Abstract
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.
Highlights
Apoptosis is the programmed cell death process that is required for tissue homeostasis and development
The Apoptosis protease-activating factor 1 (APAF1) gene is linked to 20 genes in a highly interconnected network, with 170 edges10
Prediction of the effect of APAF1 single nucleotide polymorphism (SNP) on APAF1 protein structure According to the data obtained from the NCBI dbSNP database, there were a total of 18084 SNPs in the APAF1 gene
Summary
Apoptosis is the programmed cell death process that is required for tissue homeostasis and development. Apoptosis protease-activating factor 1 (APAF1) has a crucial function in apoptosis (Bao et al, 2007). APAF1 is the molecular core of the multiprotein complex called apoptosome that takes part in the mitochondrial pathway of apoptosis among different cellular apoptosis pathways (Ferraro et al, 2003). Apoptosis consists of 2 different pathways: the intrinsic and the extrinsic pathways. Bcl-2 family members function upstream of mitochondria and regulate the intrinsic apoptotic pathway. Mitochondrial membrane permeabilization is mediated by proapoptotic Bax in the intrinsic pathway of apoptosis (Ashkenazi and Salvesen, 2014; Gu et al, 2017). After Bax activation, cytochrome c is released from the mitochondrial intermembrane space
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