Abstract
Fv and Fab antibody fragments are versatile co-crystallization partners that aid in the structural determination of otherwise “uncrystallizable” proteins, including human/mammalian membrane proteins. Accessible methods for the rapid and reliable production of recombinant antibody fragments have been long sought. In this chapter, we describe the concept and protocols of the intervening removable affinity tag (iRAT) system for the efficient production of Fv and Fab fragments in milligram quantities, which are sufficient for structural studies. As an extension of the iRAT system, we also provide a new method for the creation of genetically encoded fluorescent Fab fragments, which are potentially useful as molecular devices in various basic biomedical and clinical procedures, such as immunofluorescence cytometry, bioimaging, and immunodiagnosis.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Griffin L, Lawson A (2011) Antibody fragments as tools in crystallography. Clin Exp Immunol 165:285–291
Lieberman RL, Culver JA, Entzminger KC et al (2011) Crystallization chaperone strategies for membrane proteins. Methods 55:293–302
Hino T, Arakawa T, Iwanari H et al (2012) G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody. Nature 482:237–240
Nomura N, Verdon G, Kang HJ et al (2015) Structure and mechanism of the mammalian fructose transporter GLUT5. Nature 526:397–401
Asada H, Horita S, Hirata K et al (2018) Crystal structure of the human angiotensin II type 2 receptor bound to an angiotensin II analog. Nat Struct Mol Biol 25:570–576
Nagarathinam K, Nakada-Nakura Y, Parthier C et al (2018) Outward open conformation of a Major Facilitator Superfamily multidrug/H+ antiporter provides insights into switching mechanism. Nat Commun 9:4005
Toyoda Y, Morimoto K, Suno R et al (2019) Ligand binding to human prostaglandin E receptor EP4 at the lipid-bilayer interface. Nat Chem Biol 15:18–26
Wu S, Avila-Sakar A, Kim J et al (2012) Fabs enable single particle cryoEM studies of small proteins. Structure 20:582–592
Koehl A, Hu H, Maeda S et al (2018) Structure of the μ-opioid receptor-Gi protein complex. Nature 558:547–552
Nomura Y, Sato Y, Suno R et al (2016) The intervening removable affinity tag (iRAT) production system facilitates Fv antibody fragment-mediated crystallography. Protein Sci 25:2268–2276
Horita S, Nomura Y, Sato Y et al (2016) High-resolution crystal structure of the therapeutic antibody pembrolizumab bound to the human PD-1. Sci Rep 6:35297
Ono M, Horita S, Sato Y et al (2018) Structural basis for tumor necrosis factor blockade with the therapeutic antibody golimumab. Protein Sci 27:1038–1046
Koerber JT, Hornsby MJ, Wells JA (2015) An improved single-chain Fab platform for efficient display and recombinant expression. J Mol Biol 427:576–586
Fields C, O’Connell D, Xiao S et al (2013) Creation of recombinant antigen-binding molecules derived from hybridomas secreting specific antibodies. Nat Protoc 8:1125–1148
Lucast LJ, Batey RT, Doudna JA (2001) Large-scale purification of a stable form of recombinant tobacco etch virus protease. Biotechniques 30:544–546, 548, 550 passim
Abdulrahman W, Radu L, Garzoni F et al (2015) The production of multiprotein complexes in insect cells using the baculovirus expression system. Methods Mol Biol 1261:91–114
Markiv A, Beatson R, Burchell J et al (2011) Expression of recombinant multi-coloured fluorescent antibodies in gor-/trxB- E. coli cytoplasm. BMC Biotechnol 11:117
Gross LA, Baird GS, Hoffman RC et al (2000) The structure of the chromophore within DsRed, a red fluorescent protein from coral. Proc Natl Acad Sci U S A 97:11990–11995
Acknowledgments
We thank Shoichiro Horita, Hidetsugu Asada, and Tomoko Uemura for sharing their experiences on Sf9-baculovirus expression. The creation of the iRAT-based fluorescent Fab was conceived after being inspired by the pioneering work on multicolored fluorescent scFv by Markiv et al. [17]. This work was funded by the Strategic Basic Research Program from the Japan Science and Technology Agency (JST), the Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS) from the Japan Agency of Medical Research and Development (AMED), the Research on Development of New Drugs from the AMED, and the Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (JSPS) (Nos. 15K06968 and 18K05334).
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Nomura, N., Nomura, Y., Sato, Y., Iwata, S. (2021). The Intervening Removable Affinity Tag (iRAT) System for the Production of Recombinant Antibody Fragments. In: Poterszman, A. (eds) Multiprotein Complexes. Methods in Molecular Biology, vol 2247. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1126-5_5
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1126-5_5
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1125-8
Online ISBN: 978-1-0716-1126-5
eBook Packages: Springer Protocols