Skip to main content

Biosensor Detection Systems: Engineering Stable, High-Affinity Bioreceptors by Yeast Surface Display

  • Protocol
Biosensors and Biodetection

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 504))

Summary

Over the past two decades, the field of biosensors has been developing fast, portable, and convenient detection tools for various molecules of interest, both biological and environmental. Although much attention is paid to the transduction portion of the sensor, the actual bioreceptor that binds the ligand is equally critical. Tight, specific binding by the bioreceptor is required to detect low levels of the relevant ligand, and the bioreceptor must be stable enough to survive immobilization, storage, and in ideal cases, regeneration on the biosensing device. Often, naturally-occurring bioreceptors or antibodies that are specific for a ligand either express affinities that may be too low to detect useful levels, or the proteins are too unstable to be used and reused as a biosensor. Further engineering of these receptors can improve their utility. Here, we describe in detail the use of yeast surface display techniques to carry out directed evolution of bioreceptors to increase both the stability of the molecules and their affinity for the ligands. This powerful technique has enabled the production of stabilized, single-chain antibodies, T cell receptors, and other binding molecules that exhibit affinity increases for their ligands of up to 1 million-fold and expression of stable molecules in E. coli.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Luppa, P. B., Sokoll, L. J. and Chan, D. W. (2001) Immunosensors — principles and applications to clinical chemistry. Clin Chim Acta 314, 1–26

    Article  CAS  PubMed  Google Scholar 

  2. Pejcic, B., De Marco, R. and Parkinson, G. (2006) The role of biosensors in the detection of emerging infectious diseases. Analyst 131, 1079–1090

    Article  CAS  PubMed  Google Scholar 

  3. Stefan, R. I., van Staden, J. F. and Aboul-Enein, H. Y. (2000) Immunosensors in clinical analysis. Fresenius J Anal Chem 366, 659–668

    Article  CAS  PubMed  Google Scholar 

  4. Warsinke, A., Benkert, A. and Scheller, F. W. (2000) Electrochemical immunoassays. Fre-senius J Anal Chem 366, 622–634

    Article  CAS  Google Scholar 

  5. Peruski, A. H. and Peruski, L. F., Jr. (2003) Immunological methods for detection and identification of infectious disease and biological warfare agents. Clin Diagn Lab Immunol 10, 506–513

    CAS  PubMed  Google Scholar 

  6. Goodchild, S., Love, T., Hopkins, N. and Mayers, C. (2006) Engineering antibodies for biosensor technologies. Adv Appl Micro-biol 58, 185–226

    Article  CAS  Google Scholar 

  7. Boder, E. T. and Wittrup, K. D. (1997) Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol 15, 553–557

    Article  CAS  PubMed  Google Scholar 

  8. Kondo, A. and Ueda, M. (2004) Yeast cell-surface display — applications of molecular display. Appl Microbiol Biotechnol 64, 28–40

    Article  CAS  PubMed  Google Scholar 

  9. Boder, E. T. and Wittrup, K. D. (2000) Yeast surface display for directed evolution of protein expression, affinity, and stability. Methods Enzymol 328, 430–444

    Article  CAS  PubMed  Google Scholar 

  10. Feldhaus, M. J., Siegel, R. W., Opresko, L. K., Coleman, J. R., Feldhaus, J. M., Yeung, Y. A., Cochran, J. R., Heinzelman, P. , Colby, D., Swers, J., Graff, C., Wiley, H. S. and Wittrup, K. D. (2003) Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library. Nat Biotechnol 21, 163–170

    Article  CAS  PubMed  Google Scholar 

  11. Yeung, Y. A. and Wittrup, K. D. (2002) Quantitative screening of yeast surface-displayed polypeptide libraries by magnetic bead capture. Biotechnol Prog 18, 212–220

