Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeast

Molecular and Cellular Proteomics

Volumn 3, Issue 3, 2004, Pages 209-225

  Baxter, Susan M ^a   Rosenblum, Jonathan S ^b   Knutson, Stacy ^a   Nelson, Melanie R ^a   Montimurro, Jennifer S ^a   Di Gennaro, Jeannine A ^a   Speir, Jeffrey A ^a   Burbaum, Jonathan J ^b   Fetrow, Jacquelyn S ^a,b  

^a GeneFormatics   (United States)

^b ACTIVX BIOSCIENCES INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIHYDROFOLATE REDUCTASE; PROTEOME; SERINE DEHYDRATASE; TUMOR SUPPRESSOR PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; CATALYSIS; CHEMICAL REACTION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ASSAY; ENZYME STRUCTURE; EUKARYOTE; GENETIC DATABASE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEOMICS; REVIEW; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SCORING SYSTEM; SEQUENCE ANALYSIS; YEAST;

AMINO ACID SEQUENCE; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; FLUORESCENT DYES; MOLECULAR PROBE TECHNIQUES; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEIN FOLDING; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SERINE ENDOPEPTIDASES;

EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE;

EID: 2642574128     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M300082-MCP200     Document Type: Review

References (69)

1. Balmain, A., Gray, J., and Ponder, B. (2003) The genetics and genomics of cancer. Nat. Genet. 33, (suppl.) 238-244
2. Huang, E., Ishida, S., Pittman, J., Dressman, H., Bild, A., Kloos, M., D'Amico, M., Pestell, R. G., West, M., and Nevins, J. R. (2003) Gene expression phenotypic models that predict the activity of oncogenic pathways. Nat. Genet. 34, 226-230
3. Dressman, M. A., Baras, A., Malinowski, R., Alvis, L. B., Kwon, I., Walz, T. M., and Polymeropoulos, M. H. (2003) Gene expression profiling detects gene amplification and differentiates tumor types in breast cancer. Cancer Res. 63, 2194-2199
4. Ross, D. T., Scherf, U., Eisen, M. B., Perou, C. M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S. S., Van de Rijn, M., Waltham, M., Pergamenschikov, A., Lee, J. C., Lashkari, D., Shalon, D., Myers, T. G., Weinstein, J. N., Botstein, D., and Brown, P. O. (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat. Genet. 24, 227-235
5. Gygi, S. P., Rochon, Y., Franza, B. R., and Aebersold, R. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell Biol. 19, 1720-1730
6. Futcher, B., Latter, G. I., Monardo, P., McLaughlin, C. S., and Garrels, J. I. (1999) A sampling of the yeast proteome. Mol. Cell Biol. 19, 7357-7368
7. Gygi, S. P., Corthals, G. L., Zhang, Y., Rochon, Y., and Aebersold, R. (2000) Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. U. S. A. 97, 9390-9395
8. Washburn, M. P., Wolters, D., and Yates, J. R., 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247
9. Washburn, M. P., Ulaszek, R., Deciu, C., Schieltz, D. M., and Yates, J. R., 3rd (2002) Analysis of quantitative proteomic data generated via multi-dimensional protein identification technology. Anal. Chem. 74, 1650-1657
10. Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., and Gygi, S. P. (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2, 43-50
11. Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature 425, 737-741
12. Koller, A., Washburn, M. P., Lange, B. M., Andon, N. L., Deciu, C., Haynes, P. A., Hays, L., Schieltz, D., Ulaszek, R., Wei, J., Wolters, D., and Yates, J. R., 3rd (2002) Proteomic survey of metabolic pathways in rice. Proc. Natl. Acad. Sci. U. S. A. 99, 11969-11974
13. Al-Lazikani, B., Sheinerman, F. B., and Honig, B. (2001) Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases. Proc. Natl. Acad. Sci. U. S. A. 98, 14796-14801
14. Mackey, A. J., Haystead, T. A., and Pearson, W. R. (2002) Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences. Mol. Cell. Proteomics. 1, 139-147
15. Fetrow, J. S., and Skolnick, J. (1998) Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J. Mol. Biol. 281, 949-968
16. Gutteridge, A., Bartlett, G. J., and Thornton, J. M. (2003) Using a neural network and spatial clustering to predict the location of active sites in enzymes. J. Mol. Biol. 330, 719-734
17. Stark, A., Sunyaev, S., and Russell, R. B. (2003) A model for statistical significance of local similarities in structure. J. Mol. Biol. 326, 1307-1316
18. Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., Moore, L., Adams, S. L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183
19. Patricelli, M. P., Giang, D. K., Stamp, L. M., and Burbaum, J. J. (2001) Direct visualization of serine hydrolase activities in complex proteomes using fluorescent active site-directed probes. Proteomics 1, 1067-1071
