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Selection of Affibody Affinity Proteins from Phagemid Libraries

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Phage Display

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2702))

Abstract

Herein, we describe a general protocol for the selection of target-binding affinity protein molecules from a phagemid-encoded library. The protocol is based on our experience with phage display selections of non-immunoglobulin affibody affinity proteins but can in principle be applied to perform biopanning experiments from any phage-displayed affinity protein library available in a similar phagemid vector. The procedure begins with an amplification of the library from frozen bacterial glycerol stocks via cultivation and helper phage superinfection, followed by a step-by-step instruction of target protein preparation, selection cycles, and post-selection analyses. The described procedures in this standard protocol are relatively conservative and rely on ordinary reagents and equipment available in most molecular biology laboratories.

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References

  1. Nilsson B, Moks T, Jansson B, Abrahmsen L, Elmblad A, Holmgren E, Henrichson C, Jones TA, Uhlen M (1987) A synthetic IgG-binding domain based on staphylococcal protein A. Protein Eng 1(2):107–113

    Article  CAS  PubMed  Google Scholar 

  2. Nord K, Gunneriusson E, Ringdahl J, Stahl S, Uhlen M, Nygren PA (1997) Binding proteins selected from combinatorial libraries of an alpha-helical bacterial receptor domain. Nat Biotechnol 15(8):772–777

    Article  CAS  PubMed  Google Scholar 

  3. Gebauer M, Skerra A (2020) Engineered protein scaffolds as next-generation therapeutics. Annu Rev Pharmacol Toxicol 60:391–415

    Article  CAS  PubMed  Google Scholar 

  4. Stahl S, Graslund T, Eriksson Karlstrom A, Frejd FY, Nygren PA, Lofblom J (2017) Affibody molecules in biotechnological and medical applications. Trends Biotechnol 35(8):691–712

    Article  PubMed  Google Scholar 

  5. Vazquez-Lombardi R, Phan TG, Zimmermann C, Lowe D, Jermutus L, Christ D (2015) Challenges and opportunities for non-antibody scaffold drugs. Drug Discov Today 20(10):1271–1283

    Article  CAS  PubMed  Google Scholar 

  6. Tolmachev V, Orlova A (2020) Affibody molecules as targeting vectors for PET imaging. Cancers (Basel) 12(3):651

    Article  CAS  PubMed  Google Scholar 

  7. Hober S, Lindbo S, Nilvebrant J (2019) Bispecific applications of non-immunoglobulin scaffold binders. Methods 154:143–152

    Article  CAS  PubMed  Google Scholar 

  8. Ding H, Altai M, Yin W, Lindbo S, Liu H, Garousi J, Xu T, Orlova A, Tolmachev V, Hober S, Graslund T (2020) HER2-specific pseudomonas exotoxin a PE25 based fusions: influence of targeting domain on target binding, toxicity, and in vivo biodistribution. Pharmaceutics 12(4):391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Malm M, Bass T, Gudmundsdotter L, Lord M, Frejd FY, Stahl S, Lofblom J (2014) Engineering of a bispecific affibody molecule towards HER2 and HER3 by addition of an albumin-binding domain allows for affinity purification and in vivo half-life extension. Biotechnol J 9(9):1215–1222

    Article  CAS  PubMed  Google Scholar 

  10. Yu F, Gudmundsdotter L, Akal A, Gunneriusson E, Frejd F, Nygren PA (2014) An affibody-adalimumab hybrid blocks combined IL-6 and TNF-triggered serum amyloid A secretion in vivo. MAbs 6(6):1598–1607

    Article  PubMed  PubMed Central  Google Scholar 

  11. Johan N, Sophia H (2013) The albumin-binding domain as a scaffold for protein engineering. Comput Struct Biotechnol J 6:e201303009

    Google Scholar 

  12. Sochaj-Gregorczyk AM, Serwotka-Suszczak AM, Otlewski J (2016) A novel Affibody-Auristatin E conjugate with a potent and selective activity against HER2+ cell lines. J Immunother 39(6):223–232

