Abstract
The enormous potential of combinatorial approaches for studying problems in biology and chemistry has been clearly demonstrated over the last several years. In particular, phage display has become one of the major techniques for the use of combinatorial peptide and protein libraries. The reasons for the success of phage display are, at least, threefold: (1) phage display of combinatorial libraries creates a direct link between phenotype (the selectable properties of interest from the displayed library) and genotype (their sequences); (2) it offers the possibility to select and amplify single clones out of large libraries; (3) it allows in vitro as well as in vivo selections in order to evolve peptides and proteins with novel activities. Reported applications include selections of peptides as lead compounds in pharmaceutical research, redesign of protein structures and protein—protein interactions, screening of cDNA libraries and enzyme design. This diversity in applications has been made possible by the development of a variety of display formats and selection schemes and an increasing understanding of the biology of filamentous bacteriophages.
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References
Atwell S, Ultsch M, De Voss AM, Wells JA (1997a) Structural plasticity in a remodeled protein—protein interface. Science 278: 1125–1128
Atwell S, Ridgway JBB, Wells JA, Carter P (1997b) Stable heterodimers from remodeling the domain interface of a homodimer using a phage display library. J Mol Biol 270: 26–35
Baca M, Scanlan TS, Stephenson RC, Wells JA (1997) Phage Display of a catalytic antibody to optimize affinity for transition state binding. Proc Natl Acad Sci USA 94: 10063–10068
Barbas III CF, Kang AS, Lerner RA, Benkovic SJ (1991) Assembly of combinatorial antibody libraries on phage surface: the gene III site. Proc Natl Acad Sci USA 88: 7978–7982
Bass S, Greene R, Wells JA (1990) Hormone phage: an enrichment method for variant proteins with altered binding properties. Proteins 8: 309–314
Bass SH, Mulkerrin MG, Wells JA (1991) A systematic mutational analysis of hormone-binding deter-minants in the human growth hormone receptor. Proc Natl Acad Sci USA 88: 4498–4502
Biocca S, Cattaneo A (1995) Intracellular immunization: antibody targeting to subcellular compartments. Trends Cell Biol 5: 59–63
Boder ET, Wittrup KD (1997) Yeast surface display for screening combinatorial polypeptide libraries. Nature Biotechnol 15: 553–557
Bothmann H, Plückthun A (1998) Selection for a periplasmic factor improving phage display and functional periplasmic expression. Nature Biotechnol 16: 376–380
Boublik Y, Di Bonito P, Jones IM (1995) Eukaryotic virus display: Engineering the major surface glycoprotein of the Autographa californica nuclear polyhedrosis virus ( AcNPV) for the presentation of foreign proteins on the virus surface. BioTechnology 13: 1079–1084
Braisted A, Wells JA (1996) Minimizing a binding domain from protein A. Proc Natl Acad Sci USA 93: 5688–5692
Chen R, Henning U (1996) A periplasmic protein (Skp) of Escherichia cou selectively binds a class of outer membrane proteins. Mol Microbiol 19: 1287–1294
Chiswell DJ and McCafferty J (1992) Phage antibodies: will new ‘coliclonal’ antibodies replace monoclonal antibodies? Trends in Biotechnol 10: 80–84
Choo Y, Klug A (1994) Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc Natl Acad Sci USA 91: 11163–11167
