Molecular mechanism of apoptosis: Prediction of three-dimensional structure of caspase-6 and its interactions by homology modeling

Biochemical and Biophysical Research Communications

Volumn 308, Issue 3, 2003, Pages 497-504

  Sattar, Rabia ^a   Ali, S Abid ^a   Abbasi, Atiya ^a  

^a UNIVERSITY OF KARACHI   (Pakistan)

Author keywords

Apoptosis; Caspase 6; Caspase 8; Cysteine proteinases; Enzyme inhibitor complex; Homology modeling; Programmed cell death; Structure prediction

Indexed keywords

ALDEHYDE DERIVATIVE; ASPARTIC ACID; CASPASE 6; CASPASE 8;

APOPTOSIS; ARTICLE; ENZYME ACTIVITY; ENZYME GLYCOSYLATION; ENZYME STRUCTURE; MOLECULAR DYNAMICS; PREDICTION; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY;

EID: 0042666796     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-291X(03)01394-9     Document Type: Article

References (34)

1. Darzynkieweiz Z., Gong X., Hara J., Traganos F. Cell Growth and Apoptosis. 1995;143-167 Oxford University Press, Oxford, UK.
2. Cosulich S., Clarke P. Apoptosis: does stress kill. Curr. Biol. 6:1996;1586-1588.
3. Chang H.Y., Nishitoh H., Yang X., Ichijo H., Baltimore D. Activation of apoptosis signals regulating kinase 1 (ASK1) by the adapter protein Daxx. Science. 281:1998;1860-1863.
4. Thornberry N.A., Bull J.R., Calaycay K.T., Chapman A.D.et al. A novel heterodimeric cysteine protease is required for interleukin-1beta processing in monocytes. Nature. 356:1992;768-774.
5. Nicholson D.W., Ali A., Thornberry N.A., Valliancourt J.P., Ding C.K., Gallant M., Gareau P.R.et al. Identifications and inhibition of the ICE/CED3 protease necessary for mammalian caspases. Nature. 376:1995;37-43.
6. Wilson K.P., Black J.F., Thomson J.T., Kim E.K., Grifth J.P., Navia M.N. Structure and mechanism of interleukin-1β converting enzymes. Nature. 370:1994;270-274.
7. Rotonda J.A., Garcia-Calvo M. The three-dimensional structure of human granzyme B compared to caspase-3, key mediators of cell death with cleavage specificity for aspartic acid in P1. Chem. Biol. 8:2001;357-368.
8. Liu X., Kim C.N., Yang J., Jemmerson R., Wang X. DFF a heterodimeric protein that functions down stream of caspase-3 to trigger DNA fragmentation and apoptosis. Cell. 89:1997;175-184.
9. Srinivasula S.M., Fernandes-Alnemri T., Zangirilli J., Robertson N., Armstrong R.C., Wang L., Trapani J.A., Tomaselli K.J., Litwack G., Alnmeri E.S. The Ced-3/interleukin 1β converting enzyme-like homolog Mch6 and the lamin-cleaving enzyme Mch2α are substrates for the apoptotic mediator CPP32. J. Biol. Chem. 271:1996;27099-27106.
10. Cauwels A., Janssen B., Waeytens A., Cauvelier C., Brouckaert P. Caspase inhibition cause hyper acute tumor necrosis factor induced shock via oxidation stress and phospholipase A2. Nat. Immunol. 4:2003;387-393.
11. 2 homodimer. Cell. 78:1994;343-352.
12. (a) Mittl P.R.E., Macro S.D., Krebs J.F., Bai X., Karanewsky P.S., Priestle J.P., Kevin J.T., Grutter M.C. Structure of recombinant human CPP32 in complex with the tetrapeptide acetyl-Asp-Val-Ala-Asp fluoromethyl ketone. J. Biol. Chem. 272:1997;6539-6547
13. (b) Rotonda J., Nicholson D.W., Fazil K.M., Gallant M., Gareau Y., Labelle M., Peterson E.P., Rasper D.M. The three dimensional structure of apopain/CPP32, a key mediator of apoptosis. Nat. Struct. Biol. 3:1996;619-625.
14. Wei Y., Fox T., Chambers S.P., Sintchak J., Coll J.T., Golec J.M., Swenson L., Wilson K.P., Charifson P.S. The structures of caspases-1, -3, -7 and-8 reveal the basis for substrate and inhibitor selectivity. Chem. Biol. 7:2000;423-432.
