Exploring antibody recognition of sequence space through random-sequence peptide microarrays

Molecular and Cellular Proteomics

Volumn 10, Issue 3, 2011, Pages

  Halperin, Rebecca F ^a   Stafford, Phillip ^a   Johnston, Stephen Albert ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; EPITOPE; MONOCLONAL ANTIBODY; POLYCLONAL ANTIBODY; PEPTIDE; PEPTIDE LIBRARY; PROTEIN P53;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; FEASIBILITY STUDY; HUMAN; MOLECULAR LIBRARY; MOLECULAR RECOGNITION; PEPTIDE MAPPING; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN ENGINEERING; PROTEIN MICROARRAY; ALGORITHM; CHEMISTRY; IMMUNOLOGY; METHODOLOGY; MOLECULAR GENETICS; PROTEIN DATABASE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; ANTIBODIES; DATABASES, PROTEIN; EPITOPES; MOLECULAR SEQUENCE DATA; PEPTIDE LIBRARY; PEPTIDES; PROTEIN ARRAY ANALYSIS; PROTEIN BINDING; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; TUMOR SUPPRESSOR PROTEIN P53;

EID: 79953228541     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M110.000786     Document Type: Article

References (27)

1. Fack, F., Hügle-Dörr, B., Song, D. Queitsch, I., Petersen, G., and Bautz, E. K. F. (1997) Epitope mapping by phage display: random versus gene-fragment libraries. J Immunol Methods. 206, 43-52
2. Reineke, U. (2009) Antibody epitope mapping using de novo generated synthetic Peptide libraries. Methods Mol. Biol. 524, 203-211
3. Irving, M. B., Pan, O., and Scott, J. K. (2001) Random-peptide libraries and antigen-fragment libraries for epitope mapping and the development of vaccines and diagnostics. Curr. Opin. Chem. Biol. 5, 314-324
4. Wang, L. F., and Yu, M. (2004) Epitope identification and discovery using phage display libraries: applications in vaccine development and diagnostics. Curr. Drug Targets. 5, 1-15
5. Yip, Y. L., and Ward, R. L. (1999) Epitope discovery using monoclonal antibodies and phage peptide libraries. Comb. Chem. High Throughput Screen. 2, 125-138
6. Gershoni, J. M., Roitburd-Berman, A., Siman-Tov, D. D., Tarnovitski Freund, N., and Weiss, Y. (2007) Epitope mapping: the first step in developing epitope-based vaccines. BioDrugs. 21, 145-156 (Pubitemid 46827848)
7. Cortese, R., Felici, F., Galfre, G., Luzzago, A., Monaci, P., and Nicosia, A. (1994) Epitope discovery using peptide libraries displayed on phage. Trends Biotechnol. 12, 262-267 (Pubitemid 24221972)
8. Bongartz, J., Bruni, N., and Or-Guil, M. (2009) Epitope mapping using randomly generated Peptide libraries. Methods Mol. Biol. 524, 237-246.
9. Williams, B. A., Diehnelt, C. W., Belcher, P., Greving, M., Woodbury, N. W., Johnston, S. A., and Chaput, J. C. (2009) Creating Protein Affinity Reagents by Combining Peptide Ligands on Synthetic DNA Scaffolds. J. Am. Chem. Soc. 131, 17233-17241
10. Boltz, K. W., Gonzalez-Moa, M. J., Stafford, P., Johnston, S. A., and Svarovsky, S. A. (2009) Peptide microarrays for carbohydrate recognition. Analyst 134, 650-652
11. Morales Betanzos, C., Gonzalez-Moa, M. J., Boltz, K. W., Vander Werf, B. D., Johnston, S. A., and Svarovsky, S. A. (2009) Bacterial glycoprofiling by using random sequence peptide microarrays. Chembiochem 10, 877-888
12. Legutki, J. B., Mitchell, M. D., Stafford, P., and Johnston, S. A. (2010) A general method for characterization of humoral immunity induced by a vaccine or infection. Vaccine, doi:10.1016/j.vaccine.2010.04.061
13. Reineke, U., Ivascu, C., Schlief, M., Landgraf, C., Gericke, S., Zahn, G., Herzel, H., Volkmer-Engert, R., and Schneider-Mergener, J. (2002) Identification of distinct antibody epitopes and mimotopes from a peptide array of 5520 randomly generated sequences. J. Immunol. Methods 267, 37-51 (Pubitemid 34804811)
14. Stephen, C. W., Helminen, P., and Lane, D. P. (1995) Characterisation of epitopes on human p53 using phage-displayed peptide libraries: insights into antibody-peptide interactions. J. Mol. Biol. 248, 58-78
15. Breitling, F., and Little, M. (1986) Carboxy-terminal regions on the surface of tubulin and microtubules. Epitope locations of YOL1/34, DM1A and DM1B. J. Mol. Biol. 189, 367-370
16. Afonin, P. V., Fokin, A. V., Tsygannik, I. N., Mikhailova, I. Y., Onoprienko, L. V., Mikhaleva, I. I., Ivanov, V. T., Mareeva, T. Y., Nesmeyanov, V. A., Li, N., Pangborn, W. A., Duax, W. L., and Pletnev, V. Z. (2001) Crystal structure of an anti-interleukin-2 monoclonal antibody Fab complexed with an antigenic nonapeptide. Protein Sci. 10, 1514-1521
17. Rigoutsos, I., and Floratos, A. (1998) Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics 14, 55-67 (Pubitemid 28397726)
18. Jonassen, I. (1997) Efficient discovery of conserved patterns using a pattern graph. Comput. Appl. Biosci. 13, 509-522
19. Bailey, T. L., Williams, N., Misleh, C., and Li, W. W. (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34, W369-73
20. Frith, M. C., Saunders, N. F., Kobe, B., and Bailey, T. L. (2008) Discovering Sequence Motifs with Arbitrary Insertions and Deletions. PLOS Comput. Biol. 4, e1000071
21. Mandava, S., Makowski, L., Devarapalli, S., Uzubell, J., and Rodi, D.J. (2004) RELIC A bioinformatics server for combinatorial peptide analysis and identification of protein-ligand interaction sites. Proteomics 4, 1439-1460 (Pubitemid 38648034)
22. Bastas, G., Sompuram, S. R., Pierce, B., Vani, K., and Bogen, S. A. (2008) Bioinformatic Requirement for Protein Database Searching Using Predicted Epitopes from Disease-associated Antibodies. Mol. Cell. Proteomics 7, 247-256
23. Michaud, G. A., Salcius, M., Zhou, F., Bangham, R., Bonin, J., Guo, H., Snyder, M., Predki, P. F., and Schweitzer, B. I. (2003) Analyzing antibody specificity with whole proteome microarrays. Nat. Biotechnol. 21, 1509-1512
24. Zhou, Z. H., Tzioufas, A. G., and Notkins, A. L. (2007) Properties and function of polyreactive antibodies and antigen-binding B-cells. J. Autoimmun. 29, 219-228
25. James, L. C., Roversi, P., and Tawfik, D. S. (2003) Antibody multispecificity mediated by conformational diversity. Science 299, 1362-1367 (Pubitemid 36254643)
26. Mariuzza, R. A. (2006) Multiple paths to multispecificity. Immunity 24, 359-361
27. Gao, X., Pellois, J. P., Na, Y., Kim, Y., Gulari, E., and Zhou, X. (2004) High density peptide microarrays. In situ synthesis and applications. Mol. Divers. 8, 177-187