Phylogenetic assessment and in silico characterization of cytochrome b protein of three alpheid shrimps

Abstract

Cytochrome b (cyt b) is one of the cytochrome proteins involved in electron transport in the respiratory chain of mitochondria. Cyt b is the only gene among the cytochrome complex coded by mitochondrial DNA. It is the most widely used gene for phylogenetic assessment and inter species variation studies. Here, the amino acid sequence of cyt b in three snapping shrimps such as, Alpheus lobidens, A. randali, A. bellulus was analysed and the results showed higher similarity in A. lobidens and A. randali as reflected in the phylogenetic tree. This study describes the applications of bioinformatics tools to predict the physico-chemical characters of cyt b protein. This protein was composed of least percentage of Cys (0.8%) and highest percentage of Leu (13.8%). The maximum molecular weight (MW) was predicted as 42.62 KDa in A. randali. The theoretical pI value was ranged from 8.35 to 8.36 and confirmed that cyt b was alkali in nature. The instability index value was in the range of 42.29 to 46.94 which showed the protein was more stable. The secondary structure of this protein was primarily composed of α-helixes and random coil, revealing the stable structure. The comparative modelling was performed by Swiss model where the 3-D crystal structure of bovine cyt bc1 (6haw1.c) was used as template. Ramachandran plot analysis showed that most of the amino acids (>92%) falling on the favoured region. Seven conserved motifs were identified by MEME analysis. The modelled 3-D structure of this protein was validated by PROCHECK and QMEAN. The transmembrane protein topology and helix probability curve was predicted by TMHMM server. Protein-protein interactions was analysed by STRING tool and found the network of cyt b with related proteins. The results of this study may provide valuable insights into fundamental characteristics of cyt b in Alpheid shrimps.