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

Turkish journal of biology

article

TUĞBA KAMAN¹  ÖMER FARUK KARASAKAL¹  EBRU ÖZKAN OKTAY¹  KORKUT ULUCAN¹  MUHSİN KONUK¹ 

[1] Department of Physiology and Animal Biotechnology, Faculty of Biology and Biotechnology, University of Science, Vietnam National University;Laboratory of Tissue Engineering and Biomedical Materials, University of Science, Vietnam National University

关键词: APAF1;    apoptosis;    neurodegenerative diseases;    single nucleotide polymorphism (SNP);    in silico;   

DOI  :  10.3906/biy-1905-18

学科分类：生物科学（综合）

来源: Scientific and Technical Research Council of Turkey - TUBITAK

【 摘 要 】

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 via in silico analysis. 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.

【 授权许可】

Unknown