Rapid selection of high-affinity binders using ribosome display

Methods in Molecular Biology

Volumn 805, Issue , 2012, Pages 261-286

  Dreier, Birgit ^a   Plückthun, Andreas ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Affinity maturation; Designed Ankyrin Repeat Proteins; In vitro selection; In vitro translation; Ribosome display

Indexed keywords

PROTEIN;

ARTICLE; CHEMISTRY; ENZYME SPECIFICITY; GENETICS; METABOLISM; PEPTIDE LIBRARY; POLYMERASE CHAIN REACTION; PROTEIN BINDING; PROTEIN FOLDING; RIBOSOME;

PEPTIDE LIBRARY; POLYMERASE CHAIN REACTION; PROTEIN BINDING; PROTEIN FOLDING; PROTEINS; RIBOSOMES; SUBSTRATE SPECIFICITY;

EID: 84555189984     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-379-0_15     Document Type: Article

References (43)

1. Hanes, J. & Plückthun, A. (1997) In vitro selection and evolution of functional proteins by using ribosome display. Proc. Natl. Acad. Sci. U S A 94, 4937-4942. (Pubitemid 27214714)
2. Hanes, J., Jermutus, L., Weber-Bornhauser, S., Bosshard, H. R. & Plückthun, A. (1998) Ribosome display Efficiently selects and evolves high-affi nity antibodies in vitro from immune libraries. Proc. Natl. Acad. Sci. U S A 95, 14130-14135. (Pubitemid 28549332)
3. Mattheakis, L. C., Bhatt, R. R. & Dower, W. J. (1994) An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc. Natl. Acad. Sci. U. S. A. 91, 9022-9026.
4. Hanes, J., Jermutus, L. & Plückthun, A. (2000) Selecting and evolving functional proteins in vitro by ribosome display. Methods Enzymol. 328, 404-430.
5. Plückthun, A. (2012) Ribosome Display: a perspective. Methods Mol. Biol. 805, 3-28.
6. Hanes, J., Schaffi tzel, C., Knappik, A. & Plückthun, A. (2000) Picomolar affi nity antibodies from a fully synthetic naive library selected and evolved by ribosome display. Nat. Biotechnol. 18, 1287-1292.
7. Luginbühl, B., Kanyo, Z., Jones, R. M., Fletterick, R. J., Prusiner, S. B., Cohen, F. E., Williamson, R. A., Burton, D. R. & Plückthun, A. (2006) Directed evolution of an anti-prion protein scFv fragment to an affi nity of 1 pM and its structural interpretation. J. Mol. Biol. 363, 75-97. (Pubitemid 44414837)
8. Zahnd, C., Wyler, E., Schwenk, J. M., Steiner, D., Lawrence, M. C., McKern, N. M., Pecorari, F., Ward, C. W., Joos, T. O. & Plückthun, A. (2007) A designed ankyrin repeat protein evolved to picomolar affi nity to Her2. J. Mol. Biol. 369, 1015-1028. (Pubitemid 46754059)
9. Dreier, B., Mikheeva, G., Belousova, N., Parizek, P., Boczek, E., Jelesarov, I., Forrer, P., Plückthun, A. & Krasnykh, V. (2011) Her2-specifi c multivalent adapters confer designed tropism to adenovirus for gene targeting. J. Mol. Biol. 405, 410-426.
10. Stemmer, W. P. (1994) Rapid evolution of a protein in vitro by DNA shuffl ing. Nature 370, 389-391. (Pubitemid 24259765)
11. Zaccolo, M., Williams, D. M., Brown, D. M. & Gherardi, E. (1996) An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. J. Mol. Biol. 255, 589-603. (Pubitemid 26107188)
12. Zahnd, C., Spinelli, S., Luginbühl, B., Amstutz, P., Cambillau, C. & Plückthun, A. (2004) Directed in vitro evolution and crystallographic analysis of a peptide binding scFv antibody with low picomolar affi nity. J. Biol. Chem. 279, 18870-18877. (Pubitemid 38623314)
13. Zahnd, C., Sarkar, C. A. & Plückthun, A. (2010) Computational analysis of off-rate selection experiments to optimize affi nity maturation by directed evolution. Protein Eng. Des. Sel. 23, 175-184.
