An experimental framework for improved selection of binding proteins using SNAP display

Journal of Immunological Methods

Volumn 405, Issue , 2014, Pages 47-56

  Houlihan, Gillian ^a,b   Gatti Lafranconi, Pietro ^a   Kaltenbach, Miriam ^a   Lowe, David ^b   Hollfelder, Florian ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b MEDIMMUNE   (United States)

Author keywords

Directed evolution; In vitro compartmentalization; In vitro selection; Protein engineering; SNAP display; Therapeutic protein

Indexed keywords

BINDING PROTEIN; METHOTREXATE;

ANALYZER; ARTICLE; BINDING AFFINITY; BIOTINYLATION; CELL LYSATE; CONTROLLED STUDY; DNA TEMPLATE; EMULSION; ESCHERICHIA COLI; IN VITRO SELECTION; IN VITRO STUDY; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN SYNTHESIS; REAL TIME POLYMERASE CHAIN REACTION; RIBOSOME; SNAP DISPLAY;

ESCHERICHIA COLI;

DIRECTED EVOLUTION; IN VITRO COMPARTMENTALIZATION; IN VITRO SELECTION; PROTEIN ENGINEERING; SNAP DISPLAY; THERAPEUTIC PROTEIN;

CARRIER PROTEINS; CLONING, MOLECULAR; DNA; MODELS, GENETIC; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PEPTIDE LIBRARY; PROTEIN BINDING; PROTEIN BIOSYNTHESIS; PROTEIN STRUCTURE, TERTIARY; PROTEINS; TRANSCRIPTION, GENETIC;

EID: 84897114564     PISSN: 00221759     EISSN: 18727905     Source Type: Journal    
DOI: 10.1016/j.jim.2014.01.006     Document Type: Article

References (53)

