Quantitative specificity-based display library screening identifies determinants of antibody-epitope binding specificity

Protein Science

Volumn 18, Issue 9, 2009, Pages 1926-1934

  Hall, Sejal S ^a   Daugherty, Patrick S ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of California   (United States)

Author keywords

Antibody; Cell display; Directed evolution; Peptide epitope; Specificity

Indexed keywords

ANTIBODY; ANTIGEN; EPITOPE;

ANTIBODY AFFINITY; ANTIBODY LABELING; ANTIBODY SPECIFICITY; ANTIGEN BINDING; ARTICLE; BINDING AFFINITY; FLOW CYTOMETRY; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; QUANTITATIVE ANALYSIS; SCREENING;

AMINO ACID SEQUENCE; ANTIBODIES; ANTIBODY SPECIFICITY; BINDING SITES, ANTIBODY; EPITOPES; MOLECULAR SEQUENCE DATA; PEPTIDE LIBRARY;

EID: 69249085259     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.203     Document Type: Article

References (34)

1. Daugherty PS, Chen G, Olsen MJ, Iverson BL, Georgiou G (1998) Antibody affinity maturation using bacterial surface display. Protein Eng 11:825-832.
2. Boder ET, Midelfort KS, Wittrup KD (2000) Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc Natl Acad Sci USA 97:10701-10705.
3. Bessette PH, Rice JJ, Daugherty PS (2004) Rapid isolation of high-affinity protein binding peptides using bacterial display. Protein Eng Des Sel 17:731-739.
4. Clackson T, Wells JA (1994) In vitro selection from protein and peptide libraries. Trends Biotechnol 12:173-184.
5. Szwajkajzer D, Carey J (1997) Molecular and biological constraints on ligand-binding affinity and specificity. Biopolymers 44:181-198.
6. Levin AM, Weiss GA (2006) Optimizing the affinity and specificity of proteins with molecular display. Mol Biosyst 2:49-57.
7. Brown CK, Modzelewski RA, Johnson CS, Wong MK (2000) A novel approach for the identification of unique tumor vasculature binding peptides using an E. coli peptide display library. Ann Surg Oncol 7:743-749.
8. Lunder M, Bratkovic T, Doljak B, Kreft S, Urleb U, Strukelj B, Plazar N (2005) Comparison of bacterial and phage display peptide libraries in search of target-binding motif. Appl Biochem Biotechnol 127:125-131.
9. Harvey BR, Georgiou G, Hayhurst A, Jeong KJ, Iverson BL, Rogers GK (2004) Anchored periplasmic expression, a versatile technology for the isolation of high-affinity antibodies from Escherichia coli-expressed libraries. Proc Natl Acad Sci USA 101:9193-9198.
10. Rice JJ, Schohn A, Bessette PH, Boulware KT, Daugherty PS (2006) Bacterial display using circularly permuted outer membrane protein OmpX yields high affinity peptide ligands. Protein Sci 15:825-836.
11. Garcia-Rodriguez C, Levy R, Arndt JW, Forsyth CM, Razai A, Lou J, Geren I, Stevens RC, Marks JD (2007) Molecular evolution of antibody cross-reactivity for two subtypes of type A botulinum neurotoxin. Nat Biotechnol 25:107-116.
12. Mintz PJ, Kim J, Do KA, Wang X, Zinner RG, Cristofanilli M, Arap MA, Hong WK, Troncoso P, Logothetis CJ, Pasqualini R, Arap W (2003) Fingerprinting the circulating repertoire of antibodies from cancer patients. Nat Biotechnol 21:57-63.
13. Vidal CI, Mintz PJ, Lu K, Ellis LM, Manenti L, Giavazzi R, Gershenson DM, Broaddus R, Liu J, Arap W, Pasqualini R (2004) An HSP90-mimic peptide revealed by fingerprinting the pool of antibodies from ovarian cancer patients. Oncogene 23:8859-8867.
14. Kouzmitcheva GA, Petrenko VA, Smith GP (2001) Identifying diagnostic peptides for lyme disease through epitope discovery. Clin Diagn Lab Immunol 8:150-160.
15. Somers V, Govarts C, Hellings N, Hupperts R, Stinissen P (2005) Profiling the autoantibody repertoire by serological antigen selection. J Autoimmun 25:223-228.
