PEPTIDE DISPLAY LIBRARIES: DESIGN AND CONSTRUCTION*

REFERENCES

• Smith G. P. Filamentous Fusion Phage: Novel Expression Vectors That Display Cloned Antigens on the Virion Surface. Science 1985; 228: 1315–1317
   PubMed Web of Science ®Google Scholar
• Sanger F. DNA Sequencing with Chain-Terminating Inhibitors. Proc. Natl. Acad. Sci. USA 1977; 74: 5463–5467
   PubMed Web of Science ®Google Scholar
• Kunkel T. A., Roberts J. D., Zakour R. A. Rapid and Efficient Site-Specific Mutagenesis without Phenotypic Selection. Meth. Enzymol. 1987; 154: 367–382
   PubMed Web of Science ®Google Scholar
• Parmley S. F., Smith G. P. Antibody-Selectable Filamentous fd Phage Vectors. Affinity Purification of Target Genes. Gene 1988; 73: 305–318
   Google Scholar
• Scott J. K., Smith G. P. Searching for Peptide Ligands with an Epitope Library. Science 1990; 249: 386–390
   PubMed Web of Science ®Google Scholar
• Vieira J., Messing J. Production of Single-Stranded Plasmid DNA. Meth. Enzymol. 1987; 153: 3–11
   PubMed Web of Science ®Google Scholar
• Feiss M. Lambda II, A. Becker, R. W. Hendrix, J. W. Roberts, F. W. Stahl, R. W. Weisberg. Cold Spring Harbor Lab Press, Plainview, NY 1983; 279–304
   Google Scholar
• Stemberg N., Hoess R. H. Display of Peptides and Proteins on the Surface of Bacteriophage λ. Proc. Natl. Acad. Sci. USA 1995; 92: 1609–1613
   Google Scholar
• Maruyama I. N., Maruyama H. I., Brenner S. λfoo: A λ Phage Vector for the Expression of Foreign Proteins. Proc. Natl. Acad. Sci. USA 1994; 91: 8273–8277
   PubMed Web of Science ®Google Scholar
• Lu Z., Murray K. S., Van Cleave V., La Vallie E. R., Stahl M. L., McCoy J. M. Expression of Thioredoxin Random Peptide Libraries on the Surface as Functional Fusion to Flagellin: A System Designed for Exploring Protein–Protein Interactions. BioTechnology 1995; 13: 366–372
   PubMed Web of Science ®Google Scholar
• La Vallie E. R., Diblasio E. A., Kovacic S., Grant K. L., Schendel P. F., McCoy J. M. A Thioredoxin Gene Fusion Expression System that Circumvents Inclusion Body Formation in the E. coli Cytoplasm. BioTechnology 1993; 11: 1187–1193
   Google Scholar
• La Vallie E. R., Stahi M. L. Cloning of the Flagellin Gene from Bacillus subtilis and Complementation Studies of an In Vitro-Derived Deletion Mutation. J. Bacteriol. 1989; 171: 3085–3094
   Google Scholar
• Wilson A. R., Beveridge T. J. Bacterial Flagellar Filaments and Their Component Flagellins. Can. J. Microbiol. 1993; 39: 451–472
   PubMed Web of Science ®Google Scholar
• Model P., Russel M. Filamentous Bacteriophage. The Bacteriophages, R. Calendar. Plenum Press, New York 1988; 375–456
   Google Scholar
• Greenwood J., Willis A. E., Perham R. N. Multiple Display Foreign Peptides on a Filamentous Bacteriophage: Peptides from Plasmodium falciparum Circumsporozoite Protein as Antigens. J. Mol. Biol. 1991; 220: 821–827
   PubMed Web of Science ®Google Scholar
• Kang A. S., Barbas C. F., Janda K. D., Benkovic S. J., Lerner R. A. Linkage of Recognition and Replication Functions by Assembling Combinatorial Antibody Fab Libraries Along Phage Surfaces. Proc. Natl. Acad. Sci. USA 1991; 88: 4363–4366
   PubMed Web of Science ®Google Scholar
• Banner D. W., Nave C., Marvin D. A. Structure of the Protein and DNA in fd Filamentous Bacterial Virus. Nature 1981; 289: 814–816
   Google Scholar
