Analysis of Insulin-Like Growth Factor I and its Receptor of an Indian Major Carp Labeo rohita: An in silico Approach

Analysis of Insulin-Like Growth Factor I and its Receptor of an Indian Major Carp Labeo rohita: An in silico Approach

MOJ Proteomics Bioinform 2017, 6(3): 00195

Samik Acharya,A.D.Upadhyay,A.K.Roy and Rumpi Ghosh

Bioinformatics Center, India *Corresponding author: Ajit Kumar Roy, Bioinformatics Center, College of Fisheries, Lembucherra, Tripura, Central Agricultural University (Imphal), PIN: 799210, India, Email:

Received: May 03, 2017 | Published: November 01, 2017

Abstract

The Insulin-like growth factor I (IGF-I) is produced from the liver by involving growth hormone through the axis of pituitary/hepatic-GH/IGF-I system. IGF-I and its receptors (IGF-IR) are expressed in various extrahepatic tissues. The circulatory IGF-I promotes the systemic body growth by effecting cells of muscle, cartilage, bones etc. Various hormones such as: growth hormone (GH), Insulinlike growth factor-I (IGF-I) and their related receptors are available in different tissues of fishes which performs the growth promoting activities. Therefore, in silico analysis of IGF-I and its receptor, IGF-IR was carried out in Indian major carp, Labeo rohita to understand physicochemical properties as well as the 3D structure of these proteins. The IGF-I and IGF-IR protein sequences (accession number AME16981.1 and AQV11106.1, respectively) were analyzed by Expasy’s prot param for the physicochemical characteristics, SOPMA for prediction of secondary structures and SWISSMODEL/Workspace for template search and Swiss-Pdb-Viewer for 3D structure of the concerned proteins. The results suggested that IGF-I is an unstable, hydrophilic and basic nature of protein; whereas IGF-IR is unstable, hydrophilic and acidic in nature. The secondary structure of IGF-I showed the presence of alpha helix 32.30%, extended strands 11.18% and 6.83% beta turns along with random coiling of 49.69% whereas in IGF-IR alpha helixes are 27.03% followed by 40.26% of random coiling, extended strands with 22.12% and beta turn with 10.60%. The validation of predicted 3D structures by RAMPAGE exhibited 96.7% residues in favoured region and 3.3% in outlier region in case of IGF-I, whereas IGF-IR represented 92.2% of residues in the favoured region, 6.8% in allowed region and 1.0% in outlier region. The Ramachandran plot analysis indicated that both the model is expected to be correct in prediction. Such predicted 3D structure of IGF-I and IGF-IR can also be utilized for molecular docking and simulation studies in future. Hence, the study also reduces the gap generated due to large amount of data with available sequences and solved structures by various laboratory techniques, such as: X-ray crystallography and NMR spectroscopy, which are tedious in implication. Keywords: Insulin-like growth factor I and its receptor; In silico analysis; 3D structure.

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