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In silico approach to the analysis of SNPs in the human APAF1 gene

The apoptotic protease activating factor 1 (APAF1) gene encodes a cytoplasmic protein that initiates apoptosis and is a crucial factor in the mitochondria-dependent death pathway. APAF1 is implicated in many pathways such as apoptosis, neurodegenerative diseases, and cancer. The purpose of this stud...

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Autores principales: KAMAN, Tuğba, KARASAKAL, Ömer Faruk, ÖZKAN OKTAY, Ebru, ULUCAN, Korkut, KONUK, Muhsin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Scientific and Technological Research Council of Turkey 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6911258/
https://www.ncbi.nlm.nih.gov/pubmed/31892812
http://dx.doi.org/10.3906/biy-1905-18
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author KAMAN, Tuğba
KARASAKAL, Ömer Faruk
ÖZKAN OKTAY, Ebru
ULUCAN, Korkut
KONUK, Muhsin
author_facet KAMAN, Tuğba
KARASAKAL, Ömer Faruk
ÖZKAN OKTAY, Ebru
ULUCAN, Korkut
KONUK, Muhsin
author_sort KAMAN, Tuğba
collection PubMed
description The apoptotic protease activating factor 1 (APAF1) gene encodes a cytoplasmic protein that initiates apoptosis and is a crucial factor in the mitochondria-dependent death pathway. APAF1 is implicated in many pathways such as apoptosis, neurodegenerative diseases, and cancer. The purpose of this study was to predict deleterious/damaging SNPs in the APAF1 gene viain silicoanalysis. To this end, APAF1 missense SNPs were obtained from the NCBI dbSNP database. In silico analysis of the missense SNPs was carried out by using publicly available online software tools. The stabilization and three-dimensional modeling of mutant proteins were also determined by using the I-Mutant 2.0 and Project HOPE webservers, respectively. In total, 772 missense SNPs were found in the APAF1 gene from the NCBI dbSNP database, 18 SNPs of which were demonstrated to be deleterious or damaging. Of those, 13 SNPs had a decreasing effect on protein stability, while the other 5 SNPs had an increasing effect. Based on the modeling results, some dissimilarities of mutant type amino acids from wild-type amino acids such as size, charge, and hydrophobicity were revealed. The SNPs predicted to be deleterious in this study might be used in the selection of target SNPs for genotyping in disease association studies. Therefore, we could suggest that the present study could pave the way for future experimental studies.
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spelling pubmed-69112582019-12-31 In silico approach to the analysis of SNPs in the human APAF1 gene KAMAN, Tuğba KARASAKAL, Ömer Faruk ÖZKAN OKTAY, Ebru ULUCAN, Korkut KONUK, Muhsin Turk J Biol Article The apoptotic protease activating factor 1 (APAF1) gene encodes a cytoplasmic protein that initiates apoptosis and is a crucial factor in the mitochondria-dependent death pathway. APAF1 is implicated in many pathways such as apoptosis, neurodegenerative diseases, and cancer. The purpose of this study was to predict deleterious/damaging SNPs in the APAF1 gene viain silicoanalysis. To this end, APAF1 missense SNPs were obtained from the NCBI dbSNP database. In silico analysis of the missense SNPs was carried out by using publicly available online software tools. The stabilization and three-dimensional modeling of mutant proteins were also determined by using the I-Mutant 2.0 and Project HOPE webservers, respectively. In total, 772 missense SNPs were found in the APAF1 gene from the NCBI dbSNP database, 18 SNPs of which were demonstrated to be deleterious or damaging. Of those, 13 SNPs had a decreasing effect on protein stability, while the other 5 SNPs had an increasing effect. Based on the modeling results, some dissimilarities of mutant type amino acids from wild-type amino acids such as size, charge, and hydrophobicity were revealed. The SNPs predicted to be deleterious in this study might be used in the selection of target SNPs for genotyping in disease association studies. Therefore, we could suggest that the present study could pave the way for future experimental studies. The Scientific and Technological Research Council of Turkey 2019-12-13 /pmc/articles/PMC6911258/ /pubmed/31892812 http://dx.doi.org/10.3906/biy-1905-18 Text en Copyright © 2019 The Author(s) This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Article
KAMAN, Tuğba
KARASAKAL, Ömer Faruk
ÖZKAN OKTAY, Ebru
ULUCAN, Korkut
KONUK, Muhsin
In silico approach to the analysis of SNPs in the human APAF1 gene
title In silico approach to the analysis of SNPs in the human APAF1 gene
title_full In silico approach to the analysis of SNPs in the human APAF1 gene
title_fullStr In silico approach to the analysis of SNPs in the human APAF1 gene
title_full_unstemmed In silico approach to the analysis of SNPs in the human APAF1 gene
title_short In silico approach to the analysis of SNPs in the human APAF1 gene
title_sort in silico approach to the analysis of snps in the human apaf1 gene
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6911258/
https://www.ncbi.nlm.nih.gov/pubmed/31892812
http://dx.doi.org/10.3906/biy-1905-18
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