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

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Abstract
Apoptosis, or programmed cell death, plays a central role in the development and homeostasis of an organism. The breakdown of cellular proteins in apoptosis is mediated by caspases, which comprise a highly conserved family of cysteine proteases with specificity for aspartic acid residues at the P1 positions of their substrates. Multiple lines of evidence show that caspase‐9 is critical for an apoptosis pathway mediated via the mitochondria. In this study, the three‐dimensional structure of the catalytic domain of caspase‐9 and its interaction with the inhibitor acetyl‐Asp‐Val‐Ala‐Asp fluoromethyl ketone (Ac‐DVAD‐fmk) have been predicted by a segment matching modeling procedure. As expected, the predicted caspase‐9 structure shows both a high similarity in the overall folding topology and remarkable differences in the surface loop regions as compared to other caspase family members such as caspase‐1, ‐3 and ‐8, for which crystal structures have been determined. This kind of comparative analysis reflects the convergence–divergence duality among the caspases. Moreover, some subtle differences have been observed between caspase‐9 and caspase‐3 in the subsite contacts with the covalently linked inhibitor Ac‐DVAD‐fmk. Based on the X‐ray structural analysis of caspase‐8, a main chain carbonyl oxygen appears to be involved in a catalytic triad with the active site Cys and His residues. The corresponding carbonyl oxygen in caspase‐9, together with other expected features of the catalytic apparatus, appears in our model. The predicted structure of caspase‐9 can serve as a reference for subsite analysis relative to rational design of highly selective caspase inhibitors for therapeutic application.