In vivo biotinylated proteins as targets for phage-display selection experiments

Protein Expression and Purification

Volumn 37, Issue 1, 2004, Pages 243-252

  Scholle, Michael D ^a   Collart, Frank R ^a   Kay, Brian K ^a  

^a ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

Affinity selection; AviTag; biotinylated proteins; Combinatorial peptides; Ligation independent cloning; Target preparation

Indexed keywords

BACTERIAL PROTEIN; HYBRID PROTEIN; PEPTIDE LIBRARY; PROTEIN;

ARTICLE; BIOTINYLATION; CHEMISTRY; GENE VECTOR; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME;

BACTERIAL PROTEINS; BASE SEQUENCE; BIOTINYLATION; GENETIC VECTORS; HUMANS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PEPTIDE LIBRARY; PROTEINS; RECOMBINANT FUSION PROTEINS;

BACTERIA (MICROORGANISMS); VECTORS;

EID: 3042594038     PISSN: 10465928     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pep.2004.05.012     Document Type: Article

References (50)

1. Roberts R.W., Szostak J.W. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc. Natl. Acad. Sci. USA. 94:1997;12297-12302
2. ′ -terminal end to the C-terminal end of its encoded protein on the ribosome in vitro FEBS Lett. 414:1997;405-408
3. Hanes J., Jermutus L., Pluckthun A. Selecting and evolving functional proteins in vitro by ribosome display. Methods Enzymol. 328:2000;404-430
4. Smith G.P. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science. 228:1985;1315-1317
5. Sidhu S.S., Lowman H.B., Cunningham B.C., Wells J.A. Phage display for selection of novel binding peptides. Methods Enzymol. 328:2000;333-363
6. 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. 269:1994;23853-23856
7. Felici F., Castagnoli L., Musacchio A., Jappelli R., Cesareni G. Selection of antibody ligands from a large library of oligopeptides expressed on a multivalent exposition vector. J. Mol. Biol. 222:1991;301-310
8. Castillo J., Goodson B., Winter J. T7 displayed peptides as targets for selecting peptide specific scFvs from M13 scFv display libraries. J. Immunol. Methods. 257:2001;117-122
9. McCafferty J., Griffiths A.D., Winter G., Chiswell D.J. Phage antibodies: filamentous phage displaying antibody variable domains. Nature. 348:1990;552-554
10. Schier R., Marks J.D., Wolf E.J., Apell G., Wong C., McCartney J.E., Bookman M.A., Huston J.S., Houston L.L., Weiner L.M., et al. In vitro and in vivo characterization of a human anti-c-erbB-2 single-chain Fv isolated from a filamentous phage antibody library. Immunotechnology. 1:1995;73-81
11. Binz H.K., Stumpp M.T., Forrer P., Amstutz P., Pluckthun A. Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins. J. Mol. Biol. 332:2003;489-503
12. Koide A., Bailey C.W., Huang X., Koide S. The fibronectin type III domain as a scaffold for novel binding proteins. J. Mol. Biol. 284:1998;1141-1151
13. Nord K., Nord O., Uhlen M., Kelley B., Ljungqvist C., Nygren P.A. Recombinant human factor VIII-specific affinity ligands selected from phage-displayed combinatorial libraries of protein A. Eur. J. Biochem. 268:2001;4269-4277
14. Skerra A. Lipocalins as a scaffold. Biochim. Biophys. Acta. 1482:2000;337-350
15. Xu L., Aha P., Gu K., Kuimelis R.G., Kurz M., Lam T., Lim A.C., Liu H., Lohse P.A., Sun L., Weng S., Wagner R.W., Lipovsek D. Directed evolution of high-affinity antibody mimics using mRNA display. Chem. Biol. 9:2002;933-942
16. Aslanidis C., de Jong P.J. Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res. 18:1990;6069-6074
17. Dieckman L., Gu M., Stols L., Donnelly M.I., Collart F.R. High throughput methods for gene cloning and expression. Protein Expr. Purif. 25:2002;1-7
18. Li C., Evans R.M. Ligation independent cloning irrespective of restriction site compatibility. Nucleic Acids Res. 25:1997;4165-4166
19. Stols L., Gu M., Dieckman L., Raffen R., Collart F.R., Donnelly M.I. A new vector for high-throughput, ligation-independent cloning encoding a tobacco etch virus protease cleavage site. Protein Expr. Purif. 25:2002;8-15
20. Butler J.E., Ni L., Brown W.R., Joshi K.S., Chang J., Rosenberg B., Voss E.W. Jr. The immunochemistry of sandwich ELISAs-VI. Greater than 90% of monoclonal and 75% of polyclonal anti-fluorescyl capture antibodies (CAbs) are denatured by passive adsorption. Mol. Immunol. 30:1993;1165-1175
21. Yamabhai M., Hoffman N.G., Hardison N.L., McPherson P.S., Castagnoli L., Cesareni G., Kay B.K. Intersectin, a novel adaptor protein with two Eps15 homology and five Src homology 3 domains. J. Biol. Chem. 273:1998;31401-31407
