificity against virtually any target. A conventional antibody is still considered the prototype of a binding molecule. It is therefore not surprising that antibodies are routinely used in basic scientific and biomedical research, analytical workflows, molecular diagnostics etc. and represent the fastest growing sector in the field of biotechnology. However, several limitations associated with conventional antibodies, including stringent requirement of animal immunizations, mammalian cells for expression, issues on stability and aggregation, bulkier size and the overall time and cost of production has propelled evolution of concepts along alternative antigen binders. Rapidly evolving protein engineering approaches and high throughput screening platforms have further complemented the development of myriads of classes of non-conventional protein binders including antibody derived as well as non-antibody based molecular scaffolds. These non-canonical binders are finding use across disciplines of which diagnostics and therapeutics are the most noteworthy.
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Affiliation(s)
- Rajeev Kumar Pandey
- Research and Development-Protein Biology, Thermo Fisher Scientific, Bangalore, India
| | - Sanjana Mehrotra
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
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12
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Inavalli VVGK, Puente Muñoz V, Draffin JE, Tønnesen J. Fluorescence microscopy shadow imaging for neuroscience. Front Cell Neurosci 2024; 18:1330100. [PMID: 38425431 PMCID: PMC10902105 DOI: 10.3389/fncel.2024.1330100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Fluorescence microscopy remains one of the single most widely applied experimental approaches in neuroscience and beyond and is continuously evolving to make it easier and more versatile. The success of the approach is based on synergistic developments in imaging technologies and fluorophore labeling strategies that have allowed it to greatly diversify and be used across preparations for addressing structure as well as function. Yet, while targeted labeling strategies are a key strength of fluorescence microscopy, they reciprocally impose general limitations on the possible types of experiments and analyses. One recent development that overcomes some of these limitations is fluorescence microscopy shadow imaging, where membrane-bound cellular structures remain unlabeled while the surrounding extracellular space is made to fluoresce to provide a negative contrast shadow image. When based on super-resolution STED microscopy, the technique in effect provides a positive image of the extracellular space geometry and entire neuropil in the field of view. Other noteworthy advantages include the near elimination of the adverse effects of photobleaching and toxicity in live imaging, exhaustive and homogeneous labeling across the preparation, and the ability to apply and adjust the label intensity on the fly. Shadow imaging is gaining popularity and has been applied on its own or combined with conventional positive labeling to visualize cells and synaptic proteins in their parenchymal context. Here, we highlight the inherent limitations of fluorescence microscopy and conventional labeling and contrast these against the pros and cons of recent shadow imaging approaches. Our aim is to describe the brief history and current trajectory of the shadow imaging technique in the neuroscience field, and to draw attention to its ease of application and versatility.
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Affiliation(s)
| | - Virginia Puente Muñoz
- Department of Neurosciences, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
- Neuronal Excitability Lab, Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Jonathan E. Draffin
- Neuronal Excitability Lab, Achucarro Basque Center for Neuroscience, Leioa, Spain
- Aligning Science Across Parkinson’s (ASAP), Collaborative Research Network, Chevy Chase, MD, United States
| | - Jan Tønnesen
- Department of Neurosciences, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
- Neuronal Excitability Lab, Achucarro Basque Center for Neuroscience, Leioa, Spain
- Aligning Science Across Parkinson’s (ASAP), Collaborative Research Network, Chevy Chase, MD, United States
- Instituto Biofisika (CSIC/UPV), Leioa, Spain
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13
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Arnold B, Riegger RJ, Okuda EK, Slišković I, Keller M, Bakisoglu C, McNicoll F, Zarnack K, Müller-McNicoll M. hGRAD: A versatile "one-fits-all" system to acutely deplete RNA binding proteins from condensates. J Cell Biol 2024; 223:e202304030. [PMID: 38108808 PMCID: PMC10726014 DOI: 10.1083/jcb.202304030] [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: 04/12/2023] [Revised: 09/18/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023] Open
Abstract
Nuclear RNA binding proteins (RBPs) are difficult to study because they often belong to large protein families and form extensive networks of auto- and crossregulation. They are highly abundant and many localize to condensates with a slow turnover, requiring long depletion times or knockouts that cannot distinguish between direct and indirect or compensatory effects. Here, we developed a system that is optimized for the rapid degradation of nuclear RBPs, called hGRAD. It comes as a "one-fits-all" plasmid, and integration into any cell line with endogenously GFP-tagged proteins allows for an inducible, rapid, and complete knockdown. We show that the nuclear RBPs SRSF3, SRSF5, SRRM2, and NONO are completely cleared from nuclear speckles and paraspeckles within 2 h. hGRAD works in various cell types, is more efficient than previous methods, and does not require the expression of exogenous ubiquitin ligases. Combining SRSF5 hGRAD degradation with Nascent-seq uncovered transient transcript changes, compensatory mechanisms, and an effect of SRSF5 on transcript stability.
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Affiliation(s)
- Benjamin Arnold
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ricarda J. Riegger
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ellen Kazumi Okuda
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- International Max Planck Research School for Cellular Biophysics, Frankfurt am Main, Germany
| | - Irena Slišković
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mario Keller
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Cem Bakisoglu
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - François McNicoll
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kathi Zarnack
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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14
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Xiong S, Liu Z, Yi X, Liu K, Huang B, Wang X. NanoLAS: a comprehensive nanobody database with data integration, consolidation and application. Database (Oxford) 2024; 2024:baae003. [PMID: 38300518 PMCID: PMC10833066 DOI: 10.1093/database/baae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/15/2023] [Accepted: 01/06/2024] [Indexed: 02/02/2024]
Abstract
Nanobodies, a unique subclass of antibodies first discovered in camelid animals, are composed solely of a single heavy chain's variable region. Their significantly reduced molecular weight, in comparison to conventional antibodies, confers numerous advantages in the treatment of various diseases. As research and applications involving nanobodies expand, the quantity of identified nanobodies is also rapidly growing. However, the existing antibody databases are deficient in type and coverage, failing to satisfy the comprehensive needs of researchers and thus impeding progress in nanobody research. In response to this, we have amalgamated data from multiple sources to successfully assemble a new and comprehensive nanobody database. This database has currently included the latest nanobody data and provides researchers with an excellent search and data display interface, thus facilitating the progression of nanobody research and their application in disease treatment. In summary, the newly constructed Nanobody Library and Archive System may significantly enhance the retrieval efficiency and application potential of nanobodies. We envision that Nanobody Library and Archive System will serve as an accessible, robust and efficient tool for nanobody research and development, propelling advancements in the field of biomedicine. Database URL: https://www.nanolas.cloud.
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Affiliation(s)
| | - Zhengwen Liu
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China
| | - Xin Yi
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China
| | - Kai Liu
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China
| | - Bingding Huang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China
| | - Xin Wang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China
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15
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Baronaite U, Cachat E. Preparation of Chromobodies for the Detection of Cell Surface Epitopes. Methods Mol Biol 2024; 2774:303-314. [PMID: 38441773 DOI: 10.1007/978-1-0716-3718-0_20] [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: 03/07/2024]
Abstract
Chromobodies are nanobodies genetically fused to fluorescent proteins, which were developed to visualize endogenous intracellular antigens. These versatile bioimaging nanotools can also be used to detect cell surface epitopes, and we describe here how we use them as an alternative to conjugated antibodies. This way, we routinely test the binding efficiency of nanobodies for their cognate cell surface antigens, before integrating them as sensing domains into complex synthetic receptor architectures.
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Affiliation(s)
- Ugne Baronaite
- Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- Institute for Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Elise Cachat
- Centre for Engineering Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
- Institute for Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
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16
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Chen YL, Xie XX, Zheng P, Zhu C, Ma H, Khalid Z, Xie YJ, Dang YZ, Ye Y, Sheng N, Zhong N, Lei WH, Zhang C, Zhang LJ, Jin T, Cao MJ. Selection, identification and crystal structure of shark-derived single-domain antibodies against a green fluorescent protein. Int J Biol Macromol 2023; 247:125852. [PMID: 37460076 DOI: 10.1016/j.ijbiomac.2023.125852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/22/2023]
Abstract
Shark variable domain of new antigen receptors (VNARs) are the smallest naturally occurring binding domains with properties of low complexity, small size, cytoplasmic expression, and ease of engineering. Green fluorescent protein (GFP) molecules have been analyzed in conventional microscopy, but their spectral characteristics preclude their use in techniques offering substantially higher resolution. Besides, the GFP molecules can be quenched in acidic environment, which makes it necessary to develop anti-GFP antibody to solve these problems. In view of the diverse applications of GFP and unique physicochemical features of VNAR, the present study aims to generate VNARs against GFP. Here, we identified 36 VNARs targeting eCGP123, an extremely stable GFP, by phage display from three immunized sharks. These VNARs bound to eCGP123 with affinity constant KD values ranging from 6.76 to 605 nM. Among them, two lead VNARs named aGFP-14 and aGFP-15 with nanomolar eCGP123-binding affinity were selected for in-depth characterization. aGFP-14 and aGFP-15 recognized similar epitopes on eCGP123. X-ray crystallography studies clarified the mechanism by which aGFP14 interacts with eCGP123. aGFP-14 also showed cross-reaction with EGFP, with KD values of 47.2 nM. Finally, immunostaining analyses demonstrated that aGFP-14 was able to bind effectively to the EGFP expressed in both cultured cells and mouse brain tissues, and can be used as a fluorescence amplifier for EGFP. Our research demonstrates a feasible idea for the screening and production of shark-derived VNARs. The two high-affinity VNARs developed in the study contribute to the diversity of GFP sdAbs and may enhance the applications of GFP.
