In-silico Analysis and Homology Modeling of Cytochrome C Oxidase Sub Unit I from Indian Major Carp, <i>Labeo rohita</i>

Abstract

Labeo rohita is the popular table fish in the whole Indian sub-continent. Cytochrome c oxidase sub unit I (COX/COI) is the largest protein coding gene in the metazoan mitochondrial genome and COI is the most frequently studied region of the teleost mitochondrial genome. It is the terminal member of the respiratory chain catalyzing the reduction of dioxygen to water by ferrocytochrome C. In this study, COI of L. rohita (56.86KDa) has been characterized, and the 3- D structure was predicted by using Modeller version 9.12 by homology modeling. The secondary structure has been predicted using PSIPRED and TMHMM server, and the predicted model has been validated in RAMPAGE server. The protein statistics was carried out by using Protopram tool in Expasy server. The predicted 3-D model showed that 99.8% of residues have Φ and Ψ angle in the favored and allowed regions. It was found to be a transmembrane protein and consisted of an N-terminal signal peptide. The isoelectric focusing point, instability index, aliphatic index, grand average hydropathicity, extinction coefficient, absorbance and number of negatively charged and positively charged amino acids were; 6.05, 26.52, 109.81, 0.749, 121180, 2.142, 25 and 16 respectively, revealing the structure and properties of COI protein. The COX/CO-I protein sequences of Catla catla, Cirrhinus mrigala, Labeo rohita, C. cirrhosus and Danio rerio were also taken for the divergence study and mutation analysis.