Clackson T, Wells JA (1994) In vitro selection from protein and peptide libraries. Trends Biotechnol 12: 173–184
Cortese R, Monaci P, Nicosia A, Luzzago A, Felici F, Galfré G, Pessi A, Tramontao A, Sollazzo M (1995) Identification of biologically active peptides using random libraries displayed on phage. Curr Opin Biotechnol 6: 73–80
Crameri R, Suter M (1993) Display of biologically active proteins on the surface of filamentous phages: a cDNA cloning system for selection of functional gene products linked to the genetic information responsible for their production. Gene 137: 69–75
Crameri R, Jaussi R, Menz G, Blaser K (1994) Display of expression products of cDNA libraries on phage surface: a versatile screening system for selective isolation of genes by specific gene-product/ ligand interaction. Eur J Biochem 226: 53–58
Cwirla SE, Peters EA, Barrett RW, Dower WJ (1990) Peptides on phage: a vast library of peptides for identifying ligands. Proc Natl Acad Sci USA 87: 6378–6382
Devlin JJ, Panganiban LC, Devlin PE (1990) Random peptide libraries: a source of specific protein binding molecules. Science 249: 404–406
Dokland T, Murialdo H (1993) Structural transitions during maturation of bacteriophage lambda capsids. J Mol Biol 233: 682–694
Duenas M, Borrebaeck CAK (1994) Clonal selection and amplification of phage displayed antibodies by linking antigen recognition and phage replication. Bio/Technology 12: 999–1002
Dunn IS (1995) Assembly of functional bacteriophage lambda virions incorporating COOH-terminal peptide or protein fusions with the major tail protein. J Mol Biol 248: 497–506
Dunn IS (1996) Phage display of proteins. Curr Opin Biotechnol 7: 547–553
Endemann H, Model P (1995) Location of filamentous phage minor coat proteins in phage and in infected cells. J Mol Biol 250: 496–506
Efimov VP, Nepluev IV, Mesyanzhinov VV (1995) Bacteriophage T4 as a surface display vector. Virus Genes 10: 173–177
Fujii I, Fukuyama S, Iwabuchi Y, Tanimura R (1998) Evolving catalytic antibodies in a phage-displayed combinatorial library. Nature Biotechnol 16: 463–467
Gao C, Lavey BJ, Lo C-HL, Datta A, Wentworth Jr. P, Janda KD (1998) Direct selection for catalysis from combinatorial antibody libraries using a boronic acid probe: Primary amide bond hydrolysis. J Am Chem Soc 120: 2211–2217
Gao C, Lin C-H, Lo C-HL, Mao S, Wirsching P, Lerner RA, Janda KD (1997) Making chemistry selectable by linking it to infectivity. Proc Natl Acad USA 94: 11777–11782
Garrard LJ, Yang M, O’Connell MP, Kelley RF, Henner DJ (1991) Fab assembly and enrichment in a monovalent phage display system. Bio/Technology 9: 1373–1377
Giebel LB, Cass RT, Milligan DL, Young DC, Arze R, Johnson CR (1995) Screening of cyclic peptide phage libraries identifies ligands that bind streptavidin with high affinities. Biochemistry 34: 15430–15435
Goldsmith ME, Konigsberg WH (1977) Adsorption protein of bacteriophage fd: Isolation, molecular properties, and location in virus. Biochemistry 16: 2686–2694
Gram H, Strittmatter U, Lorenz M, Gluck D, Zenke G (1993) Phage display as a rapid gene expression system: Production of bioactive cytokine-phage and generation of neutralizing monoclonal antibodies. J Immunol Methods 161: 169–176
Gramatikoff K, Georgiev O, Schaffner W (1994) Direct interaction rescue, a novel filamentous phage technique to study protein-protein interactions. Nue Acids Res 22: 5761–5762