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Affiliation(s)
- Yu-Lei Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xin-Xin Xie
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Peiyi Zheng
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Chenchen Zhu
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Huan Ma
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Zunera Khalid
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Yang-Jie Xie
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Yi-Zhao Dang
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Yaxin Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Nengyin Sheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ning Zhong
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Wen-Hui Lei
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | | | - Ling-Jing Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Tengchuan Jin
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China.
| | - Min-Jie Cao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China.
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17
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Stahl P, Kollenda S, Sager J, Schmidt L, Schroer MA, Stauber RH, Epple M, Knauer SK. Tuning Nanobodies' Bioactivity: Coupling to Ultrasmall Gold Nanoparticles Allows the Intracellular Interference with Survivin. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300871. [PMID: 37035950 DOI: 10.1002/smll.202300871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Nanobodies are highly affine binders, often used to track disease-relevant proteins inside cells. However, they often fail to interfere with pathobiological functions, required for their clinical exploitation. Here, a nanobody targeting the disease-relevant apoptosis inhibitor and mitosis regulator Survivin (SuN) is utilized. Survivin's multifaceted functions are regulated by an interplay of dynamic cellular localization, dimerization, and protein-protein interactions. However, as Survivin harbors no classical "druggable" binding pocket, one must aim at blocking extended protein surface areas. Comprehensive experimental evidence demonstrates that intracellular expression of SuN allows to track Survivin at low nanomolar concentrations but failed to inhibit its biological functions. Small angle X-ray scattering of the Survivin-SuN complex locates the proposed interaction interface between the C-terminus and the globular domain, as such not blocking any pivotal interaction. By clicking multiple SuN to ultrasmall (2 nm) gold nanoparticles (SuN-N), not only intracellular uptake is enabled, but additionally, Survivin crosslinking and interference with mitotic progression in living cells are also enabled. In sum, it is demonstrated that coupling of nanobodies to nanosized scaffolds can be universally applicable to improve their function and therapeutic applicability.
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Affiliation(s)
- Paul Stahl
- Molecular Biology II, Department of Biology, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Sebastian Kollenda
- Inorganic Chemistry, Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Jonas Sager
- Inorganic Chemistry, Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Laura Schmidt
- Molecular Biology II, Department of Biology, Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Martin A Schroer
- Nanoparticle Process Technology, Department of Engineering, University of Duisburg-Essen, Lotharstr. 1, 47057, Duisburg, Germany
| | - Roland H Stauber
- Molecular and Cellular Oncology/ENT, University Medical Center Mainz (UMM), Langenbeckstrasse 1, 55131, Mainz, Germany
| | - Matthias Epple
- Inorganic Chemistry, Department of Chemistry, Center for Nanointegration Duisburg-Essen (CENIDE) and Center of Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Shirley K Knauer
- Molecular Biology II, Department of Biology, Center of Medical Biotechnology (ZMB) and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
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18
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Breine A, Van Holsbeeck K, Martin C, Gonzalez S, Mannes M, Pardon E, Steyaert J, Remaut H, Ballet S, Van der Henst C. Bypassing the Need for Cell Permeabilization: Nanobody CDR3 Peptide Improves Binding on Living Bacteria. Bioconjug Chem 2023. [PMID: 37418494 PMCID: PMC10360062 DOI: 10.1021/acs.bioconjchem.3c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Membrane interaction constitutes to be an essential parameter in the mode of action of entities such as proteins, as well as cell-penetrating and antimicrobial peptides, resulting in noninvasive or lytic activities depending on the membrane compositions and interactions. Recently, a nanobody able to interact with the top priority, multidrug-resistant bacterial pathogen Acinetobacter baumannii was discovered, although binding took place with fixed cells only. To potentially overcome this limitation, linear peptides corresponding to the complementarity-determining regions (CDR) were synthesized and fluorescently labeled. Microscopy data indicated clear membrane interactions of the CDR3 sequence with living A. baumannii cells, indicating both the importance of the CDR3 as part of the parent nanobody paratope and the improved binding ability and thus avoiding the need for permeabilization of the cells. In addition, cyclization of the peptide with an additionally introduced rigidifying 1,2,3-triazole bridge retains its binding ability while proteolytically protecting the peptide. Overall, this study resulted in the discovery of novel peptides binding a multidrug-resistant pathogen.
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Affiliation(s)
- A Breine
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - K Van Holsbeeck
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - C Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - S Gonzalez
- CNRS, BioCIS, CY Cergy-Paris Université, 95000 Neuville sur Oise, France
| | - M Mannes
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - E Pardon
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - J Steyaert
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - H Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium
| | - S Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - C Van der Henst
- Microbial Resistance and Drug Discovery, VIB-VUB Center for Structural Biology, VIB, Flanders Institute for Biotechnology, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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19
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Zhang X, Galenkamp NS, van der Heide NJ, Moreno J, Maglia G, Kjems J. Specific Detection of Proteins by a Nanobody-Functionalized Nanopore Sensor. ACS NANO 2023; 17:9167-9177. [PMID: 37127291 PMCID: PMC10184537 DOI: 10.1021/acsnano.2c12733] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Nanopores are label-free single-molecule analytical tools that show great potential for stochastic sensing of proteins. Here, we described a ClyA nanopore functionalized with different nanobodies through a 5-6 nm DNA linker at its periphery. Ty1, 2Rs15d, 2Rb17c, and nb22 nanobodies were employed to specifically recognize the large protein SARS-CoV-2 Spike, a medium-sized HER2 receptor, and the small protein murine urokinase-type plasminogen activator (muPA), respectively. The pores modified with Ty1, 2Rs15d, and 2Rb17c were capable of stochastic sensing of Spike protein and HER2 receptor, respectively, following a model where unbound nanobodies, facilitated by a DNA linker, move inside the nanopore and provoke reversible blockade events, whereas engagement with the large- and medium-sized proteins outside of the pore leads to a reduced dynamic movement of the nanobodies and an increased current through the open pore. Exploiting the multivalent interaction between trimeric Spike protein and multimerized Ty1 nanobodies enabled the detection of picomolar concentrations of Spike protein. In comparison, detection of the smaller muPA proteins follows a different model where muPA, complexing with the nb22, moves into the pore, generating larger blockage signals. Importantly, the components in blood did not affect the sensing performance of the nanobody-functionalized nanopore, which endows the pore with great potential for clinical detection of protein biomarkers.
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Affiliation(s)
- Xialin Zhang
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | | | - Julián Moreno
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
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20
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Galazzo L, Bordignon E. Electron paramagnetic resonance spectroscopy in structural-dynamic studies of large protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 134-135:1-19. [PMID: 37321755 DOI: 10.1016/j.pnmrs.2022.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Macromolecular protein assemblies are of fundamental importance for many processes inside the cell, as they perform complex functions and constitute central hubs where reactions occur. Generally, these assemblies undergo large conformational changes and cycle through different states that ultimately are connected to specific functions further regulated by additional small ligands or proteins. Unveiling the 3D structural details of these assemblies at atomic resolution, identifying the flexible parts of the complexes, and monitoring with high temporal resolution the dynamic interplay between different protein regions under physiological conditions is key to fully understanding their properties and to fostering biomedical applications. In the last decade, we have seen remarkable advances in cryo-electron microscopy (EM) techniques, which deeply transformed our vision of structural biology, especially in the field of macromolecular assemblies. With cryo-EM, detailed 3D models of large macromolecular complexes in different conformational states became readily available at atomic resolution. Concomitantly, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy (EPR) have benefited from methodological innovations which also improved the quality of the information that can be achieved. Such enhanced sensitivity widened their applicability to macromolecular complexes in environments close to physiological conditions and opened a path towards in-cell applications. In this review we will focus on the advantages and challenges of EPR techniques with an integrative approach towards a complete understanding of macromolecular structures and functions.
