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

Autor: Muhsin Konuk, Ömer Faruk Karasakal, Ebru Özkan Oktay, Korkut Ulucan, Tuğba Kaman
Přispěvatelé: Kaman T., Karasakal O. F. , Ozkan Oktay E., ULUCAN K., Konuk M.
Rok vydání: 2019
Předmět:
APOPTOSOME
Physiology
Mutant
APAF1
apoptosis
neurodegenerative diseases
single nucleotide polymorphism (SNP)
in silico
02 engineering and technology
VARIANTS
Sağlık Bilimleri
Fundamental Medical Sciences
Biochemistry
BIOLOGY & BIOCHEMISTRY
Tıbbi Biyoloji
0302 clinical medicine
Biyokimya
Biyoloji ve Biyokimya
Missense mutation
neurodegenerative diseases
Medical Biology
RISK
Temel Bilimler
apoptosis
Life Sciences
Biyokimya (tıbbi)
Tıp
in silico
030220 oncology & carcinogenesis
BİYOLOJİ
Medicine
Natural Sciences
General Agricultural and Biological Sciences
dbSNP
In silico
0206 medical engineering
Temel Tıp Bilimleri
BIOLOGY
Life Sciences (LIFE)
Single-nucleotide polymorphism
Computational biology
Biology
Microbiology
Article
03 medical and health sciences
APAF1
single nucleotide polymorphism (SNP)
Yaşam Bilimleri
Health Sciences
Genetics
Molecular Biology
Genotyping
Gene
Biochemistry (medical)
Cell Biology
020601 biomedical engineering
Yaşam Bilimleri (LIFE)
Zdroj: Turkish Journal of Biology
Volume: 43, Issue: 6 371-381
ISSN: 1303-6092
1300-0152
DOI: 10.3906/biy-1905-18
Popis: 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.
Databáze: OpenAIRE
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