Prediction of the tertiary structure of a caspase-9/inhibitor complex

Apoptosis, or programmed cell death, plays a central role in the developmen t and homeostasis of an organism. The breakdown of cellular proteins in apo ptosis is mediated by caspases, which comprise a highly conserved family of cysteine proteases with specificity for aspartic acid residues at the P1 p ositions of their substrates, Multiple lines of evidence show that caspase- 9 is critical for an apoptosis pathway mediated via the mitochondria, In th is study, the three-dimensional structure of the catalytic domain of caspas e-9 and its interaction with the inhibitor acetyl-Asp-Val-Ala-Asp fluoromet hyl ketone (Ac-DVAD-fmk) have been predicted by a segment matching modeling procedure. As expected, the predicted caspase-9 structure shows both a hig h similarity in the overall folding topology and remarkable differences in the surface loop regions as compared to other caspase family members such a s caspase-1, -3 and -8, for which crystal structures have been determined. This kind of comparative analysis reflects the convergence-divergence duali ty among the caspases, Moreover, some subtle differences have been observed between caspase-9 and caspase-3 in the subsite contacts with the covalentl y linked inhibitor Ac-DVAD-fmk. Based on the X-ray structural analysis of c aspase-8, a main chain carbonyl oxygen appears to be involved in a catalyti c triad with the active site Cys and His residues. The corresponding carbon yl oxygen in caspase-9, together with other expected features of the cataly tic apparatus, appears in our model. The predicted structure of caspase-9 c an serve as a reference for subsite analysis relative to rational design of highly selective caspase inhibitors for therapeutic application. (C) 2000 Federation of European Biochemical Societies.