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Affiliation(s)
- Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
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21
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Yong Joon Kim J, Sang Z, Xiang Y, Shen Z, Shi Y. Nanobodies: Robust miniprotein binders in biomedicine. Adv Drug Deliv Rev 2023; 195:114726. [PMID: 36754285 DOI: 10.1016/j.addr.2023.114726] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 12/30/2022] [Accepted: 02/02/2023] [Indexed: 02/10/2023]
Abstract
Variable domains of heavy chain-only antibodies (VHH), also known as nanobodies (Nbs), are monomeric antigen-binding domains derived from the camelid heavy chain-only antibodies. Nbs are characterized by small size, high target selectivity, and marked solubility and stability, which collectively facilitate high-quality drug development. In addition, Nbs are readily expressed from various expression systems, including E. coli and yeast cells. For these reasons, Nbs have emerged as preferred antibody fragments for protein engineering, disease diagnosis, and treatment. To date, two Nb-based therapies have been approved by the U.S. Food and Drug Administration (FDA). Numerous candidates spanning a wide spectrum of diseases such as cancer, immune disorders, infectious diseases, and neurodegenerative disorders are under preclinical and clinical investigation. Here, we discuss the structural features of Nbs that allow for specific, versatile, and strong target binding. We also summarize emerging technologies for identification, structural analysis, and humanization of Nbs. Our main focus is to review recent advances in using Nbs as a modular scaffold to facilitate the engineering of multivalent polymers for cutting-edge applications. Finally, we discuss remaining challenges for Nb development and envision new opportunities in Nb-based research.
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Affiliation(s)
- Jeffrey Yong Joon Kim
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA; Medical Scientist Training Program, University of Pittsburgh School of Medicine and Carnegie Mellon University, Pittsburgh, PA, USA
| | - Zhe Sang
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA
| | - Yufei Xiang
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA
| | - Zhuolun Shen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yi Shi
- Center of Protein Engineering and Therapeutics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1, Gustave L. Levy Pl, New York, NY 10029, USA.
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22
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Lan Z, Li L, Sun Y, Meng X, Shi Z, Du M, Wang H, Sun Z, Cui Q, Wang L, Geng T, Zhou S, Wang Y, Hu F, Duan C, Geng Y, Zhu Y, Dai Y. A procedure for producing an anti-AXL nanobody in E. coli. Protein Expr Purif 2023; 207:106268. [PMID: 37023993 DOI: 10.1016/j.pep.2023.106268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/28/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023]
Abstract
As one of the receptors of the TAM family, AXL plays a vital role in stem cell maintenance, angiogenesis, immune escape of viruses and drug resistance against tumors. In this study, the truncated extracellular segment containing two immunoglobulin-like domains of human AXL (AXL-IG), which has been confirmed to bind growth arrest specific 6 (GAS6) by structural studies [1], was expressed in a prokaryotic expression system and then purified. Immunizing camelid with the purified AXL-IG as antigen could lead to the production of unique nanobodies composed of only variable domain of heavy chain of heavy-chain antibody (VHH), which are around 15 kD and stable. We screened out a nanobody A-LY01 specific binding to AXL-IG. We further determined the affinity of A-LY01 to AXL-IG and revealed that A-LY01 could specifically recognize full-length AXL on the surface of HEK 293T/17 cells. Our study provides appropriate support for the development of diagnostic reagents and antibody therapeutics targeting AXL.
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Affiliation(s)
- Zhongyun Lan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, 201306, China; State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lingyun Li
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yili Sun
- Drug Discovery Shandong Laboratory, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong, 264117, China
| | - Xiangjing Meng
- Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan, 250101, China
| | - Zhenzhong Shi
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Mengyang Du
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hui Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zengchao Sun
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Qianqian Cui
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lu Wang
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Tengjie Geng
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Siyu Zhou
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi'ang Wang
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangzheng Hu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chonggang Duan
- Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan, 250101, China
| | - Yong Geng
- State Key Laboratory of Drug Research, The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yongheng Zhu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, 201306, China.
| | - Yuanyuan Dai
- Department of Pharmacy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China; National Cancer Center/National Clinical Research Center for Cancer/Hebei Cancer Hospital, Chinese Academy of Medical Sciences, Langfang, 065001, China.
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23
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van den Bor J, Bergkamp ND, Anbuhl SM, Dekker F, Comez D, Perez Almeria CV, Bosma R, White CW, Kilpatrick LE, Hill SJ, Siderius M, Smit MJ, Heukers R. NanoB 2 to monitor interactions of ligands with membrane proteins by combining nanobodies and NanoBRET. CELL REPORTS METHODS 2023; 3:100422. [PMID: 37056381 PMCID: PMC10088090 DOI: 10.1016/j.crmeth.2023.100422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/31/2023] [Accepted: 02/17/2023] [Indexed: 03/14/2023]
Abstract
The therapeutic potential of ligands targeting disease-associated membrane proteins is predicted by ligand-receptor binding constants, which can be determined using NanoLuciferase (NanoLuc)-based bioluminescence resonance energy transfer (NanoBRET) methods. However, the broad applicability of these methods is hampered by the restricted availability of fluorescent probes. We describe the use of antibody fragments, like nanobodies, as universal building blocks for fluorescent probes for use in NanoBRET. Our nanobody-NanoBRET (NanoB2) workflow starts with the generation of NanoLuc-tagged receptors and fluorescent nanobodies, enabling homogeneous, real-time monitoring of nanobody-receptor binding. Moreover, NanoB2 facilitates the assessment of receptor binding of unlabeled ligands in competition binding experiments. The broad significance is illustrated by the successful application of NanoB2 to different drug targets (e.g., multiple G protein-coupled receptors [GPCRs] and a receptor tyrosine kinase [RTK]) at distinct therapeutically relevant binding sites (i.e., extracellular and intracellular).
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Affiliation(s)
- Jelle van den Bor
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Nick D. Bergkamp
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Stephanie M. Anbuhl
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- QVQ Holding B.V., Utrecht, the Netherlands
| | - Françoise Dekker
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Dehan Comez
- Cell Signalling Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
| | - Claudia V. Perez Almeria
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Reggie Bosma
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Carl W. White
- Cell Signalling Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
| | - Laura E. Kilpatrick
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
- Division of Bimolecular Science and Medicinal Chemistry, School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Stephen J. Hill
- Cell Signalling Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
| | - Marco Siderius
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Martine J. Smit
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Raimond Heukers
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- QVQ Holding B.V., Utrecht, the Netherlands
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24
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Chen YL, Xie XX, Zhong N, Sun LC, Lin D, Zhang LJ, Weng L, Jin T, Cao MJ. Research Progresses and Applications of Fluorescent Protein Antibodies: A Review Focusing on Nanobodies. Int J Mol Sci 2023; 24:4307. [PMID: 36901737 PMCID: PMC10002328 DOI: 10.3390/ijms24054307] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/16/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
Since the discovery of fluorescent proteins (FPs), their rich fluorescence spectra and photochemical properties have promoted widespread biological research applications. FPs can be classified into green fluorescent protein (GFP) and its derivates, red fluorescent protein (RFP) and its derivates, and near-infrared FPs. With the continuous development of FPs, antibodies targeting FPs have emerged. The antibody, a class of immunoglobulin, is the main component of humoral immunity that explicitly recognizes and binds antigens. Monoclonal antibody, originating from a single B cell, has been widely applied in immunoassay, in vitro diagnostics, and drug development. The nanobody is a new type of antibody entirely composed of the variable domain of a heavy-chain antibody. Compared with conventional antibodies, these small and stable nanobodies can be expressed and functional in living cells. In addition, they can easily access grooves, seams, or hidden antigenic epitopes on the surface of the target. This review provides an overview of various FPs, the research progress of their antibodies, particularly nanobodies, and advanced applications of nanobodies targeting FPs. This review will be helpful for further research on nanobodies targeting FPs, making FPs more valuable in biological research.
