Phage display for engineering and analyzing protein interaction interfaces

Current Opinion in Structural Biology

Volumn 17, Issue 4, 2007, Pages 481-487

  Sidhu, Sachdev S ^a   Koide, Shohei ^b  

^a GENENTECH INC   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; BINDING PROTEIN;

ENERGY TRANSFER; NONHUMAN; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN ENGINEERING; PROTEIN INTERACTION; PROTEIN SECRETION; REVIEW;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; HUMANS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE LIBRARY; PROTEIN BINDING; PROTEIN ENGINEERING; PROTEIN INTERACTION MAPPING;

EID: 34548838274     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2007.08.007     Document Type: Review

References (60)

1. Gascoigne N.R., and Zal T. Molecular interactions at the T cell-antigen-presenting cell interface. Curr Opin Immunol 16 (2004) 114-119
2. Pawson T., and Nash P. Protein-protein interactions define specificity in signal transduction. Genes & Dev 14 (2000) 1027-1047
3. Warren A.J. Eukaryotic transcription factors. Curr Opin Struct Biol 12 (2002) 107-114
4. Schaedel O., and Reiter Y. Antibodies and their fragments as anti-cancer agents. Curr Pharm Des 12 (2006) 363-378
5. Trikha M., Yan L., and Nakada M.T. Monoclonal antibodies as therapeutics in oncology. Curr Opin Biotechnol 13 (2002) 609-614
6. Georgiou G., Stathopoulos C., Daugherty P.S., Nayak A.R., Iverson B.L., and Curtiss R.R. Display of heterologous proteins on the surface of microorganisms: from the screening of combinatorial libraries to live recombinant vaccines. Nat Biotechnol 15 (1997) 29-34
7. Harvey B.R., Georgiou G., Hayhurst A., Jeong K.J., Iverson B.L., and Rogers G.K. Anchored periplasmic expression, a versatile technology for the isolation of high-affinity antibodies from Escherichia coli-expressed libraries. Proc Natl Acad Sci U S A 101 (2004) 9193-9198
8. Lipovsek D., and Pluckthun A. In vitro protein evolution by ribosome display and mRNA display. J Immunol Methods 290 (2004) 51-67
9. Reiersen H., Lobersli I., Loset G.A., Hvattum E., Simonsen B., Stacy J.E., McGregor D., FitzGerald K., Welschof M., Brekke O.H., et al. Covalent antibody display-an in vitro antibody-DNA library selection system. Nucl Acids Res 33 (2005) e10
10. Urban J.H., Schneider R.M., Compte M., Finger C., Cichutek K., Alvarez-Vallina L., and Buchholz C.J. Selection of functional human antibodies from retroviral display libraries. Nucl Acids Res 33 (2005) e35
11. Wittrup K.D. Protein engineering by cell-surface display. Curr Opin Biotechnol 12 (2001) 395-399
12. Mazor Y., Van Blarcom T., Mabry R., Iverson B.L., and Georgiou G. Isolation of engineered, full-length antibodies from libraries expressed in Escherichia coli. Nature Biotechnol 25 (2007) 563-565
13. Smith G.P. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228 (1985) 1315-1317
14. Binz H.K., and Pluckthun A. Engineered proteins as specific binding reagents. Curr Opin Biotechnol 16 (2005) 459-469
15. Hosse R.J., Rothe A., and Power B.E. A new generation of protein display scaffolds for molecular recognition. Protein Sci 15 (2006) 14-27
16. Mathonet P., and Fastrez J. Engineering of non-natural receptors. Curr Opin Struct Biol 14 (2004) 505-511
17. Sidhu S.S., Lowman H.B., Cunningham B.C., and Wells J.A. Phage display for selection of novel binding peptides. Methods Enzymol 328 (2000) 333-363
18. Uchiyama F., Tanaka Y., Minari Y., and Tokui N. Designing scaffolds of peptides for phage display libraries. J Biosci Bioeng 99 (2005) 448-456
19. Paschke M., and Hohne W. A twin-arginine translocation (Tat)-mediated phage display system. Gene 350 (2005) 79-88
20. Droge M.J., Boersma Y.L., Braun P.G., Buining R.J., Julsing M.K., Selles K.G., van Dijl J.M., and Quax W.J. Phage display of an intracellular carboxylesterase of Bacillus subtilis: comparison of Sec and Tat pathway export capabilities. Appl Environ Microbiol 72 (2006) 4589-4595
21. Thammawong P., Kasinrerk W., Turner R.J., and Tayapiwatana C. Twin-arginine signal peptide attributes effective display of CD147 to filamentous phage. Appl Microbiol Biotechnol 69 (2006) 697-703
22. Steiner D., Forrer P., Stumpp M.T., and Pluckthun A. Signal sequences directing cotranslational translocation expand the range of proteins amenable to phage display. Nat Biotechnol 24 (2006) 823-831. A new phage display system using an alternative cotranslational signal was developed that efficiently displays highly stable proteins. Systematic comparisons of different signal sequences unambiguously show its impact on expanding the range of proteins that can be engineered and analyzed using phage display.
