Comparative homology modeling of human rhodopsin with several templates of bovine rhodopsin

Abstract

Rhodopsin is a visual pigment, which belongs to G-coupled protein receptor (GPCR) family, present in rod cells of retina. The molecular structure of rhodopsin has been studied by cryo-electron microscopic, Nuclear Magnetic Resonance (NMR) and X-ray crystallographic techniques in bovine. A humble effort has been made to identify and remove the loopholes in the existing structure (1EDS) and model the 3D structure of rhodopsin to its entire length and loops. Our studies describe the molecular structure of human rhodopsin based on homology search among seven selected bovine templates (140 models created), which were then analyzed completely through model evaluation softwares to build one complete structure of human rhodopsin. This structure will prove to be helpful in studying different biological and chemical reactions occurring in visual process, as well as hold a promising future for agonist/drug development.

Key words: Homology modeling, human rhodopsin, bovine templates, sequence alignment, model building, energy profiles.