    Article  CAS  PubMed  Google Scholar 

  12. Richman, S. A., Healan, S. J., Weber, K. S., Donermeyer, D. L., Dossett, M. L., Green-berg, P. D., Allen, P. M. and Kranz, D. M. (2006) Development of a novel strategy for engineering high-affinity proteins by yeast display. Protein Eng Des Sel 19, 255–264

    Article  CAS  PubMed  Google Scholar 

  13. Wang, X. X. and Shusta, E. V. (2005) The use of scFv-displaying yeast in mammalian cell surface selections. J Immunol Methods 304, 30–42

    Article  CAS  PubMed  Google Scholar 

  14. Boder, E. T., Midelfort, K. S. and Wittrup, K. D. (2000) Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc Natl Acad Sci U S A 97, 10701–10705

    Article  CAS  PubMed  Google Scholar 

  15. Kieke, M. C., Cho, B. K., Boder, E. T., Kranz, D. M. and Wittrup, K. D. (1997) Isolation of anti-T cell receptor scFv mutants by yeast surface display. Protein Eng 10, 1303–1310

    Article  CAS  PubMed  Google Scholar 

  16. Feldhaus, M. J. and Siegel, R. W. (2004) Yeast display of antibody fragments: a discovery and characterization platform. J Immunol Methods 290, 69–80

    Article  CAS  PubMed  Google Scholar 

  17. Kieke, M. C., Shusta, E. V., Boder, E. T., Teyton, L., Wittrup, K. D. and Kranz, D. M. (1999) Selection of functional T cell receptor mutants from a yeast surface-display library. Proc Natl Acad Sci U S A 96, 5651–5656

    Article  CAS  PubMed  Google Scholar 

  18. Richman, S. A. and Kranz, D. M. (2007) Display, engineering, and applications of antigen-specific T cell receptors. Biomol Eng 24, 361–373

    Article  CAS  PubMed  Google Scholar 

  19. Weber, K. S., Donermeyer, D. L., Allen, P. M. and Kranz, D. M. (2005) Class II-restricted T cell receptor engineered in vitro for higher affinity retains peptide specificity and function. Proc Natl Acad Sci U S A 102, 19033–19038

    Article  CAS  PubMed  Google Scholar 

  20. Jones, L. L., Brophy, S. E., Bankovich, A. J., Colf, L. A., Hanick, N. A., Garcia, K. C. and Kranz, D. M. (2006) Engineering and characterization of a stabilized alpha1/alpha2 module of the class I major histocompatibil-ity complex product Ld. J Biol Chem 281, 25734–25744

    Article  CAS  PubMed  Google Scholar 

  21. Starwalt, S. E., Masteller, E. L., Bluestone, J. A. and Kranz, D. M. (2003) Directed evolution of a single-chain class II MHC product by yeast display. Protein Eng 16, 147–156

    Article  CAS  PubMed  Google Scholar 

  22. Esteban, O. and Zhao, H. (2004) Directed evolution of soluble single-chain human class II MHC molecules. J Mol Biol 340, 81–95

    Article  CAS  PubMed  Google Scholar 

  23. Boder, E. T., Bill, J. R., Nields, A. W., Mar-rack, P. C. and Kappler, J. W. (2005) Yeast surface display of a noncovalent MHC class II heterodimer complexed with antigenic peptide. Biotechnol Bioeng 92, 485–491

    Article  CAS  PubMed  Google Scholar 

  24. Dam, J., Guan, R., Natarajan, K., Dimasi, N., Chlewicki, L. K., Kranz, D. M., Schuck, P., Margulies, D. H. and Mariuzza, R. A. (2003) Variable MHC class I engagement by Ly49 natural killer cell receptors demonstrated by the crystal structure of Ly49C bound to H-2K(b). Nat Immunol 4, 1213–1222

    Article  CAS  PubMed  Google Scholar 

  25. Cochran, J. R., Kim, Y. S., Lippow, S. M., Rao, B. and Wittrup, K. D. (2006) Improved mutants from directed evolution are biased to orthologous substitutions. Protein Eng Des Sel 19, 245–253

    Article  CAS  PubMed  Google Scholar 

  26. Buonpane, R. A., Churchill, H. R. O., Moza, B., Sundberg, E. J., Peterson, M. L., Schliev-ert, P. M., and Kranz, D. M. (2007) Neutralization of Staphylococcal enterotoxin B by soluble, high-affinity receptor antagonists. Nat Med 13(6), 725–729.

