Discovering disease-associated enzymes by proteome reactivity profiling

Chemistry and Biology

Volumn 11, Issue 11, 2004, Pages 1523-1531

  Barglow, Katherine T ^a   Cravatt, Benjamin F ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETAMIDE DERIVATIVE; ALCOHOL DEHYDROGENASE; CHLOROACETAMIDE; HYDROXYPYRUVATE REDUCTASE; PEPTIDE LIBRARY;

ANIMAL; ARTICLE; BIOLOGY; BRAIN; DISEASE MODEL; DRUG DESIGN; ENZYMOLOGY; GENERAL ASPECTS OF DISEASE; GENETICS; HEART MUSCLE; HUMAN; LIVER; METABOLISM; MOLECULAR PROBE; MOUSE; MOUSE MUTANT; NON INSULIN DEPENDENT DIABETES MELLITUS; OBESITY; PROTEOMICS; UPREGULATION;

ACETAMIDES; ALCOHOL OXIDOREDUCTASES; ANIMALS; BRAIN; COMPUTATIONAL BIOLOGY; DIABETES MELLITUS, TYPE 2; DISEASE; DISEASE MODELS, ANIMAL; DRUG DESIGN; HUMANS; HYDROXYPYRUVATE REDUCTASE; LIVER; MICE; MICE, OBESE; MOLECULAR PROBES; MYOCARDIUM; OBESITY; PEPTIDE LIBRARY; PROTEOMICS; UP-REGULATION;

EID: 8844268481     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2004.08.023     Document Type: Article

References (41)