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Affiliation(s)
- Yu-Lei Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xin-Xin Xie
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Ning Zhong
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Le-Chang Sun
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Duanquan Lin
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Ling-Jing Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Ling Weng
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Tengchuan Jin
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Min-Jie Cao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
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25
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Brookes JC, Gray ER, Loynachan CN, Gut MJ, Miller BS, P S Brogan A, McKendry RA. Thermodynamic analysis of an entropically driven, high-affinity nanobody-HIV p24 interaction. Biophys J 2023; 122:279-289. [PMID: 36527237 PMCID: PMC9892613 DOI: 10.1016/j.bpj.2022.12.019] [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: 07/10/2022] [Revised: 11/17/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Protein-protein interactions are fundamental to life processes. Complementary computational, structural, and biophysical studies of these interactions enable the forces behind their specificity and strength to be understood. Antibody fragments such as single-chain antibodies have the specificity and affinity of full antibodies but a fraction of their size, expediting whole molecule studies and distal effects without exceeding the computational capacity of modeling systems. We previously reported the crystal structure of a high-affinity nanobody 59H10 bound to HIV-1 capsid protein p24 and deduced key interactions using all-atom molecular dynamics simulations. We studied the properties of closely related medium (37E7) and low (48G11) affinity nanobodies, to understand how changes of three (37E7) or one (48G11) amino acids impacted these interactions; however, the contributions of enthalpy and entropy were not quantified. Here, we report the use of qualitative and quantitative experimental and in silico approaches to separate the contributions of enthalpy and entropy. We used complementary circular dichroism spectroscopy and molecular dynamics simulations to qualitatively delineate changes between nanobodies in isolation and complexed with p24. Using quantitative techniques such as isothermal titration calorimetry alongside WaterMap and Free Energy Perturbation protocols, we found the difference between high (59H10) and medium (37E7) affinity nanobodies on binding to HIV-1 p24 is entropically driven, accounted for by the release of unstable waters from the hydrophobic surface of 59H10. Our results provide an exemplar of the utility of parallel in vitro and in silico studies and highlight that differences in entropic interactions between amino acids and water molecules are sufficient to drive orders of magnitude differences in affinity.
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Affiliation(s)
- Jennifer C Brookes
- London Centre for Nanotechnology, Faculty of Maths and Physical Sciences, University College London, London, United Kingdom
| | - Eleanor R Gray
- London Centre for Nanotechnology, Faculty of Maths and Physical Sciences, University College London, London, United Kingdom
| | - Colleen N Loynachan
- Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Michelle J Gut
- London Centre for Nanotechnology, Faculty of Maths and Physical Sciences, University College London, London, United Kingdom
| | - Benjamin S Miller
- London Centre for Nanotechnology, Faculty of Maths and Physical Sciences, University College London, London, United Kingdom
| | - Alex P S Brogan
- Department of Chemistry, King's College London, London, United Kingdom
| | - Rachel A McKendry
- London Centre for Nanotechnology, Division of Medicine and Faculty of Maths and Physical Sciences, University College London, London, United Kingdom.
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26
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Aktalay A, Ponsot F, Bossi ML, Belov VN, Hell SW. Cleavable Linker Incorporation into a Synthetic Dye-Nanobody-Fluorescent Protein Assembly: FRET, FLIM and STED Microscopy. Chembiochem 2022; 23:e202200395. [PMID: 35838445 PMCID: PMC9804610 DOI: 10.1002/cbic.202200395] [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: 07/13/2022] [Indexed: 01/05/2023]
Abstract
A bright and photostable fluorescent dye with a disulfide (S-S) linker and maleimide group (Rho594-S2-mal), as cleavable and reactive sites, was synthesized and conjugated with anti-GFP nanobodies (NB). The binding of EGFP (FRET donor) with anti-GFP NB labeled with one or two Rho594-S2-mal residues was studied in vitro and in cellulo. The linker was cleaved with dithiothreitol recovering the donor (FP) signal. The bioconjugates (FP-NB-dye) were applied in FRET-FLIM assays, confocal imaging, and superresolution STED microscopy.
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Affiliation(s)
- Ayse Aktalay
- Department of Optical NanoscopyMax Planck Institute for Medical Research (MPI-MR)Jahnstraße 2969120HeidelbergGermany
| | - Flavien Ponsot
- Department of NanoBiophotonicsMax Planck Institute for Multidisciplinary Sciences (MPI-NAT)Am Fassberg 1137077GöttingenGermany
| | - Mariano L. Bossi
- Department of Optical NanoscopyMax Planck Institute for Medical Research (MPI-MR)Jahnstraße 2969120HeidelbergGermany
| | - Vladimir N. Belov
- Department of NanoBiophotonicsMax Planck Institute for Multidisciplinary Sciences (MPI-NAT)Am Fassberg 1137077GöttingenGermany
| | - Stefan W. Hell
- Department of Optical NanoscopyMax Planck Institute for Medical Research (MPI-MR)Jahnstraße 2969120HeidelbergGermany
- Department of NanoBiophotonicsMax Planck Institute for Multidisciplinary Sciences (MPI-NAT)Am Fassberg 1137077GöttingenGermany
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27
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Schlör A, Hirschberg S, Amor GB, Meister TL, Arora P, Pöhlmann S, Hoffmann M, Pfaender S, Eddin OK, Kamhieh-Milz J, Hanack K. SARS-CoV-2 neutralizing camelid heavy-chain-only antibodies as powerful tools for diagnostic and therapeutic applications. Front Immunol 2022; 13:930975. [PMID: 36189209 PMCID: PMC9517167 DOI: 10.3389/fimmu.2022.930975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
IntroductionThe ongoing COVID-19 pandemic situation caused by SARS-CoV-2 and variants of concern such as B.1.617.2 (Delta) and recently, B.1.1.529 (Omicron) is posing multiple challenges to humanity. The rapid evolution of the virus requires adaptation of diagnostic and therapeutic applications.ObjectivesIn this study, we describe camelid heavy-chain-only antibodies (hcAb) as useful tools for novel in vitro diagnostic assays and for therapeutic applications due to their neutralizing capacity.MethodsFive antibody candidates were selected out of a naïve camelid library by phage display and expressed as full length IgG2 antibodies. The antibodies were characterized by Western blot, enzyme-linked immunosorbent assays, surface plasmon resonance with regard to their specificity to the recombinant SARS-CoV-2 Spike protein and to SARS-CoV-2 virus-like particles. Neutralization assays were performed with authentic SARS-CoV-2 and pseudotyped viruses (wildtype and Omicron).ResultsAll antibodies efficiently detect recombinant SARS-CoV-2 Spike protein and SARS-CoV-2 virus-like particles in different ELISA setups. The best combination was shown with hcAb B10 as catcher antibody and HRP-conjugated hcAb A7.2 as the detection antibody. Further, four out of five antibodies potently neutralized authentic wildtype SARS-CoV-2 and particles pseudotyped with the SARS-CoV-2 Spike proteins of the wildtype and Omicron variant, sublineage BA.1 at concentrations between 0.1 and 0.35 ng/mL (ND50).ConclusionCollectively, we report novel camelid hcAbs suitable for diagnostics and potential therapy.
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Affiliation(s)
| | - Stefan Hirschberg
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Transfusion Medicine, Berlin, Germany
| | | | - Toni Luise Meister
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | - Prerna Arora
- Infection Biology Unit, German Primate Center– Leibniz Institute for Primate Research, Göttingen, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center– Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, University Göttingen, Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center– Leibniz Institute for Primate Research, Göttingen, Germany
| | - Stephanie Pfaender
- Department for Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
| | | | - Julian Kamhieh-Milz
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Transfusion Medicine, Berlin, Germany
- Wimedko GmbH, Berlin, Germany
| | - Katja Hanack
- New/era/mabs GmbH, Potsdam, Germany
- Department of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Katja Hanack,
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28
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Olson KM, Campbell A, Alt A, Traynor JR. Finding the Perfect Fit: Conformational Biosensors to Determine the Efficacy of GPCR Ligands. ACS Pharmacol Transl Sci 2022; 5:694-709. [PMID: 36110374 PMCID: PMC9469492 DOI: 10.1021/acsptsci.1c00256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
G protein-coupled receptors (GPCRs) are highly druggable targets that adopt numerous conformations. A ligand's ability to stabilize specific conformation(s) of its cognate receptor determines its efficacy or ability to produce a biological response. Identifying ligands that produce different receptor conformations and potentially discrete pharmacological effects (e.g., biased agonists, partial agonists, antagonists, allosteric modulators) is a major goal in drug discovery and necessary to develop drugs with better effectiveness and fewer side effects. Fortunately, direct measurements of ligand efficacy, via receptor conformational changes are possible with the recent development of conformational biosensors. In this review, we discuss classical efficacy models, including the two-state model, the ternary-complex model, and multistate models. We describe how nanobody-, transducer-, and receptor-based conformational biosensors detect and/or stabilize specific GPCR conformations to identify ligands with different levels of efficacy. In particular, conformational biosensors provide the potential to identify and/or characterize therapeutically desirable but often difficult to measure conformations of receptors faster and better than current methods. For drug discovery/development, several recent proof-of-principle studies have optimized conformational biosensors for high-throughput screening (HTS) platforms. However, their widespread use is limited by the fact that few sensors are reliably capable of detecting low-frequency conformations and technically demanding assay conditions. Nonetheless, conformational biosensors do help identify desirable ligands such as allosteric modulators, biased ligands, or partial agonists in a single assay, representing a distinct advantage over classical methods.
