Turnover-based in vitro selection and evolution of biocatalysts from a fully synthetic antibody library

Nature Biotechnology

Volumn 21, Issue 6, 2003, Pages 679-685

  Cesaro Tadic, Sandro ^a   Lagos, Dimitrios ^b,c   Honegger, Annemarie ^a   Rickard, James H ^b   Partridge, Lynda J ^b   Blackburn, G Michael ^b   Plückthun, Andreas ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b UNIVERSITY OF SHEFFIELD   (United Kingdom)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODIES; BIOCATALYSTS; GENES;

VITRO SELECTION;

BIOTECHNOLOGY;

CATALYTIC ANTIBODY; HAPTEN; PHOSPHATE;

ANTIBODY LIBRARY; ANTIBODY STRUCTURE; ARTICLE; BINDING AFFINITY; BIOCATALYST; COMPLEMENTARITY DETERMINING REGION; ENZYME LINKED IMMUNOSORBENT ASSAY; MUTAGENESIS; PHAGE DISPLAY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

ANTIBODIES; ANTIBODY FORMATION; CATALYSIS; DIRECTED MOLECULAR EVOLUTION; HUMANS; IMMUNOGLOBULIN FRAGMENTS; PEPTIDE LIBRARY; PROTEIN ENGINEERING;

EID: 0038023153     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt828     Document Type: Article

References (46)

