Chapter 9: Phage-display Methodology for the Study of Protein–Protein Interactions—References
Alting-Mees M.A. and Short J.M. 1993. Polycos vectors: A system for packaging filamentous phage and phagemid vectors using lambda phage packaging extract. Gene 137: 93–100.
Andersson E. and Matsunaga T. 1995. Evolution of immunoglobulin heavy chain variable region genes: A VH family can last for 150-200 million years or longer. Immunogenetics 41: 18–28.
Barbas C.F.I., III, Burton D.R., Scott J., and Silverman G.J. 2001. Phage display: A laboratory manual. Cold Spring Laboratory Harbor Press, Cold Spring Harbor, New York.
Braisted A.C. and Wells J.A. 1996. Minimizing a binding domain from protein A. Proc. Natl. Acad. Sci. 93: 5688–5692.
Burton D.R. and Barbas C.F. 1993. Human antibodies to HIV-1 by recombinant DNA methods. Chem. Immunol. 56: 112–126.
Cary S.P., Lee J., Wagenknecht R., and Silverman G.J. 2000. Characterization of superantigen-induced clonal deletion with a novel clan III-restricted avian monoclonal antibody: Exploiting evolutionary distance to create antibodies specific for a conserved VH region surface. J. Immunol. 164: 4730–4741.
Chiswell D.J. and McCafferty J. 1992. Phage antibodies: Will new "coliclonal" antibodies replace monoclonal antibodies? Trends Biotechnol. 10: 80–84.
Clackson T. and Wells J.A. 1994. In vitro selection from protein and peptide libraries. Trends Biotechnol. 12: 173–184.
Crameri R. and 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.
Cwirla S.E., Peters E.A., Barrett R.W., and Dower W.J. 1990. Peptides on phage: A vast library of peptides for identifying ligands. Proc. Natl. Acad. Sci. 87: 6378–6382.
Deisenhofer J. 1981. Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-Å resolution. Biochemistry 20: 2361–2370.
Djojonegoro B.M., Benedik M.J., and Willson R.C. 1994. Bacteriophage surface display of an immunoglobulin-binding domain of Staphylococcus aureus protein A. Biotechnology 12: 169–172.
Dunn I.S. 1995. Assembly of functional bacteriophage lambda virions incorporating C-terminal peptide or protein fusions with the major tail protein. J. Mol. Biol. 248: 497–506.
Efimov V.P., Nepluev I.V., and Mesyanzhinov V.V. 1995. Bacteriophage T4 as a surface display vector. Virus Genes 10: 173–177.
Fields S. and Song O.K. 1989. A novel genetic system to detect protein-protein interactions. Nature 340: 245–246.
Fisch I., Kontermann R.E., Finnern R., Hartley O., Soler-Gonzalez A.S., Griffiths A.D., and Winter G. 1996. A strategy of exon shuffling for making large peptide repertoires displayed on filamentous bacteriophage. Proc. Natl. Acad. Sci. 93: 7761–7766.
Folgori A., Tafi R., Meola A., Felici F., Galfré G., Cortese R., Monaci P., and Nicosia A. 1994. A general strategy to identify mimotopes of pathological antigens using only random peptide libraries and human sera. EMBO J. 13: 2236–2243.
Fransen M., Van Veldhoven P.P., and Subramani S. 1999. Identification of peroxisomal proteins by using M13 phage protein VI phage display: Molecular evidence that mammalian peroxisomes contain a 2,4-dienoul-CoA reductase. Biochem. J. 340: 561–568.
Fuh G. and Sidhu S.S. 2000. Efficient phage display of polypeptides fused to the carboxy-terminus of the M13 gene-3 minor coat protein. FEBS Lett. 480: 231–234.
Fuh G., Pisabarro M.T., Li Y., Quan C., Lasky L.A., and Sidhu S.S. 2000. Analysis of PDZ domain-ligand interactions using carboxyl-terminal phage display. J. Biol. Chem. 275: 21486–21491.
Gao C., Mao S., Lo C.H., Wursching P., Lerner R.A., and Janda K.D. 1999. Making artificial antibodies: A format for phage display of combinatorial heterodimeric arrays. Proc. Natl. Acad. Sci. 96: 6025–6030.
Germino F.J., Wang Z.X., and Weissman S.M. 1993. Screening for in vivo protein-protein interaction. Proc. Natl. Acad. Sci. 90: 933–937.
Goodyear C.S. and Silverman G.J. 2003. Death by a B-cell superantigen: In vivo VH targeted apoptotic supra-clonal B-cell deletion by a staphylococcal toxin. J. Exp. Med. 197: 1125–1139.
Goodyear C.S. and Silverman G.J. 2004. Staphylococcal toxin induced preferential and prolonged deletion of innate-like B lymphocytes. Proc. Natl. Acad. Sci. 101: 11392–11397.
Goodyear C.S., Narita M., and Silverman G.J. 2004. In vivo VL targeted activation-induced apoptotic supra-clonal deletion by a microbial B-cell toxin. J. Immunol. 172: 2870–2877.