1. Barendt P.A., Ng D.T., McQuade C.N., Sarkar C.A. Streamlined protocol for mRNA display. ACS Comb. Sci. 2013, 15:77.
2. Bertschinger J., Neri D. Covalent DNA display as a novel tool for directed evolution of proteins in vitro. Protein Eng. Des. Sel. 2004, 17:699.
3. Binz H.K., Amstutz P., Kohl A., Stumpp M.T., Briand C., Forrer P., Grutter M.G., Pluckthun A. High-affinity binders selected from designed ankyrin repeat protein libraries. Nat. Biotechnol. 2004, 22:575.
4. Boder E.T., Wittrup K.D. Yeast surface display for screening combinatorial polypeptide libraries. Nat. Biotechnol. 1997, 15:553.
5. Bonsor D.A., Sundberg E.J. Dissecting protein-protein interactions using directed evolution. Biochemistry 2011, 50:2394.
6. Buonpane R.A., Churchill H.R., Moza B., Sundberg E.J., Peterson M.L., Schlievert P.M., Kranz D.M. Neutralization of staphylococcal enterotoxin B by soluble, high-affinity receptor antagonists. Nat. Med. 2007, 13:725.
7. Chodorge M., Fourage L., Ravot G., Jermutus L., Minter R. In vitro DNA recombination by L-Shuffling during ribosome display affinity maturation of an anti-Fas antibody increases the population of improved variants. Protein Eng. Des. Sel. 2008, 21:343.
8. Courtois F., Olguin L.F., Whyte G., Bratton D., Huck W.T., Abell C., Hollfelder F. An integrated device for monitoring time-dependent in vitro expression from single genes in picolitre droplets. Chembiochem 2008, 9:439.
9. Diamante L., Gatti-Lafranconi P., Schaerli Y., Hollfelder F. In vitro affinity screening of protein and peptide binders by megavalent bead surface display. Protein Eng. Des. Sel. 2013, 26:713.
10. Douthwaite J.A., Jackson R.H. Ribosome Display and Related Technologies: Methods and Protocols 2012, Humana Press, New York.
11. Farr G.A., Hull M., Mellman I., Caplan M.J. Membrane proteins follow multiple pathways to the basolateral cell surface in polarized epithelial cells. J. Cell Biol. 2009, 186:269.
12. Fujii I. Antibody affinity maturation by random mutagenesis. Methods in Molecular Biology 2004, vol. 248:345. Humana Press. B. Lo (Ed.).
13. Fukuda N., Ishii J., Shibasaki S., Ueda M., Fukuda H., Kondo A. High-efficiency recovery of target cells using improved yeast display system for detection of protein-protein interactions. Appl. Microbiol. Biotechnol. 2007, 76:151.
14. Garrard L.J., Yang M., O'Connell M.P., Kelley R.F., Henner D.J. Fab assembly and enrichment in a monovalent phage display system. Biotechnology (N.Y.) 1991, 9:1373.
15. Georgiou G., Stathopoulos C., Daugherty P.S., Nayak A.R., Iverson B.L., Curtiss R. Display of heterologous proteins on the surface of microorganisms: from the screening of combinatorial libraries to live recombinant vaccines. Nat. Biotechnol. 1997, 15:29.
16. Hanes J., Pluckthun A. In vitro selection and evolution of functional proteins by using ribosome display. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:4937.
17. Hanes J., Jermutus L., Weber-Bornhauser S., Bosshard H.R., Pluckthun A. Ribosome display efficiently selects and evolves high-affinity antibodies in vitro from immune libraries. Proc. Natl. Acad. Sci. U. S. A. 1998, 95:14130.
18. Hanes J., Schaffitzel C., Knappik A., Pluckthun A. Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display. Nat. Biotechnol. 2000, 18:1287.
19. Hawkins R.E., Russell S.J., Winter G. Selection of phage antibodies by binding affinity. Mimicking affinity maturation. J. Mol. Biol. 1992, 226:889.
20. Hinner M.J., Johnsson K. How to obtain labeled proteins and what to do with them. Curr. Opin. Biotechnol. 2010, 21:766.
21. Hoogenboom H.R., de Bruine A.P., Hufton S.E., Hoet R.M., Arends J.W., Roovers R.C. Antibody phage display technology and its applications. Immunotechnology 1998, 4:1.
22. Houlihan G., Lowe D., Hollfelder F. SNAP display-an in vitro method for the selection of protein binders. Curr. Pharm. Des. 2013, 19:5421.
23. Hussain A.F., Amoury M., Barth S. SNAP-Tag Technology: a powerful tool for site specific conjugation of therapeutic and imaging agents. Curr. Pharm. Des. 2013, 19:5437.
24. Javadi Y., Itzhaki L.S. Tandem-repeat proteins: regularity plus modularity equals design-ability. Curr. Opin. Struct. Biol. 2013, 23:622.
25. Juillerat A., Heinis C., Sielaff I., Barnikow J., Jaccard H., Kunz B., Terskikh A., Johnsson K. Engineering substrate specificity of O6-alkylguanine-DNA alkyltransferase for specific protein labeling in living cells. Chembiochem 2005, 6:1263.
26. Kaltenbach M., Hollfelder F. SNAP display: in vitro protein evolution in microdroplets. Methods Mol Biol 2012, vol. 805:101.
27. Kaltenbach M., Stein V., Hollfelder F. SNAP dendrimers: multivalent protein display on dendrimer-like DNA for directed evolution. Chembiochem 2011, 12:2208.
