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In silico screening, genotyping, molecular dynamics simulation and activity studies of SNPs in pyruvate kinase M2.

Kalaiarasan P, Kumar B, Chopra R, Gupta V, Subbarao N, Bamezai RN - PLoS ONE (2015)

Bottom Line: SNPeffect and HOPE showed three substitutions (C31F, Q310P and S437Y) in-silico as deleterious and functionally important.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.

View Article: PubMed Central - PubMed

Affiliation: School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India.

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.

No MeSH data available.


Related in: MedlinePlus

Schematic representation of the study.SNPs was categorized based on their location in the gene. The nsSNPs and mutation were analyzed together.
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pone.0120469.g001: Schematic representation of the study.SNPs was categorized based on their location in the gene. The nsSNPs and mutation were analyzed together.

Mentions: The data mining for SNPs in Human PKM2 was carried out on dbSNP135 databases (https://www.ncbi.nlm.nih.gov/SNP/). Mutation information of the gene was retrieved from Human mutation database. A total of 49 variations was selected in PKM2, which included 29 nsSNPs, 15 intronic, 3 close to UTR (2–5’UTR and 1–3’UTR), and 2 mutations, the latter reported by us for the first time [5]. Fig. 1 provides the detailed work flow of the study; where SNPs were selected by prioritization based on their minor allele frequency (>5%) in the publicly available dataset from the National Centre for Biotechnology Information (NCBI) Enterz SNP and the International HapMap project:Han Chinese, Japanese (Asian populations), and African (Ancesteral) populations. Few of the SNPs were included on their presence in the promoter, exonic, intronic-boundary, or unstranslated regions (UTRs), covering 2 kb upstream and downstream of the PKM2 gene. The sequence for all SNPs was downloaded from the dbSNP database in NCBI before the assay design.


In silico screening, genotyping, molecular dynamics simulation and activity studies of SNPs in pyruvate kinase M2.

Kalaiarasan P, Kumar B, Chopra R, Gupta V, Subbarao N, Bamezai RN - PLoS ONE (2015)

Schematic representation of the study.SNPs was categorized based on their location in the gene. The nsSNPs and mutation were analyzed together.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4359060&req=5

pone.0120469.g001: Schematic representation of the study.SNPs was categorized based on their location in the gene. The nsSNPs and mutation were analyzed together.
Mentions: The data mining for SNPs in Human PKM2 was carried out on dbSNP135 databases (https://www.ncbi.nlm.nih.gov/SNP/). Mutation information of the gene was retrieved from Human mutation database. A total of 49 variations was selected in PKM2, which included 29 nsSNPs, 15 intronic, 3 close to UTR (2–5’UTR and 1–3’UTR), and 2 mutations, the latter reported by us for the first time [5]. Fig. 1 provides the detailed work flow of the study; where SNPs were selected by prioritization based on their minor allele frequency (>5%) in the publicly available dataset from the National Centre for Biotechnology Information (NCBI) Enterz SNP and the International HapMap project:Han Chinese, Japanese (Asian populations), and African (Ancesteral) populations. Few of the SNPs were included on their presence in the promoter, exonic, intronic-boundary, or unstranslated regions (UTRs), covering 2 kb upstream and downstream of the PKM2 gene. The sequence for all SNPs was downloaded from the dbSNP database in NCBI before the assay design.

Bottom Line: SNPeffect and HOPE showed three substitutions (C31F, Q310P and S437Y) in-silico as deleterious and functionally important.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.

View Article: PubMed Central - PubMed

Affiliation: School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India.

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.

No MeSH data available.


Related in: MedlinePlus