15. Blanchard H., Kodendapani L., Mittl P.R., Macro S.D., Krebs J.F., Wu J.C., Tomaselli K.J., Gutter G. The three-dimensional structure of caspase-8: an initiator enzyme in apoptosis. Struct. Fold. 7:1999;1125-1133.
16. Endres M., Namura S., Shimizu-Sasamata M., Waeber C., Zhang L., Gomez-Isla T., Hyman B.T., Moskowitz M.A. Attenuation of delayed neuronal death after mild focal ischemia in mice by inhibition of the caspase family. J. Cereb. Blood Flow Metab. 18:1998;238-247.
17. Yakovlev A.G., Knoblach S.M., Fan L., Fox G.B., Goodnight R., Faden A.I.et al. Activation of CPP32-like caspases contributes to neuronal apoptosis and neurological dysfunction after traumatic brain injury. J. Neurosci. 17:1997;7415-7424.
18. Rodriguez I., Matsuura K., Ody C., Nagata S., Vassalli P.et al. Systemic injection of a tripeptide inhibits the intracellular activation of CPP32-like proteases in vivo and fully protects mice against Fas-mediated fulminate liver destruction and death. J. Exp. Med. 184:1996;2067-2072.
19. Bairoch A., Boeekmann B. The SWISS-PROT protein sequence data bank. Nucl. Acid Res. 19:1991;2247-2249.
20. Pearson W.R. Effective protein sequence comparison. Methods Enzymol. 183:1990;63-98.
21. Althschul S.F., Madden T.L., Scaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Basic local alignment search tools. Nucl. Acid Res. 25:1997;3389-3402.
22. Berstein F.C., Koetzle T.F., Williams G.J., Meyer E.E., Brice M.D., Rodgers J.R., Kennard O., Schimanouchi T., Tasumi M. Protein data bank. J. Mol. Biol. 112:1997;535-542.
23. Watt W.K.A., Koeplinger A.M., Mildner R.L., Heninrikson A.G., Tomasselli K.D., Watenpaugh The atomic resolution structure of human caspase-8, a key activator of apoptosis. Struct. Fold. Des. 7:1999;1135-1143.
24. Šali A., Blundell T. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 234:1993;779-815.
25. Šali A., Blundell T. Definition of general topological equivalence in protein structure. J. Mol. Biol. 212:1990;403-428.
26. Laskowaski M.J., Kato L. PROCHECK. Annu. Rev. Biochem. 49:1980;593-626.
27. Vriend G. A molecular modeling and drug design program. J. Mol. Graph. 8:1990;52-55.
28. Chou K.C., Alferdo G.T., Robert L.H. Prediction of tertiary structure of a caspase-9/inhibitor complex. FEBS Lett. 470:2001;249-256.
29. Nancy A.T., Thomas A.R., Erin P.P., Dita M.R., Tracy T.et al. A combinatorial approach define specificities of members of the caspase family and granzyme. Br. J. Biol. Chem. 272:1997;17907-17911.
30. Bairoch A., Bucher P., Hoffman K. The PROSITE data base, its status in 1997. Nucl. Acid Res. 25:1997;217-221.
31. Cardone M.H., Roy N., Stennicke H.R., Salvesen G.S., Franke T.F., Stanbridge E., Frisch S., Reed J.C. Regulation of cell death protease caspase-9 by phosphorylation. Science. 282:1998;1318-1321.
32. Fujita E., Jinbo A., Matuzaki H., Konishi H., Kikkawa U., Momoi T. Akt phosphorylation site found in human caspase-9. Biochem. Biophys. Res. Commun. 264:1999;550-555.
33. Stennicke H.R., Deveraux Q., Humke E.W., Reed J.C., Dixit V.M., Salvesen G.S. Caspase-9 can be activated without proteolytic processing. J. Biol. Chem. 274:1999;8359-8362.
34. Stennicke H.R., Jurgensmeier J.M., Shin H., Deveraux Q., Wolf B.B., Yang X., Zhau Q., Ellerby H.M., Ellerby L.M., Bredesen D.et al. Pro-caspase-3 is a major physiologic target of caspase-8. J. Biol. Chem. 273:1998;27084-27090.