• Luzzago A., Felici F., Tramontano A., Pessi A., Cortese R. Mimicking of Discontinuous Epitopes by Phage-Displayed Peptides, I. Epitope Mapping of Human H Ferritin Using a Phage Library of Constrained Peptides. Gene 1993; 128: 51–57
   PubMed Web of Science ®Google Scholar
• Devlin J. J., Panganiban L. C., Devlin P. E. Random Peptide Libraries: A Source of Specific Protein Binding Molecules. Science 1990; 249: 404–406
   PubMed Web of Science ®Google Scholar
• Simons G. F.M., Konings R. N.H., Schoenmakers J. G.G. Genes VI, VII and IX of Phage M13 Code for Minor Capsid Proteins of the Virion. Proc. Natl. Acad. Sci. USA 1981; 78: 4194–4198
   Google Scholar
• Jespers L. S., Messens J. H., De Keyser A., et al. Surface Expression and Ligand-Based selection of cDNAs Fused to Filamentous Phage Gene VI. BioTechnology 1995; 13: 378–382
   PubMedGoogle Scholar
• Stemberg N., Weisberg R. Packaging of Coliphage Lambda DNA, II. The Role of the Gene D Protein. J. Mol. Biol. 1977; 117: 733–759
   Google Scholar
• Imber R., Tsugita A., Wurtz M., Hohn T. Outer Surface Protein of Bacteriophage Lambda. J. Mol. Biol. 1980; 139: 277–295
   Google Scholar
• Dokland T., Murialdo H. Structural Transitions during Maturation of Bacteriophage Lambda Capsids. J. Mol. Biol. 1993; 233: 682–694
   Google Scholar
• Buchwald M., Murialdo H., Siminovitch L. The Morphogenesis of Bacteriophage Lambda. II. Identification of the Principal Structural Proteins. Virology 1979; 42: 390–400
   Google Scholar
• Casjens S. R., Hendrix R. W. Locations and Amounts of Major Structural Proteins in Bacteriophage Lambda. J. Mol. Biol. 1974; 88: 535–545
   Google Scholar
• Katsura I. Structure and Function of the Major Tail Protein of Bacteriophage Lambda. Mutants having Small Major Tail Protein Molecules in Their Virion. J. Mol. Biol. 1981; 146: 493–512
   Google Scholar
• Von Heijne G. Patterns of Amino Acids near Signal Sequence Cleavage Sites. Eur. J. Biochem. 1983; 133: 17–21
   PubMedGoogle Scholar
• Von Heijne G. A New Method for Predicting Signal Sequence Cleavage Sites. Nucleic Acids Res. 1986; 14: 4683–4690
   PubMed Web of Science ®Google Scholar
• Kuwajima G. Construction of a Minimum-Size Functional Flagellin of E. coli. J. Bacteriol. 1988; 170: 3305–3309
   PubMed Web of Science ®Google Scholar
• Katti S. K., LeMaster D. M., Eklund H. Crystal Structure of Thioredoxin from E. coli at 1.68 Angstroms Resolution. J. Mol. Biol. 1990; 212: 167–184
   PubMed Web of Science ®Google Scholar
• Smith G. P., Scott J. K. Libraries of Peptides and Proteins Displayed on Filamentous Phage. Meth. Enzymol. 1993; 217: 228–257
   PubMed Web of Science ®Google Scholar
• Mandecki W. A Method for Construction of Long Randomized Open Reading Frames and Polypeptides. Protein Eng. 1990; 3: 221–226
   Google Scholar
• LaBean T. H., Kauffman S. A. Design of Synthetic Gene Libraries Encoding Random Sequence Proteins with Desired Ensemble Characteristics. Protein Sci. 1993; 2: 1249–1254
   Google Scholar
• Clackson T., Wells J. A. In Vitro Selection from Protein and Peptide Libraries. Trends Biotechnol. 1994; 12: 173–184
   PubMed Web of Science ®Google Scholar
• Scott J. K. Discovering Peptide Ligands Using Epitope Libraries. Trends Biotechnol. 1992; 17: 241–245
   Google Scholar
