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Online Journal of Bioinformatics©
Volume 22 (3): 301-314, 2021.
Homology model protein GATA4 nucleotide polymorphisms in congenital heart disease
Dinesh SM1, Prashantha Karunakar2 and Nallur B Ramachandra1
1. Genomics Laboratory, Department of Studies in Zoology, University of Mysore, Mysore-570006, Karnataka,2. Department of Biotechnology and Bioinformatics, Kuvempu University, Shankarghatta, Shivamogga - 577451, Karnataka, India
Dinesh SM, Karunakar P, Ramachandra NB., Homology model protein GATA4 nucleotide polymorphisms in congenital heart disease, Onl J Bioinform., 22 (3): 301-314, 2021. Congenital heart disease (CHD) is the most common type of birth defect, affecting 1% of all live births and a leading cause of death. Single nucleotide polymorphisms (SNPs) in GATA4 are associated with CHD phenotypes. We separated SNPs from non-synonymous SNPs (nsSNPs), in coding regions to determine amino acid variation in protein products by in silico model of 48 nsSNPs of GATA4 involved in CHD. We edited nsSNPs control sequence for amino acid polymorphisms (SAP) and protein secondary structure to create a 3-D structure of mutated proteins of the GATA4 nsSNPs to reveal side chain differences. We found 48 mutated proteins in GATA4 nsSNPs, with 755G, 1037C>T, 1129A>G and 1130G>A showed changes in turns 155C>T, 487C>T and 1220C>A in sheets and 278G>C in helix. We found 687G>T responsible for changes in sheet and helix, 779G>A and 855T>C helix and turns 17C>T, 82C>T, 905A>G and 1207C>A helix and sheet and 1295T>C helix, sheet and turns. 3-D showed differences in side chain due to mutation by nsSNPs involved in CHD. Results suggest SNPs and SAPs may affect function of GATA4 in heart development.
Key words: Congenital heart disease; Single nucleotide polymorphisms; GATA4; 3-D structure.