23. Koide A., Gilbreth R.N., Esaki K., Tereshko V., and Koide S. High-affinity single-domain binding proteins with a binary-code interface. Proc Natl Acad Sci U S A 104 (2007) 6632-6637. A simple combinatorial library of Tyr and Ser in two recognition loops of the FN3 scaffold produced tight binders for naive proteins. It presents the first atomic structure of FN3-based binders, which demonstrates the dominance of Tyr in mediating protein-protein interactions and the importance of conformational diversity in engineering specific molecular recognition.
24. Herman R.E., Badders D., Fuller M., Makienko E.G., Houston Jr. M.E., Quay S.C., and Johnson P.H. The Trp cage motif as a scaffold for the display of a randomized peptide library on bacteriophage T7. J Biol Chem 282 (2007) 9813-9824. A large synthetic combinatorial library from a small scaffold, Trp cage, was built using the T7 phage display system and was used to generate binding molecules to streptavidin and to cell surface.
25. Bradbury A. Antibodies in proteomics I: generating antibodies. Trends Biotechnol 21 (2003) 275-281
26. Brekke O.H., and Loset G.A. New technologies in therapeutic antibody development. Curr Opin Pharmacol 3 (2003) 544-550
27. Hoogenboom H.R. Selecting and screening recombinant antibody libraries. Nat Biotechnol 23 (2005) 1105-1116
28. Dobson CL, Minter RR, Hart-Shorrock CP: Naive antibody libraries from natural repertoires. In Phage Display in Biotechnology and Drug Discovery, edn 1. Edited by Sidhu SS. Taylor and Francis Group; 2005:659-708 [Carmen A (Series Editor): Drug Discovery, vol. 3].
29. Kretzschmar T., and von Ruden T. Antibody discovery: phage display. Curr Opin Biotechnol 13 (2002) 598-602
30. Barbas III C.F., Amberg W., Simoncsits A., Jones T.M., and Lerner R.A. Selection of human anti-hapten antibodies from semisynthetic libraries. Gene 137 (1993) 57-62
31. Griffiths A.D., Williams S.C., Hartley O., Tomlinson I.M., Waterhouse P., Crosby W.L., Kontermann R.E., Jones P.T., Low N.M., Allison T.J., et al. Isolation of high affinity human antibodies directly from large synthetic repertoires. EMBO J 13 (1994) 3245-3260
32. Hoet R.M., Cohen E.H., Kent R.B., Rookey K., Schoonbroodt S., Hogan S., Rem L., Frans N., Daukandt M., Pieters H., et al. Generation of high-affinity human antibodies by combining donor-derived and synthetic complementarity-determining-region diversity. Nat Biotechnol 23 (2005) 344-348
33. Lee C.V., Liang W.C., Dennis M.S., Eigenbrot C., Sidhu S.S., and Fuh G. High-affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold. J Mol Biol 340 (2004) 1073-1093
34. Fellouse F.A., Bing L., Compaan D.M., Peden A.A., Hymowitz S.G., and Sidhu S.S. Molecular recognition by a binary code. J Mol Biol 348 (2005) 1153-1162
35. Fellouse F.A., Wiesmann C., and Sidhu S.S. Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition. Proc Natl Acad Sci U S A 101 (2004) 12467-12472
36. Knappik A., Ge L., Honegger A., Pack P., Fischer M., Wellnhofer G., Hoess A., Wolle J., Pluckthun A., and Virnekas B. Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides. J Mol Biol 296 (2000) 57-86
37. Sidhu S.S., Li B., Chen Y., Fellouse F.A., Eigenbrot C., and Fuh G. Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions. J Mol Biol 338 (2004) 299-310
38. Silacci M., Brack S., Schirru G., Marlind J., Ettorre A., Merlo A., Viti F., and Neri D. Design, construction, and characterization of a large synthetic human antibody phage display library. Proteomics 5 (2005) 2340-2350
39. H single domain with a germ-line scaffold. J Mol Biol 337 (2004) 893-903
40. Fellouse FA, Esaki K, Birtalan S, Raptis D, Cancasci VJ, Koide A, Jhurani P, Vasser M, Wiesmann C, Kossiakoff AA et al.: High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. J Mol Biol, doi:10.1016/j.jmb.2007.08.005. Conformational and chemical diversity was systematically added into a simple antibody library restricted to a single framework and dominated by tyrosine and serine. Despite the simplicity of the design, numerous high affinity antibodies were generated against a large panel of antigens in a high-throughput manner. Libraries of this type should be useful in proteomics applications that will require the rapid generation and analysis of antibodies against large arrays of diverse antigens.
