Impact of mutation on podocin protein involved in type 2 nephrotic syndrome: Insights into docking and molecular dynamics simulation study

Abstract

Podocin is expressed in the nephrotic tissues and its mutation inside the gene have been associated to familial idiopathic type 2 nephrotic syndrome. Here we have analyzed the most affected mutation position R138Q of human podocin protein which occurs at SPFH_PODOCIN domain of the titled protein. Molecular docking study has been carried out through AutoDock vina to study the molecular interaction between mutant and wild type models of the studied protein with biological active compounds of Boerhaavia diffusa plant extracts. Both boeravinone B and F are having higher binding energy as compared to others in mutant protein. Furthermore, molecular dynamics simulation study was carried out of with a trajectory of 50 ns for both the wild type and mutant model. This study reveals that, flexibility nature decreases in the mutant protein. The recognition of disease related non-synonymous single nucleotide polymorphisms and analysis of their effects by computational approaches has potential to provided knowledge for the diagnosis, and treatment of diseases like nephrotic syndrome. (C) 2019 Published by Elsevier B.V.