SARS-CoV-2 Spike Glikoproteinlerinin Farklı Ülkelerde Karşılaştırmalı Biyoinformatik Analizleri

Year 2022, , 68 - 74, 30.06.2022

Barış Kurt

https://doi.org/10.31594/commagene.1079045

Abstract

Bu çalışmada, biyoinformatik yaklaşımlar kullanılarak 23 farklı ülkeden SARS-CoV-2 spike (S) glikoproteininin 27 protein dizisi analiz edildi. Bu kapsamda saçak glikoproteinlerinin post-translasyonel modifikasyonları, sekans ve domain analizleri, filogenetik analizleri ve 3 boyutlu yapı analizleri gerçekleştirilmiştir. Ayrıca, insan ACE2 proteini ile SARS-CoV-2 saçak proteini S1 reseptör bağlama alanının (SS1) moleküler yerleştirme analizi yapıldı. Tüm SARS-CoV-2'lerin Spike_rec_bind (PF09408) ve Corona_S2 (PF01601) alan yapılarını içermesine rağmen, C-terminal S2 bölgesinin S1 bölgesinden daha çeşitli olduğu bulundu. Öngörülen N-glikosilasyon ve fosforilasyon bölgelerinin sırasıyla 17 ve 19, 136 ve 168 arasında olduğu belirlendi. Filogenetik analizde, SARS-CoV-2'lerin yarasa RaTG13 ve pangolin CoV-2 ile MERS CoV ve yarasa SARS CoV'den daha fazla benzerliğe sahip olduğu bulundu. İnsan SARS-CoV-2 ve yarasa RaTG13'ün tahmin edilen 3D protein yapıları, 0.76 ile 0.78 arasında değişen yüksek benzerlik gösterdi. Yerleştirme analizleri, Asp30, Lys31, His34, Glu35, Glu37, Asp38, Asn330 ve Gln325 rezidülerinin, SARS-CoV-2'nin N-terminal S1 alt birimi için ACE2 proteininde bağlayıcı kalıntılar olduğunu ortaya çıkardı. Bulgular özellikle ilaç geliştirme ve ilaç tasarımı çalışmaları için önemlidir.

Keywords

Kovid-19, koronavirus, saçak proteini, moleküler kenetleme, in siliko analizler

Comparative Bioinformatics Analyses of SARS-CoV-2 Spike Glycoproteins in Different Countries

Abstract

In this study, 27 protein sequences of SARS-CoV-2 spike (S) glycoprotein from 23 different countries were analyzed using bioinformatics approaches. In this context, post-translational modifications, sequence and domain analyses, phylogenetic analysis, and 3D structure analysis of the spike glycoprotein proteins were performed. Also, molecular docking analysis of the SARS-CoV-2 spike protein S1 receptor-binding domain (SS1) with human ACE2 protein was conducted. It was found that although all SARS-CoV-2s include Spike_rec_bind (PF09408) and Corona_S2 (PF01601) domain structures, the C-terminal S2 region was more diverse than the S1 region. The predicted N-glycosylation and phosphorylation sites were determined to be between 17 and 19 and 136 and 168, respectively. In phylogenetic analysis, SARS-CoV-2s were found to have more similarity with bat RaTG13 and pangolin CoV-2 than MERS CoV and bat SARS CoV. The predicted 3D protein structures of human SARS-CoV-2 and bat RaTG13 showed high similarity, ranging from 0.76 to 0.78. The docking analyses revealed that Asp30, Lys31, His34, Glu35, Glu37, Asp38, Asn330, and Gln325 residues were binding residues in the ACE2 protein for the N-terminal S1 subunit of SARS-CoV-2. The findings are particularly important for the studies of drug development and drug design.

Keywords

Covid-19, coronavirus, spike protein, molecular docking, in silico analyses

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