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

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