A Comparative Study on Retinol Binding Protein in Two Freshwater Fishes, Danio rerio and Cyprinus carpio

Retinol-binding proteins (RBP) are a family of proteins with diverse functions. They are carrier proteins that bind retinol. An in silico study has been performed for 3D structure prediction and molecular phylogenetic analysis of RBP from two freshwater fishes, Danio rerio and Cyprinus carpio. The analyses were performed using sequence data of rbp gene and retinol binding protein, extracted from Gen Bank and UNIPROKB/SWISSPROT databases respectively. The evolutionary analyses of rbp gene have been conducted in MEGA5 by Maximum Likelihood and Maximum Parsimony methods. The present study represents the application of comparative modeling for 3D structure prediction of RBP and molecular phylogenetic analyses of rbp gene in MEGA5, using two different methods namely Maximum Parsimony and Maximum Likelihood. The predicted structures were deposited to Protein Model Database (PMDB) after statistical verification. The study shows that rbp gene of Cyprinus carpio is the closest ortholog of the rbp gene of Denio rerio. The structures of RBP can be helpful in structural biology for further investigations on active sites, molecular mechanism of function and structure based phylogeny. The structure will be helpful in the further understanding of the RBP-retinol complex interacts with transthyretin in freshwater fishes. The phylogenetic tree revealed the evolutionary relationship of RBP family.