Analysis of Seven Human Respiratory Coronavirus (CoV) S Proteins from a Bioinformatics Approach
Antigenic epitope, COVID-19, SARS-CoV, S protein
Abstract
The coronavirus disease 2019 (COVID-19) has caused a huge pandemic repercussion across the globe and it is mainly contributed by the human severe acute respiratory syndrome coronavirus (SARS-CoV-2). There are seven human respiratory coronaviruses identified to date, namely HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, MERS-CoV, SARS-CoV and SARS-CoV-2. A recently published bioinformatic human CoV comparison only covered four human CoV. Therefore, in this study, a bioinformatics approach-based analyses route was taken to dissect the S proteins of all the available (seven) human respiratory coronaviruses publicly available in the GenBank database. The antigenic epitope amount is postulated to be the most accurate bioindicator among all in determining the severity of a particular human respiratory coronavirus. Other powerful bioinformatic indicators are global similarity index, maximum likelihood phylogenetic analysis as well as domain analysis. The data generated in this study can be channelled to the vaccine and antiviral drug development to combat the current and future spread of the human respiratory coronaviruses.
References
Chou, K.C. & Shen, H.B. (2010). A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0. PLoS ONE, 5: e9931. DOI: 10.1371/journal.pone.0009931
Cicaloni, V., Costanti, F., Pasqui, A., Bianchini, M., Niccolai, N. & Bongini, P. (2022). A bioinformatics approach to investigate structural and non-structural proteins in human coronavirus. Frontiers in Genetics, 13: 891418. DOI: 10.3389/fgene.2022.891418
Chatterjee, B. & Thakur, S.S. (2022). SARS-CoV-2 infection triggers phosphorylation: Potential target for anti-COVID-19 therapeutics. Frontiers in Immunology, 13: 829474. DOI: 10.3389/fimmu.2022.829474
Fung, T.S., & Liu, D.X. (2018). Post-translational modifications of coronavirus proteins: Roles and function. Future Virology, 13(6): 405-430. DOI: 10.2217/fvl-2018-0008
Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D. & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In Walker, J.M. (Ed.), The Proteomics Protocols Handbook. Humana Press, New Jersey, pp. 571-607.
Guruprasad, K., Reddy, B.V.B. & Pandit, M.W. (1990). Correlation between stability of a protein and its dipeptide composition: A novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering, Design and Selection, 4(2): 155-161. DOI: 10.1093/protein/4.2.155.
Huang, Y., Yang, C., Xu, X.F., Xu, W. & Liu, S. (2020). Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacologica Sinica, 41: 1141-1149. DOI: 0.1038/s41401-020-0485-4
Jaiswal, V.J. & Lee, H.J. (2022). Conservation and evolution of antigenic determinants of SARS-CoV-2: An insight for immune escape and vaccine design. Frontiers in Immunology, 13: 832106. DOI: 10.3389/fimmu.2022.832106.
Kelley, L.A., Mezulis, S., Yates, C.M., Wass, M.N. & Sternberg, M.J.E. (2015). The Phyre2 web portal for protein modelling, prediction and analysis. Nature Protocols, 10(6): 845-858. DOI: 10.1038/nprot.2015.053
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution, 35(6): 1547-1549. DOI: 10.1093/molbev/msy096.
Lim, L.W.K. (2023). Blended learning in animal biotechnology during pre-COVID-19, COVID-19 and post COVID-19 recovery phase periods across the globe: A step forward or backward. International Journal of Zoology and Animal Biology, 6(2): 1-5. DOI: 10.23880/izab-16000451
Lim, L.W.K. (2022). Comparative genomic analysis reveals the origin and global distribution of melon necrotic virus isolates. Gene Reports, 29: 101685. DOI: 10.1016/j.genrep.2022.101685
Lim, L.W.K., Hung, I.M. & Chung, H.H. (2022a). Cucumber mosaic virus: Global genome comparison and beyond. Malaysian Journal of Microbiology, 18(1): 79-92. DOI: 10.21161/mjm.211276
Lim, L.W.K., Liew, J.X. & Chung, H.H. (2022b). Piper yellow mottle virus: A deep dive into the genome. Gene Reports, 29: 101680. DOI: 10.1016/j.genrep.2022.101680
Matyášek, R., Řehůřková, K., Marošiová, K.B. & Kovařík, A. (2021). Mutational asymmetries in the SARS-CoV-2 genome may lead to increased hydrophobicity of virus proteins. Genes, 12(6): 826. DOI: 10.3390/genes12060826
Niu, Z., Xu, S., Zhang, J., Zou, Z., Ren, L., Liu, X., Zhang, S., Zou, H., Hu, X., Wang, J., Zhang, L. & Zhou, Y. (2023). Bioinformatic analysis of the S protein of human respiratory coronavirus. Molecular Phylogenetics and Evolution, 181: 107704. DOI: 10.1016/j.ympev.2023.107704
Pawlowski, P.H. (2021). Charged amino acids may promote coronavirus SARS-CoV-2 fusion with the host cell. AIMS Biophysics, 8(1): 111-120. DOI: 10.3934/biophy.2021008
Reis, C.A., Tauber, R. & Blanchard, V. (2021). Glycosylation is a key in SARS-CoV-2 infection. Journal of Molecular Medicine, 99(8): 1023-1031. DOI: 10.1007/s00109-021-02092-0
Xia, S., Zhu, Y., Liu, M., Lan, Q., Xu, W., Wu, Y., Ying, T., Liu, S., Shi, Z., Jiang, S. & Lu, L. (2020). Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein. Cellular & Molecular Immunology, 17: 765-767. DOI: 10.1038/s41423-020-0374-2
Xia, X. (2021). Domains and functions of spike protein in SARS-CoV-2 in the context of vaccine design. Viruses, 13(1): 109. DOI: 10.3390/v13010109.
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