• Giebel L. B., Cass R. T., Milligan D. L., Young D. C., Arze R., Johnson C. R. Screening of Cyclic Peptide Phage Libraries Identifies Ligands That bind Streptavidin with High Affinities. Biochemistry 1995; 34: 15430–15435
   PubMed Web of Science ®Google Scholar
• Pasqualini R., Koivunen E., Ruoslahti E. A Peptide Isolated from Phage Display Libraries is a Structural and Functional Mimic of an RGD-Binding Site on Integrins. J. Cell. Biol. 1995; 130(5)1189–1196
   Google Scholar
• Wrighton N. C., Farrel F. X., Chang R., et al. Small Peptides as Potent Mimetics of the Protein Hormone Erythropoietin. Science 1996; 273: 458–463
   PubMed Web of Science ®Google Scholar
• Pasqualini R., Ruoslahti E. Organ Targeting In Vivo Using Phage Display Peptide Libraries. Nature 1996; 380: 364–366
   PubMed Web of Science ®Google Scholar
• Couet J., Li S., Okamoto T., Ikezu T., Lisanti M. P. Identification of Peptide and Protein Ligands for the Caveolin-Scaffolding Domain. J. Biol. Chem. 1997; 272: 6525–6533
   PubMed Web of Science ®Google Scholar
• Li M. Use of a Modified Bacteriophage to Probe the Interactions Between Peptides and Ion Channel Receptors in Mammalian Cells. Nat. Biotechnol. 1997; 15: 559–563
   Google Scholar
• Mukhija S., Erni B. Phage Display Selection of Peptides Against Enzyme I of the Phosphoenolpyruvate-Sugar Phosphotransferase System. Mol. Microbiol. 1997; 25: 1159–1166
   Google Scholar
• Balass M., Heldman Y., Cabilly S., Givol D., Katchalski-Katzir E., Fuchs S. Identification of a Hexapeptide That Mimics a Conformation-Dependent Binding Site of Acetylcholine Receptor by Use of a Phage-Epitope Library. Proc. Natl. Acad. Sci. USA 1993; 90: 10638–10642
   Google Scholar
• Gaynor B., Putterman C., Valdon P., Spatz L., Scharff M. D., Diamond B. Peptide Inhibition of Glomerular Deposition of an Anti-DNA Antibody. Proc. Natl. Acad. Sci. USA 1997; 94: 1955–1960
   PubMed Web of Science ®Google Scholar
• Nord K., Gunneriusson E., Ringdahi J., Stahl S., Uhlen M., Nygren P. Binding Proteins Selected from Combinatorial Libraries of an α-Helical Bacterial Receptor Domain. Nat. Biotechnol. 1997; 15: 772–777
   PubMed Web of Science ®Google Scholar
• Sato A., Ida N., Fukuyama M., Miwa K., Kazami J., Nakamura H. Identification from a Phage Display Library of Peptides That Bind to Toxic Shock Syndrome Toxin-1 and that Inhibit its Binding to Major Histocompatibility Complex (MHC) Class II Molecules. Biochemistry 1996; 35: 10441–10447
   PubMed Web of Science ®Google Scholar
• Yanofsky S. D., Baldwin D. N., Butler J. H., et al. High Affinity Type I Interleukin 1 Receptor Antagonists Discovered by Screening Recombinant Peptide Libraries. Proc. Natl. Acad. Sci. USA 1996; 93: 7381–7386
   PubMed Web of Science ®Google Scholar
• Markland W., Ley A. C., Ladner R. C. Iterative Optimization of High-Affinity Protease Inhibitors Using Phage Display. 2. Plasma Kallikrein and Thrombin. Biochemistry 1996; 35: 8058–8067
   PubMed Web of Science ®Google Scholar
• Castaño A. R., Tangri S., Miller J. E.W., et al. Peptide Binding and Presentation by Mouse CD1. Science 1995; 269: 223–226
   PubMed Web of Science ®Google Scholar
• Cheng X., Juliano R. L. Identification of a Biologically Significant DNA-Binding Peptide Motif by Use of a Random Phage Display Library. Gene 1996; 171: 1–8
   PubMed Web of Science ®Google Scholar