14. Schaffi tzel, C., Zahnd, C., Amstutz, P., Luginbühl, B. & Plückthun, A. (2001). In vitro selection and evolution of protein-ligand interactions by ribosome display. In Protein-Protein Interactions, A Molecular Cloning Manual (Golemis, E., ed.), pp. 535-567. Cold Spring Harbor Laboratory Press, New York.
15. Schaffi tzel, C., Zahnd, C., Amstutz, P., Luginbühl, B. & Plückthun, A. (2005). In vitro selection and evolution of protein-ligand interactions by ribosome display. In Proteinprotein interactions: A molecular cloning manual 2nd edit. (Golemis, E. & Adams, P., eds.), pp. 517-548. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
16. Dreier, B. & Plückthun, A. (2010) Ribosome Display, a technology for selecting and evolving proteins from large libraries. Methods Mol. Biol. 687, 283-306.
17. Binz, H. K., Stumpp, M. T., Forrer, P., Amstutz, P. & Plückthun, A. (2003) Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J. Mol. Biol. 332, 489-503. (Pubitemid 37020959)
18. Binz, H. K., Amstutz, P., Kohl, A., Stumpp, M. T., Briand, C., Forrer, P., Grütter, M. G. & Plückthun, A. (2004) High-affi nity binders selected from designed ankyrin repeat protein libraries. Nat. Biotechnol. 22, 575-582. (Pubitemid 38590636)
19. Amstutz, P., Binz, H. K., Parizek, P., Stumpp, M. T., Kohl, A., Grütter, M. G., Forrer, P. & Plückthun, A. (2005) Intracellular kinase inhibitors selected from combinatorial libraries of designed ankyrin repeat proteins. J. Biol. Chem. 280, 24715-24722. (Pubitemid 40941033)
20. Zahnd, C., Pécorari, F., Straumann, N., Wyler, E. & Plückthun, A. (2006) Selection and characterization of Her2 binding-designed ankyrin repeat proteins. J. Biol. Chem. 281, 35167-35175. (Pubitemid 46036556)
21. Schweizer, A., Roschitzki-Voser, H., Amstutz, P., Briand, C., Gulotti-Georgieva, M., Prenosil, E., Binz, H. K., Capitani, G., Baici, A., Plückthun, A. & Grütter, M. G. (2007) Inhibition of caspase-2 by a designed ankyrin repeat protein: specifi city, structure, and inhibition mechanism. Structure 15, 625-636. (Pubitemid 46702685)
22. Huber, T., Steiner, D., Räthlisberger, D. & Plückthun, A. (2007) In vitro selection and characterization of DARPins and Fab fragments for the co-crystallization of membrane proteins: The Na(+)-citrate symporter CitS as an example. J. Struct. Biol. 159, 206-221. (Pubitemid 47095399)
23. Veesler, D., Dreier, B., Blangy, S., Lichière, J., Tremblay, D., Moineau, S., Spinelli, S., Tegoni, M., Plückthun, A., Campanacci, V. & Cambillau, C. (2009) Crystal structure of a DARPin neutralizing inhibitor of lactococcal phage TP901-1: comparison of DARPin and camelid VHH binding mode J. Biol. Chem. 384, 30718-30726.
24. Schatz, P. J. (1993) Use of peptide libraries to map the substrate specifi city of a peptide-modifying enzyme: a 13 residue consensus peptide specifi es biotinylation in Escherichia coli. Biotechnology (N. Y.) 11, 1138-1143. (Pubitemid 23307458)
25. Wade, H. E. & Robinson, H. K. (1966) Magnesium ion-independent ribonucleic acid depolymerases in bacteria. Biochem. J. 101, 467-479.
26. Laminet, A. A. & Plückthun, A. (1989) The precursor of ?-lactamase: Purifi cation, properties and folding kinetics. EMBO J. 8, 1469-1477. (Pubitemid 19274373)