Gramatikoff K, Schaffner W, Georgiev O (1995) The leucine zipper of c-Jun binds to ribosomal protein Ll8a: a role in Jun protein regulation? Biol Chem Hoppe-Seyler 376: 321–325
Grant RA, Lin TC, Konigsberg W, Webster RE (1981) Structure of the filamentous bacteriophage fl: Location of the A, C and D minor coat proteins. J Biol Chem 256: 539–546
Gray CW, Brown RS, Marvin DA (1981) Adsorption complex of filamentous fd virus. J Mol Biol 146: 621–627
Greisman HA, Pabo CO (1997) A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science 275: 657–661
Griffith AD, Duncan AR (1998) Strategies for selection of antibodies by phage display. Curr Opin Biotechnol 9: 102–108
Gu H, Kim D, Baker D (1997) Contrasting roles for symmetrically disposed (3-turns in the folding of a small protein. J Mol Biol 274: 588–596
Gu H, Yi Q, Bray ST, Riddle DS, Shiau AK, Baker D (1995) A phage display system for studying the sequence determinants of protein folding. Protein Sci 4: 1108–1117
Hansson LO, Widersten M, Mannervik B (1997) Mechanism-based phage display selection of active-site mutants of human glutathione transférase Al-1 catalyzing SNAr reactions. Biochemistry 36: 11252–11260
Holliger P, Riechmann L (1997) A conserved infection pathway for filamentous bacteriophages is suggested by the structure of the membrane penetration domain of the minor coat protein g3p from phage fd. Structure 5: 265–275
Hottiger M, Gramatikoff K, Georgiev O, Chaponnier C, Schaffner W, Hubscher U (1995) The large subunit of HIV-1 reverse transcriptase interacts with l-actin. Nuc Acids Res 23: 736–741
Iannolo G, Minenkova O, Petruzzelli R, Cesareni G (1995) Modifying filamentous phage capside: Limits in the size of the major capsid protein. J Mol Biol 248: 835–844
Jacobson A (1972) Role of F pili in the penetration of bacteriophage fl. J Virol 10: 835–843
Jamieson AC, Kim S-H, Wells JA (1994) In vitro selection of zinc fingers with altered DNA-binding specificity. Biochemistry 33: 5689–5695
Janda KD, Lo C-HL, Li T, Barbas CF III, Wirsching P, Lerner RA (1994) Direct selection for a catalytic mechanism from combinatorial antibody libraries. Proc Natl Acad Sci USA 91: 2532–2536
Janda KD, Lo L-C, Lo C-HL, Sim M-M, Wang R, Wong C-H, Lerner RA (1997) Chemical selection for catalysis in combinatorial antibody libraries. Science 275: 945–948
Jiang J, Abu-Shilbayeh L, Rao VB (1997) Display of a PorA peptide from Neisseria meningitidis on the bacteriophage T4 capsid surface. Infect Immun 65: 4770–4777
Jespers LS, De Keyser A, Stanssens PE (1996) LambdaZLG6: a phage lambda vector for high-efficiency cloning and surface expression of cDNA libraries on filamentous phage. Gene 173: 179–181
Jespers LS, Messens JH, De Keyser A, Eeckhout D, Van Den Brande I, Gansemans YG, Lauwereys MJ, Vlasuk GP, Stanssens PE (1995) Surface expression and ligand-based selection of cDNAs fused to filamentous phage gene VI. Bio/Technology 13: 378–382
Kang AS, Barbas III CF, Janda KD, Benkovic SJ, Lerner RA (1991) Linkage of recognition and replication functions by assembling combinatorial antibody Fab libraries along phage surface. Proc Natl Acad Sci USA 88: 4363–4366
Katz BA (1995) Binding to protein targets of peptidic leads discovered by phage display: crystal structures of streptavidin-bound linear and cyclic peptide ligands containing the HPQ sequence. Biochemistry 34: 15421–15429
