Prediction of the tertiary structure and substrate binding site of caspase-8

A model of the complex between cyclin-dependent kinase 5 and the activation domain of neuronal Cdk5 activator

Tau protein kinase II (TPKII) is a heterodimer comprising a catalytic cyclin-dependent kinase subunit (Cdk5) and a regulatory protein called neuronal Cdk5 activator (Nck5a). TPKII is somewhat reminiscent, therefore, of the Cdk2-cyclin complex important in cell cycle regulation. In fact, although the amino acid sequence of Nck5a has little similarity to those of cyclins, recent experimental results obtained by site-directed mutagenesis studies have indicated that its activation domain, Nck5a*, may adopt a conformation of the cyclin-fold structure. Based on this structural inference, a 3-dimensional model of the Cdk5-Nck5a*-ATP complex was derived from the X-ray structure of Cdk2-cyclinA-ATP complex. The computed structure for TPKII is fully compatible with experimental data derived from studies of the Cdk5-Nck5a system, and also predicts which amino acid residues might be involved in formation of the Cdk5-Nck5a* interface and ATP binding pocket in TPKII. The computational structure also shows the interactive region of Nck5a* and the T-loop of Cdk5, a critical region in TPKII which functions as a gate-control-lever of the catalytic cleft. Furthermore, a physical mechanism is put forth to explain why the activation of TPKII is not dependent upon phosphorylation of the Cdk5 subunit, a puzzle long-standing in this area. These findings provide a model with which to consider design of compounds which might serve as inhibitors of TPKII.

Non-specific effects of methyl ketone peptide inhibitors of caspases

Caspases are a family of cysteine proteases which play a crucial role in apoptosis and inflammation. The involvement of caspases in these processes can be demonstrated by their irreversible inhibition with fluoromethyl ketone and chloromethyl ketone derivatives of peptides resembling the cleavage site of known caspase substrates. These inhibitors irreversibly alkylate the cysteine residue in the active site of caspases. In this study we show that a biotinylated fluoromethyl ketone peptide inhibitor of caspases (z-VAD.fmk) also efficiently affinity-labeled cathepsin B and cathepsin H. In addition, the caspase inhibitors z-VAD.fmk, z-DEVD.fmk and Ac-YVAD.cmk also efficiently inhibited cathepsin B activity in vitro and in tissue culture cells at concentrations that are generally used to demonstrate the involvement of caspases.

Solution structure of the RAIDD CARD and model for CARD/CARD interaction in caspase-2 and caspase-9 recruitment

Apoptosis requires recruitment of caspases by receptor-associated adaptors through homophilic interactions between the CARDs (caspase recruitment domains) of adaptor proteins and prodomains of caspases. We have solved the CARD structure of the RAIDD adaptor protein that recruits ICH-1/caspase-2. It consists of six tightly packed helices arranged in a topology homologous to the Fas death domain. The surface contains a basic and an acidic patch on opposite sides. This polarity is conserved in the ICH-1 CARD as indicated by homology modeling. Mutagenesis data suggest that these patches mediate CARD/CARD interaction between RAIDD and ICH-1. Subsequent modeling of the CARDs of Apaf-1 and caspase-9, as well as Ced-4 and Ced-3, showed that the basic/acidic surface polarity is highly conserved, suggesting a general mode for CARD/CARD interaction.