Subsite cooperativity in protease specificity

Biological Chemistry

Volumn 390, Issue 5-6, 2009, Pages 401-407

  Ng, Natasha M ^a   Pike, Robert N ^a   Boyd, Sarah E ^a  

^a MONASH UNIVERSITY   (Australia)

Author keywords

Cooperativity; Protease; Specificity; Subsites

Indexed keywords

BLOOD CLOTTING FACTOR 10A; CLOSTRIPAIN; HIV 1 PROTEASE; HIV 2 PROTEASE; HUMAN IMMUNODEFICIENCY VIRUS PROTEIN; PAPAIN; PROTEINASE; SUBTILISIN; THROMBIN; TRYPSIN; UNCLASSIFIED DRUG;

APOPTOSIS; CELL CYCLE REGULATION; CELL DIFFERENTIATION; CELL GROWTH; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME KINETICS; ENZYME SPECIFICITY; HEMOSTASIS; NONHUMAN; PRIORITY JOURNAL; REVIEW; STRUCTURE ANALYSIS; SUBSITE COOPERATIVITY;

ANIMALS; CATALYTIC DOMAIN; HUMANS; KINETICS; PEPTIDE HYDROLASES; SUBSTRATE SPECIFICITY;

EID: 67649617069     PISSN: 14316730     EISSN: 14374315     Source Type: Journal    
DOI: 10.1515/BC.2009.065     Document Type: Review

References (37)

