Computational analysis of non-synonymous single nucleotide polymorphism in the bovine PKLR gene Computational analysis of bovine PKLR gene

Pyruvate kinase (PKLR) is a potential candidate gene for milk production traits in cows. The main aim of this work is to investigate the potentially deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in the PKLR gene by using several computational tools. In silico tools including SIFT, Polyphen-2, SNAP2 and Panther indicated only 18 nsSNPs out of 170 were considered deleterious. The analysis of proteins' stability change due to amino acid substitution performed by the use of the I-mutant, MUpro, CUPSTAT, SDM and Dynamut confirmed that 9 nsSNPs decreased protein stability. ConSurf analysis predicted that all 18 nsSNPs were evolutionary moderately or highly conserved. Two different domains of PKLR protein were revealed by the InterPro tool with 12 nsSNPs positioned in the Pyruvate Kinase barrel domain and 6 nsSNP present in the Pyruvate Kinase C Terminal. The PKLR 3D model was predicted by MODELLER software and validated via Ramachandran plot and Prosa which indicated a good quality model. The analysis of energy minimizations for the native and mutated structures was performed by SWISS PDB viewer with GROMOS 96 program and showed that 3 structural and 4 functional residues had total energy higher than the native model. These findings indicate that these mutant structures (rs441424814, rs449326723, rs476805413, rs472263384, rs474320860, rs475521477, rs441633284) were less stable than the native model. Molecular Dynamics simulations were performed to confirm the impact of nsSNPs on the protein structure and function. The present study provides useful information about functional SNPs that have an impact on PKLR protein in cattle.Communicated by Ramaswamy H. Sarma

Automated summary

This study investigates the potentially deleterious nsSNPs in the PKLR gene for milk production traits in cows using computational tools. In silico analysis reveals that out of 170 nsSNPs, only 18 are considered deleterious. Protein stability analysis confirms that 9 nsSNPs decrease protein stability. ConSurf analysis predicts that all 18 nsSNPs are evolutionarily conserved. Two different domains of PKLR protein are identified, with 12 nsSNPs in the Pyruvate Kinase barrel domain and 6 nsSNPs in the Pyruvate Kinase C Terminal. Molecular dynamics simulations confirm the impact of nsSNPs on protein structure and function. This study provides valuable information about functional SNPs that affect PKLR protein in cattle.