In Silico Domain Structural Model Analysis of Coronavirus ORF1ab Polyprotein

Mohammed I. Jameel; Rabar J. Noori; Soma F. Rasul

doi:10.14500/aro.10829

Mohammed I. Jameel Department of Medical Microbiology, Faculty of Science and Health, Koya University, Koya KOY45, Kurdistan Region – F.R. Iraq https://orcid.org/0000-0002-2964-2520
Rabar J. Noori Department of Medical Microbiology, Faculty of Science and Health, Koya University, Koya KOY45, Kurdistan Region – F.R. Iraq https://orcid.org/0000-0003-1439-9182
Soma F. Rasul Department of Medical Microbiology, Faculty of Science and Health, Koya University, Koya KOY45, Kurdistan Region – F.R. Iraq http://orcid.org/0000-0003-3773-7156

Keywords: Coronavirus, Ligand, Modeling, ORF1ab

Abstract

The world today is battling with a coronavirus infection that is considered a global pandemic. Coronavirus infection is mainly attribute to the varying technique of the replication and release of different genomic components of the virus. The present study aims to establish the physical and chemical features, as well as the basic structural and functional properties of Coronavirus ORF1ab domain. A molecular approach was adopt in this study using the Swiss Model and Phyre2 server whereas the prediction of the active ligand binding sites was done using Phyre2. The analysis of the structure of the protein showed that it has good structural and heat stability, as well as better hydrophilic features and acidic in nature. Based on the Homology modeling, only two binding active sites were noted with catalytic function being mediated by Zn2+ as the metallic heterogeneous ligand for binding sites prediction. The proteins mostly exhibited helical secondary configurations. This study can help in predicting and understanding the role of this domain protein in active coronavirus infection.

Downloads

Download data is not yet available.

Author Biographies

Mohammed I. Jameel, Department of Medical Microbiology, Faculty of Science and Health, Koya University, Koya KOY45, Kurdistan Region – F.R. Iraq

Mohammed I. Jameel is a Lecturer at the Department of Medical Microbiology, Faculty of Science and Health at Koya University, Kurdistan Region, F.R. Iraq. He got a B.Sc. degree in Biotechnology and the M.Sc. degree in Bioinformatics. His research interest includes microarray, whole genome sequencing data analysis, Metagenomics and R programming.

Rabar J. Noori, Department of Medical Microbiology, Faculty of Science and Health, Koya University, Koya KOY45, Kurdistan Region – F.R. Iraq

Rabar J. Noori is a Lecturer in the Department of Medical Microbiology, Faculty of Science and Health at Koya University, Kurdistan Region, F.R. Iraq. He got the B.Sc. degree in Agriculture and the M.Sc. degree in Agriculture for sustainable development. His research interest includes: water and soil microbiology, Integrated pest management. Mr. Rabar is a member of Kurdistan Agricultural Engineering Union.

Soma F. Rasul, Department of Medical Microbiology, Faculty of Science and Health, Koya University, Koya KOY45, Kurdistan Region – F.R. Iraq

Soma Fatah Rasul is a Lecturer at the Department of Medical microbiology, Faculty of Science and Health, Koya University. She got the B.Sc. degree in agriculture machinery from Koya University, the M.Sc. degree in agriculture engineering from USQ-Australia. Her research interests are in agriculture science, food science, post harvesting, precision agriculture and smart farming and renewable energy.

References

Gasteiger, J. and Walker, M., 2005. The Proteomics Protocols Handbook. Springer, Berlin, p.571.

Geourjon, C. and Deleage, G.C., 1995. SOPMA: Significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Computer Applied Bioscience, 681(11), pp.681-684.

Gil, S.C. and Von Hippel, P.H., 1989. Calculation of protein extinction coefficients from amino acid sequence data. Analytical Biochemistry, 182(2), pp.319-326.

Hamp, T., Kassner, R., Seemayer, S., Vicedo, E., Schaefer, C., Achten, D., Auer, F., Boehm, A., Braun, T., Hecht, M., Heron, M., Hönigschmid, P., Hopf, T.A., Kaufmann, S.A., Kiening, M., Krompass, D., Landerer, C., Mahlich, Y., Roos, M. and Rost, B., 2013. Homology-based inference sets the bar high for protein function prediction. BMC Journal Bioinformatics, 14(7), pp.502-511.

