Determination of Deleterious SNPs in APH1A Gene Related to Alzheimer’s Disease by In Silico Methods

Öz

Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by pathological accumulation of β-amyloid (Aβ) senile plaques and neurofibrillary tangles. γ-secretase produces the amyloid β peptide (Aβ), which causes AD. γ-secretase is a macromolecular complex and the protein encoded by the APH1A gene is located in this complex. In this study, it was aimed to determine the possible deleterious effects of missense single nucleotide polymorphisms (SNPs) in APH1A gene on the protein structure and stabilization via in silico methods. PolyPhen-2 and SIFT were used to predict deleterious SNPs, I-Mutant 2.0 software was used to detect protein stabilization changes and Project HOPE software tool was used to make three-dimensional modeling of wild and mutant type proteins. The results showed that 257 SNPs among a total of 3567 SNPs in the APH1A gene were missense SNPs. According to the in silico analysis of the 257 SNPs it has been determined that rs11548266, rs74126634, rs145324799, rs199961673, rs370361277, rs370719475 and rs376071112 polymorphisms may have deleterious effects. The results of in silico analysis provide data for genotyping of SNPs which have deleterious effects on protein structure and stabilization rather than genotyping of entire 3567 SNPs in the APH1A gene associated with Alzheimer's disease. Therefore, deleterious SNPs may be used in the selection of SNPs and experimental design which are the most important stages of genotyping studies. Thus, we envisaged that the obtained results will contribute to the further studies either experimental or in silico on Alzheimer's disease.

Anahtar Kelimeler

• APH1A,Polymorphism,Alzheimer’s Disease,In silico

Alzheimer Hastalığı ile İlişkilendirilen APH1A Genindeki Zararlı SNP’lerin In Silico Yöntemler ile Belirlenmesi

Öz

Alzheimer hastalığı (AH), β-amiloid (Aβ) senil plakların ve nörofibriler yumakların patolojik birikimi ile karakterize olan ilerleyici bir nörodejeneratif hastalıktır. γ-sekretaz, AH nedeni olan amiloid β peptidi (Aβ) üretmektedir. γ-sekretaz makromoleküler bir komplekstir ve APH1A geninin kodladığı protein bu komplekste yer almaktadır. Bu çalışmada, APH1A genindeki yanlış anlamlı (missense) tek nükleotid polimorfizmlerinin (SNP) proteinin yapısı ve stabilizasyonu üzerindeki olası zararlı etkilerinin in silico yöntemler kullanılarak belirlenmesi amaçlanmıştır. Zararlı SNP’lerin tahmin edilmesi için PolyPhen-2 ve SIFT yazılım araçları, protein stabilizasyonu değişimlerinin tespit edilmesi için I-Mutant 2.0 yazılımı, yabanıl ve mutant tip proteinlerin üç boyutlu modellemeleri için Project HOPE yazılım aracı kullanılmıştır. Sonuçlar, APH1A geninde yer alan toplam 3567 SNP’nin 257 tanesinin yanlış anlamlı SNP olduğunu göstermiştir. 257 SNP’nin in silico analizlerine göre, rs11548266, rs74126634, rs145324799, rs199961673, rs370361277, rs370719475 ve rs376071112 polimorfizmlerinin zararlı etkilerinin olabileceği belirlenmiştir. Çalışmamızda gerçekleştirdiğimiz in silico analizler, Alzheimer hastalığı ile ilgili APH1A geninde yer alan 3567 SNP’nin tamamının genotiplenmesi yerine proteinin yapısı ve stabilizasyonuna zararlı etkisi olabilecek SNP’lerin genotiplenmesine ilişkin veri sağlamaktadır. Dolayısıyla, zararlı olduğu tespit edilen SNP’ler genotipleme çalışmalarının en önemli basamağı olan SNP seçiminde ve deney tasarımında kullanılabilecektir. Bu nedenle, elde ettiğimiz sonuçların Alzheimer hastalığı ile ilgili gelecekte yapılacak olan hem deneysel hem de in silico çalışmalara katkı sağlayacağı düşünülmektedir.

Anahtar Kelimeler

• APH1A,Polimorfizm,Alzheimer Hastalığı,In silico

Kaynakça

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