Changes in Protein Structure Caused by SARS CoV-2 nsp1 Mutations

Yıl 2020, , 68 - 76, 31.12.2020

Ekrem Akbulut , Bülent Kar

https://doi.org/10.29132/ijpas.793377

Öz

Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) is a positive-polarity single-stranded RNA virus. COVID19 disease caused by the virus has killed more than 900 thousand people in a short period of ten months. There is no effective and specific drug and vaccine yet to combat the virus. Drug and vaccine development studies require a comprehensive understanding of the structural and functional properties of the virus. The high mutation rate of the rapidly spreading virus is one of the biggest obstacles to the continuity of the efficiency of vaccines and drugs to be developed. SARS CoV-2 non-structural protein 1 (nsp1), which is involved in the onset of cellular viral infection, is a potential candidate protein for prophylaxis. It is important to know the structure of nsp1, which prevents translation of host cell. In this study, the changes that can be caused by nsp1 mutations in 222 European isolates in protein structure were modeled using trRosetta, an artificial intelligence-based modeling software. Sequence information obtained from the NCBI Virus database was aligned with the MAFFT multiple sequence alignment program. Mutation analyzes were performed with RDP4 software. The mutant protein primary construct was created with the MegaX software. Protein quality scores were analyzed using the QMEAN algorithm. The physical chemistry properties of the proteins were made with the ProtParam ExPAsy program. Conformational analyzes of the obtained protein structures were made with PyMOL. It has been determined that nsp1 mutations seen in SARS CoV-2 European isolates may cause conformational and topological changes in the protein secondary and tertiary structure. It is thought that the change seen in the region between the P153 and N178 residues, which includes the SARS CoV-2 catalytic region, may affect the functional properties of the protein. It is thought that the obtained data can provide important data for preventive and therapeutic approaches.

Anahtar Kelimeler

SARS CoV-2, COVID19, nsp1, homology model

SARS CoV-2 nsp1 Mutasyonlarının Protein Yapıda Ortaya Çıkardığı Değişimler

Öz

Şiddetli akut solunum yolu sendromu koronavirüsü 2 (SARS CoV-2) pozitif polariteli ve tek iplikli bir RNA virüsüdür. Virüsün sebep olduğu COVID19 hastalığı on ay gibi kısa bir sürede 900 binden fazla insanın ölümüne neden oldu. Virüs ile mücadelede etkin ve spesifik bir ilaç ve aşı henüz bulunmamaktadır. İlaç ve aşı geliştirme çalışmaları virüsün yapısal ve fonksiyonel özelliklerinin kapsamlı bir şekilde anlaşılmasını gerekli kılmaktadır. Hızlı yayılım gösteren virüsün yüksek mutasyon hızı geliştirilecek aşı ve ilaçların etkinliklerini sürdürebilmelerinin önündeki en büyük engellerden biridir. Hücresel boyutta viral enfeksiyonun başlangıcında yer alan SARS CoV-2 yapısal olmayan protein 1 (nsp1) önleyici tedavi için potansiyel hedef proteindir. Konak hücre translasyonunu engelleyen nsp1’in yapısının bilinmesi önemlidir. Bu çalışmada 222 Avrupa izolatında görülen nsp1 mutasyonlarının protein yapıda ortaya çıkarabileceği değişimler yapay zekâ tabanlı bir modelleme yazılımı olan trRosetta kullanılarak modellenmiştir. NCBI Virüs veritabanından elde edilen dizi bilgileri MAFFT çoklu dizi hizalama programı ile hizalanmıştır. Mutasyon analizleri RDP4 yazılımı ile yapılmıştır. Mutant protein primer yapı MegaX yazılımı ile oluşturulmuştur. Protein kalite skorları QMEAN algoritması kullanılarak analiz edilmiştir. Proteinleri fizikokimyasla özellikleri ProtParam ExPAsy programı ile yapılmıştır. Elde edilen protein yapıların konformasyonel analizleri PyMOL ile yapılmıştır. SARS CoV-2 Avrupa izolatlarında görülen nsp1 mutasyonlarının protein sekonder ve tersiyer yapısında konformasyonel ve topolojik değişimlere neden olabileceği tespit edilmiştir. SARS CoV-2 katalitik bölgeyi içine alan P153 ve N178 rezidüleri arasında kalan bölgede görülen değişimin proteinin fonksiyonel özelliklerini etkileyebileceği düşünülmektedir. Elde edilen verilerin önleyici ve tedavi edici yaklaşımlara önemli veriler sunabileceği düşünülmektedir.

