Mixture-based peptide libraries for identifying protease cleavage motifs

Methods in Molecular Biology

Volumn 539, Issue , 2009, Pages 79-91

  Turk, Benjamin E ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Edman sequencing; Enzyme specificity; High throughput screening; Peptide libraries; Proteases

Indexed keywords

PEPTIDE; PEPTIDE HYDROLASE; PEPTIDE LIBRARY;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CHEMISTRY; ENZYME SPECIFICITY; METABOLISM;

AMINO ACID SEQUENCE; BINDING SITES; PEPTIDE HYDROLASES; PEPTIDE LIBRARY; PEPTIDES; SUBSTRATE SPECIFICITY;

EID: 73649086108     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-003-8_5     Document Type: Article

References (21)

1. Lopez-Otin, C. and Overall, C. M. (2002) Protease degradomics: a new challenge for proteomics. Nat. Rev. Mol. Cell. Biol. 3, 509-519. (Pubitemid 34733432)
2. Rawlings, N. D., Tolle, D. P., and Barrett, A. J. (2004) MEROPS: the peptidase database. Nucleic Acids Res. 32, D160-D164. (Pubitemid 38081629)
3. Mahajan, N. P., Harrison-Shostak, D. C., Michaux, J., Herman, B. (1999) Novel mutant green fluorescent protein protease substrates reveal the activation of specific caspases during apoptosis. Chem. Biol. 6, 401-409. (Pubitemid 29363172)
4. Vanderklish, P. W., Kr ushel, L. A., Holst, B. H., Gally, J. A., Crossin, K. L., Edelman, G. M. (2000) Marking synaptic activity in dendritic spines with a calpain substrate exhibiting fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA 97, 2253-2258. (Pubitemid 30134055)
5. 129 Xe NMR biosensors for matrix metalloproteinase detection. J. Am. Chem. Soc. 128, 13274-13283. (Pubitemid 44527699)
6. Turk, B. E., Huang, L. L., Piro, E. T., and Cantley, L. C. (2001) Determination of protease cleavage site motifs using mixture-based oriented peptide libraries. Nat. Biotechnol. 19, 661-667. (Pubitemid 32625438)
7. Boyd, S. E., Pike, R. N., Rudy, G. B., Whisstock, J. C., and Garcia de la Banda, M. (2005) PoPS: a computational tool for modeling and predicting protease specificity. J. Bioinform. Comput. Biol. 3, 551-585. (Pubitemid 41015279)
8. Meldal, M., Svendsen, I., Breddam, K., and Auzanneau, F. I. (1994) Portion-mixing peptide libraries of quenched fluorogenic substrates for complete subsite mapping of endoprotease specificity. Proc. Natl. Acad. Sci. USA 91, 3314-3318. (Pubitemid 24130227)
9. Backes, B. J., Harris, J. L., Leonetti, F., Craik, C. S., and Ellman, J. A. (2000) Synthesis of positional-scanning libraries of fluorogenic peptide substrates to define the extended substrate specificity of plasmin and thrombin. Nat. Biotechnol. 18, 187-193. (Pubitemid 30091180)
10. Matthews, D. J. and Wells, J. A. (1993) Substrate phage: selection of protease substrates by monovalent phage display. Science 260, 1113-1117. (Pubitemid 23186784)
11. 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, 14868-14870. (Pubitemid 36014093)
12. Dekker, N., Cox, R. C., Kramer, R. A., and Egmond, M. R. (2001) Substrate specificity of the integral membrane protease OmpT determined by spatially addressed peptide libraries. Biochemistry 40, 1694-1701. (Pubitemid 32144039)
13. Turk, B. E., Cantley, L. C. (2004) Using peptide libraries to identify optimal cleavage motifs for proteolytic enzymes. Methods 32, 398-405. (Pubitemid 38299331)
14. Martins, L. M., Turk, B. E., Cowling, V., et al. (2003) Binding specificity and regulation of the serine protease and PDZ domains of HtrA2/Omi. J. Biol. Chem. 278, 49417-49427.
15. Cuerrier, D., Moldoveanu, T., and Davies, P. L. (2005) Determination of peptide substrate specificity for m -calpain by a peptide librarybased approach: the importance of primed side interactions. J. Biol. Chem. 280, 40632 40641. (Pubitemid 41780554)
16. Murata, C. E., Goldberg, D. E. (2003) Plasmodium falciparum falcilysin: a metallopro-tease with dual specificity. J. Biol. Chem. 278, 38022-38028. (Pubitemid 37175333)
17. Turk, B. E., Lee, D. H., Yamakoshi, Y., et al. (2006) MMP-20 is predominately a toothspecific enzyme with a deep catalytic pocket that hydrolyzes type V collagen. Biochemistry 45, 3863-3874.
18. Turk, B. E., Wong, T. Y., Schwarzenbacher, R., et al. (2004) The structural basis for substrate and inhibitor selectivity of the anthrax lethal factor. Nat. Struct. Mol. Biol. 11, 60-66. (Pubitemid 38173442)
19. Udenfriend, S., Stein, S., Bohlen, P., Dairman, W., Leimgruber, W., and Weigele, M. (1972) Fluo-rescamine: a reagent for assay of amino acids, peptides, proteins, and primary amines in the picomole range. Science 178, 871-872.
20. Lam, K. S., Lake, D., Salmon, S. E., et al. (1996) A one-bead one-peptide combinatorial library method for B-cell epitope mapping. Methods 9, 482-493. (Pubitemid 26273469)
21. Ostresh, J. M., Winkle, J. H., Hamashin, V. T., and Houghten, R. A. (1994) Peptide libraries: determination of relative reaction rates of protected amino acids in competitive couplings. Biopolymers 34, 1681-1689. (Pubitemid 24357583)