Computational analysis for the determination of deleterious nsSNPs in human MTHFR gene. (June 2018)

• Record Type: Journal Article
• Authors: Desai, Mansi; Chauhan, J.B.
• Is Part Of: Computational biology and chemistry. Volume 74(2018)
• Page Start: 20
• Page End: 30
• Publication Date: 2018-06
• Subjects: SIFT sorting intolerant from tolerant -- PolyPhen polymorphism phenotyping -- PROVEAN protein variation effect analyzer -- PhD-SNP predictor of human deleterious single nucleotide polymorphisms -- SNPs&GO single nucleotide polymorphisms and gene ontology -- MTHFR methylenetetrahydrofolate reductase -- nsSNPs non-synonymous single nucleotide polymorphism -- THF tetrahydrofolate -- FAD flavin adenine dinucleotide -- NCBI National Center for Biological Information -- OMIM online mendelian inheritance in man -- PhD-SNP predictor of human deleterious single nucleotide polymorphisms -- PTM post translational modification; In silico analysis -- Human MTHFR gene polymorphism -- Single nucleotide polymorphisms -- Folate metabolism -- Deleterious prediction; Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2018.02.022
• Languages: English
• ISSNs: 1476-9271

Abstract

Graphical abstract: Highlights: The structural and functional consequences of nsSNPs of human MTHFR gene was analyzed through computational tools. R157Q, L323P and W500C were predicted highly deleterious and affecting protein stability. R157, L323 and W500 were predicted highly conserved and also involved in ligand binding interactions. R157 and W500 were predicted to be involved in post translational modifications. R157Q and L323P alters the H-bonding interaction with other amino acids in MTHFR protein. Abstract: Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme involved in folate metabolism and plays a central role in DNA methylation and biosynthesis. MTHFR mutations may alter the cellular folate supply which in turn affects nucleic acid synthesis, DNA methylation and chromosomal damage. The identification of number of SNPs in the human genome growing nowadays and hence, the evaluation of functional & structural consequences of these SNPs is very laborious by means of experimental analysis. Therefore, in the present study, recently developed various computational algorithms have been used which can predict the functional and structural consequences of the SNPs. Various computational tools like SIFT, PolyPhen2, PROVEAN, SNAP2, nsSNPAnalyzer, SNPs&GO, PhD-SNP, PMut, I-Mutant, iPTREE-STAB and MUpro were used to predict most deleterious SNPs. Additionally, ConSurf was used to find amino acids conservation and NCBI conserved domain search tool to find conserved domains in MTHFR. Post translational modification sites were predicted using ModPred. SPARKS-X was used to generate 3D structure of the native and mutant MTHFR protein, ModRefiner for further refinement, Varify3D and RAMPAGE to validate structure. Ligand binding sites were predicted using FTsite, RaptorX binding and COACH. Three SNPs i.e . R157Q, L323P and W500C predicted the most deleterious in all the tools used for functional and stability analysis. Moreover, both residues R157, L323 and W500 were predicted highly conserved, buried and structural residues by ConSurf. Post translational modification sites were also predicted at R157 and W500. The ligand binding sites were predicted at R157, L323 and W500.