Journal Article

Molecular modeling and simulation analysis of glaucoma pathway

Patel, Ashish, Verma, Mukesh Kumar, Choubey, Jyotsna, Choudhari, Jyoti Kant

2016

Overview

Glaucoma is a group of disease characterized by progressive optic nerve degeneration and retinal ganglion cells (RGCs). The RGCs and evaluation elevated intraocular pressure are the most common cause for glaucoma. In this study, RGC death pathway of glaucoma was modeled to predict the response of the protein receptor, ligand, inhibitor and other regulatory units, which are involved in RGC death pathway in glaucoma. In the pathway modeling six aspects were considered, namely extrinsic pathway, intrinsic pathway, endoplasmic reticulum stress, neurotrophins signaling response, oxidative stress response and calpain activation induced RGC degeneration. The pathway has been designed a compressive pathway of molecular interaction on a cellular level based on published literature for analyzing the expression of the species. The CellDesigner software was used to designing the pathway and store it systems biology markup language (SBML). The SBML squeezer plugin is used to apply the kinetic equation such as a general mass action equation, Michaelis–Menten equation, and Hill equation for pathway simulation. The pathway of glaucoma was showed the over/down expression of the protein species.

• Publisher: Springer Vienna,Springer Nature B.V
• Subject: Apoptosis / Applications of Graph Theory and Complex Networks / Bioinformatics / Brain-derived neurotrophic factor / Calpain / Cell death / Computational Biology/Bioinformatics / Computer Science / Cytochrome / Cytoplasm / Degeneration / Disease / Endoplasmic reticulum / Enzymes / Glaucoma / Health Informatics / Intraocular pressure / Kinases / Kinetic equations / Kinetics / Modelling / Molecular interactions / Molecular modelling / Neurotrophic factors / Optic nerve / Original Article / Oxidative stress / Photoreceptors / Proteins / Retinal ganglion cells / Software / Tumor necrosis factor-TNF