Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools

Ömer Faruk KARASAKAL, (Üsküdar Üniversitesi, Sağlık Hizmetleri Meslek Yüksekokulu, Tıbbi Laboratuvar Teknikleri, İstanbul, Türkiye)
Ebru ÖZKAN OKTAY, (Üsküdar Üniversitesi, Sağlık Hizmetleri Meslek Yüksekokulu, Laboratuvar Teknolojisi, İstanbul, Türkiye)
Tuğba KAMAN (Üsküdar Üniversitesi, Sağlık Hizmetleri Meslek Yüksekokulu, Tıbbi ve Aromatik Bitkiler, İstanbul, Türkiye)
Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi
6 2
Yıl: 2023 Cilt: 25 Sayı: 2 Sayfa Aralığı: 489 - 500 Metin Dili: İngilizce DOI: 10.25092/baunfbed.1197932 İndeks Tarihi: 21-07-2023

Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools

Öz:
Apolipoprotein E (APOE) is one of the main proteins responsible for cholesterol transport. It has three major isoforms, APOE2, APOE3, and APOE4. The purpose of this study is to investigate the possible effects of single nucleotide variations (SNVs) in the APOE gene, which cause amino acid substitution, on the function, structure and stabilization of the APOE protein using bioinformatics/s tools. SNVs and protein sequence information were obtained from NCBI and UniProt databases. Bioinformatical analysis was performed using a series of tools such as SIFT, PolyPhen-2, SNPs&GO, Mutation Assessor, PROVEAN, SNAP2, I-Mutant-3, MUPro, and Project HOPE. As a result, 321 missense SNVs were analyzed and rs7412 (R176C), rs769455 (R163C), rs11542029 (R50C), rs121918393 (R154S), rs121918394 (K164Q), rs200703101 (R154P), rs387906567 (R160C), rs11542040 (P102T), rs11542041 (R132S) and rs41382345 (E139V) were predicted to be deleterious/disease related after functional analysis and pathological effect analysis via all of the bioinformatics/s tools. According to the protein stabilization results, it was determined that all SNVs decreased protein stabilization with the MUPro software tool, and two SNVs (rs121918394, rs41382345) increased protein stabilization with the I-Mutant-3 software tool. The models of protein and amino acid properties were obtained via Project HOPE for all high-risk SNVs. We hope our analysis will be valuable for further proteomic, genomic, and clinical research.
Anahtar Kelime: Apolipoprotein E (APOE) cholesterol in silico single nucleotide variation (SNV)

Biyoinformatik araçlar aracılığıyla insan APOE (Apolipoprotein E) genindeki yanlış anlamlı SNV'lerin değerlendirilmesi

Öz:
Apolipoprotein E (APOE), kolesterol taşınmasından sorumlu ana proteinlerden biridir. APOE2, APOE3 ve APOE4 olmak üzere üç ana izoformu vardır. Bu çalışmanın amacı, APOE geninde amino asit yer değiştirmesine neden olan tek nükleotid varyantlarının (SNV'ler) APOE proteininin işlevi, yapısı ve stabilizasyonu üzerindeki olası etkilerini biyoinformatik araçlar kullanarak araştırmaktır. SNV'ler ve protein dizi bilgisi, NCBI ve UniProt veritabanlarından elde edilmiştir. Biyoinformatik analiz, SIFT, PolyPhen-2, SNPs&GO, Mutation Assessor, PROVEAN, SNAP2, I-Mutant-3, MUPro ve Project HOPE gibi bir dizi araç kullanılarak yapılmıştır. Sonuç olarak 321 yanlış anlamlı SNV analiz edilmiş ve rs7412 (R176C), rs769455 (R163C), rs11542029 (R50C), rs121918393 (R154S), rs121918394 (K164Q), rs200703101 (R154P), rs387906567 (R160C), 102rsT11542040 rs11542041 (R132S) ve rs41382345 (E139V)'nin tüm biyoinformatik araçları aracılığıyla fonksiyonel analiz ve patolojik etki analizinden sonra zararlı/hastalık ile ilgili olduğu tahmin edilmiştir. Protein stabilizasyon sonuçlarına göre, MUPro yazılım aracı ile tüm SNV'lerin protein stabilizasyonunu azalttığı ve I-Mutant-3 yazılım aracı ile iki SNV'nin (rs121918394, rs41382345) protein stabilizasyonunu arttırdığı belirlenmiştir. Protein ve amino asit özellikleri modelleri, tüm yüksek riskli SNV'ler için Project HOPE aracılığıyla elde edilmiştir. Analizimizin daha fazla proteomik, genomik ve klinik araştırmalar için değerli olacağını umuyoruz.
Anahtar Kelime: Apolipoprotein E (APOE) kolesterol in silico tek nükleotid varyantı (SNV)

Belge Türü: Makale Makale Türü: Araştırma Makalesi Erişim Türü: Erişime Açık
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APA Karasakal Ö, Özkan Oktay E, Kaman T (2023). Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools. , 489 - 500. 10.25092/baunfbed.1197932
Chicago Karasakal Ömer Faruk,Özkan Oktay Ebru,Kaman Tugba Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools. (2023): 489 - 500. 10.25092/baunfbed.1197932
MLA Karasakal Ömer Faruk,Özkan Oktay Ebru,Kaman Tugba Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools. , 2023, ss.489 - 500. 10.25092/baunfbed.1197932
AMA Karasakal Ö,Özkan Oktay E,Kaman T Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools. . 2023; 489 - 500. 10.25092/baunfbed.1197932
Vancouver Karasakal Ö,Özkan Oktay E,Kaman T Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools. . 2023; 489 - 500. 10.25092/baunfbed.1197932
IEEE Karasakal Ö,Özkan Oktay E,Kaman T "Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools." , ss.489 - 500, 2023. 10.25092/baunfbed.1197932
ISNAD Karasakal, Ömer Faruk vd. "Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools". (2023), 489-500. https://doi.org/10.25092/baunfbed.1197932
APA Karasakal Ö, Özkan Oktay E, Kaman T (2023). Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 25(2), 489 - 500. 10.25092/baunfbed.1197932
Chicago Karasakal Ömer Faruk,Özkan Oktay Ebru,Kaman Tugba Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25, no.2 (2023): 489 - 500. 10.25092/baunfbed.1197932
MLA Karasakal Ömer Faruk,Özkan Oktay Ebru,Kaman Tugba Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi, vol.25, no.2, 2023, ss.489 - 500. 10.25092/baunfbed.1197932
AMA Karasakal Ö,Özkan Oktay E,Kaman T Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi. 2023; 25(2): 489 - 500. 10.25092/baunfbed.1197932
Vancouver Karasakal Ö,Özkan Oktay E,Kaman T Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi. 2023; 25(2): 489 - 500. 10.25092/baunfbed.1197932
IEEE Karasakal Ö,Özkan Oktay E,Kaman T "Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools." Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 25, ss.489 - 500, 2023. 10.25092/baunfbed.1197932
ISNAD Karasakal, Ömer Faruk vd. "Evaluation of missense SNVs within human APOE (Apolipoprotein E) gene via bioinformatics tools". Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi 25/2 (2023), 489-500. https://doi.org/10.25092/baunfbed.1197932
Sayfa Oluşturulma Tarihi
24-04-2024 8:30

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