20. Kidd, D., Liu, Y., and Cravatt, B. F. (2001) Profiling serine hydrolase activities in complex proteomes. Biochemistry 40, 4005-4015
21. 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
22. Greenbaum, D., Baruch, A., Hayrapetian, L., Darula, Z., Burlingame, A., Medzihradszky, K. F., and Bogyo, M. (2002) Chemical approaches for functionally probing the proteome. Mol. Cell. Proteomics 1, 60-68
23. Allen, J., Davey, H. M., Broadhurst, D., Heald, J. K., Rowland, J. J., Oliver, S. G., and Kell, D. B. (2003) High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat. Biotechnol. 21, 692-696
24. Davie, E. W., Fujikawa, K., Kurachi, K., and Kisiel, W. (1979) The role of serine proteases in the blood coagulation cascade. Adv. Enzymol. Relat. Areas Mol. Biol. 48, 277-318
25. Patricelli, M. P., and Cravatt, B. F. (2001) Characterization and manipulation of the acyl chain selectivity of fatty acid amide hydrolase. Biochemistry 40, 6107-6115
26. Pinho, M. G., de Lencastre, H., and Tomasz, A. (2001) An acquired and a native penicillin-binding protein cooperate in building the cell wall of drug-resistant staphylococci. Proc. Natl. Acad. Sci. U. S. A. 98, 10886-10891
27. Satoh, T., and Hosokawa, M. (1998) The mammalian carboxylesterases: From molecules to functions. Annu. Rev. Pharmacol. Toxicol. 38, 257-288
28. Dodson, G., and Wlodawer, A. (1998) Catalytic triads and their relatives. Trends Biochem. Sci. 23, 347-352
29. Paetzel, M., and Dalbey, R. E. (1997) Catalytic hydroxyl/amine dyads within serine proteases. Trends Biochem. Sci. 22, 28-31
30. Perrot, M., Sagliocco, F., Mini, T., Monribot, C., Schneider, U., Shevchenko, A., Mann, M., Jeno, P., and Boucherie, H. (1999) Two-dimensional gel protein database of Saccharomyces cerevisiae (update 1999). Electrophoresis 20, 2280-2298
31. Shevchenko, A., Jensen, O. N., Podtelejnikov, A. V., Sagliocco, F., Wilm, M., Vorm, O., Mortensen, P., Boucherie, H., and Mann, M. (1996) Linking genome and proteome by mass spectrometry: Large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. U. S. A. 93, 14440-14445
32. Garrels, J. I., McLaughlin, C. S., Warner, J. R., Futcher, B., Latter, G. I., Kobayashi, R., Schwender, B., Volpe, T., Anderson, D. S., Mesquita-Fuentes, R., and Payne, W. E. (1997) Proteome studies of Saccharomyces cerevisiae: Identification and characterization of abundant proteins. Electrophoresis 18, 1347-1360
33. Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B., Arkin, A. P., Astromoff, A., El-Bakkoury, M., Bangham, R., Benito, R., et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391
34. Lu, L., Arakaki, A. K., Lu, H., and Skolnick, J. (2003) Multimeric threading-based prediction of protein-protein interactions on a genomic scale: Application to the Saccharomyces cerevisiae proteome. Genome Res. 13, 1146-1154
35. Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E. S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254
36. Bader, G. D., and Hogue, C. W. (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol. 20, 991-997
37. Washburn, M. P., Koller, A., Oshiro, G., Ulaszek, R. R., Plouffe, D., Deciu, C., Winzeler, E., and Yates, J. R., 3rd (2003) Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 100, 3107-3112
38. Hellman, U., Wernstedt, C., Gonez, J., and Heldin, C. H. (1995) Improvement of an "In-Gel" digestion procedure for the micropreparation of internal protein fragments for amino acid sequencing. Anal. Biochem. 224, 451-455
39. Stone, K. L., DeAngelis, R., LoPresti, M., Jones, J., Papov, V. V., and Williams, K. R. (1998) Use of liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) for routine identification of enzymatically digested proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Electrophoresis 19, 1046-1052
40. Di Gennaro, J. A., Siew, N., Hoffman, B. T., Zhang, L., Skolnick, J., Neilson, L. I., and Fetrow, J. S. (2001) Enhanced functional annotation of protein sequences via the use of structural descriptors. J. Struct. Biol. 134, 232-245
41. Fetrow, J. S., Godzik, A., and Skolnick, J. (1998) Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: Identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. J. Mol. Biol. 282, 703-711
42. Zuegg, J., Gruber, K., Gugganig, M., Wagner, U. G., and Kratky, C. (1999) Three-dimensional structures of enzyme-substrate complexes of the hydroxynitrile lyase from Hevea brasiliensis. Protein Sci. 8, 1990-2000
43. Gruber, K., Gugganig, M., Wagner, U. G., and Kratky, C. (1999) Atomic resolution crystal structure of hydroxynitrile lyase from Hevea brasiliensis. Biol. Chem. 380, 993-1000
