Apoptosis plays an important role in maintaining the normal function of various tissues and organs in different species. Caspase-3 is a terminal caspases which plays an important role in the execution of apoptosis in all vertebrates. It was cloned from zebra fish embryos and its properties were identified through Western blotting and biological activity. In the cells over-expressing caspase-3, Western blotting with an anti-His-tag antibody confirmed the presence of caspase-3 in the three bands that were proposed to correspond to the precursor form (33 kDa), the mature forms processed at the prodomain alone (29 kDa, large subunit) and small sub unit (13 kD). Fish kidney cells were transiently co-transfected with the beta-galactosidase reporter gene and either vector alone (mock), pZCASP3His (caspase-3) or pZCASP3His mutant (caspase-3 mutant). After 72 h following transfection of fish kidney cells, 35% of cells transfected with the zebra fish caspase-3 construct, pZCASP3His, showed apoptotic morphology when compared with cells transfected with the mock vector or an expression construct (pZCASP3His mutant) encoding the caspase-3 mutant lacking Cys. The fusion proteins were expressed in Escherichia coli, isolated from cell lysates by nickel-affinity column chromatography, and cleaved with thrombin. A thrombin cleavage recognition site was positioned at the fusion junction to release the caspase-3 from the fusion protein. Phylogenetic analysis showed that the cloned zebra fish caspase was a member of the caspase-3 subfamily with approximately 60% identity with caspase-3 from Xenopus, chicken and mammals. We have obtained structural information by X-ray crystallography. Orthorhombic crystals of the caspase-3 that diffracted to 1.8 A were obtained in a mixture of 0.1 M imidazole (pH 6.0) and 0.4 M NaOAc (pH 7.0 -7.5), containing 30% glycerol. The space group is C222 with cell dimensions of a = 36.07 A, b = 38.80 A, c = 135.20 A.

In tumorigenesis, cancer genetics and the related mutations have been the main topic of study these days. Caspases have been found to be actively involved in the process of apoptosis. Malfunction of apoptosis is one of the causes for cancerous tumors and different caspase mutations are related to that process. It has been found that two groups of caspases involved in this process apoptosis which are initiator caspases and executioner caspases. SNPs have been extensively studied over the last decade, due to their association with a number of genetic diseases. Human SNPs have always been a source of information related to the complex changes associated with their origin. SNPs which can change the resulting amino acid i.e., nonsynonymous SNPs (nsSNPs) are of prime concern these days because of their direct relation with the disease or the respective individual. In this study our focus is not only to detect the nsSNPs available in the human caspase data but to further evaluate the potentially damaging nsSNPs. Using the computational approach we have been able to obtain almost seventy eight nsSNPs, among these few of the nsSNPs seem to have serious consequences, as they have been cross verified from a variety of SNP prediction tools. The functional as well as structural impact of the nsSNPs is determined and discussed. Our predicted nsSNPs on human caspases may be associated with cancer risk.

Human death receptors (TNFR1, FAS, DR3, DR4, DR5, DR6 and TNFBR), primarily from tumor necrosis receptor super family, play an essential role in the process of the extrinsic pathway of apoptosis. We performed conserved domain, amino acid residues analysis in which cysteine residues were found to be highly conserved for all the family members. Sixteen (16) highly conserved residues were observed in TNFR1, DR3 and TNFBR; and in case of Fas, only seven (7) residues are highly conserved. From molecular phylogenetics, we found that DR5 and DR4, TNFR1 and DR3 and TNFR1 and DR3 had the same point of origin. Alternatively, Fas was found to be distant from the rest of the death receptors. A network map was developed to explain these proteins are not only interlinked among themselves, but also interlinked with several other proteins. We have also observed from this system that scores of all the nodes ranges from 0.996 to 0.999.

Caspases belong to the family of cysteinyl aspartate-a specific proteases which control the programmed cell death process, or apoptosis. In this paper, we have performed a structural bioinformatics analysis of the conserved domains and residues, WebLogo generation and active sites identification related to apoptosis activator and apoptosis executioner caspase-cascades. Here, we have also shown conservation patterns of backbone structures of activator and executioner caspase-cascades. It has been noted that the numbers of highly conserved amino acid residues are very high in caspase-12 (36 aa) and low in caspase-7 (18 aa). We have observed that highly conserved amino acids residues like LYS154, PRO155, LYS156 are present in caspase-3 and caspase-6. In apoptosis and executioner caspases, these amino acids may play an active role. From WebLogo, it has been observed that the stack height is very low between the sequences 231 to 240; 2.3 bits stack height has been observed in 1st sequence position and 236th position where WebLogo stack height is very low. We have identified 10 active sites in caspase-3, caspase-6, caspase-7 which may be helpful in drug development using caspase-cascades. Here, we have also performed literature survey about the drug development using caspase-cascades.

No abstract