Current Bioinformatics

Yi-Ping Phoebe Chen
Department of Computer Science and Information Technology
La Trobe University
Melbourne
Australia

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Conserved Domains, Residues, WebLogo and Active Sites of Caspase- Cascades Related to Apoptotic Signaling Pathway

Author(s): Chiranjib Chakraborty, Jinny Tomar, Vishnu Kumar Gera.

Abstract:

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.

Keywords: Active sites, apoptosis pathway, caspase, conserved domains, Web Logo, Amino Acids, Cancer, Inhibitor of apoptosis protein family, intestinal and cerebral injury, proteome

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Article Details

VOLUME: 7
ISSUE: 4
Year: 2012
Page: [392 - 401]
Pages: 10
DOI: 10.2174/157489312803900929
Price: $58