1. Schmidt-Dannert, C. Directed evolution of single proteins, metabolic pathways, and viruses. Biochemistry 40, 13125-13136 (2001).
2. Farinas, E.T., Bulter, T. & Arnold, F.H. Directed enzyme evolution. Curr. Opin. Biotechnol. 12, 545-551 (2001).
3. Griffiths, A.D. & Tawfik, D.S. Man-made enzymes - from design to in vitro compartmentalisation. Curr. Opin. Biotechnol. 11, 338-353 (2000).
4. Kazlauskas, R.J. Molecular modeling and biocatalysis: explanations, predictions, limitations, and opportunities. Curr. Opin. Chem. Biol. 4, 81-88 (2000).
5. Blackburn, G.M., Datta, A., Denham, H. & Wentworth, P. Jr. Catalytic antibodies. Adv. Phys. Org. Chem. 31, 249-392 (1998).
6. Hilvert, D. Critical analysis of antibody catalysis. Annu. Rev. Biochem. 69, 751-793 (2000).
7. Wentworth, P. Jr. & Janda, K.D. Catalytic antibodies: structure and function. Cell Biochem. Biophys. 35, 63-87 (2001).
8. Wirsching, P., Ashley, J.A., Lo, C.H., Janda, K.D. & Lerner, R.A. Reactive immunization. Science 270, 1775-1782 (1995).
9. Barbas, C.F., et al. Immune versus natural selection: antibody aldolases with enzymic rates but broader scope. Science 278, 2085-2092 (1997).
10. Gao, C. et al. Making chemistry selectable by linking it to infectivity. Proc. Natl. Acad. Sci. USA 94, 11777-11782 (1997).
11. Amstutz, P. et al. In vitro selection for catalytic activity with ribosome display. J. Am. Chem. Soc. 124, 9396-9403 (2002).
12. Janda, K.D. et al. Chemical selection for catalysis in combinatorial antibody libraries. Science 275, 945-948 (1997).
13. Soumillion, P. et al. Phage display of enzymes and in vitro selection for catalytic activity. Appl. Biochem. Biotechnol 47, 175-190 (1994).
14. Tanaka, F., Lerner, R.A. & Barbas, C.F. Reconstructing aldolase antibodies to alter their substrate specificity and turnover. J. Am. Chem. Soc. 122, 4835-4836 (2000).
15. Danielsen, S. et al. In vitro selection of enzymatically active lipase variants from phage libraries using a mechanism-based inhibitor. Gene 272, 267-274 (2001).
16. Knappik, A. et al. Fully synthetic Human Combinatorial Antibody Libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides. J., Mol. Biol. 296, 57-86 (2000).
17. Krebs, B. et al. High-throughput generation and engineering of recombinant human antibodies. J. Immunol. Methods 254, 67-84 (2001).
18. Betley, J.R. et al. Direct screening for phosphatase activity by turnover-based capture of protein catalysts. Angew. Chem., Int. Edn. Engl. 41, 775-777 (2002).
19. Myers, J.K., Cohen, J.D. & Widlanski, T.S. Substituent effects on the mechanism-based inactivation of prostatic acid phosphatase. J. Am. Chem. Soc. 117, 11049-11054 (1995).
20. Born, T.L., Myers, J.K., Widlanski, T.S. & Rusnak, F. 4-(Fluoromethyl)phenyl phosphate acts as a mechanism-based inhibitor of calcineurin. J. Biol. Chem. 270, 25651-25655 (1995).
21. Loubinoux, B., Miazimbakana, J. & Gerardin, P. Reactivity of new precursors of quinone methides. Tetrahedron Lett. 30, 1939-1942 (1989).
22. Vayron, P. et al. Toward antibody-catalyzed hydrolysis of organophosphorus poisons. Proc. Natl. Acad. Sci. USA 97, 7058-7063 (2000).
23. Scanlan, T.S., Prudent, J.R. & Schultz, P.G. Antibody-catalyzed hydrolysis of phosphate monoesters. J. Am. Chem. Soc. 113, 9397-9398 (1991).
24. Wentworth, P. Jr. et al. A bait and switch hapten strategy generates catalytic antibodies for phosphodiester hydrolysis. Proc. Natl. Acad. Sci. USA 95, 5971-5975 (1998).
25. Wentworth, P. & Janda, K.D. Catalytic antibodies. Curr. Opin. Chem. Biol. 2, 138-144 (1998).
26. Spivak, D.A., Hoffman, T.Z., Moore, A.H., Taylor, M.J. & Janda, K.D. A comparison of flexible and constrained haptens in eliciting antibody catalysts for paraoxon hydrolysis. Bioorg. Med. Chem. 7, 1145-1150 (1999).
27. Stec, B., Hehir, M.J., Brennan, C., Nolte, M. & Kantrowitz, E.R. Kinetic and X-ray structural studies of three mutant E. coli alkaline phosphatases: insights into the catalytic mechanism without the nucleophile Serr102. J. Mol. Biol. 277, 647-662 (1998).
28. Coleman, J.E. Structure and mechanism of alkaline phosphatase. Annu. Rev. Biophys. Biomol. Struct. 21, 441-483 (1992).
29. Thatcher, G.R.J. & Kluger, R. Mechanism and catalysis of nucleophilic substitution in phosphate esters. Adv. Phys. Org. Chem. 25, 99-265 (1989).
30. Peracchi, A. Enzyme catalysis: removing chemically 'essential' residues by site-directed mutagenesis. Trends Biochem. Sci. 26, 497-503 (2001).
31. Davies, D.R., Padlan, E.A. & Sheriff, S. Antibody-antigen complexes. Annu. Rev. Biochem. 59, 439-473 (1990).
32. Zaccolo, M., Williams, D.M., Brown, D.M. & Gherardi, E. An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. J. Mol. Biol. 255, 589-603 (1996).
33. Arnold, F.H. When blind is better: protein design by evolution. Nat. Biotechnol. 16, 617-618 (1998).
34. Chen, Y.L., Tang, T.Y. & Cheng, K.J. Directed evolution to produce an alkalophilic variant from a Neocallimastix patriciarum xylanase. Can. J. Microbiol. 47, 1088-1094 (2001).
35. Christians, F.C. & Loeb, L.A. Novel human DNA alkyltransferases obtained by random substitution and genetic selection in bacteria. Proc. Natl. Acad. Sci. USA 93, 6124-6128 (1995).
36. Martinez, M.A., Pezo, V., Marliere, P. & Wain-Hobson, S. Exploring the functional robustness of an enzyme by in vitro evolution. EMBO J. 15, 1203-1210 (1995).
37. Oue, S., Okamoto, A., Yano, T. & Kagamiyama, H. Redesigning the substrate specificity of an enzyme by cumulative effects of the mutations of non-active site residues. J. Biol. Chem. 274, 2344-2349 (1999).
38. Daugherty, P.S., Chen, G., Iverson, B.L. & Georgiou, G. Quantitative analysis of the effect of the mutation frequency on the affinity maturation of single chain Fv antibodies. Proc. Natl. Acad. Sci. USA 97, 2029-2034 (2000).
39. Takahashi, N., Kakinuma, H., Liu, L., Nishi, Y. & Fujii, I. In vitro abzyme evolution to optimize antibody recognition for catalysis. Nat. Biotechnol. 19, 563-567 (2001).
40. Ladner, R.C. & Ley, A.C. Novel frameworks as a source of high-affinity ligands. Curr. Opin. Biotechnol. 12, 406-410 (2001).
41. 8-barrel enzyme to catalyze related reactions in two different metabolic pathways. Proc. Natl. Acad. Sci. USA 97, 9925-9930 (2000).
42. Hanes, J., Schaffitzel, C., Knappik, A. & Plückthun, A. Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display. Nat. Biotechnol. 18, 1287-1292 (2000).
43. Wolfenden, R., Ridgway, C. & Young, G. Spontaneous hydrolysis of ionized phosphate monoesters and diesters and the proficiencies of phosphohydrolases as catalysts. J. Am. Chem. Soc. 120, 833-834 (1998).
44. O'Brien, P.J. & Herschlag, D. Alkaline phosphatase revisited: hydrolysis of alkyl phosphates. Biochemistry 41, 3207-3225 (2002).
45. Honegger, A. & Plückthun, A. Yet another numbering scheme for immunoglobulin variable domains: an automatic modeling and analysis tool. J. Mol. Biol. 309, 657-670 (2001).
46. Kabat, E.A. & Wu, T.T. Identical V region amino acid sequences and segments of sequences in antibodies of different specificities. Relative contributions of VH and VL genes, minigenes, and complementarity-determining regions to binding of antibody-combining sites. J. Immunol. 147, 1709-1719 (1991).