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PLoS One. 2016 May 6;11(5):e0153999. doi: 10.1371/journal.pone.0153999. eCollection 2016.

A Comprehensive In Silico Analysis on the Structural and Functional Impact of SNPs in the Congenital Heart Defects Associated with NKX2-5 Gene-A Molecular Dynamic Simulation Approach.

Author information

1
Center for Genetics and Inherited Diseases, Taibah University, Madinah, Kingdom of Saudi Arabia.
2
Molecular Biomedicine Program, Research Center, King Faisal Specialist Hospital & Research Center, Riyadh, Kingdom of Saudi Arabia.
3
Innovative Informatica Technologies, HIG, HUDA, Mayuri Nagar, Miyapur, Hyderabad, 500 049, India.
4
Department of Biochemistry and Biotechnology, Annamalai University, Annamalai Nagar, Tamilnadu, India.
5
Department of Food Science and Nutrition, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman.
6
Aging and Dementia Research Group, Sultan Qaboos University, Muscat, Oman.

Abstract

Congenital heart defects (CHD) presented as structural defects in the heart and blood vessels during birth contribute an important cause of childhood morbidity and mortality worldwide. Many Single nucletotide polymorphisms (SNPs) in different genes have been associated with various types of congenital heart defects. NKX 2-5 gene is one among them, which encodes a homeobox-containing transcription factor that plays a crucial role during the initial phases of heart formation and development. Mutations in this gene could cause different types of congenital heart defects, including Atrial septal defect (ASD), Atrial ventricular block (AVB), Tetralogy of fallot and ventricular septal defect. This highlights the importance of studying the impact of different SNPs found within this gene that might cause structural and functional modification of its encoded protein. In this study, we retrieved SNPs from the database (dbSNP), followed by identification of potentially deleterious Non-synonymous single nucleotide polymorphisms (nsSNPs) and prediction of their effect on proteins by computational screening using SIFT and Polyphen. Furthermore, we have carried out molecular dynamic simulation (MDS) in order to uncover the SNPs that would cause the most structural damage to the protein altering its biological function. The most important SNP that was found using our approach was rs137852685 R161P, which was predicted to cause the most damage to the structural features of the protein. Mapping nsSNPs in genes such as NKX 2-5 would provide valuable information about individuals carrying these polymorphisms, where such variations could be used as diagnostic markers.

PMID:
27152669
PMCID:
PMC4859487
DOI:
10.1371/journal.pone.0153999
[Indexed for MEDLINE]
Free PMC Article

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