Computational protocol: In-silico analysis of caspase-3 and -7 proteases from blood-parasitic Schistosoma species (Trematoda) and their human host

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Protocol publication

[…] Two Caspase-3 sequences (EMBL:CAX76583.1 and ref:XP_002574296.1) from S. mansoni and S. japonicum, respectively and two Caspase-7 sequences (ref:XP_002574645.1 and ref: XP_002580143.1) from S. mansoni were retrieved from GenBank [], National Center for Biotechnology Information (NCBI). A total of only 62 and 22 3-D structures for Caspase-3 and Caspase-7, respectively were found from humans in Protein Data Bank (http://www.pdb.org). Basic Local Alignment Search Tool (BLAST)p [] was used to retrieve template hits for homology modelling and only the human caspase crystal structures could be mined for the initial 3-D structure modelling. Sequence similarities and identities of templates with corresponding schistosomal caspases are outlined in (see supplementary material). Pairwise alignment of corresponding templates and targets (supplementary material) showed some gaps, which adopted loop structures during homology modelling. Initial 3-D models were generated using automated homology modelling software Modeler9v8 [] that generate a 3-D model by satisfaction of spatial restraints. The models were further refined by loop modelling, side chain modelling and energy minimization with the aid of Modeler9v8, SCWRL-4.0 [] and Swiss- PDBViewer4.0 Gromacs96 program [], respectively for getting more optimized and energetically favoured structures. Structure Analysis and Verification Server (SAVES) [http://nihserver.mbi.ucla.edu/SAVES/] and pKNOT v.2 web server [http://pknot.life.nctu.edu.tw/] were used for evaluation of the stereochemical qualities and protein knot in the modeled structures []. [...] For the structure-based sequence alignment of modeled caspases of Schistosoma spp with those of human, MUSTANG programs [] were used for the purpose of calculating the root mean square deviation (RMSD) amongst modeled structures. Orientation vectors of modeled α-helices and β-sheets as well as crystal structures were calculated by an open source perl script developed by Thomas Holder (www.pymolwiki.org). Additional perl scripts were developed to calculate the angle and distance between the two vectors. […]

Pipeline specifications

Software tools BLASTN, SCWRL, Swiss-PdbViewer, GROMACS, pKNOT, MUSTANG
Application Protein structure analysis
Organisms Homo sapiens
Diseases Hematologic Diseases, Infection