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Affiliation(s)
- Keith M. Olson
- Department
of Pharmacology and Edward F Domino Research Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Andra Campbell
- Department
of Pharmacology and Edward F Domino Research Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Andrew Alt
- Department
of Pharmacology and Edward F Domino Research Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - John R. Traynor
- Department
of Pharmacology and Edward F Domino Research Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United
States
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29
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Jamieson SA, Pudjihartono M, Horne CR, Viloria JS, Dunlop JL, McMillan HD, Day RC, Keeshan K, Murphy JM, Mace PD. Nanobodies identify an activated state of the TRIB2 pseudokinase. Structure 2022; 30:1518-1529.e5. [PMID: 36108635 DOI: 10.1016/j.str.2022.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/02/2022] [Accepted: 08/19/2022] [Indexed: 12/23/2022]
Abstract
Tribbles proteins (TRIB1-3) are pseudokinases that recruit substrates to the COP1 ubiquitin ligase. TRIB2 was the first Tribbles ortholog to be implicated as a myeloid leukemia oncogene, because it recruits the C/EBPα transcription factor for ubiquitination by COP1. Here we report identification of nanobodies that bind the TRIB2 pseudokinase domain with low nanomolar affinity. A crystal structure of the TRIB2-Nb4.103 complex identified the nanobody to bind the N-terminal lobe of TRIB2, enabling specific recognition of TRIB2 in an activated conformation that is similar to the C/EBPα-bound state of TRIB1. Characterization in solution revealed that Nb4.103 can stabilize a TRIB2 pseudokinase domain dimer in a face-to-face manner. Conversely, a distinct nanobody (Nb4.101) binds through a similar epitope but does not readily promote dimerization. In combination, this study identifies features of TRIB2 that could be exploited for the development of inhibitors and nanobody tools for future investigation of TRIB2 function.
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Affiliation(s)
- Sam A Jamieson
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Michael Pudjihartono
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Christopher R Horne
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Jessica L Dunlop
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Hamish D McMillan
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Robert C Day
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, Scotland
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.
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30
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Ishizuka Y, Mergiya TF, Baldinotti R, Xu J, Hallin EI, Markússon S, Kursula P, Bramham CR. Development and Validation of Arc Nanobodies: New Tools for Probing Arc Dynamics and Function. Neurochem Res 2022; 47:2656-2666. [PMID: 35307777 PMCID: PMC9463278 DOI: 10.1007/s11064-022-03573-5] [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: 01/21/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 11/06/2022]
Abstract
Activity-regulated cytoskeleton-associated (Arc) protein plays key roles in long-term synaptic plasticity, memory, and cognitive flexibility. However, an integral understanding of Arc mechanisms is lacking. Arc is proposed to function as an interaction hub in neuronal dendrites and the nucleus, yet Arc can also form retrovirus-like capsids with proposed roles in intercellular communication. Here, we sought to develop anti-Arc nanobodies (ArcNbs) as new tools for probing Arc dynamics and function. Six ArcNbs representing different clonal lines were selected from immunized alpaca. Immunoblotting with recombinant ArcNbs fused to a small ALFA-epitope tag demonstrated binding to recombinant Arc as well as endogenous Arc from rat cortical tissue. ALFA-tagged ArcNb also provided efficient immunoprecipitation of stimulus-induced Arc after carbachol-treatment of SH-SY5Y neuroblastoma cells and induction of long-term potentiation in the rat dentate gyrus in vivo. Epitope mapping showed that all Nbs recognize the Arc C-terminal region containing the retroviral Gag capsid homology domain, comprised of tandem N- and C-lobes. ArcNbs E5 and H11 selectively bound the N-lobe, which harbors a peptide ligand binding pocket specific to mammals. Four additional ArcNbs bound the region containing the C-lobe and C-terminal tail. For use as genetically encoded fluorescent intrabodies, we show that ArcNbs fused to mScarlet-I are uniformly expressed, without aggregation, in the cytoplasm and nucleus of HEK293FT cells. Finally, mScarlet-I-ArcNb H11 expressed as intrabody selectively bound the N-lobe and enabled co-immunoprecipitation of full-length intracellular Arc. ArcNbs are versatile tools for live-cell labeling and purification of Arc, and interrogation of Arc capsid domain specific functions.
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Affiliation(s)
- Yuta Ishizuka
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway.
- Department of Pathophysiology and Metabolism, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan.
| | - Tadiwos F Mergiya
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
- Mohn Center for Research on the Brain, University of Bergen, Bergen, Norway
| | - Rodolfo Baldinotti
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
- Mohn Center for Research on the Brain, University of Bergen, Bergen, Norway
| | - Ju Xu
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
| | - Erik I Hallin
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
| | - Sigurbjörn Markússon
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Clive R Bramham
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway.
- Mohn Center for Research on the Brain, University of Bergen, Bergen, Norway.
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31
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Cong ATQ, Witter TL, Schellenberg MJ. High-efficiency recombinant protein purification using mCherry and YFP nanobody affinity matrices. Protein Sci 2022; 31:e4383. [PMID: 36040252 PMCID: PMC9413470 DOI: 10.1002/pro.4383] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/28/2022] [Accepted: 04/05/2022] [Indexed: 11/11/2022]
Abstract
Mammalian cell lines are important expression systems for large proteins and protein complexes, particularly when the acquisition of post-translational modifications in the protein's native environment is desired. However, low or variable transfection efficiencies are challenges that must be overcome to use such an expression system. Expression of recombinant proteins as a fluorescent protein fusion enables real-time monitoring of protein expression, and also provides an affinity handle for one-step protein purification using a suitable affinity reagent. Here, we describe a panel of anti-GFP and anti-mCherry nanobody affinity matrices and their efficacy for purification of GFP/YFP or mCherry fusion proteins. We define the molecular basis by which they bind their target proteins using X-ray crystallography. From these analyses, we define an optimal pair of nanobodies for purification of recombinant protein tagged with GFP/YFP or mCherry, and demonstrate these nanobody-sepharose supports are stable to many rounds of cleaning and extended incubation in denaturing conditions. Finally, we demonstrate the utility of the mCherry-tag system by using it to purify recombinant human topoisomerase 2α expressed in HEK293F cells. The mCherry-tag and GFP/YFP-tag expression systems can be utilized for recombinant protein expression individually or in tandem for mammalian protein expression systems where real-time monitoring of protein expression levels and a high-efficiency purification step is needed.
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Affiliation(s)
- Anh T. Q. Cong
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesotaUSA
| | - Taylor L. Witter
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesotaUSA
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32
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Morales RTT, Ko J. Future of Digital Assays to Resolve Clinical Heterogeneity of Single Extracellular Vesicles. ACS NANO 2022; 16:11619-11645. [PMID: 35904433 PMCID: PMC10174080 DOI: 10.1021/acsnano.2c04337] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Extracellular vesicles (EVs) are complex lipid membrane vehicles with variable expressions of molecular cargo, composed of diverse subpopulations that participate in the intercellular signaling of biological responses in disease. EV-based liquid biopsies demonstrate invaluable clinical potential for overhauling current practices of disease management. Yet, EV heterogeneity is a major needle-in-a-haystack challenge to translate their use into clinical practice. In this review, existing digital assays will be discussed to analyze EVs at a single vesicle resolution, and future opportunities to optimize the throughput, multiplexing, and sensitivity of current digital EV assays will be highlighted. Furthermore, this review will outline the challenges and opportunities that impact the clinical translation of single EV technologies for disease diagnostics and treatment monitoring.
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Affiliation(s)
- Renee-Tyler T Morales
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jina Ko
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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33
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Nezammahalleh H, Ghanati F, Rezaei S, Badshah MA, Park J, Abbas N, Ali A. Biochemical Interactions through Microscopic Techniques: Structural and Molecular Characterization. Polymers (Basel) 2022; 14:2853. [PMID: 35890632 PMCID: PMC9318543 DOI: 10.3390/polym14142853] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/06/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022] Open
Abstract
Many researchers and scientists have contributed significantly to provide structural and molecular characterizations of biochemical interactions using microscopic techniques in the recent decade, as these biochemical interactions play a crucial role in the production of diverse biomaterials and the organization of biological systems. The properties, activities, and functionalities of the biomaterials and biological systems need to be identified and modified for different purposes in both the material and life sciences. The present study aimed to review the advantages and disadvantages of three main branches of microscopy techniques (optical microscopy, electron microscopy, and scanning probe microscopy) developed for the characterization of these interactions. First, we explain the basic concepts of microscopy and then the breadth of their applicability to different fields of research. This work could be useful for future research works on biochemical self-assembly, biochemical aggregation and localization, biological functionalities, cell viability, live-cell imaging, material stability, and membrane permeability, among others. This understanding is of high importance in rapid, inexpensive, and accurate analysis of biochemical interactions.
