References
- Baric, R. S., Nelson, G. W., Fleming, J. O., Deans, R. J., Keck, J. G., Casteel, N., & Stohlman, S. A. (1988). Interactions between coronavirus nucleocapsid protein and viral RNAs: Implications for viral transcription. Journal of Virology, 62(11), 4280–4287. https://doi.org/https://doi.org/10.1128/JVI.62.11.4280-4287.1988
- Berendsen, H. J. C., Grigera, J. R., & Straatsma, T. P. (1987). The missing term in effective pair potentials. The Journal of Physical Chemistry, 91(24), 6269–6271.
- Chen, H., & Zhou, H. X. (2005). Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data. Proteins, 61(1), 21–35. https://doi.org/https://doi.org/10.1002/prot.20514
- Chenavas, S., Crepin, T., Delmas, B., Ruigrok, R. W., & Slama-Schwok, A. (2013). Influenza virus nucleoprotein: Structure, RNA binding, oligomerization and antiviral drug target. Future Microbiology, 8(12), 1537–1545. https://doi.org/https://doi.org/10.2217/fmb.13.128
- Cong, Y., Ulasli, M., Schepers, H., Mauthe, M., V’kovski, P., Kriegenburg, F., Thiel, V., de Haan, C. A. M., & Reggiori, F. (2020). Nucleocapsid protein recruitment to replication-transcription complexes plays a crucial role in coronaviral life cycle. Journal of Virology, 94(4), e01925–19. https://doi.org/https://doi.org/10.1128/JVI.01925-19.
- Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/https://doi.org/10.1063/1.464397
- DeLano, W. L. (2002). The PyMOL molecular graphics system. http://pymol.org
- Gerritz, S. W., Cianci, C., Kim, S., Pearce, B. C., Deminie, C., Discotto, L., McAuliffe, B., Minassian, B. F., Shi, S., Zhu, S., Zhai, W., Pendri, A., Li, G., Poss, M. A., Edavettal, S., McDonnell, P. A., Lewis, H. A., Maskos, K., Mörtl, M., … Krystal, M. (2011). Inhibition of influenza virus replication via small molecules that induce the formation of higher-order nucleoprotein oligomers. Proceedings of the National Academy of Sciences of the United States of America, 108(37), 15366–15371. https://doi.org/https://doi.org/10.1073/pnas.1107906108
- Gil, C., Ginex, T., Maestro, I., Nozal, V., Barrado-Gil, L., Cuesta-Geijo, M. A., … Martinez, A. (2020). COVID-19: Drug Targets and Potential Treatments. Journal of Medicinal Chemistry., https://doi.org/https://doi.org/10.1021/acs.jmedchem.0c00606
- Gordon, D. E., Jang, G. M., Bouhaddou, M., Xu, J., Obernier, K., White, K. M., O’Meara, M. J., Rezelj, V. V., Guo, J. Z., Swaney, D. L., Tummino, T. A., Hüttenhain, R., Kaake, R. M., Richards, A. L., Tutuncuoglu, B., Foussard, H., Batra, J., Haas, K., Modak, M., … Krogan, N. J. (2020). A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 583(7816), 459–468. doi: https://doi.org/10.1038/s41586-020-2286-9
- Grifoni, A., Sidney, J., Zhang, Y., Scheuermann, R. H., Peters, B., & Sette, A. (2020). A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2. Cell Host & Microbe, 27(4), 671–680. https://doi.org/https://doi.org/10.1016/j.chom.2020.03.002
- Gupta, R., Charron, J., Stenger, C. L., Painter, J., Steward, H., Cook, T. W., Faber, W., Frisch, A., Lind, E., Bauss, J., Li, X., Sirpilla, O., Soehnlen, X., Underwood, A., Hinds, D., Morris, M., Lamb, N., Carcillo, J. A., Bupp, C., … & Prokop, J. W. (2020). SARS-CoV2 (COVID-19) Structural/Evolution Dynamicome: Insights into functional evolution and human genomics. Journal of Biological Chemistry, 295(33), 11742-11753. https://doi.org/https://doi.org/10.1074/jbc.RA120.014873
- He, R., Dobie, F., Ballantine, M., Leeson, A., Li, Y., Bastien, N., Cutts, T., Andonov, A., Cao, J., Booth, T. F., Plummer, F. A., Tyler, S., Baker, L., & Li, X. (2004). Analysis of multimerization of the SARS coronavirus nucleocapsid protein. Biochemical and Biophysical Research Communications, 316(2), 476–483. https://doi.org/https://doi.org/10.1016/j.bbrc.2004.02.074
- He, R., Leeson, A., Ballantine, M., Andonov, A., Baker, L., Dobie, F., Li, Y., Bastien, N., Feldmann, H., Strocher, U., Theriault, S., Cutts, T., Cao, J., Booth, T. F., Plummer, F. A., Tyler, S., & Li, X. (2004). Characterization of protein-protein interactions between the nucleocapsid protein and membrane protein of the SARS coronavirus. Virus Research, 105(2), 121–125. https://doi.org/https://doi.org/10.1016/j.virusres.2004.05.002
- Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/https://doi.org/10.1002/(SICI)1096-987X(199709)18:12 < 1463::AID-JCC4 > 3.0.CO;2-H
- Holmes, K. V., & Enjuanes, L. (2003). Virology. The SARS coronavirus: A postgenomic era. Science (New York, N.Y.).), 300(5624), 1377–1378. https://doi.org/https://doi.org/10.1126/science.1086418
- Hung, H.-C., Liu, C.-L., Hsu, J. T.-A., Horng, J.-T., Fang, M.-Y., Wu, S.-Y., Ueng, S.-H., Wang, M.-Y., Yaw, C.-W., & Hou, M.-H. (2012). Development of an anti-influenza drug screening assay targeting nucleoproteins with tryptophan fluorescence quenching. Analytical Chemistry, 84(15), 6391–6399. https://doi.org/https://doi.org/10.1021/ac2022426
- Ivanov, P., Kedersha, N., & Anderson, P. (2019). Stress granules and processing bodies in translational control. Cold Spring Harbor Perspectives in Biology, 11(5), doi: https://doi.org/10.1101/cshperspect.a032813.