41. Fuh G., Wu P., Liang W.-C., Ultsch M., Lee C.V., Moffat B., and Wiesmann C. Structure-function studies of two synthetic anti-vascular endothelial growth factor Fabs and comparison with the Avastin™ Fab. J Biol Chem 281 (2006) 6625-6631
42. Lee C.V., Hymowitz S.G., Wallweber H.J.A., Gordon N.C., Billeci K.L., Tsai S.-P., Compaan D.M., Yin J.P., Gong Q., Kelley R.F., et al. Synthetic anti-BR3 antibodies that mimic BAFF binding and target both human and murine B cells. Blood 108 (2006) 3103-3111
43. HH properties. J Immunol Methods 263 (2002) 97-109
44. Hs by a phage selection. J Biol Chem 280 (2005) 41395-41403
45. HH domains illustrate the dominant role of binding-site shape in determining the strong binding preference of these domains for active site clefts.
46. Persson H., Lantto J., and Ohlin M. A focused antibody library for improved hapten recognition. J Mol Biol 357 (2006) 607-620. A 'cavity' library was constructed with an anti-hapten antibody as the framework and diversity restricted to positions commonly involved in hapten binding. The library proved to be extremely effective in targeting small-molecule haptens. This study demonstrates that focused libraries with design features tailored to particular antigen classes may be especially effective for synthetic antibody development.
47. Sheridan C. Pharma consolidates its grip on post-antibody landscape. Nat Biotechnol 25 (2007) 365-366
48. Schweizer A., Roschitzki-Voser H., Amstutz P., Briand C., Gulotti-Georgieva M., Prenosil E., Binz H.K., Capitani G., Baici A., Pluckthun A., et al. Inhibition of caspase-2 by a designed ankyrin repeat protein: specificity, structure, and inhibition mechanism. Structure 15 (2007) 625-636. Ankyrin repeat proteins that bind and inhibit caspase-2 were produced. A crystal structure revealed the structural basis for allosteric inhibition where the inhibitor stabilizes an inactive conformation.
49. Zahnd C., Wyler E., Schwenk J.M., Steiner D., Lawrence M.C., McKern N.M., Pecorari F., Ward C.W., Joos T.O., and Pluckthun A. A designed ankyrin repeat protein evolved to picomolar affinity to her2. J Mol Biol 369 (2007) 1015-1028
50. Kawe M., Forrer P., Amstutz P., and Pluckthun A. Isolation of intracellular proteinase inhibitors derived from designed ankyrin repeat proteins by genetic screening. J Biol Chem 281 (2006) 40252-40263
51. Binz H.K., Amstutz P., Kohl A., Stumpp M.T., Briand C., Forrer P., Grutter M.G., and Pluckthun A. High-affinity binders selected from designed ankyrin repeat protein libraries. Nat Biotechnol 22 (2004) 575-582
52. Bond C.J., Wiesmann C., Marsters Jr. J.C., and Sidhu S.S. A structure-based database of antibody variable domain diversity. J Mol Biol 348 (2005) 699-709
53. Pancer Z., Amemiya C.T., Ehrhardt G.R., Ceitlin J., Gartland G.L., and Cooper M.D. Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature 430 (2004) 174-180
54. Forrer P., Stumpp M.T., Binz H.K., and Pluckthun A. A novel strategy to design binding molecules harnessing the modular nature of repeat proteins. FEBS Lett 539 (2003) 2-6
55. Fellouse F.A., Barthelemy P.A., Kelley R.F., and Sidhu S.S. Tyrosine plays a dominant functional role in the paratope of a synthetic antibody derived from a four amino acid code. J Mol Biol 357 (2006) 100-114
56. Sidhu S.S., and Kossiakoff A.A. Exploring and designing protein function with restricted diversity. Curr Opin Chem Biol (2007)
57. Pal G., Kouadio J.-L.K., Artis D.R., Kossiakoff A.A., and Sidhu S.S. Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning. J Biol Chem 281 (2006) 22378-22385. 'Quantitative saturation' scanning was developed, where a small number of interface residues are fully randomized and quantitative energetics information is deduced from a large sequence database of functional variants.
58. Kotz J.D., Bond C.J., and Cochran A.G. Phage-display as a tool for quantifying protein stability determinants. Eur J Biochem 271 (2004) 1623-1629
59. Lendel C., Dogan J., and Hard T. Structural basis for molecular recognition in an affibody:affibody complex. J Mol Biol 359 (2006) 1293-1304
60. Korndorfer I.P., Schlehuber S., and Skerra A. Structural mechanism of specific ligand recognition by a lipocalin tailored for the complexation of digoxigenin. J Mol Biol 330 (2003) 385-396