16. Govarts C, Somers K, Hupperts R, Stinissen P, Somers V (2007) Exploring cDNA phage display for autoantibody profiling in the serum of multiple sclerosis patients: optimization of the selection procedure. Ann NY Acad Sci 1109:372-384.
17. Hansen MH, Ostenstad B, Sioud M (2001) Antigen-specific IgG antibodies in stage IV long-time survival breast cancer patients. Mol Med 7:230-239.
18. Wang X, Yu J, Sreekumar A, Varambally S, Shen R, Giacherio D, Mehra R, Montie JE, Pienta KJ, Sanda MG, Kantoff PW, Rubin MA, Wei JT, Ghosh D, Chinnaiyan AM (2005) Autoantibody signatures in prostate cancer. N Engl J Med 353:1224-1235.
19. Fabian MA, Biggs WH III, Treiber DK, Atteridge CE, Azimioara MD, Benedetti MG, Carter TA, Ciceri P, Edeen PT, Floyd M, et al. (2005) A small molecule-kinase interaction map for clinical kinase inhibitors. Nat Biotechnol 23:329-336.
20. Bessette PH, Hu X, Soh HT, Daugherty PS (2007) Microfluidic library screening for mapping antibody epitopes. Anal Chem 79:2174-2178.
21. Rice JJ, Daugherty PS (2008) Directed evolution of a biterminal bacterial display scaffold enhances the display of diverse peptides. Protein Eng Des Sel 21:435-442.
22. Jones S, Thornton JM (1996) Principles of protein-protein interactions. Proc Natl Acad Sci USA 93:13-20.
23. Silverman J, Liu Q, Bakker A, To W, Duguay A, Alba BM, Smith R, Rivas A, Li P, Le H, Whitehorn E, Moore KW, Swimmer C, Perlroth V, Vogt M, Kolkman J, Stemmer WP (2005) Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains. Nat Biotechnol 23:1556-1561.
24. Sparks AB, Rider JE, Hoffman NG, Fowlkes DM, Quillam LA, Kay BK (1996) Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCgamma, Crk, and Grb2. Proc Natl Acad Sci USA 93:1540-1544.
25. Carothers JM, Oestreich SC, Szostak JW (2006) Aptamers selected for higher-affinity binding are not more specific for the target ligand. J Am Chem Soc 128:7929-7937.
26. de Haard HJ, van Neer N, Reurs A, Hufton SE, Roovers RC, Henderikx P, de Bruine AP, Arends JW, Hoogenboom HR (1999) A large non-immunized human Fab fragment phage library that permits rapid isolation and kinetic analysis of high affinity antibodies. J Biol Chem 274:18218-18230.
27. You X, Nguyen AW, Jabaiah A, Sheff MA, Thorn KS, Daugherty PS (2006) Intracellular protein interaction mapping with FRET hybrids. Proc Natl Acad Sci USA 103:18458-18463.
28. Austin RJ, Ja WW, Roberts RW (2008) Evolution of class-specific peptides targeting a hot spot of the Galphas subunit. J Mol Biol 377:1406-1418.
29. Chames P, Coulon S, Baty D (1998) Improving the affinity and the fine specificity of an anti-cortisol antibody by parsimonious mutagenesis and phage display. J Immunol 161:5421-5429.
30. Zanoni G, Navone R, Lunardi C, Tridente G, Bason C, Sivori S, Beri R, Dolcino M, Valletta E, Corrocher R, Puccetti A (2006) In celiac disease, a subset of autoantibodies against transglutaminase binds toll-like receptor 4 and induces activation of monocytes. PLoS Med 3:1637-1653.
31. Bostrom J, Yu SF, Kan D, Appleton BA, Lee CV, Billeci K, Man W, Peale F, Ross S, Wiesmann C, Fuh G (2009) Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site. Science 323:1610-1614.
32. Lee CV, Hymowitz SG, Wallweber HJ, Gordon NC, Billeci KL, Tsai SP, Compaan DM, Yin J, Gong Q, Kelley RF, DeForge LE, Martin F, Starovasnik MA, Fuh G (2006) Synthetic anti-BR3 antibodies that mimic BAFF binding and target both human and murine B cells. Blood 108:3103-3111.
33. Casadaban MJ, Cohen SN (1980) Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J Mol Biol 138:179-207.
34. Hu X, Bessette PH, Qian J, Meinhart CD, Daugherty PS, Soh HT (2005) Marker-specific sorting of rare cells using dielectrophoresis. Proc Natl Acad Sci USA 102:15757-15761.