We have determined the non-synonymous Single-Nucleotide Polymorphisms (nsSNPs) of PLD2 gene and its variations in different populations to understand its role in hypertension. Out of 350 SNPs, six are found to be non-synonymous, of which two showed significant damaging effect and SNP variability with large differences among the Minor Allele Frequency (MAF) observed in various populations. The amino acid change found for rs2286672 is from arginine to cysteine, i.e., from largest amino acid containing guanidino group to a small amino acid containing sulfhydryl group, and for rs3764897, it is from glycine to serine, i.e., from a hydrophobic amino acid to a hydrophilic amino acid. Hence, owing to the complete change in side chains and polarity of the amino acid residues brought about by these SNPs, the structure of the protein might be altered and hence the function might be affected, leading to dysregulation of blood pressure. © 2013 Inderscience Enterprises Ltd.

Rajendran P

Department of Mathematics

School of Advanced Sciences

Vellore Campus

Anand A

Department of Biotechnology

School of Bio Sciences and Technology

Kundu A

Ramakrishnan P

Dharwar N.V

Vellore Institute of Technology (VIT) is a private university located in&nbsp;Tamil Nadu, India. Founded in 1984, as Vellore Engineering College, the institution offers 20 undergraduate, 34 postgraduate, four integrated and four research programs. It has campuses in Vellore, Amravati, Bhopal and Chennai.

VIT is one of the top ranked private universities in India according to NIRF, THE and QS Rankings.&nbsp;Govt. of India has recognized&nbsp;VIT, Vellore as an&nbsp;Institution of Eminence. This has allowed VIT to take independent quality initiatives and move up in world ranking.

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VIT University

Analysis of non-synonymous single-nucleotide polymorphisms and population variability of PLD2 gene associated with hypertension

International Journal of Bioinformatics Research and Applications

Mutations in the gene encoding vesicle-associated membrane protein (VAPB) cause amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder. The VAPB gene is mapped to chromosome number 20 and can be found at cytogenetic location 20q13.33 of the chromosome. VAPB is seen to play a significant role in the unfolded protein response (UPR), which is a process that suppresses the accumulation of unfolded proteins in the endoplasmic reticulum. Earlier studies have reported two points; which we have analyzed in our study. Firstly, the mutation P56S in the VAPB is seen to increase the stability of the protein and secondly, the mutation P56S in VAPB is seen to interrupt the functioning of the gene and loses its ability to be involved in the activation of the IRE1/XBP1 pathway which leads to ALS. With correlation on the previous research studies on the stability of this protein, we carried out Molecular dynamics (MD) simulation. We analyzed the SNP results of 17 nsSNPs obtained from dbSNP using SIFT, polyphen, I-Mutant, SNP&amp;GO, PhDSNP and Mutpred to predict the role of nsSNPs in VAPB. MD simulation is carried out and plots for RMSD, RMSF, Rg, SASA, H-bond and PCA are obtained to check and prove the stability of the wild type and the mutant protein structure. The protein is checked for its aggregation and the results obtained show changes in the protein structure that might result in the loss of function. © 2014 Elsevier Ltd.

Journal of Theoretical Biology

Protein aggregation due to nsSNP resulting in P56S VABP protein is associated with amyotrophic lateral sclerosis

Cell Biochemistry and Biophysics

Computational Study of ADD1 Gene Polymorphism Associated with Hypertension

BMC Genetics

Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project

Journal of Human Hypertension

Non-synonymous single-nucleotide polymorphisms associated with blood pressure and hypertension

Bioinformatics

Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques

Neuropeptide Y gene functional polymorphism influences susceptibility to hypertension in Indian population

PLoS ONE

A Genome-Wide Association Study of the Metabolic Syndrome in Indian Asian Men

Journal	International Journal of Bioinformatics Research and Applications
Publisher	Inderscience Publishers
ISSN	1744-5485
Open Access	0