• Krook M., Mosbach K., Lindbladh C. Selection of Peptides with Affinity for Single-Stranded DNA Using a Phage Display Library. Biochem. Biophys. Res. Commun. 1994; 204(2)849–854
   Google Scholar
• Dyson M. R., Murray K. Selection of Peptide Inhibitors of Interactions Involved in Complex Protein Assemblies: Association of the Core and Surface Antigens of Hepatitis B Virus. Proc. Natl. Acad. Sci. USA 1995; 92: 2194–2198
   PubMed Web of Science ®Google Scholar
• Cheadle C., Ivashchenko Y., South V., et al. Identification of a Src SH3 Domain Binding Motif by Screening a Random Phage Display Library. J. Biol. Chem. 1994; 269: 24034–24039
   PubMed Web of Science ®Google Scholar
• Sparks A. B., Quilliam L. A., Thorn J. M., Der C. J., Kay B. K. Identification and Characterization of Src SH3 Ligands from Phage-Displayed Random Peptide Libraries. J. Biol. Chem. 1994; 269(39)23853–23856
   Google Scholar
• Renschler M. F., Bhatt R. R., Dower W. J., Levy R. Synthetic Peptide Ligands of the Antigen Binding Receptor Induce Programmed Cell Death in a Human B Cell Lynphoma. Proc. Natl. Acad. Sci. USA 1994; 91: 3623–3627
   PubMed Web of Science ®Google Scholar
• Daniels D. A., Lane D. P. The Characterization of p53 Binding Phage Isolated from Phage Peptide Display Libraries. J. Mol. Biol. 1994; 243: 639–652
   Google Scholar
• Balass M., Katchalski-Katzir E., Fuchs S. The α-Bungarotoxin Binding Site on the Nicotinic Acetylcholine Receptor: Analysis Using a Phage-Epitope Library. Proc. Natl. Acad. Sci. USA 1997; 94: 6054–6058
   PubMed Web of Science ®Google Scholar
• Scott J. K., Loganathan D., Easley R. B., Gong X., Goldstein I. J. A Family of Concanavalin A-Binding Peptides from a Hexapeptide Epitope Library. Proc. Natl. Acad. Sci. USA 1992; 89: 5398–5402
   PubMed Web of Science ®Google Scholar
• Oldemburg K. R., Loganathan D., Goldstein I. J., Schultz P. G., Gallop M. A. Peptide Ligands for Sugar-Binding Protein Isolated from a Random Peptide Library. Proc. Natl. Acad. Sci. USA 1992; 89: 5393–5397
   Google Scholar
• Tabler M., Benos P., Dörr M. Representation of Unique Sequences in Libraries of Randomized Nucleic Acids. Nucleic Acids Res. 1996; 24: 3437–3438
   Google Scholar
• Reidhaar-Olson J. F., Sauer R. T. Combinatorial Cassette Mutagenesis as a Probe of the Informational Content of Protein Sequences. Science 1988; 241: 53–57
   PubMed Web of Science ®Google Scholar
• Chen K., Arnold F. H. Enzyme Engineering for Nonaqueous Solvents: Random Mutagenesis to Enhance Activity of Subtilisin E in Polar Organic Media. Bio/Technology 1991; 9: 1073–1077
   PubMedGoogle Scholar
• Holm L., Koivula A., Lehtovaara P., Hemminki A., Knowles J. Random Mutagenesis Used to Probe the Structure and Function of Bacillus stearothermophilus α-Amylase. Protein Eng. 1990; 3: 181–191
   Google Scholar
• Merino E., Osuna F., Bolívar F., Soberón X. A General PCR-Based Method for Single or Combinatorial Oligonucleotide-Directed Mutagenesis on pUC-M13 Vectors. Bio/Techniques 1992; 12: 508–510
   Google Scholar
• Hermes J. D., Parekh S. M., Blacklow S. C., Köster H., Knowles J. R. A Reliable Method for Random Mutagenesis: The Generation of Mutant Libraries Using Spiked Oligodeoxyribonucleotide Primers. Gene 1989; 84: 143–151
   PubMedGoogle Scholar
• Del Río G., Osuna J., Soberón X. Combinatorial Libraries of Proteins: Analysis of Efficiency of Muthagenesis Techniques. Bio/Techniques 1994; 17: 1132–1138
