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Evolving catalytic antibodies in a phage-displayed combinatorial library

Nature Biotechnology volume 16, pages 463–467 (1998)Cite this article

Abstract

In vitro affinity maturation for evolving catalytic antibodies has been demonstrated by generating a diverse repertoire of the appropriate complementarity-determining regions on a phage surface. Phage display is followed by a selection based on binding to an altered antigen that was not used at the time of immunization, and provides variants with new catalytic activity and substrate specificity. This library format reduces the time needed to isolate the desired catalytic antibody fragments to under 2 weeks.

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References

  1. Lerner, A.R., Benkovic, S.J., and Schultz, P.G. 1991. At the crossroads of chemistry and immunology: Catalytic antibodies. Science 252: 659–667.

    Article  CAS  PubMed  Google Scholar 

  2. Schultz, P.G. and Lerner, R.A. 1995. From molecular diversity to catalysis: Lessons from the immune system. Science 269: 1835–1842.

    Article  CAS  PubMed  Google Scholar 

  3. Patten, P.A., Gray, N.S., Yang, P.L., Mark, C.B., Wedemayer, G.J., Boniface, J.J. et al. 1996 The immunological evolution of catalysis. Science 271: 1086–1091.

    Article  CAS  PubMed  Google Scholar 

  4. Hawkins, R.E., Russell, S.J., and Winter, G. 1992. Selection of phage antibodies by binding affinity mimicking affinity maturation. J. Med. Biol. 226: 889–896.

    CAS  Google Scholar 

  5. Barbas III, C.F., Bain, J.D., Hoekstra, D.M., and Lerner, R.A. 1992. Semisynthetic combinatorial antibody libraries: A chemical solution to the diversity problem. Proc. Natl. Acad. Sci. USA 89: 4457–4461.

    Article  Google Scholar 

  6. Marks, J.D., Hoogenboom, H.H., Griffiths, A.D., and Winter, G. 1992. Molecular evolution of proteins on filamentous phage. J. Biol. Chem. 267: 16007–16010.

    CAS  PubMed  Google Scholar 

  7. Jackson, J.R., Sathe, G., Rosenberg, A., and Sweet, R. 1995. In vitro antibody maturation. J. Immunol. 154: 3310–3319.

    CAS  PubMed  Google Scholar 

  8. Barbas, C.F. and Burton, D.R. 1996. Selection and evolution of high-affinity human anti-viral antibodies. TIBTECH 14: 230–234.

    Article  CAS  Google Scholar 

  9. Iwabuchi, Y., Miyashita, H., Tanimura, R., Kinoshita, K., Kikuchi, M., and Fujii, I. 1994. Regio- and stereoselective deprotection of acylated carbohydrates via catalytic antibodies. J. Am. Chem. Soc. 116: 771–772.

    Article  CAS  Google Scholar 

  10. Schmidt, R.R. 1986. New methods for the synthesis of glycosides and oligosaccharides-Are there alternatives to the Koenigs-Knorr method?. Angew. Chem. Int. Ed. Engl. 25: 212–234, and references cited therein.

    Article  Google Scholar 

  11. Jackson, D.Y., Prudent, J.R., Baldwin, E.P., and Schultz, P.G. 1991. A mutage-nesis study of a catalytic antibody. Proc. Natl. Acad Sci. USA 88: 58–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Roberts, V.A., Stewart, J., Benkovic, S.J., and Getzoff, E.D. 1994. Catalytic antibody model and mutagenesis implicate arginine in transition-state stabilization. J. Mol. Biol. 235: 1098–1116.

    Article  CAS  PubMed  Google Scholar 

  13. Miyashita, H., Hara, T., Tanimura, R., Fukurama, S., Cagnon, C., Kohara, A., and Fujii, I. 1997. Site-directed mutagenesis of active site contact residues in a hydrolytic abzyme: Evidence for an essential histidine involved in transition state stabilization. J. Mol. Biol. 267: 1247–1257.

    Article  CAS  PubMed  Google Scholar 

  14. Chothia, C. and Lesk, A. 1987. Canonical structures for the hypervariable regions of immunoglobulins. J. Mol Biol. 196: 901–917.

    Article  CAS  PubMed  Google Scholar 

  15. Chothia, C., Lesk, A.M., Tramontano, A., Levitt, M., Smith-Gill, S.J., Air, G. et al. 1989. Conformations of immunoglobulin hypervariable regions. Nature 342: 877–883.

    Article  CAS  PubMed  Google Scholar 

  16. Kabat, E.A., Wu, T.T., Perry, H.M., Gottes-man, K.S., and Foeller, C. 1991 Sequences of proteins of immunological interest, 5th ed. United States Department of Health and Human Services, National Institutes of Health, Bethesda, MD.