    Article  CAS  PubMed  Google Scholar 

  13. Engfeldt T, Renberg B, Brumer H, Nygren PA, Karlstrom AE (2005) Chemical synthesis of triple-labelled three-helix bundle binding proteins for specific fluorescent detection of unlabelled protein. Chembiochem 6(6):1043–1050

    Article  CAS  PubMed  Google Scholar 

  14. Lindgren J, Ekblad C, Abrahmsen L, Eriksson Karlstrom A (2012) A native chemical ligation approach for combinatorial assembly of affibody molecules. Chembiochem 13(7):1024–1031. https://pubmed.ncbi.nlm.nih.gov/24688717/

  15. Galindo Casas M, Stargardt P, Mairhofer J, Wiltschi B (2020) Decoupling protein production from cell growth enhances the site-specific incorporation of noncanonical amino acids in E. coli. ACS Synth Biol 9(11):3052–3066

    Article  CAS  PubMed  Google Scholar 

  16. Kanje S, Hober S (2015) In vivo biotinylation and incorporation of a photo-inducible unnatural amino acid to an antibody-binding domain improve site-specific labeling of antibodies. Biotechnol J 10(4):564–574

    Article  CAS  PubMed  Google Scholar 

  17. Rouet R, Jackson KJL, Langley DB, Christ D (2018) Next-generation sequencing of antibody display repertoires. Front Immunol 9:118

    Article  PubMed  PubMed Central  Google Scholar 

  18. Zambrano N, Froechlich G, Lazarevic D, Passariello M, Nicosia A, De Lorenzo C, Morelli MJ, Sasso E (2022) High-throughput monoclonal antibody discovery from phage libraries: challenging the current preclinical pipeline to keep the pace with the increasing mAb demand. Cancers (Basel) 14(5):1325

    Article  CAS  PubMed  Google Scholar 

  19. Ferrara F, Teixeira AA, Naranjo L, Erasmus MF, D’Angelo S, Bradbury ARM (2020) Exploiting next-generation sequencing in antibody selections – a simple PCR method to recover binders. MAbs 12(1):1701792

    Article  PubMed  PubMed Central  Google Scholar 

  20. Nannini F, Senicar L, Parekh F, Kong KJ, Kinna A, Bughda R, Sillibourne J, Hu X, Ma B, Bai Y, Ferrari M, Pule MA, Onuoha SC (2021) Combining phage display with SMRTbell next-generation sequencing for the rapid discovery of functional scFv fragments. MAbs 13(1):1864084

    Article  PubMed  Google Scholar 

  21. Noh J, Kim O, Jung Y, Han H, Kim JE, Kim S, Lee S, Park J, Jung RH, Kim SI, Park J, Han J, Lee H, Yoo DK, Lee AC, Kwon E, Ryu T, Chung J, Kwon S (2019) High-throughput retrieval of physical DNA for NGS-identifiable clones in phage display library. MAbs 11(3):532–545

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Spiliotopoulos A, Owen JP, Maddison BC, Dreveny I, Rees HC, Gough KC (2015) Sensitive recovery of recombinant antibody clones after their in silico identification within NGS datasets. J Immunol Methods 420:50–55

    Article  CAS  PubMed  Google Scholar 

  23. Astrand M, Nilvebrant J, Bjornmalm M, Lindbo S, Hober S, Lofblom J (2016) Investigating affinity-maturation strategies and reproducibility of fluorescence-activated cell sorting using a recombinant ADAPT library displayed on staphylococci. Protein Eng Des Sel 29(5):187–195

    Article  PubMed  Google Scholar 

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Acknowledgments

We would like to acknowledge former and present members of the KTH lab who have helped improving this protocol over the years.

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Correspondence to Johan Nilvebrant .

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Giang, K.A., Nygren, PÅ., Nilvebrant, J. (2023). Selection of Affibody Affinity Proteins from Phagemid Libraries. In: Hust, M., Lim, T.S. (eds) Phage Display. Methods in Molecular Biology, vol 2702. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3381-6_19

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  • DOI: https://doi.org/10.1007/978-1-0716-3381-6_19

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3380-9

  • Online ISBN: 978-1-0716-3381-6

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