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Affiliation(s)
- Hassan Nezammahalleh
- Faculty of Biological Science, Tarbiat Modares University, Tehran 14115-111, Iran; (H.N.); (F.G.)
- Research and Development Department, Hamyarapply Group, Tehran 14115-111, Iran
| | - Faezeh Ghanati
- Faculty of Biological Science, Tarbiat Modares University, Tehran 14115-111, Iran; (H.N.); (F.G.)
| | - Shima Rezaei
- Department of Microbiology, Faculty of Biological Science, Ardebil Branch, Islamic Azad University, Ardebil 5615731567, Iran;
| | - Mohsin Ali Badshah
- Department of Chemical and Biomolecular Engineering, University of California-Irvine, Irvine, CA 92697, USA;
| | - Joobee Park
- Plamica Labs, Batten Hall, 125 Western Ave, Allston, MA 02163, USA;
| | - Naseem Abbas
- Department of Mechanical Engineering, Sejong University, Seoul 05006, Korea
| | - Ahsan Ali
- Department of Mechanical Engineering, Gachon University, Seongnam-si 13120, Korea
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34
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Preparation and identification of a single domain antibody specific for adenovirus vectors and its application to the immunoaffinity purification of adenoviruses. AMB Express 2022; 12:80. [PMID: 35723787 PMCID: PMC9207862 DOI: 10.1186/s13568-022-01422-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/11/2022] [Indexed: 11/10/2022] Open
Abstract
Adenovirus belongs to the family of Adenoviridae. As a vaccine carrier, it has high safety and stimulates the body to produce cellular immunity and humoral immunity. This study prepared an adenoviral vector-specific single-domain antibody for use in adenovirus identification and purification. We successfully constructed a single domain antibody phage display library with a capacity of 1.8 × 109 by immunizing and cloning the VHH gene from Bactrian camel. After the second round of biopanning, clones specific for adenovirus were screened using phage ELISA. Twenty-two positive clones were obtained, and two clones with the highest binding affinity from ELISA were selected and named sdAb 5 and sdAb 31 for further application. The recombinant single-domain antibody was solublely expressed in E. coli and specifically bound to adenoviruses rAd26, ChAd63 and HAd5 in ELISA and live cell immunofluorescence assays. We established an effective method for immunoaffinity purification of adenovirus by immobilizing the single domain antibody to Sepharose beads, and it may be used to selectively capture adenoviruses from cell culture medium. The preparation of the adenovirus-specific single-domain antibody lays a foundation for the one-step immunoaffinity purification and identification of adenoviruses.
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35
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Macias LA, Wang X, Davies BW, Brodbelt JS. Mapping paratopes of nanobodies using native mass spectrometry and ultraviolet photodissociation. Chem Sci 2022; 13:6610-6618. [PMID: 35756525 PMCID: PMC9172568 DOI: 10.1039/d2sc01536f] [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: 03/16/2022] [Accepted: 05/16/2022] [Indexed: 11/21/2022] Open
Abstract
Following immense growth and maturity of the field in the past decade, native mass spectrometry has garnered widespread adoption for the structural characterization of macromolecular complexes. Routine analysis of biotherapeutics by this technique has become commonplace to assist in the development and quality control of immunoglobulin antibodies. Concurrently, 193 nm ultraviolet photodissociation (UVPD) has been developed as a structurally sensitive ion activation technique capable of interrogating protein conformational changes. Here, UVPD was applied to probe the paratopes of nanobodies, a class of single-domain antibodies with an expansive set of applications spanning affinity reagents, molecular imaging, and biotherapeutics. Comparing UVPD sequence fragments for the free nanobodies versus nanobody·antigen complexes empowered assignment of nanobody paratopes and intermolecular salt-bridges, elevating the capabilities of UVPD as a new strategy for characterization of nanobodies. Ultraviolet photodissociation mass spectrometry is used to probe the paratopes of nanobodies, a class of single-domain antibodies, and to determine intersubunit salt-bridges and explore the nanobody·antigen interfaces.![]()
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Affiliation(s)
- Luis A Macias
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Xun Wang
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
| | - Bryan W Davies
- Department of Molecular Biosciences, University of Texas at Austin Austin TX 78712 USA
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36
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Moliner-Morro A, McInerney GM, Hanke L. Nanobodies in the limelight: Multifunctional tools in the fight against viruses. J Gen Virol 2022; 103. [PMID: 35579613 DOI: 10.1099/jgv.0.001731] [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: 11/18/2022] Open
Abstract
Antibodies are natural antivirals generated by the vertebrate immune system in response to viral infection or vaccination. Unsurprisingly, they are also key molecules in the virologist's molecular toolbox. With new developments in methods for protein engineering, protein functionalization and application, smaller antibody-derived fragments are moving in focus. Among these, camelid-derived nanobodies play a prominent role. Nanobodies can replace full-sized antibodies in most applications and enable new possible applications for which conventional antibodies are challenging to use. Here we review the versatile nature of nanobodies, discuss their promise as antiviral therapeutics, for diagnostics, and their suitability as research tools to uncover novel aspects of viral infection and disease.
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Affiliation(s)
- Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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37
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Camelid Single-Domain Antibodies: Promises and Challenges as Lifesaving Treatments. Int J Mol Sci 2022; 23:ijms23095009. [PMID: 35563400 PMCID: PMC9100996 DOI: 10.3390/ijms23095009] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 02/07/2023] Open
Abstract
Since the discovery of camelid heavy-chain antibodies in 1993, there has been tremendous excitement for these antibody domains (VHHs/sdAbs/nanobodies) as research tools, diagnostics, and therapeutics. Commercially, several patents were granted to pioneering research groups in Belgium and the Netherlands between 1996–2001. Ablynx was established in 2001 with the aim of exploring the therapeutic applications and development of nanobody drugs. Extensive efforts over two decades at Ablynx led to the first approved nanobody drug, caplacizumab (Cablivi) by the EMA and FDA (2018–2019) for the treatment of rare blood clotting disorders in adults with acquired thrombotic thrombocytopenic purpura (TPP). The relatively long development time between camelid sdAb discovery and their entry into the market reflects the novelty of the approach, together with intellectual property restrictions and freedom-to-operate issues. The approval of the first sdAb drug, together with the expiration of key patents, may open a new horizon for the emergence of camelid sdAbs as mainstream biotherapeutics in the years to come. It remains to be seen if nanobody-based drugs will be cheaper than traditional antibodies. In this review, I provide critical perspectives on camelid sdAbs and present the promises and challenges to their widespread adoption as diagnostic and therapeutic agents.
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38
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Marino M, Holt MG. AAV Vector-Mediated Antibody Delivery (A-MAD) in the Central Nervous System. Front Neurol 2022; 13:870799. [PMID: 35493843 PMCID: PMC9039256 DOI: 10.3389/fneur.2022.870799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
In the last four decades, monoclonal antibodies and their derivatives have emerged as a powerful class of therapeutics, largely due to their exquisite targeting specificity. Several clinical areas, most notably oncology and autoimmune disorders, have seen the successful introduction of monoclonal-based therapeutics. However, their adoption for treatment of Central Nervous System diseases has been comparatively slow, largely due to issues of efficient delivery resulting from limited permeability of the Blood Brain Barrier. Nevertheless, CNS diseases are becoming increasingly prevalent as societies age, accounting for ~6.5 million fatalities worldwide per year. Therefore, harnessing the full therapeutic potential of monoclonal antibodies (and their derivatives) in this clinical area has become a priority. Adeno-associated virus-based vectors (AAVs) are a potential solution to this problem. Preclinical studies have shown that AAV vector-mediated antibody delivery provides protection against a broad range of peripheral diseases, such as the human immunodeficiency virus (HIV), influenza and malaria. The parallel identification and optimization of AAV vector platforms which cross the Blood Brain Barrier with high efficiency, widely transducing the Central Nervous System and allowing high levels of local transgene production, has now opened a number of interesting scenarios for the development of AAV vector-mediated antibody delivery strategies to target Central Nervous System proteinopathies.