    Google Scholar 

  17. Barbas, C.F., Kang, A.S., Lerner, R.A., and Benkovic, S.J. 1991. Assembly of combinatorial antibody libraries on phage surfaces: the gene III site. Proc Natl. Acad. Sci. USA 88: 7978–7982.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Jacobs, J.W. 1991. New perspectives on catalytic antibodies. Bio/Technology 9: 258–262.

    CAS  Google Scholar 

  19. Stewart, J.D. and Benkovic, S.J. 1995. Transition-state stabilization as a measure of the efficiency of antibody catalysis. Nature 375: 388–391.

    Article  CAS  PubMed  Google Scholar 

  20. Fujii, I., Tanaka, F., Miyashita, H., Tanimura, R., and Kinoshita, K. 1995. Correlation between antigen-combining-site structures and functions within a panel of catalytic antibodies generated against a single transition state analog. J. Am. Chem. Soc. 117: 6199–6209.

    Article  CAS  Google Scholar 

  21. Baca, M., Scanlan, T.S., Stephenson, R.C., and Wells, J.A. 1997. Phage display of a catalytic antibody to optimize for transition-state analog binding. Proc. Natl. Acad. Sci. USA 94: 10063–10068.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Zhou, G.W., Guo, J., Huang, W., Fletterick, R.J., and Scanlan, T.S. 1994. Crystal structure of a catalytic antibody with a serine protease active site. Science 265: 1059–1064.

    Article  CAS  PubMed  Google Scholar 

  23. Guo, J., Huang, W., and Scanlan, T.S. 1994. Kinetic and Mechanistic characterization of an efficient hydrolytic antibody: Evidence for the formation of an acyl intermediate. J. Am. Chem. Soc. 116: 6062–6069.

    Article  CAS  Google Scholar 

  24. Murphy, D.J. 1995. Revisiting ground-state and transition-state effects, the split-site model, and the “fundamentalist position” of enzyme catalysis. Biochemistry 34: 4507–4510.

    Article  CAS  PubMed  Google Scholar 

  25. Wells, T.N.C. and Fersht, A.R. 1986. Use of binding energy in catalysis analyzed by mutagenesis of the tyrosyl-tRNA synthetase. Biochemistry 25: 1881–1886.

    Article  CAS  PubMed  Google Scholar 

  26. Fersht, A. 1985. Enzyme substrate complementarity and the use of binding energy in catalysis, pp. 324–327 in Enzyme structure and mechanism, 2nd ed. W.H. Freeman and Company, New York.

    Google Scholar 

  27. Wedemayer, G.J., Patten, P.A., Wang, L.H., Schultz, P.G., and Stevens, R.C. 1997. Structural insights into the evolution of an antibody combining site. Science 276: 1665–1669.

    Article  CAS  PubMed  Google Scholar 

  28. Sheriff, S., Silverton, E.W., Padlan, E.A., Cohen, G.H., Smith-Gill, S.J., Finzel, B.C., and Davies, D.R. 1987. Three-dimensional structure of an antibody-antigen complex. Proc. Natl. Acad. Sci. USA 84: 8075–8079.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Desmet, J., De Maeyer, M., Hazes, B., and Lasters, I. 1992. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356: 539–542.

    Article  CAS  PubMed  Google Scholar 

  30. Tanimura, R., Kidera, A., and Nakamura, H. 1994. Determinants of protein side-chain packing. Protein Sci. 3: 2358–2365.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Morikami, K., Nakai, T., Kidera, A., Saito, M., and Nakamura, H. 1992. PRESTO (Protein Engineering Simulation): a vectorized molecular mechanics program for biopolymers. Comp. Chem. 16: 243–248.

    Article  CAS  Google Scholar 

  32. Friguet, B., Chaffotte, A.F., Djavadi-Ohaniance, L., and Goldberg, M.E. 1985. Measurements of the true affinity constant in solution of antigen-antibody complexes by enzyme-linked immunosorbent assay. J. Immunol. Methods 77: 305–319.

    Article  CAS  PubMed  Google Scholar 

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Author notes

  1. Ikuo Fujii: Corresponding author (e-mail: fujii@bioorg.beri.co.jp).

Authors and Affiliations

  1. Biomolecular Engineering Research Institute and,

    Yoshiharu Iwabuchi

  2. Protein Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka, 565, Japan

    Shiro Fukuyama & Ryuji Tanimura

Authors
  1. Ikuo Fujii
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  2. Shiro Fukuyama
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  3. Yoshiharu Iwabuchi
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  4. Ryuji Tanimura
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Fujii, I., Fukuyama, S., Iwabuchi, Y. et al. Evolving catalytic antibodies in a phage-displayed combinatorial library. Nat Biotechnol 16, 463–467 (1998). https://doi.org/10.1038/nbt0598-463

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