Homology Modelling of Cytochrome B from Carangoides equula

The in silico analysis of homology modelling and 3D structure prediction of Cytochrome B (CYTB) protein in Carangoides equula was carried out. Primary structure prediction / physicochemical characterization were performed by computing theoretical isoelectric point, molecular weight, extinction coefficient, instability index, aliphatic index and grand average hydropathy. Performing homology modelling, a high quality of protein 3D structure has been predicted for the amino acid sequence. Cytochrome B of Carangoides equula was compared to the 1BE3 structure of Cytochrome BC1 from Bovine, where the structure predicted through SWISS-MODEL was visualized in RASMOL. Hence, the Tertiary structure was predicted using homology modelling by using template to create a model from the target sequence. The model was validated using protein structure analysis tool, RAMPAGE. The assessment of secondary structure modelled using SOPMA revealed greater percentage of residues as alpha helix and random coils against the beta sheets. These structures will provide a good foundation for functional analysis of experimentally derived crystal structures.