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Affiliation(s)
- Marika Marino
- Laboratory of Glia Biology, VIB-KU Leuven, Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Matthew G. Holt
- Laboratory of Glia Biology, VIB-KU Leuven, Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, Leuven, Belgium
- Synapse Biology Group, Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- *Correspondence: Matthew G. Holt
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39
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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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40
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Puthenveetil R, Christenson ET, Vinogradova O. New Horizons in Structural Biology of Membrane Proteins: Experimental Evaluation of the Role of Conformational Dynamics and Intrinsic Flexibility. MEMBRANES 2022; 12:227. [PMID: 35207148 PMCID: PMC8877495 DOI: 10.3390/membranes12020227] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
A plethora of membrane proteins are found along the cell surface and on the convoluted labyrinth of membranes surrounding organelles. Since the advent of various structural biology techniques, a sub-population of these proteins has become accessible to investigation at near-atomic resolutions. The predominant bona fide methods for structure solution, X-ray crystallography and cryo-EM, provide high resolution in three-dimensional space at the cost of neglecting protein motions through time. Though structures provide various rigid snapshots, only an amorphous mechanistic understanding can be inferred from interpolations between these different static states. In this review, we discuss various techniques that have been utilized in observing dynamic conformational intermediaries that remain elusive from rigid structures. More specifically we discuss the application of structural techniques such as NMR, cryo-EM and X-ray crystallography in studying protein dynamics along with complementation by conformational trapping by specific binders such as antibodies. We finally showcase the strength of various biophysical techniques including FRET, EPR and computational approaches using a multitude of succinct examples from GPCRs, transporters and ion channels.
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Affiliation(s)
- Robbins Puthenveetil
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Dr., Bethesda, MD 20892, USA
| | | | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
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41
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Müntener T, Joss D, Häussinger D, Hiller S. Pseudocontact Shifts in Biomolecular NMR Spectroscopy. Chem Rev 2022; 122:9422-9467. [PMID: 35005884 DOI: 10.1021/acs.chemrev.1c00796] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.
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Affiliation(s)
- Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Daniel Joss
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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42
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Lepeta K, Bauer M, Aguilar G, Vigano MA, Matsuda S, Affolter M. Studying Protein Function Using Nanobodies and Other Protein Binders in Drosophila. Methods Mol Biol 2022; 2540:219-237. [PMID: 35980580 DOI: 10.1007/978-1-0716-2541-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The direct manipulation of proteins by nanobodies and other protein binders has become an additional and valuable approach to investigate development and homeostasis in Drosophila. In contrast to other techniques, that indirectly interfere with proteins via their nucleic acids (CRISPR, RNAi, etc.), protein binders permit direct and acute protein manipulation. Since the first use of a nanobody in Drosophila a decade ago, many different applications exploiting protein binders have been introduced. Most of these applications use nanobodies against GFP to regulate GFP fusion proteins. In order to exert specific protein manipulations, protein binders are linked to domains that confer them precise biochemical functions. Here, we reflect on the use of tools based on protein binders in Drosophila. We describe their key features and provide an overview of the available reagents. Finally, we briefly explore the future avenues that protein binders might open up and thus further contribute to better understand development and homeostasis of multicellular organisms.
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Affiliation(s)
| | - Milena Bauer
- Biozentrum der Universität Basel, Basel, Switzerland
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43
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Kuhlemann A, Beliu G, Janzen D, Petrini EM, Taban D, Helmerich DA, Doose S, Bruno M, Barberis A, Villmann C, Sauer M, Werner C. Genetic Code Expansion and Click-Chemistry Labeling to Visualize GABA-A Receptors by Super-Resolution Microscopy. Front Synaptic Neurosci 2021; 13:727406. [PMID: 34899260 PMCID: PMC8664562 DOI: 10.3389/fnsyn.2021.727406] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/02/2021] [Indexed: 01/15/2023] Open
Abstract
Fluorescence labeling of difficult to access protein sites, e.g., in confined compartments, requires small fluorescent labels that can be covalently tethered at well-defined positions with high efficiency. Here, we report site-specific labeling of the extracellular domain of γ-aminobutyric acid type A (GABA-A) receptor subunits by genetic code expansion (GCE) with unnatural amino acids (ncAA) combined with bioorthogonal click-chemistry labeling with tetrazine dyes in HEK-293-T cells and primary cultured neurons. After optimization of GABA-A receptor expression and labeling efficiency, most effective variants were selected for super-resolution microscopy and functionality testing by whole-cell patch clamp. Our results show that GCE with ncAA and bioorthogonal click labeling with small tetrazine dyes represents a versatile method for highly efficient site-specific fluorescence labeling of proteins in a crowded environment, e.g., extracellular protein domains in confined compartments such as the synaptic cleft.
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Affiliation(s)
- Alexander Kuhlemann
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany.,Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Würzburg, Germany
| | - Dieter Janzen
- Institute of Clinical Neurobiology, University of Würzburg, Würzburg, Germany
| | - Enrica Maria Petrini
- Neuroscience and Brain Technologies Department, Istituto Italiano Di Tecnologia, Genova, Italy
| | - Danush Taban
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Dominic A Helmerich
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Martina Bruno
- Neuroscience and Brain Technologies Department, Istituto Italiano Di Tecnologia, Genova, Italy
| | - Andrea Barberis
- Neuroscience and Brain Technologies Department, Istituto Italiano Di Tecnologia, Genova, Italy
| | - Carmen Villmann
- Institute of Clinical Neurobiology, University of Würzburg, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Christian Werner
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
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44
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Li X, Liu W, Li H, Wang X, Zhao Y. Capture and purification of an untagged nanobody by mixed weak cation chromatography and cation exchange chromatography. Protein Expr Purif 2021; 192:106030. [PMID: 34920133 DOI: 10.1016/j.pep.2021.106030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/19/2022]
Abstract
Nanobodies (Nbs) are single-domain antibodies, which have potential application value in tumor-targeted therapy, immunotherapy, diagnostic probe, and molecular imaging. Typically, Nbs are captured by affinity chromatography via the addition of specific fusion tags at their N or C terminus. Nerve growth factor (NGF), which regulates the growth and development of peripheral and central neurons, maintains neuronal survival and plays a key role in both arthritis and acute and chronic pain. In this study, a method for capture and purification of an untagged Nb (anti-NGF Nb) by mixed weak cation chromatography and cation exchange chromatography was established. First, pH 4.0-5.0 was demonstrated to be the optimal loading condition for Capto MMC to capture anti-NGF by the design of experiments (DOE). Furthermore, high purity and yield products can be obtained at laboratory scale and commercial production scale by adjusting the protein pH. Additionally, direct capture of anti-NGF Nb using Capto MMC without adjusting anti-NGF Nb harvest pH was investigated. The anti-NGF Nb captured by Capto MMC was 67.2% yield, 94.5% monomer purity, and host cell protein (HCP) was reduced from 74,931 ppm to 484 ppm. The anti-NGF Nb that were further purified using Capto S ImpAct achieved 84.5% yield and 99.2% purity and 77 ppm of HCP. The scaling-up process was consistent with the results of the optimized process, further demonstrating the feasibility of this method. This outcome provides a highly promising and competitive alternative to affinity chromatography-based processing strategies for Nbs.
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Affiliation(s)
- Xin Li
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, School of Pharmacy, Yantai University, Yantai, 264005, PR China
| | - Wanhui Liu
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, School of Pharmacy, Yantai University, Yantai, 264005, PR China
| | - Heshui Li
- Shandong Boan Biotechnology Company Limited, PR China
| | - Xin Wang
- Shandong Boan Biotechnology Company Limited, PR China
| | - Yanyan Zhao
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, School of Pharmacy, Yantai University, Yantai, 264005, PR China.
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45
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Asaadi Y, Jouneghani FF, Janani S, Rahbarizadeh F. A comprehensive comparison between camelid nanobodies and single chain variable fragments. Biomark Res 2021; 9:87. [PMID: 34863296 PMCID: PMC8642758 DOI: 10.1186/s40364-021-00332-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022] Open
Abstract
By the emergence of recombinant DNA technology, many antibody fragments have been developed devoid of undesired properties of natural immunoglobulins. Among them, camelid heavy-chain variable domains (VHHs) and single-chain variable fragments (scFvs) are the most favored ones. While scFv is used widely in various applications, camelid antibodies (VHHs) can serve as an alternative because of their superior chemical and physical properties such as higher solubility, stability, smaller size, and lower production cost. Here, these two counterparts are compared in structure and properties to identify which one is more suitable for each of their various therapeutic, diagnosis, and research applications.
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Affiliation(s)
- Yasaman Asaadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Fatemeh Fazlollahi Jouneghani
- Department of Cell & Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Sara Janani
- Department of Cell & Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.