Anahtar Kelimeler

SARS CoV-2, COVID19, nsp1, homoloji model

Kaynakça

• Andersen, K.G., Rambaut, A., Lipkin, W., Holmes, E., Garry, R., 2020. The proximal origin of SARS-CoV-2. Nature Medicine, 26: 450–452.
• Benedetti, F., Marta, G., Silvia, A., Davide, Z., 2020. Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1. Journal of Translational Medicine, 18: 1–6.
• Benkert, P., Marco, B., Torsten, S., 2011. Toward the estimation of the absolute quality of ındividual protein structure models. Bioinformatics, 27: 343–350.
• Braitbard, M., Dina, S., Nir, K., 2019. Integrative structure modeling: overview and assessment. Annual Review of Biochemistry, 88: 113–135.
• Carroll, H., Beckstead, W., O'Connor, T., Ebbert, M., Clement, M., Snell, Q., Mcclellan, D., 2007. DNA reference alignment benchmarks based on tertiary structure of encoded proteins. Bioinformatics, 23: 2648–2649.
• Connor, R.F., Rachel, L.R., 2007. Unique SARS-CoV protein nsp1: bioinformatics, biochemistry and potential effects on virulence. Trends in Microbiology, 15: 51–53.
• van Dorp, L., Acman, M., Richard, D., Shaw, L., Ford, C., Ormond, L., Owen, C., Pang, J., Tan, C., Boshier, F., Ortiz, A., Balloux, F., 2020. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infection, Genetics and Evolution, 83:104351.
• Gomez, G., Abrar, F., Dodhia, M., Gonzalez, F., Nag, A., 2019. SARS coronavirus protein nsp1 disrupts localization of NUP93 from the nuclear pore complex. Biochemistry and Cell Biology, 97: 758–766.
• Jauregui, A., Savalia, D., Lowry, V., Farrell, C., Wathelet, M., 2013. Identification of residues of SARS-CoV nsp1 that differentially affect ınhibition of gene expression and antiviral signaling. PloSOne, 8: e62416.
• Kamitani, W., Huang, C., Narayanan, K., Lokugamage, K., Makino, S., 2009. A two-pronged strategy to suppress host protein synthesis by SARS coronavirus nsp1 protein. Nature Structural and Molecular Biology, 16: 1134–1140.
• Katoh, K., 2002. MAFFT: A novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Research, 30: 3059–3066.
• Katoh, K., Rozewicki, J., Yamada, K.D., 2018. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics, 20: 1160–1166.
• Kondabala, R., Vijay, K., 2019. Computational intelligence tools for protein modeling. In Advances in Intelligent Systems and Computing, 741: 949–956.
• 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: 1547–1549.
• Lokugamage, K., Narayanan, K., Huang, C., Makino, S., 2012. Severe acute respiratory syndrome coronavirus protein nsp1 is a novel eukaryotic translation inhibitor that represses multiple steps of translation initiation. Journal of Virology, 86: 13598–13608.
• Martin, D., Murrell, B., Golden, M., Khoosal, A., Muhire, B., 2015. RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution, 1: 1-5.
• McKee, D., Sternberg, A., Stange, U., Laufer, S., Naujokat, C., 2020. Candidate drugs against SARS-CoV-2 and COVID-19. Pharmacological Research, 157: 1-9.
• Mount, D.W., 2008. Using BLOSUM in sequence alignments. Cold Spring Harbor Protocols, 3: 39
