Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.

<h4>Background</h4>Elucidating the molecular dynamic behavior of Protein-DNA complex upon mutation is crucial in current genomics. Molecular dynamics approach reveals the changes on incorporation of variants that dictate the structure and function of Protein-DNA complexes. Deleterious mu...

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Autores principales:	C George Priya Doss, N Nagasundaram
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c7d0743bc3d840ad9340024731ceb224
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spelling	oai:doaj.org-article:c7d0743bc3d840ad9340024731ceb2242021-11-18T07:26:43ZInvestigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.1932-620310.1371/journal.pone.0031677https://doaj.org/article/c7d0743bc3d840ad9340024731ceb2242012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22384055/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Elucidating the molecular dynamic behavior of Protein-DNA complex upon mutation is crucial in current genomics. Molecular dynamics approach reveals the changes on incorporation of variants that dictate the structure and function of Protein-DNA complexes. Deleterious mutations in APE1 protein modify the physicochemical property of amino acids that affect the protein stability and dynamic behavior. Further, these mutations disrupt the binding sites and prohibit the protein to form complexes with its interacting DNA.<h4>Principal findings</h4>In this study, we developed a rapid and cost-effective method to analyze variants in APE1 gene that are associated with disease susceptibility and evaluated their impacts on APE1-DNA complex dynamic behavior. Initially, two different in silico approaches were used to identify deleterious variants in APE1 gene. Deleterious scores that overlap in these approaches were taken in concern and based on it, two nsSNPs with IDs rs61730854 (I64T) and rs1803120 (P311S) were taken further for structural analysis.<h4>Significance</h4>Different parameters such as RMSD, RMSF, salt bridge, H-bonds and SASA applied in Molecular dynamic study reveals that predicted deleterious variants I64T and P311S alters the structure as well as affect the stability of APE1-DNA interacting functions. This study addresses such new methods for validating functional polymorphisms of human APE1 which is critically involved in causing deficit in repair capacity, which in turn leads to genetic instability and carcinogenesis.C George Priya DossN NagasundaramPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 2, p e31677 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q C George Priya Doss N Nagasundaram Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.
description	<h4>Background</h4>Elucidating the molecular dynamic behavior of Protein-DNA complex upon mutation is crucial in current genomics. Molecular dynamics approach reveals the changes on incorporation of variants that dictate the structure and function of Protein-DNA complexes. Deleterious mutations in APE1 protein modify the physicochemical property of amino acids that affect the protein stability and dynamic behavior. Further, these mutations disrupt the binding sites and prohibit the protein to form complexes with its interacting DNA.<h4>Principal findings</h4>In this study, we developed a rapid and cost-effective method to analyze variants in APE1 gene that are associated with disease susceptibility and evaluated their impacts on APE1-DNA complex dynamic behavior. Initially, two different in silico approaches were used to identify deleterious variants in APE1 gene. Deleterious scores that overlap in these approaches were taken in concern and based on it, two nsSNPs with IDs rs61730854 (I64T) and rs1803120 (P311S) were taken further for structural analysis.<h4>Significance</h4>Different parameters such as RMSD, RMSF, salt bridge, H-bonds and SASA applied in Molecular dynamic study reveals that predicted deleterious variants I64T and P311S alters the structure as well as affect the stability of APE1-DNA interacting functions. This study addresses such new methods for validating functional polymorphisms of human APE1 which is critically involved in causing deficit in repair capacity, which in turn leads to genetic instability and carcinogenesis.
format	article
author	C George Priya Doss N Nagasundaram
author_facet	C George Priya Doss N Nagasundaram
author_sort	C George Priya Doss
title	Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.
title_short	Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.
title_full	Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.
title_fullStr	Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.
title_full_unstemmed	Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.
title_sort	investigating the structural impacts of i64t and p311s mutations in ape1-dna complex: a molecular dynamics approach.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/c7d0743bc3d840ad9340024731ceb224
work_keys_str_mv	AT cgeorgepriyadoss investigatingthestructuralimpactsofi64tandp311smutationsinape1dnacomplexamoleculardynamicsapproach AT nnagasundaram investigatingthestructuralimpactsofi64tandp311smutationsinape1dnacomplexamoleculardynamicsapproach
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Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.

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