Kelly, L.A, Mezulis, S., Yates, C.M., Wass, M.N. and Sternberg, M.J., 2015. The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols, 10(6), p.845.

Kyte, J. and Doolottle, R.F., 1982. Asimple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157(1), pp.105-132.

Li, S., Yuan, L., Dai, G., Chen, R.A., Liu, D.X. and Fung, T.S., 2020. Regulation of the ER stress response by the Ion channel activity of the infectious bronchitis coronavirus envelope protein modulates virion release, apoptosis, viral fitness, and pathogenesis. Frontiers in Microbiology, 10, p.3022.

McBride, R. and Fielding, B.C., 2012. The role of severe acute respiratory syndrome (SARS) coronavirus accessory proteins in virus pathogenesis. Viruses, 4(11), pp.2902-2923.

Ofran, Y. and Rost, B., 2007. ISIS: Interaction sites identified from sequence. Bioinformatics Journal, 23(2), pp.e13-e16.

Paraskevis, D., Kostaki, E.G., Magiorkinis, G., Panayiotakopoulos, G., Sourvinos, G. and Tsiodras, S., 2020. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event. Infection Genetics and Evolution, 79, pp.104-212.

Raik, G. and Luis, S., 2010. Strategies for protein synthetic biology. Nucleic Acids Research Journal, 38(8), pp.2663-2675.

Remmert, M., Andreas, B., Andreas, H. and Johannes, S., 2012. HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature Methods, 9(2), pp.173-178.

Rost, B., Guy, Y. and Liu, J., 2004. The predicProtein server. Nucleic Acid Research Journal, 32(2), pp.321-326.

Rothe, C., Schunk, M., Sothmann, P., Bretzel, G., Froeschl, G., Wallrauch, C., Zimmer, T., Thiel, V., Janke, C., Guggemos, W., Seilmaier, M., Drosten, C., Vollmar, P., Zwirglmaier, K., Zange, S., Wölfel, R. and Hoelscher, M., 2020.

Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. New England Journal of Medicine, 382(10), pp.970-971.

Schaecher, S.R. and Pekosz, A., 2010. Molecular Biology of the SARSCoronavirus. Springer, Berlin, pp.153-166.

To, K.K.W., Tsang, O.T., Yip, C.C., Chan, K.H., Wu, T.C., Chan, J.M., Leung, W.S., Chik, T.S., Choi, C.Y., Kandamby, D.H., Lung, D.C., Tam, A.R., Poon, R.W., Fung, A.Y., Hung, I.F., Cheng, V.C., Chan, J.F. and Yuen, K.Y., 2020. Consistent detection of 2019 novel coronavirus in saliva. Clinical Infectious Diseases, 71(15), pp.841-843.

Wu, A., Peng, Y., Huang, B., Ding, X., Wang, X., Niu, P., Meng, J., Zhu, Z., Zhang, Z., Wang, J., Sheng, J., Quan, L., Xia, Z., Tan, W., Cheng, G. and Jiang, T., 2020. Genome composition and divergence of the novel coronavirus (2019- nCoV) originating in China. Cell Host and Microbe, 27(3), pp.325-328.

Wu, F., Zhao, S., Yu, B., Chen, Y., Hu, Y., Tao, Z.W., Tian, J.H., Pei, Y.Y., Yuan, M.L., Zhang, Y.L., Dai, F.H., Liu, Y., Wang, Q.M., Zheng, J.J., Xu, L., Holmes, E.C. and Zhang, Y.Z., 2020. Anew coronavirus associated with human respiratory disease in China. Nature, 579(7798), pp.265-269.

Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., Niu, P., Zhan, F., Ma, X., Wang, D., Xu, W., Wu, G., Gao, G.F. and Tan, W., 2020. Anovel coronavirus from patients with pneumonia in China, 2019. New England Journal of Medicine, 382(8), pp.727-733.