• Mullan, L.J., 2003. Hydropathy- a window on the evasion of water. Briefings in Bioinformatics, 4: 279–282.
• Nag, A., Homayoun, V., Niharika, P., 2020. A study of nonstructural protein 1 of SARS coronavirus. The FASEB Journal, 34(S1): 1–1.
• Narayanan, K., Huang, C., Lokugamage, K., Kamitani, W., Ikegami, T., Tseng, C., Makino, S., 2008. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type 1 interferon, in infected cells. Journal of Virology, 82: 4471–4479.
• NCBI, 2020. https://www.ncbi.nlm.nih.gov/protein/YP_009725297.1 SARS CoV-2 nsp1. 11 May 2020.
• NCBI Virus, 2020. https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/ Genome information of SARS CoV-2 European isolates. 11 May 2020.
• Pachetti, M., Marini, B., Benedetti, F., Giudici, F., Mauro, E., Storici, P., Masciovecchio, C., Angeletti, S., Ciccozzi, M., Gallo, R., Zella, D., Ippodrino, R., 2020. Emerging SARS CoV-2 mutation hot spots ınclude a novel RNA-dependent-RNA polymerase variant. Journal of Translational Medicine, 18: 1–9.
• Phan, T., 2020. Genetic diversity and evolution of SARS-CoV-2. Infection, Genetics and Evolution, 81: 1-3.
• Sallenave, J.M., Loïc, G., 2020. Innate immune signaling and proteolytic pathways in the resolution or exacerbation of SARS-CoV-2 in Covid-19: Key therapeutic targets?. Frontiers in Immunology, 11: 1-20.
• Tanaka, T., Kamitani, W., Dediego, M.L., Enjuanes, L., Matsuura, Y., 2012. Severe acute respiratory syndrome coronavirus nsp1 facilitates efficient propagation in cells through a specific translational shutoff of host mRNA. Journal of Virology, 86: 11128–11137.
• Thoms, M., Buschauer, R., Ameismeier, M., Koepke, L., Denk, T., Hirschenberger, M., Kratzat, H., Hayn, M., Mackens-Kiani, T., Cheng, J., Straub, J.H., Stürzel, C.M., Fröhlich, T., Berninghausen, O., Becker, T., Kirchhoff, F., Sparrer, K.M.J., Beckman, R., 2020. Structural basis for translational shutdown and ımmune evasion by the nsp1 protein of SARS-CoV-2. Science, 8665: 1-11.
• Vankadari, N., 2020. Overwhelming mutations or SNPs of SARS-CoV-2: A point of caution. Gene, 752: 1-4.
• Wathelet, M.G., Melissa, O., Matthew, B.F., Ralph, S.B., 2007. Severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp1 and rational design of an attenuated strain. Journal of Virology, 81: 11620–11633.
• Worldometer, 2020. https://www.worldometers.info/coronavirus/coronavirus-cases/#daily-cases Coronavirus cases. 11 May 2020.
• Wu, F., Zhao, S., Yu, B., Chen, Y.M., Wang, W., Song, Z.G., Hu, Y., F.H. Tao, Z.W., Tian, J.H., Pei, Y.Y., Yuan, M.L., Zhang, Y.L., Dai, and Y.Z. Liu, Y., Wang, Q.M., Zheng, J.J., Xu, L., Holmes, E.C., Zhang, Y., 2020. Severe acute respiratory syndrome coronavirus 2 isolate wuhan-Hu-1 co - nucleotide - NCBI. Nature, 579: 265–269.
• Yang, J., Anishchenko, I., Park, H., Peng, Z., Ovchinnikov, S., Baker, D., 2020. Improved protein structure prediction using predicted ınterresidue orientations. Proceedings of the National Academy of Sciences of the United States of America 117: 1496–1503.