Knappik A, Krebber C, Plückthun A (1993) The effect of folding catalysts on the in vivo folding process of different antibody fragments expressed in Escherichia coli. Biotechnology 11: 77–83
Krebber C, Spada S, Desplancq, Krebber A, Plückthun A (1995) Co-selection of cognate antibody-antigen pairs by selectively-infective phages. FEBS Letters 377: 227–231
Krebber C,Spada S, Desplancq, Krebber A, Ge L, Plückthun A (1997) Selectively-infective phage (SIP): A mechanistic dissection of a novel in vivo selection for protein-ligand interactions. J Mol Biol 268:607–618
Ku J, Schultz PG (1996) Alternate protein frameworks for molecular recognition. Proc Natl Acad Sci USA 92: 6552–6556
Kuwabara I, Maruyama H, Mikawa YG, Zuberi RI, Liu FT, Maruyama IN (1997) Efficient epitope mapping by bacteriophage 1 surface display. Nature Biotechnol 15: 74–78
Lin TC, Webster RE, Konigsberg W (1980) Isolation and characterization of the C and D proteins coded by gene IX and gene VI in the filamentous bacteriophage fl and fd. J Biol Chem 255: 10331–10337
Lindqvist BH, Naderi S (1995) Peptide presentation by bacteriophage P4. FEMS Microbiol Rev 17: 33–39
Livnah O, Stura E, Johnson DL, Middleton SA, Mulcahy LS, Wrighton NC, Dower WJ, Jolliffe LK, Wilson IA (1996) Functional mimicry of a protein hormone by a peptide agonist: The EPO receptor complex at 2.8 A. Science 273: 464–471
Lopez J, Webster RE (1983) Morphogenesis of filamentous bacteriophage fl: Orientation of extrusion and production of polyphage. Virology 127: 177–193
Lowman HB, Wells JA (1993) Affinity maturation of human growth hormone by monovalent phage display. J Mol Biol 234: 564–578
Lubkowski J, Hennecke F, Plückthun A, Wlodawer A (1998) The structural basis of phage display elucidated by the crystal structure of the N-terminal domains of g3p. Nature Struct Biol 5: 140–147
Malik P, Terry TD, Gowda LR, Langara A, Petukhov SA, Symmons MF, Welsh LC, Marvin DA, Perham RN (1996) Role of capsid structure and membrane protein processing in determining the size and copy number of peptides displayed on the major coat protein of filamentous bacteriophage. J Mol Biol 260: 9–21
Malmborg A-C, Söderlind E, Frost L, Borrebaeck CAK (1997) Selective phage infection mediated by epitope expression on F pilus. J Mol Biol 273: 544–551
Markland W, Roberts BL, Saxena MJ, Guterman SK, Ladner RC (1991) Design, construction and function of a multicopy display vector using fusions to the major coat protein of bacteriophage M13. Gene 109: 13–19
Martin F, Toniatti C, Salvati AL, Ciliberto G, Cortese R, Sollazzo M (1996) Coupling protein design and in vitro selection strategies: improving specificity and affinity of a designed beta-protein IL-6 antagonist. J Mol Biol 255: 86–97
Maruyama IN, Maruyama HI, Brenner S (1994) Xfoo: A X phage vector for the expression of foreign proteins. Proc Natl Acad Sci USA 91: 8273–8277
Mikawa YG, Maruyama IN, Brenner S (1996) Surface display of proteins on bacteriophage X heads. J Mol Biol 262: 21–30
McCafferty J, Jackson RH, Chiswell DJ. (1992) Phage-enzymes: expression and affinity chromatography of functional alkaline phosphatase on the surface of bacteriophage. Protein Eng 4: 955–961
McConnell SJ, Hoess RH (1995) Tendamistat as a scaffold for conformationally constrained phage peptide libraries. J Mol Biol 250: 460–470
Model P, Russel M (1988) Filamentous Bacteriophage. In: Bacteriophages 2: 375–456.