27. O'Callaghan, C. H., Morris, A., Kirby, S. M. & Shingler, A. H. (1972) Novel method for detection of beta-lactamases by using a chromogenic cephalosporin substrate. Antimicrob. Agents Chemother. 1, 283-288.
28. Steiner, D., Forrer, P. & Plückthun, A. (2008) Efficient selection of DARPins with sub-nanomolar affi nities using SRP phage display. J. Mol. Biol. 382, 1211-1227.
29. Zahnd, C., Amstutz, P. & Plückthun, A. (2007) Ribosome display: selecting and evolving proteins in vitro that specifi cally bind to a target. Nat. Methods 4, 269-279. (Pubitemid 46358879)
30. Hajnsdorf, E., Braun, F., Haugel-Nielsen, J., Le Derout, J. & Regnier, P. (1996) Multiple degradation pathways of the rpsO mRNA of Escherichia coli. RNase E interacts with the 5′ and 3′ extremities of the primary transcript. Biochimie 78, 416-424. (Pubitemid 26360077)
31. Amstutz, P., Binz, H. K., Zahnd, C. & Plückthun, A. (2006). Ribosome Display: In Vitro Selection of Protein-Protein Interactions. In Cell Biology -A Laboratory Handbook 3rd edit. (Celis, J., ed.), Vol. 1, pp. 497-509. 4 vols. Elsevier Academic Press.
32. Chen, H. Z. & Zubay, G. (1983) Prokaryotic coupled transcription-translation. Methods Enzymol. 101, 674-690. (Pubitemid 13071078)
33. Pratt, J. M. (1984). Coupled transcriptiontranslation in prokaryotic cell-free systems. In Current Protocols (Hemes, B. D. & Higgins, S. J., eds.), pp. 179-209. IRL Press, Oxford.
34. Kushner, S. R. (2002) mRNA decay in Escherichia coli comes of age. J. Bacteriol. 184, 4658-4665; discussion 4657.
35. Jermutus, L., Honegger, A., Schwesinger, F., Hanes, J. & Plückthun, A. (2001) Tailoring in vitro evolution for protein affi nity or stability. Proc. Natl. Acad. Sci. U.S.A. 98, 75-80. (Pubitemid 32095866)
36. Hawkins, R. E., Russell, S. J. & Winter, G. (1992) Selection of phage antibodies by binding affi nity. Mimicking affi nity maturation. J. Mol. Biol. 226, 889-896.
37. Yang, W. P., Green, K., Pinz-Sweeney, S., Briones, A. T., Burton, D. R. & Barbas, C. F., 3rd. (1995) CDR walking mutagenesis for the affi nity maturation of a potent human anti-HIV-1 antibody into the picomolar range. J. Mol. Biol. 254, 392-403. (Pubitemid 26001779)
38. Sambrook, J. & Russel, D. W. (2001). Molecular cloning: A laboratory handbook . 3rd edit, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
39. Willuda, J., Honegger, A., Waibel, R., Schubiger, P. A., Stahel, R., Zangemeister-Wittke, U. & Plückthun, A. (1999) High thermal stability is essential for tumor targeting of antibody fragments: Engineering of a humanized anti-epithelial glycoprotein-2 (epithelial cell adhesion molecule) single-chain Fv fragment. Cancer Res. 59, 5758-5767.
40. Wärn, A. & Plückthun, A. (2001) Stability engineering of antibody single-chain F v fragments. J. Mol. Biol. 305, 989-1010.
41. Proba, K., Wärn, A., Honegger, A. & Plückthun, A. (1998) Antibody scFv fragments without disulfi de bonds made by molecular evolution. J. Mol. Biol. 275, 245-253. (Pubitemid 28030002)
42. Chames, P. & Baty, D. (2000) Antibody engineering and its applications in tumor targeting and intracellular immunization. FEMS Microbiol. Lett. 189, 1-8. (Pubitemid 30456238)
43. Honegger, A., Malebranche, A. D., Räthlisberger, D. & Plückthun, A. (2009) The infl uence of the framework core residues on the biophysical properties of immunoglobulin heavy chain variable domains. Protein Eng. Des. Sel. 22, 121-134.