22. Hemminki A., Niemi S., Hautoniemi L., Soderlund H., Takkinen K. Fine tuning of an anti-testosterone antibody binding site by stepwise optimisation of the CDRs. Immunotechnology. 4:1998;59-69
23. Hawkins R.E., Russell S.J., Winter G. Selection of phage antibodies by binding affinity. Mimicking affinity maturation. J. Mol. Biol. 226:1992;889-896
24. Fan H., Liu Y., Zhou H., Wang L., Li W., Guo L., Roeske R.W. Selection of peptide ligands that bind to acid fibroblast growth factor. IUBMB Life. 49:2000;545-548
25. D'Mello F., Howard C.R. An improved selection procedure for the screening of phage display peptide libraries. J. Immunol. Methods. 247:2001;191-203
26. Smith G.P., Scott J.K. Libraries of peptides and proteins displayed on filamentous phage. Methods Enzymol. 217:1993;228-257
27. Chapman-Smith A., Cronan J.E. Jr. The enzymatic biotinylation of proteins: a post-translational modification of exceptional specificity. Trends Biochem Sci. 24:1999;359-363
28. Cronan J.E. Jr. Biotination of proteins in vivo. A post-translational modification to label, purify, and study proteins. J. Biol. Chem. 265:1990;10327-10333
29. Samols D., Thornton C.G., Murtif V.L., Kumar G.K., Haase F.C., Wood H.G. Evolutionary conservation among biotin enzymes. J. Biol. Chem. 263:1988;6461-6464
30. Schatz P.J. Use of peptide libraries to map the substrate specificity of a peptide-modifying enzyme: a 13 residue consensus peptide specifies biotinylation in Escherichia coli. Biotechnology NY. 11:1993;1138-1143
31. Duffy S., Tsao K.L., Waugh D.S. Site-specific, enzymatic biotinylation of recombinant proteins in Spodoptera frugiperda cells using biotin acceptor peptides. Anal. Biochem. 262:1998;122-128
32. Athavankar S., Peterson B.R. Control of gene expression with small molecules: biotin-mediated acylation of targeted lysine residues in recombinant yeast. Chem. Biol. 10:2003;1245-1253
33. Viens A., Mechold U., Lehrmann H., Harel-Bellan A., Ogryzko V. Use of protein biotinylation in vivo for chromatin immunoprecipitation. Anal. Biochem. 325:2004;68-76
34. Kay B.K. Phage Display of Peptides and Proteins: A Laboratory Manual. 1996;Academic Press
35. Dougherty W.G., Parks T.D., Cary S.M., Bazan J.F., Fletterick R.J. Characterization of the catalytic residues of the tobacco etch virus 49-kDa proteinase. Virology. 172:1989;302-310
36. Dougherty W.G., Parks T.D. Molecular genetic and biochemical evidence for the involvement of the heptapeptide cleavage sequence in determining the reaction profile at two tobacco etch virus cleavage sites in cell-free assays. Virology. 172:1989;145-155
37. Dougherty W.G., Carrington J.C., Cary S.M., Parks T.D. Biochemical and mutational analysis of a plant virus polyprotein cleavage site. EMBO J. 7:1988;1281-1287
38. Piran U., Riordan W.J. Dissociation rate constant of the biotin-streptavidin complex. J. Immunol. Methods. 133:1990;141-143
39. Green N.M. Avidin Adv. Protein Chem. 29:1975;85-133
40. Keefe A.D., Wilson D.S., Seelig B., Szostak J.W. One-step purification of recombinant proteins using a nanomolar-affinity streptavidin-binding peptide, the SBP-Tag. Protein Expr. Purif. 23:2001;440-446
41. Lamla T., Erdmann V.A. Searching sequence space for high-affinity binding peptides using ribosome display. J. Mol. Biol. 329:2003;381-388
42. Devlin J.J., Panganiban L.C., Devlin P.E. Random peptide libraries: a source of specific protein binding molecules. Science. 249:1990;404-406
43. Diamandis E.P., Christopoulos T.K. The biotin-(strept)avidin system: principles and applications in biotechnology. Clin. Chem. 37:1991;625-636
44. Balass M., Morag E., Bayer E.A., Fuchs S., Wilchek M., Katchalski-Katzir E. Recovery of high-affinity phage from a nitrostreptavidin matrix in phage-display technology. Anal. Biochem. 243:1996;264-269
45. Morag E., Bayer E.A., Wilchek M. Immobilized nitro-avidin and nitro-streptavidin as reusable affinity matrices for application in avidin-biotin technology. Anal. Biochem. 243:1996;257-263
46. Morag E., Bayer E.A., Wilchek M. Reversibility of biotin-binding by selective modification of tyrosine in avidin. Biochem. J. 316(Pt 1):1996;193-199
47. Kay B.K., Kasanov J., Knight S., Kurakin A. Convergent evolution with combinatorial peptides. FEBS Lett. 480:2000;55-62
48. Kay B.K., Hamilton P.T. Identification of enzyme inhibitors from phage-displayed combinatorial peptide libraries. Comb. Chem. High Throughput Screen. 4:2001;535-543
49. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410
50. Han Z., Karatan E., Scholle M.D., McCafferty J., Kay B.K. Accelerated screening of phage-display output with alkaline phosphatase fusions. Comb. Chem. High Throughput Screen. 7:2004;55-62