28. Keppler A., Gendreizig S., Gronemeyer T., Pick H., Vogel H., Johnsson K. A general method for the covalent labeling of fusion proteins with small molecules in vivo. Nat. Biotechnol. 2003, 21:86.
29. Koide A., Bailey C.W., Huang X., Koide S. The fibronectin type III domain as a scaffold for novel binding proteins. J. Mol. Biol. 1998, 284:1141.
30. Leemhuis H., Stein V., Griffiths A.D., Hollfelder F. New genotype-phenotype linkages for directed evolution of functional proteins. Curr. Opin. Struct. Biol. 2005, 15:472.
31. Liu Y., Adams J.D., Turner K., Cochran F.V., Gambhir S.S., Soh H.T. Controlling the selection stringency of phage display using a microfluidic device. Lab Chip 2009, 9:1033.
32. Lu D., Shen J., Vil M.D., Zhang H., Jimenez X., Bohlen P., Witte L., Zhu Z. Tailoring in vitro selection for a picomolar affinity human antibody directed against vascular endothelial growth factor receptor 2 for enhanced neutralizing activity. J. Biol. Chem. 2003, 278:43496.
33. Minter R.R., Cohen E.S., Wang B., Liang M., Vainshtein I., Rees G., Eghobamien L., Harrison P., Sims D.A., Matthews C., Wilkinson T., Monk P., Drinkwater C., Fabri L., Nash A., McCourt M., Jermutus L., Roskos L., Anderson I.K., Sleeman M.A. Protein engineering and preclinical development of a GM-CSF receptor antibody for the treatment of rheumatoid arthritis. Br. J. Pharmacol. 2013, 168:200.
34. Nilssen N.R., Frigstad T., Pollmann S., Roos N., Bogen B., Sandlie I., Loset G.A. DeltaPhage-a novel helper phage for high-valence pIX phagemid display. Nucleic Acids Res. 2012, 40:e120.
35. Nord K., Gunneriusson E., Ringdahl J., Stahl S., Uhlen M., Nygren P.A. Binding proteins selected from combinatorial libraries of an alpha-helical bacterial receptor domain. Nat. Biotechnol. 1997, 15:772.
36. Odegrip R., Coomber D., Eldridge B., Hederer R., Kuhlman P.A., Ullman C., FitzGerald K., McGregor D. CIS display: In vitro selection of peptides from libraries of protein-DNA complexes. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:2806.
37. Ohashi H., Shimizu Y., Ying B.W., Ueda T. Efficient protein selection based on ribosome display system with purified components. Biochem. Biophys. Res. Commun. 2007, 352:270.
38. Roberts R.W., Szostak J.W. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:12297.
39. Schaerli Y., Hollfelder F. The potential of microfluidic water-in-oil droplets in experimental biology. Mol. Biosyst. 2009, 5:1392.
40. Scott J.K., Smith G.P. Searching for peptide ligands with an epitope library. Science 1990, 249:386.
41. Shimizu Y., Inoue A., Tomari Y., Suzuki T., Yokogawa T., Nishikawa K., Ueda T. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 2001, 19:751.
42. Silverman J., Liu Q., Bakker A., To W., Duguay A., Alba B.M., Smith R., Rivas A., Li P., Le H., Whitehorn E., Moore K.W., Swimmer C., Perlroth V., Vogt M., Kolkman J., Stemmer W.P. Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains. Nat. Biotechnol. 2005, 23:1556.
43. Smith G.P. Filamentous Fusion Phage: Novel Expression Vectors that Display Cloned Antigens on the Virion Surface. Science 1985, 228:1315.
44. Stein V. A Protein Display System Based on Human O(6)-Alkylguanine Alkyltransferase and In Vitro Compartmentalisation 2008, Department of Biochemistry, University of Cambridge, (Vol. PhD thesis).
45. Stein V., Hollfelder F. An efficient method to assemble linear DNA templates for in vitro screening and selection systems. Nucleic Acids Res. 2009, 37:e122.
46. Stein V., Sielaff I., Johnsson K., Hollfelder F. A covalent chemical genotype-phenotype linkage for in vitro protein evolution. Chembiochem 2007, 8:2191.
47. Sun X., Zhang A., Baker B., Sun L., Howard A., Buswell J., Maurel D., Masharina A., Johnsson K., Noren C.J., Xu M.Q., Correa I.R. Development of SNAP-tag fluorogenic probes for wash-free fluorescence imaging. Chembiochem 2011, 12:2217.
48. Tawfik D.S., Griffiths A.D. Man-made cell-like compartments for molecular evolution. Nat. Biotechnol. 1998, 16:652.
49. Ueda T., Kanamori T., Ohashi H. Ribosome display with the PURE technology. Methods in Molecular Biology 2010, vol. 607:219. Humana Press. Y. Endo, K. Takai, T. Ueda (Eds.).
50. Villemagne D., Jackson R., Douthwaite J.A. Highly efficient ribosome display selection by use of purified components for in vitro translation. J. Immunol. Methods 2006, 313:140.
51. Wilson D.S., Keefe A.D., Szostak J.W. The use of mRNA display to select high-affinity protein-binding peptides. Proc. Natl. Acad. Sci. U. S. A. 2001, 98:3750.
52. Zahnd C., Pecorari F., Straumann N., Wyler E., Pluckthun A. Selection and characterization of Her2 binding-designed ankyrin repeat proteins. J. Biol. Chem. 2006, 281:35167.
53. Zahnd C., Wyler E., Schwenk J.M., Steiner D., Lawrence M.C., McKern N.M., Pecorari F., Ward C.W., Joos T.O., Pluckthun A. A designed ankyrin repeat protein evolved to picomolar affinity to Her2. J. Mol. Biol. 2007, 369:1015.