In Silico characterization of growth hormone from freshwater ornamental fishes: Sequence analysis, molecular modelling and phylogeny

Abstract

The present investigation includes in Silico sequence analysis, three-dimensional (3D) structure prediction and evolutionary profile of growth hormone (GH) from 14 ornamental freshwater fishes. The analyses were performed using the sequence data of growth hormone gene (gh) and its encoded GH protein. The evolutionary analyses were performed using maximum likelihood (ML) estimate and maximum parsimony (MP) methods. Bootstrap test (1000 replicates) was performed to validate the phylogenetic tree. The tertiary structures of GH were predicted using the comparative modelling method. The suitable template for comparative modeling protein databank (PDB IDs: 1HWG A) has been selected on the basis of basic local alignment search tool (BLASTp) and fast analysis (FASTA) results. The target-template alignment, model building, loop modelling and evaluation have been performed in Modeller 9.10. The tertiary structure of GH is α-helix structure connected by loops, which forms a compressed complex maintained by two disulfide bridges. The resultant 3D models are verified by ERRAT and ProCheck programmes. After fruitful verification, the tertiary structures of GH have been deposited to protein model database (PMDB). Sequence analyses and RNA secondary structure prediction was performed by CLC genomics workbench version 4.0. The computational models of GH could be of use for further evaluation of molecular mechanism of function.

Keywords: Growth hormone, in Silico, somatotropin, growth hormone gene (gh) mRNA, freshwater ornamental fish