Graille M., Stura E.A., Corper A.L., Sutton B., Taussig M., Charbonnier J.-B., and Silverman G.J. 2000. Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: Structural basis for recognition of B-cell receptors and superantigen activity. Proc. Natl. Acad. Sci. 97: 5399–5404.
Gram H., Strittmatter U., Lorenz M., Gluck D., and 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.
Helfman D.M., Fiddes J.R., Thomas G.P., and Hughes S. 1983. Identification of clones that encode chicken tropomyosin. Proc. Natl. Acad. Sci. 80: 31–35.
Houshmand H., Fröman G., and Magnusson G. 1999. Use of bacteriophage T7 displayed peptides for determination of monoclonal antibody specificity and biosensor analysis of the binding reaction. Anal. Biochem. 268: 363–370.
Iannolo G., Minenkova O., Petruzzelli R., and Cesarini G. 1995. Modifying filamentous phage capsid: Limits in the size of the major capsid protein. J. Mol. Biol. 248: 835–844.
Jespers L.S., Messens J.H., De Keyser A., Eeckhout D., Van Den Brande I., Gansemans Y.G., Lauwereys M.J., Vlasuk G.P., and Stanssens P.E. 1995. Surface expression and ligand-based selection of cDNAs fused to filamentous phage gene VI. Biotechnology 13: 378–382.
Kast P. and Hilvert D. 1997. 3D structural information as a guide to protein engineering using genetic selection. Curr. Opin. Struct. Biol. 7: 470–479.
Katz B.A. 1997. Structural and mechanistic determinants of affinity and specificity of ligands discovered or engineered by phage display. Annu. Rev. Biophys. Biomol. Struct. 26: 27–45.
Kirkham P.M. and Schroeder H.W., Jr. 1994. Antibody structure and the evolution of immunoglobulin V gene segments. Semin. Immunol. 6: 347–360.
Kirkham P.M., Mortari F., Newton J.A., and Schroeder H.W., Jr. 1992. Immunoglobulin VH clan and family identity predicts variable domain structure and may influence antigen binding. EMBO J. 11: 603–609.
Kushwaha A., Chowdhury P.S., Arora K., Abrol S., and Chaudhary V.K. 1994. Construction and characterization of M13 bacteriophages displaying functional IgG-binding domains of staphylococcal protein A. Gene 151: 45–51.
Kuwabara I., Maruyama H., Mikawa Y.G., Zuberi R.I., Liu F.T., and Maruyama I.N. 1997. Efficient epitope mapping by bacteriophage λ surface display. Nat. Biotechnol. 15: 74–78.
Lowman H.B., Bass S.H., Simpson N., and Wells J.A. 1991. Selecting high-affinity binding protein by monovalent phage display. Biochemistry 30: 10832–10838.
Malik P., Terry T.D., Gowda L.R., Petukhov A.L.S.A., Symmons M.F., Welsh L.C., Marvin D.A., and Perham R.N. 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.
Maruyama I.N., Maruyama H.I., and Brenner S. 1994. λfoo: A lambda phage vector for the expression of foreign proteins. Proc. Natl. Acad. Sci. 91: 8273–8277.
Marvin D.A. 1998. Filamentous phage structure, infection and assembly. Curr. Opin. Struct. Biol. 8: 150–158.
McCafferty J., Griffiths A.D., Winter G., and Chiswell D.J. 1990. Phage antibodies: Filamentous phage displaying antibody variable domains. Nature 348: 552–554.
Nord K., Nilsson B., Uhlen M., and Nygren P.A. 1995. A combinatorial library of an alpha-helical bacterial receptor domain. Protein Eng. 8: 601–608.
Nord K., Gunneriusson E., Ringdahl J., Stahl S., Uhlen M., and Nygren P.A. 1997. Binding proteins selected from combinatorial libraries of an alpha-helical bacterial receptor domain. Nat. Biotechnol. 15: 772–777.
O'Neil K.T. and Hoess R.H. 1995. Phage display: Protein engineering by directed evolution. Curr. Opin. Struct. Biol. 5: 443–449.
Petersen G., Song D., Hugle-Dorr B., Oldenburg I., and Bautz E.K. 1995. Mapping of linear epitopes recognized by monoclonal antibodies with gene-fragment phage display libraries. Mol. Gen. Genet. 249: 425–431.
Qiu J.X., Kai M., Padlan E.A., and Marcus D.M. 1999. Structure-function studies of an anti-asialo GM1 antibody obtained from a phage display library. J. Neuroimmunol. 97: 172–181.
Rader C., Steinberger P., and Barbas C.F., III. 2001. Selection from antibody libraries. In Phage display: A laboratory manual (ed. C.F. Barbas III et al.), pp. 10.1–10.20. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Ren Z.J., Lewis G.K., Wingfield P.T., Locke E.G., Steven A.C., and Black L.W. 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.
Roberts B.L., Markland W., Ley A.C., Kent R.B., White D.W., Guterman S.K., and Ladner R.C. 1992. Directed evolution of a protein: Selection of a potent neutrophil elastase inhibitor. Gene 121: 9–15.