Nord K, Gunneriusson E, Ringdahl J, Stahl S, Uhlen M, Nygren PA (1997) Binding proteins selected from combinatorial libraries of an alpha-helical bacterial receptor domain. Nature Biotechnol 15: 772–777
Ohkawa I, Webster RE (1981) The orientation of the major coat protein of bacteriophage fl in the cytoplasmic membrane of Escherichia cols. J Biol Chem 256: 9951–9958
O’Neil KT, Hoess RH, Raleigh DP, DeGrado WP (1995) Thermodynamic genetics of the folding of the BI immunoglobulin-binding domain from streptococcal protein G. Proteins Struct Funct Genet 21: 11–21
Pasqualini R, Ruoslahti E (1996) Organ targeting in vivo using phage display peptide libraries. Nature 380: 364–366
Pedrazzi G, Schwesinger F, Honegger A, Krebber C, Plückthun A (1997) Affinity and folding properties both influence the selection of antibodies with the selectively infective phage ( SIP) methodology. FEBS Lett 415: 289–293
Proba K, Wörn A, Honegger A, Plückthun A (1998) Antibody scFv fragments without disulfide bonds made by molecular evolution. J Mol Biol 275: 245–253
Rakonjac J, Model P (1994) The influence of the reducing agent dithiothreitol In vitro on infectivity of fl particles. Gene 142: 153–154
Rader C, Barbas III CF (1997) Phage display of combinatorial antibody libraries. Curr Opin Biotechnol 8: 503–508
Rebar EJ, Pabo CO (1994) Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science 263: 671–673
Ren ZJ, Lewis GK, Wingfield PT, Locke EG, Steven AC, Black LW (1996) Phage display of intact domains at high copy number: a system based on SOC, the small outer capsid protein of bacteriophage T4. Protein Sci 5: 1833–1843
Riechmann L, Holliger P (1997) The COOH-terminal domain of ToIA is the coreceptor for filamentous phage infection of E. cols. Cell 90: 351–360
Saggio I, Gloaguen I, Laufer R (1995) Functional phage display of ciliary neurotrophic factor. Gene 152: 35–39
Schultz PG, Lerner RA (1995) From molecular diversity to catalysis: Lessons from the immune system. Science 269: 1835–1842
Scott JK, Smith GP (1990) Searching for peptide ligands with an epitope library. Science 249: 386–390
Smilowitz H (1974) Bacteriophage fl infection: Fate of the parental coat protein. J Virol 13: 94–99
Smith GP (1985) Filamentous fusion phage: Novel expression vectors that display cloned antigens on the virion surface. Science 228: 1315–1317
Smith GP, Patel SU, Windass JD, Thornton JM, Winter G, Griffiths AD (1998) Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage. J Mol Biol 277: 317–332
Soumillion P, Jespers L, Bouchet M, Marchand-Brynaert J, Winter G, Fastrez J (1994) Selection of 13-lactamase on filamentous bacteriophage by catalytic activity. J Mol Biol 237: 415–422
Stahl S, Uhlen M (1997) Bacterial surface display: trends and progress. Trends Biotechnol 15: 185–192
Starovasnik MA, Braistd AC, Wells JA (1997) Structural mimicry of a native protein by a minimized binding domain. Proc Natl Acad Sei USA 94: 10080–10085
Sternberg N, Hoess RH (1995) Display of peptides and proteins on the surface of bacteriophage X. Proc Natl Acad Sci USA 92: 1609–1613
Wickner W (1975) Asymmetric orientation of a phage coat protein in cytoplasmic membrane of Escherichia coli. Proc Natl Acad Sci USA 72: 4749–4753
Wrighton NC, Balasubramanian P, Barbone FP, Kashyap AK, Farrell FX, Jolliffe LK, Barrett RW, Dower WJ (1997) Increased potency of an erythropoietin peptide mimetic through covalent dimerization. Nature Biotechnol 15: 1261–1265
Wrighton NC, Farrell FX, Chang R, Kashyap AK, Barbone FP, Mulcahy LS, Johnson DL, Barrett RW, Jolliffe LK, Dower WJ (1996) Small peptides as potent mimetics of the protein hormone erythropoietin. Science 273: 458–463
Wu H, Yang W-P, Barbas III CF (1995) Building zinc fingers by selection: Toward a therapeutic application. Proc Natl Acad Sci USA 92: 344–348
Yanofsky SD, Baldwin DN, Butler JH, Holden FR, Jacobs JW, Balasubramanian P, Chinn JP, Cwirla SE, Peters-Bhatt E, Whitehorn EA, Tate EH, Akeson A, Bowlin TL, Dower WJ, Barrett RW (1996) High affinity type I interleukin 1 receptor antagonists discovered by screening recombinant peptide libraries. Proc Natl Acad Sei USA 93: 7381–7386
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Johnsson, K., Ge, L. (1999). Phage Display of Combinatorial Peptide and Protein Libraries and Their Applications in Biology and Chemistry. In: Famulok, M., Winnacker, EL., Wong, CH. (eds) Combinatorial Chemistry in Biology. Current Topics in Microbiology and Immunology, vol 243. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-60142-2_5
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