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

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. Mo...

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Bibliographic Details
Published in:Journal of molecular liquids 2019-05, Vol.281, p.549-562
Main Authors: Sahu, Satya Narayan, Moharana, Maheswata, Sahu, Rojalin, Pattanayak, Subrat Kumar
Format: Article
Language:English
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Summary: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. [Display omitted] •The physico-chemical characterization of domain in podocin protein was studied.•Identification of the effect on functional relationships of the non-synonymous SNPs•Docking study between mutant protein with compounds from Boerhaavia diffusa plant•Electrostatic solvation energy was found −241.373654 kJ/mol for mutant protein.•Less number of hydrogen bonds was found in mutant model as compared to wild type.
ISSN:0167-7322
1873-3166
DOI:10.1016/j.molliq.2019.02.120