Sambrook J. and Russell D. 2001. Molecular cloning: A laboratory manual, 3rd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Santini C., Brennan D., Mennuni C., Hoess R.H., Nicosia A., Cortese R., and Luzzago A. 1998. Efficient display of an HCV cDNA expression library as C-terminal fusion to the capsid protein D of bacteriophage lambda. J. Mol. Biol. 282: 125–135.
Sasano M., Burton D.R., and Silverman G.J. 1993. Molecular selection of human antibodies with an unconventional bacterial B cell antigen. J. Immunol. 151: 5822–5839.
Sasso E.H., Silverman G.J., and Mannik M. 1989. Human IgM molecules that bind staphylococcal protein A contain VHIII H chains. J. Immunol. 142: 2778–2783.
Sasso E.H., Silverman G.J., and Mannik M. 1991. Human IgA and IgG F(ab´)2 that bind to staphylococcal protein A belong to the VHIII subgroup. J. Immunol. 147: 1877–1883.
Schroeder H.W., Jr., Hillson J.L., and Perlmutter R.M. 1990. Structure and evolution of mammalian VH families. Int. Immunol. 2: 41–50.
Scott J.K. and Barbas C.F.I., III. 2001. Phage-display vectors. In Phage display: A laboratory manual (ed. C.F. Barbas III et al.), pp. 2.1–2.19. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Scott J.K. and Smith G.P. 1990. Searching for peptide ligands with an epitope library. Science 249: 386–390.
Seed B. and Aruffo A. 1987. Molecular cloning of the CD2 antigen, the T-cell erythrocyte receptor, by a rapid immunoselection procedure. Proc. Natl. Acad. Sci. 84: 3365–3369.
Shanmugavelu M., Baytan A.R., Chesnut J.D., and Bonning B.C. 2000. A novel protein that binds juvenile hormone esterase in fat body tissue and pericardial cells of the tobacco hornworm Manduca sexta L. J. Biol. Chem. 275: 1802–1806.
Shen S.X., Bernstein R.M., Schluter S.F., and Marchalonis J.J. 1996. Heavy-chain variable regions in carcharhine sharks: Development of a comprehensive model for the evolution of VH domains among the gnathostomes. Immunol. Cell Biol. 74: 357–364.
Sidhu S.S., Fairbrother W.J., and Deshayes K. 2003. Exploring protein-protein interactions with phage display. ChemBioChem. 4: 14–25.
Sidhu S.S., Lowman H.B., Cunningham B.C., and Wells J.A. 2000. Phage display for selection of novel binding proteins. Methods Enzymol. 328: 333–363.
Sikela J.M. and Hahn W. 1987. Screening an expression library with a ligand probe: Isolation and sequence of a cDNA corresponding to a brain calmodulin binding protein. Proc. Natl. Acad. Sci. 84: 3038–3042.
Silverman G.J. 2001. Functional domains and scaffolds. In Phage display: A laboratory manual (ed. C.F. Barbas III et al.), pp. 5.1–5.24. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Silverman G.J., Pirès R., and Bouvet J.P. 1996. An endogenous sialoprotein and a bacterial B-cell superantigen compete in their VH family-specific binding interactions with human immunoglobulins. J. Immunol. 157: 4496–4502.
Silverman G.J., Sasano M., and Wormsley S.B. 1993. Age-associated changes in binding of human B lymphocytes to a VH3-restricted unconventional bacterial antigen. J. Immunol. 151: 5840–5855.
Silverman G.J., Cary S.P., Dwyer D.C., Linda L., Wagenknecht R., and Curtiss V.E. 2000. A B-cell superantigen induced persistent "Hole" in the B-1 repertoire. J. Exp. Med. 192: 87–98.
Singh S.J.H., LeBowitz A.S., Baldwin J., and Sharp, P.A. 1988. Molecular cloning of an enhancer binding protein: Isolation by screening of an expression library with a recogntion site DNA. Cell 52: 415–423.
Smith G.P. 1985. Filamentous fusion phage: Novel expression vectors that display cloned antigens on the virion surface. Science 228: 1315–1317.
Starovasnik M.A., Braisted A.C., and Wells J.A. 1997. Structural mimicry of a native protein by a minimized binding domain. Proc. Natl. Acad. Sci. 94: 10080–10085.
Sternberg N. and Hoess R.H. 1995. Display of peptides and proteins on the surface of bacteriophage λ. Proc. Natl. Acad. Sci. 92: 1609–1613.
Tutter A. and Riblet R. 1989. Conservation of an immunoglobulin variable-region gene family indicates a specific, noncoding function. Proc. Natl. Acad. Sci. 86: 7460–7464.
Webster R.E. 2001. Filamentous phage biology. In Phage display: A laboratory manual (ed. C.F. Barbas III et al.), pp. 1.1–1.37. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Winter G., Griffiths A.D., Hawkins R.E., and Hoogenboom H.R. 1994. Making antibodies by phage display technology. Annu. Rev. Immunol. 12: 433–455.
Young R.A. and Davis R.W. 1983. Efficient isolation of genes using antibody probes. Proc. Natl. Acad. Sci. 80: 1194–1198.
<<< Chapter 8 References
Chapter 10 References >>>
|