1. Schena M., Heller R.A., Theriault T.P., Konrad K., Lachenmeier E., Davis R.W. Microarrays. biotechnology's discovery platform for functional genomics Trends Biotechnol. 16:1998;301-306
2. Kodadek T. Protein microarrays. prospects and problems Chem. Biol. 8:2001;105-115
3. Santoni V., Molloy M., Rabilloud T. Membrane proteins and proteomics. un amour impossible? Electrophoresis. 21:2000;1054-1070
4. Corthals G.L., Wasinger V.C., Hochstrasser D.F., Sanchez J.C. The dynamic range of protein expressioin. a challenge for proteomic research Electrophoresis. 21:2000;1104-1115
5. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17:1999;994-999
6. Washburn M.P., Wolters D., Yates J.R. III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19:2001;242-247
7. Kobe B., Kemp B.E. Active site-directed protein regulation. Nature. 402:1999;373-376
8. Liu Y., Patricelli M.P., Cravatt B.F. Activity-based protein profiling. the serine hydrolases Proc. Natl. Acad. Sci. USA. 96:1999;14694-14699
9. Jessani N., Cravatt B.F. The development and application of methods for activity-based protein profiling. Curr. Opin. Chem. Biol. 8:2004;54-59
10. Speers A.E., Cravatt B.F. Chemical strategies for activity-based proteomics. Chembiochem. 5:2004;41-47
11. Kidd D., Liu Y., Cravatt B.F. Profiling serine hydrolase activities in complex proteomes. Biochemistry. 40:2001;4005-4015
12. Jessani N., Liu Y., Humphrey M., Cravatt B.F. Enzyme activity profiles of the secreted and membrane proteome that depict cancer invasiveness. Proc. Natl. Acad. Sci. USA. 99:2002;10335-10340
13. Saghatelian A., Jessani N., Joseph A., Humphrey M., Cravatt B.F. Activity-based probes for the proteomic profiling of metalloproteases. Proc. Natl. Acad. Sci. USA. 101:2004;10000-10005
14. Patricelli M.P., Giang D.K., Stamp L.M., Burbaum J.J. Direct visualization of serine hydrolase activities in complex proteome using fluorescent active site-directed probes. Proteomics. 1:2001;1067-1071
15. Greenbaum D., Medzihradszky K.F., Burlingame A., Bogyo M. Epoxide electrophiles as activity-dependent cysteine protease profiling and discovery tools. Chem. Biol. 7:2000;569-581
16. Faleiro L., Kobayashi R., Fearnhead H., Lazebnik Y. Multiple species of CPP32 and Mch2 are the major active caspases present in apoptotic cells. EMBO J. 16:1997;2271-2281
17. Borodovsky A., Ovaa H., Kolli N., Gan-Erdene T., Wilkinson K.D., Ploegh H.L., Kessler B.M. Chemistry-based functional proteomics reveals novel members of the deubiquitinating enzyme family. Chem. Biol. 9:2002;1149-1159
18. Kumar S., Zhou B., Liang F., Wang W.Q., Huang Z., Zhang Z.Y. Activity-based probes for protein tyrosine phosphatases. Proc. Natl. Acad. Sci. USA. 101:2004;7943-7948
19. Adam G.C., Sorensen E.J., Cravatt B.F. Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype. Nat. Biotechnol. 20:2002;805-809
20. Adam G.C., Cravatt B.F., Sorensen E.J. Profiling the specific reactivity of the proteome with non-directed activity-based probes. Chem. Biol. 8:2001;81-95
21. Adam G.C., Sorensen E.J., Cravatt B.F. Trifunctional chemical probes for the consolidated detection and identification of enzyme activities from complex proteomes. Mol. Cell. Proteomics. 1:2002;828-835
22. Adam G.C., Burbaum J.J., Kozarich J.W., Patricelli M.P., Cravatt B.F. Mapping enzyme active sites in complex proteomes. J. Am. Chem. Soc. 126:2004;1363-1368
23. Liu S., Widom J., Kemp C.W., Crews C.M., Clardy J. Structure of human methionine aminopeptidase-2 complexed with fumagillin. Science. 282:1998;1324-1327
24. Withers S.G., Aebersold R. Approaches to labeling and identification of active site residues in glycosidases. Protein Sci. 4:1995;361-372
25. Speers A.E., Cravatt B.F. Profiling enzyme activities in vivo using click chemistry methods. Chem. Biol. 11:2004;535-546
26. Greenbaum D., Baruch A., Hayrapetian L., Darula Z., Burlingame A., Medzihradszky K.F., Bogyo M. Chemical approaches for functionally probing the proteome. Mol. Cell. Proteomics. 1:2002;60-68
27. Shoolingin-Jordan P.M., Spencer P., Sarwar M., Erskine P.E., Cheung K.M., Cooper J.B., Norton E.B. 5-Aminolaevulinic acid dehydratase. metals, mutants and mechanism Biochem. Soc. Trans. 30:2002;584-590
28. Seehra J.S., Jordan P.M. 5-Aminolevulinic acid dehydratase. alkylation of an essential thiol in the bovine-liver enzyme by active-site-directed reagents Eur. J. Biochem. 113:1981;435-446
29. Liu S., Cerione R.A., Clardy J. Structural basis for the guanine nucleotide-binding activity of tissue transglutaminase and its regulation of transamidation activity. Proc. Natl. Acad. Sci. USA. 99:2002;2743-2747
30. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA. 95:1998;14863-14868
31. Johnson P.R., Greenwood M.R., Horwitz B.A., Stern J.S. Animal models of obesity. genetic aspects Annu. Rev. Nutr. 11:1991;325-353
32. Yoon J.C., Puigserver P., Chen G., Donovan J., Wu Z., Rhee J., Adelmant G., Stafford J., Kahn C.R., Granner D.K., et al. Control of hepatic gluconeogenesis through the transcriptional coactivator PGC-1. Nature. 413:2001;131-138
33. Edvardsson U., von Lowenhielm H.B., Panfilov O., Nystrom A.C., Nilsson F., Dahllof B. Hepatic protein expression of lean mice and obese diabetic mice treated with peroxisome proliferator-activated receptor activators. Proteomics. 3:2003;468-478
34. Leung D., Hardouin C., Boger D.L., Cravatt B.F. Discovering potent and selective reversible inhibitors of enzymes in complex proteomes. Nat. Biotechnol. 21:2003;687-691
35. Karlsson M., Contreras J.A., Hellman U., Tornqvist H., Holm C. cDNA cloning, tissue distribution, and identification of the catalytic triad of monoglyceride lipase. Evolutionary relationship to esterases, lysophospholipases, and haloperoxidases. J. Biol. Chem. 272:1997;27218-27223
36. David L., Guo X.J., Villard C., Moulin A., Puigserver A. Purification and molecular cloning of porcine intestinal glycerol-ester hydrolase - evidence for its identity with carboxylesterase. Eur. J. Biochem. 257:1998;142-148
37. Xue H.H., Fujie M., Sakaguchi T., Oda T., Ogawa H., Kneer N.M., Lardy H.A., Ichiyama A. Flux of the L-serine metabolism in rat liver. The predominant contribution of serine dehydratase. J. Biol. Chem. 274:1999;16020-16027
38. Xue H.H., Sakaguchi T., Fujie M., Ogawa H., Ichiyama A. Flux of the L-serine metabolism in rabbit, human, and dog livers. Substantial contributions of both mitochondrial and peroxisomal serine:pyruvate/alanine:glyoxylate aminotransferase. J. Biol. Chem. 274:1999;16028-16033
39. Lind P. Interdependence of hepatic lipid and glucose metabolism. novel pharmacological targets for diabetes Curr. Opin. Investig. Drugs. 5:2004;395-401
40. Kurukulasuriya R., Link J.T., Madar D.J., Pei Z., Richards S.J., Rohde J.J., Souers A.J., Szczepankiewicz B.G. Potential drug targets and progress towards pharmacologic inhibition of hepatic glucose production. Curr. Med. Chem. 10:2003;123-153
41. Ross S.A., Gulve E.A., Wang M. Chemistry and biochemistry of type 2 diabetes. Chem. Rev. 104:2004;1255-1282