    Article  CAS  PubMed  Google Scholar 

  27. Koide, A., Gilbreth, R. N., Esaki, K., Ter-eshko, V. and Koide, S. (2007) High-affinity single-domain binding proteins with a binary-code interface. Proc Natl Acad Sci U S A 104, 6632–6637

    Article  CAS  PubMed  Google Scholar 

  28. Lipovsek, D., Lippow, S. M., Hackel, B. J., Gregson, M. W., Cheng, P., Kapila, A. and Wittrup, K. D. (2007) Evolution of an inter-loop disulfide bond in high-affinity antibody mimics based on fibronectin type III domain and selected by yeast surface display: molecular convergence with single-domain camelid and shark antibodies. J Mol Biol 368, 1024– 1041

    Article  CAS  PubMed  Google Scholar 

  29. Rao, B. M., Driver, I., Lauffenburger, D. A. and Wittrup, K. D. (2004) Interleukin 2 (IL-2) variants engineered for increased IL-2 receptor alpha-subunit affinity exhibit increased potency arising from a cell surface ligand reservoir effect. Mol Pharmacol 66, 864–869

    CAS  PubMed  Google Scholar 

  30. Rao, B. M., Girvin, A. T., Ciardelli, T., Lauffenburger, D. A. and Wittrup, K. D. (2003) Interleukin-2 mutants with enhanced alpha-receptor subunit binding affinity. Protein Eng 16, 1081–1087

    Article  CAS  PubMed  Google Scholar 

  31. Chao, G., Lau, W. L., Hackel, B. J., Sazin-sky, S. L., Lippow, S. M. and Wittrup, K. D. (2006) Isolating and engineering human antibodies using yeast surface display. Nat Protoc 1, 755–768

    Article  CAS  PubMed  Google Scholar 

  32. Colby, D. W., Kellogg, B. A., Graff, C. P., Yeung, Y. A., Swers, J. S. and Wittrup, K. D. (2004) Engineering antibody affinity by yeast surface display. Methods Enzymol 388, 348–358

    Article  CAS  PubMed  Google Scholar 

  33. Dong, X., Stothard, P. , Forsythe, I. J. and Wishart, D. S. (2004) PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Res 32, W660–W664

    Article  CAS  PubMed  Google Scholar 

  34. Daugherty, P. S., Chen, G., Iverson, B. L. and Georgiou, G. (2000) Quantitative analysis of the effect of the mutation frequency on the affinity maturation of single chain Fv antibodies. Proc Natl Acad Sci U S A 97, 2029–2034

    Article  CAS  PubMed  Google Scholar 

  35. Fromant, M., Blanquet, S. and Plateau, P. (1995) Direct random mutagenesis of gene-sized DNA fragments using polymerase chain reaction. Anal Biochem 224, 347–353

    Article  CAS  PubMed  Google Scholar 

  36. Meilhoc, E., Masson, J. M. and Teissie, J. (1990) High efficiency transformation of intact yeast cells by electric field pulses. Biotechnology (N Y) 8, 223–227

    Article  CAS  Google Scholar 

  37. Becker, D. M. and Lundblad, V. (1996) Introduction of DNA into yeast cells, transformation by electroporation. In: Current Protocols in Molecular Biology (Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. and Struhl, K., eds.). John Wiley & Sons, Hoboken, NJ

    Google Scholar 

  38. Shusta, E. V., Holler, P. D., Kieke, M. C., Kranz, D. M. and Wittrup, K. D. (2000) Directed evolution of a stable scaffold for T-cell receptor engineering. Nat Biotechnol 18, 754–759

