Computational analysis of non-synonymous single nucleotide polymorphism in the bovine cattle kappa-casein (CSN3) gene

Abstract

Backgroundkappa-casein is candidate gene, present on chromosome 6 of cattle, play an important role in mammary gland and properties of milk. MethodsIn the present study, we used SIFT, SNAP2, PROVEAN and PolyPhen 2 computational tools which are based on different approaches to predict deleterious nsSNPs in coding region of cattle CSN3 gene. Furthermore, protein stability and structure were predicted by I-Mutant 2.0, MuStab, ModPred, ConSurf, PSIPRED, MUSTER, Ramachandran plot, TM-score, FT site and STRING. ResultsAmong the 15 nsSNPs, 3 were predicted deleterious by SIFT, SNAP2, PROVEAN and PolyPhen 2. Additionally, R118S, S125A and S176G variant showed decrease in stability, S125A and S176G are highly conserved and role in post translational modification using I-Mutant 2.0, MuStab, ConSurf and ModPred. The 3D structure of CSN3 wild type and mutant were generated by MUSTER and validated via Ramachandran plot, showed 170 residues (90.4%) in favoured region, 14 residues in allowing the region (7.4%) and 4 residues (2.2%) in outer region which indicated good quality model. The TM-score ranging from 0.70 to 0.87 which means two structures was within same fold while higher RMSD values (1.59 to 2.31) showed that the deviation from two structures may change the functional activity of the protein. Results of GROMOS96 indicated that the stability of mutant protein was decreased. Ligand binding site 1 has a SER-125, site 2, ASP-169 and site 3, SER-125. CSN3 protein interacts with 10 different proteins. ConclusionThe S125A variant of cattle population may serve as a genetic marker for mutational analysis of CSN3.