44. Skolnick, J., and Kihara, D. (2001) Defrosting the frozen approximation: PROSPECTOR - A new approach to threading. Proteins 42, 319-331
45. Cammer, S. A., Hoffman, B. T., Speir, J. A., Canady, M. A., Nelson, M. R., Knutson, S., Gallina, M., Baxter, S. M., and Fetrow, J. S. (2003) Structure-based active site profiles for genome analysis and functional family subclassification. J. Mol. Biol. 334, 387-401
46. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680
47. Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G., and Thompson, J. D. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31, 3497-3500
48. Attwood, T. K., Beck, M. E., Flower, D. R., Scordis, P., and Selly, J. (1998) The PRINTS protein fingerprints database in its fifth year. Nucleic Acids Res. 26, 304-308
49. Attwood, T. K., Beck, M. E., Bleasby, A. J., and Parry-Smith, D. J. (1994) PRINTS - A database of protein motif fingerprints. Nucleic Acids Res. 22, 3590-3596
50. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S. R., Griffiths-Jones, S., Howe, K. L., Marshall, M., and Sonnhammer, E. L. (2002) The Pfam protein families database. Nucleic Acids Res. 30, 276-280
51. Sonnhammer, E. L., Eddy, S. R., and Durbin, R. (1997) Pfam: A comprehensive database of protein domain families based on seed alignments. Proteins Struct. Funct. Gen. 28, 405-420
52. Henikoff, J. G., and Henikoff, S. (1996) Blocks database and its applications. Methods Enzymol. 266, 88-105
53. Henikoff, J. G., Pietrokovski, S., McCallum, C. M., and Henikoff, S. (2000) Blocks-based methods for detecting protein homology. Electrophoresis 21, 1700-1706
54. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410
55. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Shang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402
56. Zhang, L., Godzik, A., Skolnick, J., and Fetrow, J. S. (1998) Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family. Fold Des. 3, 535-548
57. Fetrow, J. S., Siew, N., and Skolnick, J. (1999) Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily. FASEB J. 13, 1866-1874
58. Cousin, X., Hotelier, T., Giles, K., Toutant, J. P., and Chatonnet, A. (1998) aCHEdb: The database system for ESTHER, the alpha/beta fold family of proteins and the Cholinesterase gene server. Nucleic Acids Res. 26, 226-228
59. Campbell, D. A., and Szardenings, A. K. (2003) Functional profiling of the proteome with affinity labels. Curr. Opin. Chem. Biol. 7, 296-303
60. Kozarich, J. W. (2003) Activity-based proteomics: Enzyme chemistry redux. Curr. Opin. Chem. Biol. 7, 78-83
61. Ogris, E., Du, X., Nelson, K. C., Mak, E. K., Yu, X. X., Lane, W. S., and Pallas, D. C. (1999) A protein phosphatase methylesterase (PME-1) is one of several novel proteins stably associating with two inactive mutants of protein phosphatase 2A. J. Biol. Chem. 274, 14382-14391
62. Schuster, H., Rautenstrauss, B., Mittag, M., Stratmann, D., and Schweizer, E. (1995) Substrate and product binding sites of yeast fatty acid synthase. Stoichiometry and binding kinetics of wild-type and in vitro mutated enzymes. Eur. J. Biochem. 228, 417-424
63. Mohamed, A. H., Chirala, S. S., Mody, N. H., Huang, W. Y., and Wakil, S. J. (1988) Primary structure of the multifunctional alpha subunit protein of yeast fatty acid synthase derived from FAS2 gene sequence. J. Biol. Chem. 263, 12315-12325
64. Bertani, L. E., and Campbell, J. L. (1994) The isolation and characterization of the gene (dfr1) encoding dihydrofolate reductase (DHFR) in Schizosaccharomyces pombe. Gene 147, 131-135
65. Schultz, D. C., Vanderveer, L., Berman, D. B., Hamilton, T. C., Wong, A. J., and Godwin, A. K. (1996) Identification of two candidate tumor suppressor genes on chromosome 17p13.3. Cancer Res. 56, 1997-2002
66. Huang, J., Hu, N., Goldstein, A. M., Emmert-Buck, M. R., Tang, Z. Z., Roth, M. J., Wang, Q. H., Dawsey, S. M., Han, X. Y., Ding, T., Li, G., Giffen, C., and Taylor, P. R. (2000) High frequency allelic loss on chromosome 17p13.3-p11.1 in esophageal squamous cell carcinomas from a high incidence area in northern China. Carcinogenesis 21, 2019-2026
67. Prowse, A. H., Vanderveer, L., Milling, S. W., Pan, Z. Z., Dunbrack, R. L., Xu, X. X., and Godwin, A. K. (2002) OVCA2 is downregulated and degraded during retinoid-induced apoptosis. Int. J. Cancer 99, 185-192
68. Rost, B. (2002) Enzyme function low conserved than anticipated. J. Mol. Biol. 318, 595-608
69. Hegyi, H., and Gerstein, M. (2001) Annotation transfer for genomics: Measuring functional divergence in multi-domain proteins. Genome Res. 11, 1632-1640