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46
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Soleimanizadeh A, Dinter H, Schindowski K. Central Nervous System Delivery of Antibodies and Their Single-Domain Antibodies and Variable Fragment Derivatives with Focus on Intranasal Nose to Brain Administration. Antibodies (Basel) 2021; 10:antib10040047. [PMID: 34939999 PMCID: PMC8699001 DOI: 10.3390/antib10040047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/10/2021] [Accepted: 11/25/2021] [Indexed: 02/06/2023] Open
Abstract
IgG antibodies are some of the most important biopharmaceutical molecules with a high market volume. In spite of the fact that clinical therapies with antibodies are broadly utilized in oncology, immunology and hematology, their delivery strategies and biodistribution need improvement, their limitations being due to their size and poor ability to penetrate into tissues. In view of their small size, there is a rising interest in derivatives, such as single-domain antibodies and single-chain variable fragments, for clinical diagnostic but also therapeutic applications. Smaller antibody formats combine several benefits for clinical applications and can be manufactured at reduced production costs compared with full-length IgGs. Moreover, such formats have a relevant potential for targeted drug delivery that directs drug cargo to a specific tissue or across the blood–brain barrier. In this review, we give an overview of the challenges for antibody drug delivery in general and focus on intranasal delivery to the central nervous system with antibody formats of different sizes.
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Affiliation(s)
- Arghavan Soleimanizadeh
- Institute of Applied Biotechnology, Biberach University of Applied Science, 88400 Biberach, Germany; (A.S.); (H.D.)
- Faculty of Medicine, University of Ulm, 89081 Ulm, Germany
| | - Heiko Dinter
- Institute of Applied Biotechnology, Biberach University of Applied Science, 88400 Biberach, Germany; (A.S.); (H.D.)
- Department of Pharmacy and Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Katharina Schindowski
- Institute of Applied Biotechnology, Biberach University of Applied Science, 88400 Biberach, Germany; (A.S.); (H.D.)
- Correspondence:
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Zhang JF, Mehta S, Zhang J. Signaling Microdomains in the Spotlight: Visualizing Compartmentalized Signaling Using Genetically Encoded Fluorescent Biosensors. Annu Rev Pharmacol Toxicol 2021; 61:587-608. [PMID: 33411579 DOI: 10.1146/annurev-pharmtox-010617-053137] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
How cells muster a network of interlinking signaling pathways to faithfully convert diverse external cues to specific functional outcomes remains a central question in biology. Through their ability to convert dynamic biochemical activities to rapid and precise optical readouts, genetically encoded fluorescent biosensors have become instrumental in unraveling the molecular logic controlling the specificity of intracellular signaling. In this review, we discuss how the use of genetically encoded fluorescent biosensors to visualize dynamic signaling events within their native cellular context is elucidating the different strategies employed by cells to organize signaling activities into discrete compartments, or signaling microdomains, to ensure functional specificity.
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Affiliation(s)
- Jin-Fan Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA; .,Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA;
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, USA; .,Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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48
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Zakri AM, Al-Doss AA, Ali AA, Samara EM, Ahmed BS, Al-Saleh MA, Idris AM, Abdalla OA, Sack M. Generation and Characterization of Nanobodies Against Tomato Leaf Curl Sudan Virus. PLANT DISEASE 2021; 105:2410-2417. [PMID: 33599515 DOI: 10.1094/pdis-11-20-2407-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Begomoviruses infect food, fiber, and vegetable crop plants, including tomato, potato, bean, cotton, cucumber, and pumpkin, and damage many economically important crop plants worldwide. Tomato leaf curl Sudan virus (ToLCSDV) is the most widespread tomato-infecting begomovirus in Saudi Arabia. Using phage display technology, this study isolated two camel-derived nanobodies against purified ToLCSDV virions from a library of antigen-binding fragments (VHH or nanobody) of heavy-chain antibodies built from an immunized camel. The isolated nanobodies also cross-reacted with purified tomato yellow leaf curl virus virions and showed significant enzyme-linked immunosorbent assay reactivity with extracts from plants with typical begomovirus infection symptoms. The results can pave the way to developing diagnostics for begomovirus detection, design, and characterization of novel nanomaterials based on virus-like particles, in addition to nanobody-mediated begomovirus resistance in economically important crops, such as tomato, potato, and cucumber.
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Affiliation(s)
- Adel M Zakri
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah A Al-Doss
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed A Ali
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Emad M Samara
- Department of Animal Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Basem S Ahmed
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed A Al-Saleh
- Department of Plant Protection, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Ali M Idris
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, U.S.A
| | - Omar A Abdalla
- Department of Plant Protection, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
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Iwata T, Hirose H, Sakamoto K, Hirai Y, Arafiles JVV, Akishiba M, Imanishi M, Futaki S. Liquid Droplet Formation and Facile Cytosolic Translocation of IgG in the Presence of Attenuated Cationic Amphiphilic Lytic Peptides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105527] [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)
- Takahiro Iwata
- Institute for Chemical Research Kyoto University, Uji Kyoto 611-0011 Japan
| | - Hisaaki Hirose
- Institute for Chemical Research Kyoto University, Uji Kyoto 611-0011 Japan
| | - Kentarou Sakamoto
- Institute for Chemical Research Kyoto University, Uji Kyoto 611-0011 Japan
| | - Yusuke Hirai
- Institute for Chemical Research Kyoto University, Uji Kyoto 611-0011 Japan
| | | | - Misao Akishiba
- Institute for Chemical Research Kyoto University, Uji Kyoto 611-0011 Japan
| | - Miki Imanishi
- Institute for Chemical Research Kyoto University, Uji Kyoto 611-0011 Japan
| | - Shiroh Futaki
- Institute for Chemical Research Kyoto University, Uji Kyoto 611-0011 Japan
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50
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Eliseev IE, Ukrainskaya VM, Yudenko AN, Mikushina AD, Shmakov SV, Afremova AI, Ekimova VM, Vronskaia AA, Knyazev NA, Shamova OV. Targeting ErbB3 Receptor in Cancer with Inhibitory Antibodies from Llama. Biomedicines 2021; 9:biomedicines9091106. [PMID: 34572289 PMCID: PMC8467012 DOI: 10.3390/biomedicines9091106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 01/05/2023] Open
Abstract
The human ErbB3 receptor confers resistance to the pharmacological inhibition of EGFR and HER2 receptor tyrosine kinases in cancer, which makes it an important therapeutic target. Several anti-ErbB3 monoclonal antibodies that are currently being developed are all classical immunoglobulins. We took a different approach and discovered a group of novel heavy-chain antibodies targeting the extracellular domain of ErbB3 via a phage display of an antibody library from immunized llamas. We first produced three selected single-domain antibodies, named BCD090-P1, BCD090-M2, and BCD090-M456, in E. coli, as SUMO fusions that yielded up to 180 mg of recombinant protein per liter of culture. Then, we studied folding, aggregation, and disulfide bond formation, and showed their ultimate stability with half-denaturation of the strongest candidate, BCD090-P1, occurring in 8 M of urea. In surface plasmon resonance experiments, two most potent antibodies, BCD090-P1 and BCD090-M2, bound the extracellular domain of ErbB3 with 1.6 nM and 15 nM affinities for the monovalent interaction, respectively. The receptor binding was demonstrated by immunofluorescent confocal microscopy on four different ErbB3+ cancer cell lines. We observed that BCD090-P1 and BCD090-M2 bind noncompetitively to two distinct epitopes on the receptor. Both antibodies inhibited the ErbB3-driven proliferation of MCF-7 breast adenocarcinoma cells and HER2-overexpressing SK-BR-3 cells, with the EC50 in the range of 0.1–25 μg/mL. BCD090-M2 directly blocks ligand binding, whereas BCD090-P1 does not compete with the ligand and presumably acts through a distinct allosteric mechanism. We anticipate that these llama antibodies can be used to engineer new biparatopic anti-ErbB3 or bispecific anti-ErbB2/3 antibodies.
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Affiliation(s)
- Igor E. Eliseev
- Laboratory of Renewable Energy Sources, Alferov University, St. Petersburg 194021, Russia; (A.D.M.); (S.V.S.); (A.A.V.)
- Center for Personalized Medicine, FSBSI Institute of Experimental Medicine, St. Petersburg 197376, Russia;
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
- Correspondence:
| | - Valeria M. Ukrainskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
| | - Anna N. Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia;
| | - Anna D. Mikushina
- Laboratory of Renewable Energy Sources, Alferov University, St. Petersburg 194021, Russia; (A.D.M.); (S.V.S.); (A.A.V.)
| | - Stanislav V. Shmakov
- Laboratory of Renewable Energy Sources, Alferov University, St. Petersburg 194021, Russia; (A.D.M.); (S.V.S.); (A.A.V.)
| | | | | | - Anna A. Vronskaia
- Laboratory of Renewable Energy Sources, Alferov University, St. Petersburg 194021, Russia; (A.D.M.); (S.V.S.); (A.A.V.)
| | - Nickolay A. Knyazev
- Saint-Petersburg Clinical Scientific and Practical Center for Specialized Types of Medical Care (Oncological), St. Petersburg 197758, Russia;
| | - Olga V. Shamova
- Center for Personalized Medicine, FSBSI Institute of Experimental Medicine, St. Petersburg 197376, Russia;
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