1. Beck, Z.Q., Lin, Y-C., and Elder, J.H. (2001). Molecular basis for the relative substrate specificity of human immunodeficiency virus type 1 and feline immunodeficiency virus proteases. J. Virol. 75, 9458-9469.
2. 29 sub-sites. Biochemistry 30, 1394-1402.
3. Beyer, B.B., Johnson, J.V., Chung, A.Y., Li, T., Madabushi, A., Agbandje-McKenna, M., McKenna, R., Dame, J.B., and Dunn, B.M. (2005). Active-site specificity of digestive aspartic peptidases from the four species of Plasmodium that infect humans using chromogenic combinatorial peptide libraries. Biochemistry 44, 1768-1779.
4. Bode, W. and Huber, R. (1991). Ligand binding: proteinase-protein inhibitor reactions. Curr. Opin. Struct. Biol. 1, 45-52.
5. Boyd, S.E., Kerr, F.K., Albrecht, D.W., Garcia de la Banda, M., Ng, N.M., and Pike, R.N. (2009). Cooperative effects in the substrate specificity of the complement protease C1s. Biol. Chem. 390, 503-507.
6. Fujinaga, M., Sielecki, A.R., Read, R.J., Ardelt, W., Laskowski, M. Jr., and James, M.N.G. (1987). Crystal and molecular structures of the complex α-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 Å resolution. J. Mol. Biol. 195, 397-418.
7. Gosalia, D.N., Salisbury, C.M., Maly, D.J., Ellman, J.A., and Diamond, S.L. (2005). Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays. Proteomics 5, 1292-1298.
8. Griffiths, J.T., Phylip, J.H., Konvalinka, J., Strop, P., Gustchina, A., Wlodawer, A., Davenport, R.J., Briggs, R., Dunn, B.M., and Kay, J. (1992). Different requirements for productive interactions between the active site of HIV-1 proteinase and substrates containing -hydrophobic*hydrophobic- or -aromatic*pro-cleavage sites. Biochemistry 31, 5193-5200.
9. Grøn, H. and Breddam, K. (1992). Interdependency of the binding sites in subtilisin. Biochemistry 31, 8967-8971.
10. Grøn, H., Meldal, M., and Breddam, K. (1992). Extensive comparison of the substrate preferences of two subtilisins as determined with peptide substrates which are based on the principle of intramolecular quenching. Biochemistry 31, 6011-6018.
11. Harris, J.L., Backes, B.J., Leonetti, F., Mahrus, S., Ellman, J.A., and Craik, C.S. (2000). Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries. Proc. Natl. Acad. Sci. USA 97, 7754-7759.
12. Hong, L., Koelsch, G., Lin, X., Wu, S., Terzyan, S., Ghosh, A.K., Zhang, X.C., and Tang, J. (2000). Structure of the protease domain of memapsin 2 (β-secretase) complexed with inhibitor. Science 290, 150-153.
13. Hooper, N.M. (2002). Proteases: a primer. In: Essays in Biochemistry: Proteases in Biology and Medicine, Vol. 38, N.M. Hooper, ed. (London, UK: Portland Press), pp. 2-8.
14. Hu, J., Cwi, C.L., Smiley, D.L., Timm, D., Erickson, J.A., McGee, J.E., Yang, H.-C., Mendel, D., May, P.C., Shapiro, M., et al. (2003). Design and synthesis of statine-containing BACE inhibitors. Bioorg. Med. Chem. Lett. 13, 4335-4339.
15. Kataoka, Y., Takada, K., Oyama, H., Tsunemi, M., James, M.N.G., and Oda, K. (2005). Catalytic residues and substrate specificity of scytalidoglutamic peptidase, the first member of the eqolisin in family (G1) of peptidases. FEBS Lett. 579, 2991-2994.
16. Keil, B. (1992). Essential substrate residues for action of endopeptidases. In: Specificity of Proteolysis (Berlin, Germany: Springer-Verlag), pp. 66-73.
17. Kerr, F.K., O'Brien, G., Quinsey, N.S., Whisstock, J.C., Boyd, S., Garcia de la Banda, M., Kaiserman, D., Matthews, A.Y., Bird, P.I., and Pike, R.N. (2005). Elucidation of the substrate specificity of the C1s protease of the classical complement pathway. J. Biol. Chem. 280, 39510-39514.
18. Kisselev, A.F., Garcia-Colvo, M., Overkleeft, H.S., Peterson, E., Pennington, M.W., Ploegh, H.L., Thornberry, N.A., and Gold-bert, A.L. (2003). The caspase-like sites of proteasomes, their substrate specificity, new inhibitors and substrates, and allosteric interactions with the trypsin-like sites. J. Biol. Chem. 278, 35869-35877.
19. Mahrus, S., Trinidad, J.C., Barkan, D.T., Sali, A., Burlingame, A.L., and Wells, J.A. (2008). Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N-termini. Cell 134, 866-876.
20. Nazif, T. and Bogyo, M. (2001). Global analysis of proteasomal substrate specificity using positional-scanning libraries of covalent inhibitors. Proc. Natl. Acad. Sci. USA 98, 2967-2972.
21. Overall, C.M. and Blobel, C.P. (2007). In search of partners: linking extracellular proteases to substrates. Nat. Rev. Mol. Cell Biol. 8, 245-257.
22. Petit, S.C., Simsic, J., Loeb, D.D., Everitt, L., Hutchison, C.A. III, Swanstrom, R. (1991). Analysis of retroviral protease cleavage sites reveals two types of cleavage sites and the structural requirements of the P1 amino acid. J. Biol. Chem. 266, 14539-14547.
23. Rao, M.B., Tanksale, A.M., Ghatge, M.S., and Deshpande, V.V. (1998). Molecular and biotechnical aspects of microbial proteases. Microbiol. Mol. Biol. Rev. 62, 597-635.
24. Rawlings, N.D. and Barrett, A.J. (1999). MEROPS: the peptidase database. Nucleic Acids Res. 27, 325-331.
25. Ridky, T.W., Cameron, C.E., Cameron, J., and Leis, J. (1996). Human immunodeficiency virus, type 1 protease substrate specificity is limited by interactions between substrate amino acids bound in adjacent enzyme subsites. J. Biol. Chem. 271, 4709-4717.
26. Rögnvaldsson, T. and You, L. (2004). Why neural networks should not be used for HIV-1 protease cleavage site prediction. Bioinformatics 22, 1702-1709.
27. Ruhlmann, A., Kukla, D., Schwager, P., Bartels, K., and Huber, R. (1973). Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. Crystal structure determination and stereochemistry of the contact region. J. Mol. Biol. 77, 417-436.
28. Schechter, I. and Berger, A. (1967). On the size of the active site in proteases. I. Papain. Biochem. Biophys. Res. Commun. 27, 157-162.
29. Schellenberger, V., Turck, C.W., and Rutter, W.J. (1994). Role of the S' subsites in serine protease catalysis. active-site mapping of rat chymotrypsin, rat trypsin, a-lytic protease, and cercarial protease from Schistosoma mansoni. Biochemistry 33, 4251-4257.
30. Strop, P., Konvalinka, J., Stys, D., Pavlickova, L., Blaha, I., Velek, J., Travnicek, M., Kostka, V., and Sedlacek, J. (1991). Specificity studies on retroviral proteinase from myeloblastosis-associated virus. Biochemistry 30, 3437-3443.
31. Thornberry, N.A., Rano, R.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. (1997). A combinatorial approach defines specificities of members of the caspase family and granzyme B. J. Biol. Chem. 272, 17907-17911.
32. 39 subsites of HIV proteinases. Biochemistry 31, 4793-4800.
33. Tözsér, J., Bagossi, P., Weber, I.T., Louis, J.M., Copeland, T.D., and Oroszlan, S. (1997). Studies on the symmetry and sequence context dependence of the HIV-1 proteinase specificity. J. Biol. Chem. 272, 16807-16814.
34. Turk, D., Guncar, G., Podobnik, M., and Turk, B. (1998). Revised definition of substrate binding sites of papain-like cysteine proteases. Biol. Chem. 379, 137-147.
35. Tyndall, J.D.A., Nall, T., and Fairlie, D.P. (2005). Proteases universally recognize β-strands in their active sites. Chem. Rev. 105, 973-999.
36. Ullmann, D. and Jakubke, H.-D. (1994). The specificity of clostripain from Clostridium histolyticum: mapping the S' subsites via acyl transfer to amino acid amides and peptides. Eur. J. Biochem. 223, 865-872.
37. Vindigni, A., Dang, Q.D., and Di Cera, E. (1997). Site-specific dissection of substrate recognition by thrombin. Nat. Biotechnol. 15, 891-895.