   Google Scholar
• Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning, C. Nolan. Cold Spring Harbor Lab. Press, Cold Spring Harbor, NY 1989
   Google Scholar
• Christian R. B., Zuckermann R. N., Kerr J. M., Wang L., Malcom B. A. Simplified Methods for Construction, Assessment and Rapid Screening of Peptide Libraries in Bacteriophage. J. Mol. Biol. 1992; 227: 711–718
   PubMed Web of Science ®Google Scholar
• de la Cruz V. F., Lal A. A., McCutchan T. F. Immunogenicity and Epitope Mapping of Foreign Sequences Via Genetically Engineered Filamentous Phage. J. Biol. Chem. 1988; 263: 4318–4322
   PubMed Web of Science ®Google Scholar
• Huse W. D., Sastry L., Iverson S. A., et al. Generation of a Large Combinatorial Library of the Immunoglobulin Repertoire in Phage Lambda. Science 1989; 246: 1275–1281
   PubMed Web of Science ®Google Scholar
• Cwirla S. E., Peters E. A., Barrett R. W., Dower W. J. Peptides on Phage: A Vast Library of Peptides for Identifying Ligands. Proc. Natl. Acad. Sci. USA 1990; 87: 6378–6382
   PubMed Web of Science ®Google Scholar
• McCafferty J., Griffiths A. D., Winter G., Chiswell D. J. Phage Antibodies: Filamentous Phage Displaying Antibody Variable Domains. Nature 1990; 348: 552–554
   PubMed Web of Science ®Google Scholar
• Breitling F., Dubel S., Seehaus T., Klewinghaus I., Little M. A Surface Expression Vector for Antibodies Screening. Gene 1991; 104: 147–153
   PubMed Web of Science ®Google Scholar
• Markland W., Roberts B. L., Saxena M. J., Guterman S. K., Ladner R. C. Design, Construction and Function of a Multicopy Display Vector Using Fusion to the Major Coat Protein of Bacteriophage M13. Gene 1991; 109: 13–19
   PubMed Web of Science ®Google Scholar
• Felici F., Castagnoli L., Mustacchio A., Jappelli R., Cesareni G. Selection of Antibody Ligands from a Large Library of Oligopeptides Expressed on Multivalent Exposition Vector. J. Mol. Biol. 1991; 222: 301–310
   PubMed Web of Science ®Google Scholar
• Clackson T., Hoogenboom H. R., Griffiths A. D., Winter G. Making Antibody Fragments Using Phage Display Libraries. Nature 1991; 352: 624–628
   PubMed Web of Science ®Google Scholar
• O'Neil K. T., Hoess R. H., Jackson S. A., Ramachandran N. S., Mousa S. A., DeGrado W. F. Identification of Novel Peptide Antagonists for GPIIb/IIIa from a Conformationally Constrained Phage Peptide Library. Proteins: Structure, Function, Genet. 1992; 14: 509–515
   PubMed Web of Science ®Google Scholar
• Cull M. G., Miller J. F., Schatz P. J. Screening for Receptor Ligands Using Large Libraries of Peptides Linked to the C Terminus of the Lac Repressor. Biochemistry 1992; 89: 1865–1869
   Google Scholar
• Guzman L. M., Belin D., Carson M. J., Beckwith J. Tight Regulation, Modulation, and High-Level Expression by Vectors Containing the Arabinose PBAD Promoter. J. Bacteriol 1995; 177: 4121–4130
   PubMed Web of Science ®Google Scholar
• Koivunen E., Bingcheng W., Ruoslahti E. Phage Libraries Displaying Cyclic Peptides with different Ring Sizes: Ligand Specificities of the RGD-Directed. Integrins-Bio/Technology 1995; 13: 265–270
   PubMedGoogle Scholar
• Barbas C. F., 3d, Kang A. S., Lerner R. A., Benkovic S. J. Assembly of Combinatorial Antibody Libraries on Phage Surfaces: The Gene III Site. Proc. Natl. Acad. Sci. USA 1991; 88: 7978–7982
   PubMed Web of Science ®Google Scholar