PNA-encoded protease substrate microarrays

Chemistry and Biology

Volumn 11, Issue 10, 2004, Pages 1351-1360

  Winssinger, Nicolas ^a   Damoiseaux, Robert ^b   Tully, David C ^b   Geierstanger, Bernhard H ^b   Burdick, Keith ^d   Harris, Jennifer L ^b,c  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

^d NONE

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE HYDROLASE; PEPTIDE LIBRARY; PEPTIDE NUCLEIC ACID;

ARTICLE; CHEMISTRY; COMPARATIVE STUDY; DNA MICROARRAY; ENZYME SPECIFICITY; GENETICS; HUMAN; HYDROLYSIS; LEUKEMIA CELL LINE; METABOLISM; METHODOLOGY; PROTEOMICS;

HUMANS; HYDROLYSIS; JURKAT CELLS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PEPTIDE HYDROLASES; PEPTIDE LIBRARY; PEPTIDE NUCLEIC ACIDS; PROTEOMICS; SUBSTRATE SPECIFICITY;

EID: 5444241960     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2004.07.015     Document Type: Article

References (27)

1. Rawlings N.D., Tolle D.P., Barrett A.J. Merops. the peptidase database Nucleic Acids Res. 32:2004;D160-D164
2. Barret A.J., Rawlings N.D., Woessner J.F. Handbook of Proteolytic Enzymes. 1998;Academic Press, London
3. Krausslich H.G., Ingraham R.H., Skoog M.T., Wimmer E., Pallai P.V., Carter C.A. Activity of purified biosynthetic proteinase of human immunodeficiency virus on natural substrates and synthetic peptides. Proc. Natl. Acad. Sci. USA. 86:1989;807-811
4. Davie E.W., Fujikawa K., Kisiel W. The coagulation cascade. initiation, maintenance, and regulation Biochemistry. 30:1991;10363-10370
5. Thornberry N.A., Rano T.A., Peterson E.P., Rasper D.M., Timkey T., Garcia-Calvo M., Houtzager V.M., Nordstrom P.A., Roy S., Vaillancourt J.P., et al. A combinatorial approach defines specificities of members of the caspase family and granzyme B. Functional relationships established for key mediators of apoptosis. J. Biol. Chem. 272:1997;17907-17911
6. Backes B.J., Harris J.L., Leonetti F., Craik C.S., Ellman J.A. Synthesis of positional-scanning libraries of fluorogenic peptide substrates to define the extended substrate specificity of plasmin and thrombin. Nat. Biotechnol. 18:2000;187-193
7. Harris J.L., Backes B.J., Leonetti F., Mahrus S., Ellman J.A., Craik C.S. Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries. Proc. Natl. Acad. Sci. USA. 97:2000;7754-7759
8. Meldal M., Svendsen I., Breddam K., Auzanneau F.-I. Portion-mixing peptide libraries of quenched fluorogenic substrates for complete subsite mapping of endoprotease specificity. Proc. Natl. Acad. Sci. USA. 91:1994;3314-3318
9. Salisbury C.M., Maly D.J., Ellman J.A. Peptide microarrays for the determination of protease substrate specificity. J. Am. Chem. Soc. 124:2002;14868-14870
10. Reimer U., Reineke U., Schneider-Mergener J. Peptide arrays. from macro to micro Curr. Opin. Biotechnol. 13:2002;315-320
11. St. Hilaire P.M., Willert M., Juliano M.A., Juliano L., Meldal M. Fluorescence-quenched solid phase combinatorial libraries in the characterization of cysteine protease substrate specificity. J. Comb. Chem. 1:1999;509-523
12. Harris J., Mason D., Burdick K.W., Backes B., Chen T., Van Heeke G., Gough L., Ghaemmaghami A., Shakib F., Debaene F., et al. Activity profile of dust mite allergen extract using substrate libraries and functional proteomic microarrays. Chem. Biol. 11:2004;1361-1372., this issue
13. Winssinger N., Ficarro S., Schultz P.G., Harris J.L. Profiling protein function with small molecule microarrays. Proc. Natl. Acad. Sci. USA. 99:2002;11139-11144
14. Leytus S.P., Patterson W.L., Mangel W.F. New class of sensitive and selective fluorogenic substrates for serine proteinases. Amino acid and dipeptide derivatives of rhodamine. Biochem. J. 215:1983;253-260
15. Assfalg-Machleidt I., Rothe G., Klingel S., Banati R., Mangel W.F., Valet G., Machleidt W. Membrane permeable fluorogenic rhodamine substrates for selective determination of cathepsin L. Biol. Chem. Hoppe Seyler. 373:1992;433-440
16. Leytus S.P., Melhado L.L., Mangel W.F. Rhodamine-based compounds as fluorogenic substrates for serine proteinases. Biochem. J. 209:1983;299-307
17. Cai S.X., Zhang H.Z., Guastella J., Drewe J., Yang W., Weber E. Design and synthesis of rhodamine 110 derivative and caspase-3 substrate for enzyme and cell-based fluorescent assay. Bioorg. Med. Chem. Lett. 11:2001;39-42
18. Winssinger N., Harris J.L., Backes B.J., Schultz P.G. From split-pool libraries to spatially addressable microarrays and its application to functional proteomic profiling. Angew. Chem. Int. Ed. Engl. 40:2001;3152-3155
19. Ratilainen T., Holmen A., Tuite E., Haaima G., Christensen L., Nielsen P.E., Norden B. Hybridization of peptide nucleic acid. Biochemistry. 37:1998;12331-12342
20. Furka A., Sebestyen F., Asgedom M., Dibo G. General method for rapid synthesis of multicomponent peptide mixtures. Int. J. Pept. Protein Res. 37:1991;487-493
21. Debaene F., Mejias L., Harris J.L., Winssinger N. Synthesis of a PNA-encoded cysteine protease inhibitor library. Tetrahedron. 60:2004;8677-8690
22. Jeffery D.A., Bogyo M. Chemical proteomics and its application to drug discovery. Curr. Opin. Biotechnol. 14:2003;87-95
23. Jessani N., Cravatt B.F. The development and application of methods for activity-based protein profiling. Curr. Opin. Chem. Biol. 8:2004;54-59
24. Furie B., Furie B.C. The molecular basis of blood coagulation. Cell. 53:1988;505-518
25. Zhou Q., Snipas S., Orth K., Muzio M., Dixit V.M., Salvesen G.S. Target protease specificity of the viral serpin CrmA. Analysis of five caspases. J. Biol. Chem. 272:1997;7797-7800
26. Ioffe I.S., Otten V.F. Rhodamine dyes and related compounds. III. Reaction of m-aminophenol with phthalic anhydride in hot sulfuric acid. Zh. Obshch. Khimii. 32:1962;1477-1480
27. Czerwinski G., Wank S.A., Tarasova N.I., Hudson E.A., Resau J.H., Michejda C.J. Synthesis and properties of three fluorescent derivatives of gastrin. Lett. Pept. Sci. 1:1995;235-242