Open Access Journal of Genome Biology and Bioinformatics

In Silico Analysis and 3d Structure Prediction of mitochondrial RHO GTPase 2 Protein of Danio rerio (zebra fish) by Homology Modeling

*Roy AK
Department Of Bioinformatics, Bioinformatics Centre, Bioinformatics Centre, India

*Corresponding Author:
Roy AK
Department Of Bioinformatics, Bioinformatics Centre, Bioinformatics Centre, India
Email:akroy1946@yahoo.co.in

Published on: 2018-11-23

Abstract

The present study deals with Insilco characterization of homology-dependent modeling and 69739.7 kDa Mitochondrial RHO GTPase proteins of Danio;rerio (Brachydanio rerio) not attempted earlier for this species. The secondary structure prediction reveals the extended 43 coil Regions, 24 helix region, and 13 strands. The 3D structure of this protein was generated using Deep view/Swiss PDB viewer 3.7 by homology modeling. The predicted 3D model showed that 88.1% residues fall in the most favored region, 11.3% in additional allowed region, 0.6% generously allowed region and 0% fall in the disallowed region. Findings like isoelectric point (pI) 5.34, instability index 45.76 and aliphatic index 92.11.3D structure information of Rho GTPase protein will help us to know the role of protein in zebra fish and interaction of their ligands. The predicted structure can also be used for molecular docking studies for more insight into the structure. The rho GTPase protein analyzed in the study showed that this is an unstable protein. The resultant structure was evaluated by PROCHECK. Finally, the 3D structure was predicted by Swiss model server.

Keywords

Zebra fish Danio rerio (Brachydanio); Homology modeling; Mitochondrial Rho GTPase 2; Ramachandran plot; Secondary structure; 3D structure

Introduction

The zebra fish (Danio rerio) is a tropical freshwater fish belonging to the minnow family(Cyprinidae) of the order Cypriniformes. Native to the Himalayan region, it is a popular aquarium fish, which is frequently sold under the trade name zebra Danio. The species arose in the Ganges region in eastern India and commonly inhabits in streams, canals, ditches, ponds, and slow-moving or stagnant water bodies. Zebra fish is omnivorous, primarily eating zooplankton, phytoplankton, insects and insect larvae, although they can eat a variety of other foods. The zebra fish is also an important and widely used vertebrate model organism used in scientific research,(notably, developmental biology, toxicology, reproductive studies, teratology, genetics, neurobiology,environmental sciences, stem cell research, regenerative medicine, and evolutionary theory ) and is the first vertebrate to be cloned. It is particularly notable for its regenerative abilities and has been modified by researchers to produce several transgenic strains. The strength of this fish includes its high degree of genetic conservation with humans and its simple, inexpensive maintenance. Additionally, gene expression can be easily manipulated in zebra fish embryos, and their transparency allows for observation of developmental processes.