Struktur 3D Protein Struktural VP1 pada Enterovirus A71 Menggunakan Swiss-Model
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Submitted
30 January 2020
Published
30 June 2020
Keywords:
-
Enterovirus A71, In-Silico, Metode Homologi, Protein VP1, Swiss-Model
Abstract
Background: Protein struktural VP1 berperan sebagai pemain kunci dalam patogenesis, memiliki keunikan yang cukup menarik untuk dikaji dengan mempelajari sifat dan fungsi protein struktural VP1. Penelitian ini bertujuan untuk memprediksi struktur tiga dimensi protein VP1 pada EV-A71. Metode: Protein target diperoleh dari server UniProt dengan kode akses A0A097EV89 menggunakan template 4cey.1.A (PDB ID) dianalisis secara in silico melalui metode homologi menggunakan server SWISS-MODEL. Hasil: analisis penelitian menunjukkan protein target dan template memiliki identity 95,29 % dan tersusun dari 297 asam amino dengan nilai QMEAN -2,15. Protein struktural VP1 pada Ramachandran Plots memiliki struktur stabil, residu non-glisin pada daerah outlier hanya berkisar 0,34 % (A53 ALA) dengan Nilai rotamer outliers 1,61 %. Kesimpulan: Model struktur tiga dimensi protein yang diteliti memiliki struktur stabil dan informasi yang didapatkan berguna untuk penelitian lebih lanjut dalam pengembangan vaksin penyakit yang disebabkan oleh EV-A71.
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References
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Zhang, H., Song, L., Cong, H., & Tien, P. (2015). Nuclear Protein Sam68 Interacts with the Enterovirus 71 Internal Ribosome Entry Site and Positively Regulates Viral Protein Translation. Journal of Virology, 89(19), 10031–10043. https://doi.org/10.1128/jvi.01677-15
Apostol, L. N., Shimizu, H., Suzuki, A., Umami, R. N., Jiao, M. M. A., Tandoc, A., Saito, M., Lupisan, S., & Oshitani, H. (2019). Molecular characterization of enterovirus-A71 in children with acute flaccid paralysis in the Philippines. BMC Infectious Diseases, 19(1), 1–8. https://doi.org/10.1186/s12879-019-3955-x
Aw-Yong, K. L., NikNadia, N. M. N., Tan, C. W., Sam, I. C., & Chan, Y. F. (2019). Immune responses against enterovirus A71 infection: Implications for vaccine success. Reviews in Medical Virology, 29(5), 1–20. https://doi.org/10.1002/rmv.2073
Baker, D., & Sali, A. (2001). Protein structure prediction and structural genomics. Science, 294(93), 93–96. https://doi.org/10.1126/science.1065659
Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J., & Schwede, T. (2008). Protein structure homology modeling using SWISS-MODEL workspace. Nature Protocols, 4(1), 1–13. https://doi.org/10.1038/nprot.2008.197
Fouriana, L. (2017). Analisis In-Silico dan Struktur Tiga Dimensi Protein Struktural Envelope (E) Virus Dengue Serotipe Tiga dan Pemanfaatnnya sebagai Media Pembelajaran. Skripsi Tidak Diterbitkan.
Gorelik, L., Reid, C., Testa, M., Brickelmaier, M., Bossolasco, S., Pazzi, A., Bestetti, A., Carmillo, P., Wilson, E., McAuliffe, M., Tonkin, C., Carulli, J. P., Lugovskoy, A., Lazzarin, A., Sunyaev, S., Simon, K., & Cinque, P. (2011). Progressive multifocal leukoencephalopathy (PML) development is associated with mutations in JC virus capsid protein VP1 that change its receptor specificity. Journal of Infectious Diseases, 204(1), 103–114. https://doi.org/10.1093/infdis/jir198
Kiener, T. K., Premanand, B., & Kwang, J. (2013). Immune responses to dermatophytoses. Expert Reviews Vaccines, 12(4), 357–364. https://doi.org/10.1007/978-1-4020-6397-8_10
Kurniasih, R. (2018). Struktur Prediksi dan Identifikasi Substrat Spesifik Lakase Isolat Lokal Neorspora crassa inaCC F226. Skripsi Tidak Diterbitkan.
Lin, J. Y., Kung, Y. A., & Shih, S. R. (2019). Antivirals and vaccines for Enterovirus A71. Journal of Biomedical Science, 26(65), 1–10. https://doi.org/10.1186/s12929-019-0560-7
Lovell, S. C., Davis, I. W., Adrendall, W. B., de Bakker, P. I. W., Word, J. M., Prisant, M. G., Richardson, J. S., & Richardson, D. C. (2003). Structure Validation By Calpha Geometry: Phi,Psi And C beta Deviation. Proteins-Structure Function and Genetics, 50, 437–450. https://doi.org/10.1002/prot.10286
Ma'rifatun, R. L., & Sugiyanto, S. (2013). Model Penyebaran Penyakit Polio Dengan Pengaruh Vaksinasi. Jurnal Fourier, 2(1), 11–18. https://doi.org/10.14421/fourier.2013.21.11-18
Ooi, M. H., Wong, S. C., Lewthwaite, P., Cardosa, M. J., & Solomon, T. (2010). Clinical features, diagnosis, and management of enterovirus 71. The Lancet Neurology, 9(11), 1097–1105. https://doi.org/10.1016/S1474-4422(10)70209-X
Seprianto. (2018). Bioinformatika untuk Protein Modelling. Pusat Penelitian Bioteknologi dan Bioindustri Indonesia. Universitas Esa Unggul.
Sheu, S. Y., Schlag, E. W., Selzle, H. L., & Yang, D. Y. (2009). Hydrogen bonds in membrane proteins. Journal of Physical Chemistry B, 113(15), 5318–5326. https://doi.org/10.1021/jp810772a
Umam, Y. C., Kharis, M., & Supriyono. (2016). Model Epidemi SEIV Penyebaran Penyakit Polio pada Populasi Tak Konstan. Unnes Journal of Life Mathematics, 5(2), 100–107.
Wijaya, H., & Hasanah, F. (2016). Pangan Dengan Metode Homologi Menggunakan Program Swiss-Model. Biopropal Industri, 7(2), 83–94.
Wilson, W. R. (2001). Current Diagnosis and Treatment in Infectious Disease. McGraw – Hill Companies, Inc.
Yu, Z., Huang, Z., Sao, C., Huang, Y., Zhang, F., Ma, G., Chen, Z., Zeng, Z., Qiwen, D., & Zeng, W. (2013). Oral immunization of mice using Bifidobacterium longum expressing VP1 protein from enterovirus 71. Archives of Virology, 158(5), 1071–1077. https://doi.org/10.1007/s00705-012-1589-z
Yuan, J., Shen, L., Wu, J., Zou, X., Gu, J., Chen, J., & Mao, L. (2018). Enterovirus A71 proteins: Structure and function. Frontiers in Microbiology, 9(286), 1–12. https://doi.org/10.3389/fmicb.2018.00286
Zhang, H., Song, L., Cong, H., & Tien, P. (2015). Nuclear Protein Sam68 Interacts with the Enterovirus 71 Internal Ribosome Entry Site and Positively Regulates Viral Protein Translation. Journal of Virology, 89(19), 10031–10043. https://doi.org/10.1128/jvi.01677-15
Authors
Suprianto, S., Budiarsa, M., & Dhafir, F. (2020). Struktur 3D Protein Struktural VP1 pada Enterovirus A71 Menggunakan Swiss-Model. BIOEDUSCIENCE, 4(1), 37–47. https://doi.org/10.29405/j.bes/4137-474353
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