    Article  CAS  PubMed  Google Scholar 

  39. Shusta, E. V., Kieke, M. C., Parke, E., Kranz, D. M. and Wittrup, K. D. (1999) Yeast polypeptide fusion surface display levels predict thermal stability and soluble secretion efficiency. J Mol Biol 292, 949–956

    Article  CAS  PubMed  Google Scholar 

  40. Kowalski, J. M., Parekh, R. N., Mao, J. and Wittrup, K. D. (1998) Protein folding stability can determine the efficiency of escape from endoplasmic reticulum quality control. J Biol Chem 273, 19453–19458

    Article  CAS  PubMed  Google Scholar 

  41. Kowalski, J. M., Parekh, R. N. and Wittrup, K. D. (1998) Secretion efficiency in Saccha-romyces cerevisiae of bovine pancreatic trypsin inhibitor mutants lacking disulfide bonds is correlated with thermodynamic stability. Biochemistry 37, 1264–1273

    Article  CAS  PubMed  Google Scholar 

  42. Hagihara, Y. and Kim, P. S. (2002) Toward development of a screen to identify randomly encoded, foldable sequences. Proc Natl Acad Sci U S A 99, 6619–6624

    Article  CAS  PubMed  Google Scholar 

  43. Warrens, A. N., Jones, M. D. and Lechler, R. I. (1997) Splicing by overlap extension by PCR using asymmetric amplification: an improved technique for the generation of hybrid proteins of immunological interest. Gene 186, 29–35

    Article  CAS  PubMed  Google Scholar 

  44. Boder, E. T. and Wittrup, K. D. (1998) Optimal screening of surface-displayed polypep-tide libraries. Biotechnol Prog 14, 55–62

    Article  CAS  PubMed  Google Scholar 

  45. Park, S., Xu, Y., Stowell, X. F., Gai, F., Saven, J. G. and Boder, E. T. (2006) Limitations of yeast surface display in engineering proteins of high thermostability. Protein Eng Des Sel 19, 211–217

    Article  CAS  PubMed  Google Scholar 

  46. Stemmer, W. P. (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370, 389–391

    Article  CAS  PubMed  Google Scholar 

  47. Rajpal, A., Beyaz, N., Haber, L., Cappuc-cilli, G., Yee, H., Bhatt, R. R., Takeuchi, T., Lerner, R. A. and Crea, R. (2005) A general method for greatly improving the affinity of antibodies by using combinatorial libraries. Proc Natl Acad Sci U S A 102, 8466–8471

    Article  CAS  PubMed  Google Scholar 

  48. Garcia-Rodriguez, C., Levy, R., Arndt, J. W., Forsyth, C. M., Razai, A., Lou, J., Geren, I., Stevens, R. C. and Marks, J. D. (2007) Molecular evolution of antibody cross-reactivity for two subtypes of type A botulinum neurotoxin. Nat Biotechnol 25, 107–116

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors thank members of our laboratory and K. Dane Wit-trup and members of his lab for working out many of the conditions and methods described in this chapter. This work was supported by NIH grants AI064611 and GM55767 (to DMK), the Samuel and Ruth Engelberg/Irvington Institute postdoctoral fellowship from the Cancer Research Institute (to JDS), and predoctoral fellowship ES013571 (to SAR).

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Humana Press, a part of Springer Science+Business Media, LLC, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Richman, S.A., Kranz, D.M., Stone, J.D. (2009). Biosensor Detection Systems: Engineering Stable, High-Affinity Bioreceptors by Yeast Surface Display. In: Rasooly, A., Herold, K.E. (eds) Biosensors and Biodetection. Methods in Molecular Biology™, vol 504. Humana Press. https://doi.org/10.1007/978-1-60327-569-9_19

Download citation

  • DOI: https://doi.org/10.1007/978-1-60327-569-9_19

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-568-2

  • Online ISBN: 978-1-60327-569-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics