Application of microarrays in high-throughput enzymatic profiling

Applied Biochemistry and Biotechnology - Part B Molecular Biotechnology

Volumn 28, Issue 3, 2004, Pages 227-239

  Uttamchandani, Mahesh ^a   Huang, Xuan ^a   Chen, Grace Y J ^a   Tan, Lay Pheng ^a   Yao, Shao Q ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Enzyme; Fluorescence; Immobilization; Inhibitors; Microarray; Proteomics

Indexed keywords

ARRAYS; CELL IMMOBILIZATION; FLUORESCENCE; PROTEINS; THROUGHPUT;

ENZYMATIC ACTIVITIES; MICROARRAYS; PROTEIN IMMOBILIZATION; PROTEOMICS;

BIOTECHNOLOGY;

ARTICLE; DNA MICROARRAY; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME IMMOBILIZATION; ENZYME INHIBITION; FLUORESCENCE; HIGH THROUGHPUT SCREENING; PROTEIN FUNCTION; PROTEIN IMMOBILIZATION; PROTEIN INTERACTION; PROTEOMICS; AMINO ACID SEQUENCE; CHEMISTRY; GENETICS; REVIEW;

ENZYME;

AMINO ACID SEQUENCE; ENZYMES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 15944415329     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1385/MB:28:3:227     Document Type: Article

References (56)

1. Chen, G. Y. J., Uttamchandani, M., Lue, Y. P. R., Lesaicherre, M. L., and Yao, S. Q. (2003) Array-based technologies and their applications in proteomics. Curr. Top. Med. Chem. 3, 705-724.
2. Jeffery, D. A. and Bogyo, M. (2003) Chemical proteomics and its application to drug discovery. Curr. Opin. Biotechnol. 14, 87-95.
3. Schweitzer, B., Predki, P., and Snyder, M. (2003) Microarrays to characterize protein interactions on a whole-proteome scale. Proteomics 3, 2190-2199.
4. Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. (1995) Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray. Science 270, 467-470.
5. MacBeath, G. and Schreiber, S. L. (2000) Printing proteins as microarrays for high-throughput function determination. Science 289, 1760-1763.
6. Wilson, D. S. and Nock, S. (2003) Recent developments in protein microarray technology. Angew. Chem. Int. Ed. Engl. 42, 494-500.
7. Kodadek, T. (2001) Protein microarrays: prospects and problems. Chem. Biol. 8, 105-115.
8. Lal, S. P., Christopherson, R. I., and dos Remedios, C. G. (2002) Antibody arrays: an embryonic but rapidly growing technology. Drug Discov. Today 7, S143-S149.
9. Liu, R., Marik, J., and Lam. K. S. (2002) A novel peptide-based encoding system for "one-bead one-compound" peptidomimetic and small molecule combinatorial libraries. J. Am. Chem. Soc. 124, 7678-7680.
10. Figeys, D. (2003) Proteomics in 2002: a year of technical development and wide-ranging applications. Anal. Chem. 75, 2891-2905.
11. Ito, T., Tashiro, K., Muta, S., et al. (2000) Toward a protein-protein interaction map of budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteome. Proc. Nat. Acad. Sci. USA 97, 1143-1147.
12. Love, B., Rank, D. R., Penn, S. G., Jenkins, D. A., and Thomas, R. S. (2002) A conditional density error model for the statistical analysis of microarray data. Bioinformatics. 18, 1064-1072.
13. Brazma, A., Hingamp, P., Quackenbush, J., et al. (2001) Minimum information about a microarray experiment (MIAME): towards standards for microarray data. Nat. Genet. 29, 365-371.
14. Kuruvilla, F. G., Shamji, A. F., Sternson, S. M., Hergenrother, P. J., and Schreiber, S. L. (2002) Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays. Nature 416, 653-657.
15. Zhu, H., Bilgin, M., Bangham, R., et al. (2001) Global analysis of protein activities using proteome chips. Science 293, 2101-2105.
16. Michaud, G. A., Salcius, M., Zhou, F., et al. (2003) Analyzing antibody specificity with whole proteome microarrays. Nat. Biotechnol. 21, 1509-1512.
17. Paborsky, L. R., Dunn, K. E., Gibbs, C. S., and Dougherty, J. P. (1996) A nickel chelate microtiter plate assay for six histidine-containing proteins. Anal. Biochem. 234, 60-65.
18. Lesaicherre, M. L., Lue, Y. P. R., Chen, G. Y. J., Zhu, Q., and Yao, S. Q. (2002) Intein-mediated biotinylation of proteins and its application in a protein microarray. J. Am. Chem. Soc. 124, 8768, 8769.
19. Green, N. M., Toms, E. J. (1973) The properties of subunits of avidin coupled to sepharose. Biochem. J. 133, 687-700.
20. Lue, R. Y. P., Chen, G. Y., Hu, Y., Zhu, Q., and Yao, S. Q. (2004) Versatile protein biotinylation strategies for potential high-throughput proteomics. J. Am. Chem. Soc. 126, 1055-1062.
21. Lue, R. Y. P., Yeo, D. S. Y., Tan, L. P., Uttamchandani, M., Chen, G. Y. J., and Yao, S. Q. (2004) Novel strategies in protein microarray generation and detection. In Protein Microarrays (Schena, M., ed.), Jones and Bartlett, Sudbury, MA, pp. 13-42.
22. Lesaicherre, M. L., Uttamchandani, M., Chen, G. Y. J., and Yao, S. Q. (2002) Developing site-specific immobilization strategies of peptides in a microarray. Bioorg. Med. Chem. Lett. 12, 2079-2083.
23. Fang, Y., Frutos, A. G., and Lahiri, J. (2002) Membrane protein microarrays. J. Am. Chem. Soc. 124, 2394, 2395.
24. Iyer, V. R., Horak, C. E., Scafe, C. S., Botstein, D., Snyder, M., and Brown, P. O. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533-538.
25. Fukui S., Feizi, T., Galustian, C., Lawson, A. M, and Chai, W. (2002) Oligosaccharide microarrays for high-throughput detection and specificity assignments of carbohydrate-protein interactions. Nat. Biotechnol. 20, 1011-1017.
26. Uetz, P., Giot, L., Cagney, G., et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627.
27. Martzen, M. R., McCraith, S. M., Spinelli, S. L., et al. (1999) A biochemical genomics approach for identifying genes by the activity of their products. Science 286, 1153-1155.
28. Newman, J. R. S. and Keating, A. E. (2003) Comprehensive identification of human bZIP interactions with coiled-coil arrays. Science. 300, 2097-2101.
29. Hu, Y., Wang, G., Chen, G. Y. J., Fu, X., and Yao, S. Q. (2003) Proteome analysis of Saccharomyces cerevisiae under metal stress by two-dimensional differential gel electrophoresis (DIGE). Electrophoresis 24, 1458-1470.
30. Aebersold, R., Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207.
31. Huang, X., Tan, E. L. P., Chen, G. Y. J., and Yao, S. Q. (2003) Enzyme-targeting small molecule probes for proteomics application. Appl. Genomics Proteomics, 2, 225-238.
32. Hu, Y., Huan, X., Chen, G. Y. J., and Yao, S. Q. (2004) Recent advances in gel-based proteome profiling techniques. Mol. Biotechnol., in press.
33. Patton, W.F. (2000) A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 21, 1123-1144.
34. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999.
35. Zhu, H., Klemic, J. F., Chang, S., et al. (2000) Analysis of yeast protein kinases using protein chips. Nat. Genet. 26, 283-289.
36. Lesaicherre, M. L., Uttamchandani, M., Chen, G. Y. J., and Yao, S. Q. (2002) Antibody-based fluorescence detection of kinase activity on a peptide array. Bioorg. Med. Chem. Lett. 12, 2085-2088.
37. Uttamchandani, M., Chan, E. W. S., Chen, G. Y. J., and Yao, S. Q. (2003) Combinatorial peptide microarrays for the rapid determination of kinase specificity. Bioorg. Med. Chem. Lett. 13, 2997-3000.
38. Chen, G. Y. J., Uttamchandani, M., Zhu, Q., Wang, G., and Yao, S. Q. (2003) Developing a strategy for activity-based detection of enzymes in a protein microarray. Chembiochem. 4, 336-339.
39. Zhu, Q., Uttamchandani, M., Li, D. B., Lesaicherre, M. L., and Yao, S. Q. (2003) An enzymatic profiling system in a small-molecule microarray. Org. Lett. 5, 1257-1260.
40. Zhu, Q., Li, D. B., Uttamchandani, M., and Yao, S. Q. (2003) Facile synthesis of 7-amino-4-carbamoylmethylcoumarin (ACC)-containing solid supports and their corresponding fluorogenic protease substrates. Bioorg. Med. Chem. Lett. 13, 1033-1036.
41. Pawson, T. and Nash, P. (2003) Assembly of cell regulatory systems through protein interaction domains. Science 300, 445-452.
42. Lam, K. S., Lebl, M., and Krchnak, V. (1997) The "one-bead-one- compound" combinatorial library method. Chem. Rev. 97, 411-448.
43. Yan, B. (2002) Single-bead analysis in combinatorial chemistry. Curr. Opin. Chem. Biol. 6, 328-332.
44. Galbraith, D. W., Anderson, M. T., and Herzenberg, L. A. (1999) Flow cytometric analysis and FACS sorting of cells based on GFP accumulation. Methods Cell Biol. 58, 315-341.
45. Needels, M. C., Jones, D. G., Tate, E. H., et al. (1993) Generation and screening of an oligonucleotide-encoded synthetic peptide library. Proc. Natl. Acad. Sci. USA 90, 10,700-10,704.
46. Dostmann, W. R. G., Taylor, M. S., Nickl, C. K., Brayden, J. E., Frank, R., and Tegge, W. J. (2000) Highly specific, membrane-permeant peptide blockers of cGMP-dependent protein kinase I alpha inhibit NO-induced cerebral dilation. Proc. Natl. Acad. Sci. USA 97, 14,772-14,777.
47. Sidhu, S. S., Lowman, H. B., Cunningham, B. C., and Wells, J. A. (2000) Phage display for selection of novel binding peptides. Methods Enzymol. 328, 333-363.
48. Zhang, J., Ma, Y., Taylor, S. S., and Tsien, R. Y. (2001) Genetically encoded reporters of protein kinase A activity reveal impact of substrate tethering. Proc. Natl. Acad. Sci. USA 98, 14,997-15,002.
49. Ting, A., Kain, K. H., Klemke, R. L., and Tsien, R. Y. (2001) Genetically encoded fluorescent reporters of protein tyrosine kinase activities in living cells. Proc. Natl. Acad. Sci. USA 98, 15,003-15,008.
50. Zhu, Q., Huang, X., Chen, G. Y. J., and Yao, S. Q. (2003) Activity-based fluorescent probes that targets phosphatases. Tetrahedron Lett. 44, 2669-2672.
51. Wang, G., Uttamchandani, M., Chen, G. Y. J., and Yao, S. Q. (2003) Solid-phase synthesis of peptide vinyl sulfones and their uses in large-scale proteomic experiments. Org. Lett. 5, 737-740.
52. Wang G. and Yao, S. Q. (2003) Combinatorial synthesis of a small molecule library based on vinyl sulfone scaffold. Org. Lett. 5, 4437-4440.
53. Liau, M. L., Panicker, R. C., and Yao, S. Q. (2003) Design and synthesis of an affinity probe that targets caspases in proteomic experiments, Tetrahedron Lett. 44, 1043-1046.
54. Salisbury, C. M., Maly, D. J., and Ellman, J. A. (2002) Peptide microarrays for the determination of protease substrate specificity. J. Am. Chem. Soc. 124, 14,868-14,870.
55. Zhang, J., Campbell, R. E., Ting, A. Y., and Tsien, R. Y. (2002) Creating new fluorescent probes for cell biology. Nat. Rev. Mol. Cell Biol. 3, 906-918.
56. Yeo, S. Y. D., Srinivasan, R., Uttamchandani, M., Chen, G. Y. J., Zhu, Q., and Yao, S. Q. (2003) Cell-permeable small molecule probes for site-specific labeling of proteins. Chem. Commun. (Camb) 23, 2870, 2871.