title: In silico screening, genotyping, molecular dynamics simulation and activity studies of SNPs in pyruvate kinase M2.
abstract: Role of, 29-non-synonymous, 15-intronic, 3-close to UTR, single nucleotide polymorphisms (SNPs) and 2 mutations of Human Pyruvate Kinase (PK) M2 were investigated by in-silico and in-vitro functional studies. Prediction of deleterious substitutions based on sequence homology and structure based servers, SIFT, PANTHER, SNPs&GO, PhD-SNP, SNAP and PolyPhen, depicted that 19% emerged common between all the mentioned programs. SNPeffect and HOPE showed three substitutions (C31F, Q310P and S437Y) in-silico as deleterious and functionally important. In-vitro activity assays showed C31F and S437Y variants of PKM2 with reduced activity, while Q310P variant was catalytically inactive. The allosteric activation due to binding of fructose 1-6 bisphosphate (FBP) was compromised in case of S437Y nsSNP variant protein. This was corroborated through molecular dynamics (MD) simulation study, which was also carried out in other two variant proteins. The 5 intronic SNPs of PKM2, associated with sporadic breast cancer in a case-control study, when subjected to different computational analyses, indicated that 3 SNPs (rs2856929, rs8192381 and rs8192431) could generate an alternative transcript by influencing splicing factor binding to PKM2. We propose that these, potentially functional and important variations, both within exons and introns, could have a bearing on cancer metabolism, since PKM2 has been implicated in cancer in the recent past.
authors.affiliation: School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India.
authors.forename: Ponnusamy
authors.initials: P
authors.lastname: Kalaiarasan
authors.affiliation: National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
authors.forename: Bhupender
authors.initials: B
authors.lastname: Kumar
authors.affiliation: School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India.
authors.forename: Rupali
authors.initials: R
authors.lastname: Chopra
authors.affiliation: National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
authors.forename: Vibhor
authors.initials: V
authors.lastname: Gupta
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
authors.forename: Naidu
authors.initials: N
authors.lastname: Subbarao
authors.affiliation: National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India; School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
authors.forename: Rameshwar N K
authors.initials: RN
authors.lastname: Bamezai
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D001483:Base Sequence; D003001:Cloning, Molecular; D017931:DNA Primers / Q000235:genetics; D057225:Data Mining; D004789:Enzyme Activation / Q000235:genetics; D005635:Fructosediphosphates / Q000378:metabolism; D005838:Genotype; D006801:Humans; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011770:Pyruvate Kinase / Q000235:genetics* / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D017931:DNA Primers; D005635:Fructosediphosphates; D011770:Pyruvate Kinase; C029063:fructose-1,6-diphosphate