- Jendele, L., Krivak, R., Skoda, P., Novotny, M., & Hoksza, D. (2019). PrankWeb: A web server for ligand binding site prediction and visualization. Nucleic Acids Research, 47(W1), W345–W349. https://doi.org/https://doi.org/10.1093/nar/gkz424
- Kindrachuk, J., Ork, B., Hart, B. J., Mazur, S., Holbrook, M. R., Frieman, M. B., Traynor, D., Johnson, R. F., Dyall, J., Kuhn, J. H., Olinger, G. G., Hensley, L. E., & Jahrling, P. B. (2015). Antiviral potential of ERK/MAPK and PI3K/AKT/mTOR signaling modulation for Middle East respiratory syndrome coronavirus infection as identified by temporal kinome analysis. Antimicrobial Agents and Chemotherapy, 59(2), 1088–1099. https://doi.org/https://doi.org/10.1128/AAC.03659-14
- Kumar, V., Prakash, A., Pandey, P., Lynn, A. M., & Hassan, M. I. (2018). TFE-induced local unfolding and fibrillation of SOD1: Bridging the experiment and simulation studies. The Biochemical Journal, 475(10), 1701–1719. https://doi.org/https://doi.org/10.1042/BCJ20180085
- Kuo, L., & Masters, P. S. (2002). Genetic evidence for a structural interaction between the carboxy termini of the membrane and nucleocapsid proteins of mouse hepatitis virus. Journal of Virology, 76(10), 4987–4999. https://doi.org/https://doi.org/10.1128/jvi.76.10.4987-4999.2002
- Lejal, N., Tarus, B., Bouguyon, E., Chenavas, S., Bertho, N., Delmas, B., Ruigrok, R. W. H., Di Primo, C., & Slama-Schwok, A., AAC (2013). Structure-based discovery of the novel antiviral properties of naproxen against the nucleoprotein of influenza A virus. Antimicrobial Agents and Chemotherapy, 57(5), 2231–2242. https://doi.org/https://doi.org/10.1128/AAC.02335-12
- Lin, S. Y., Liu, C. L., Chang, Y. M., Zhao, J., Perlman, S., & Hou, M. H. (2014). Structural basis for the identification of the N-terminal domain of coronavirus nucleocapsid protein as an antiviral target. Journal of Medicinal Chemistry, 57(6), 2247–2257. https://doi.org/https://doi.org/10.1021/jm500089r
- Lo, Y. S., Lin, S. Y., Wang, S. M., Wang, C. T., Chiu, Y. L., Huang, T. H., & Hou, M. H. (2013). Oligomerization of the carboxyl terminal domain of the human coronavirus 229E nucleocapsid protein. FEBS Letters, 587(2), 120–127. https://doi.org/https://doi.org/10.1016/j.febslet.2012.11.016
- Lu, X., Pan, J., Tao, J., & Guo, D. (2011). SARS-CoV nucleocapsid protein antagonizes IFN-β response by targeting initial step of IFN-β induction pathway, and its C-terminal region is critical for the antagonism. Virus Genes, 42(1), 37–45. https://doi.org/https://doi.org/10.1007/s11262-010-0544-x
- Luo, H., Chen, J., Chen, K., Shen, X., & Jiang, H. (2006). Carboxyl terminus of severe acute respiratory syndrome coronavirus nucleocapsid protein: Self-association analysis and nucleic acid binding characterization. Biochemistry, 45(39), 11827–11835. https://doi.org/https://doi.org/10.1021/bi0609319
- McBride, R., van Zyl, M., & Fielding, B. C. (2014). The coronavirus nucleocapsid is a multifunctional protein. Viruses, 6(8), 2991–3018. https://doi.org/https://doi.org/10.3390/v6082991
- Monod, A., Swale, C., Tarus, B., Tissot, A., Delmas, B., Ruigrok, R. W., Crépin, T., & Slama-Schwok, A. (2015). Learning from structure-based drug design and new antivirals targeting the ribonucleoprotein complex for the treatment of influenza. Expert Opinion on Drug Discovery, 10(4), 345–371. https://doi.org/https://doi.org/10.1517/17460441.2015.1019859
- Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639–1662.
- Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/https://doi.org/10.1002/jcc.21256
- Nakagawa, K., Narayanan, K., Wada, M., & Makino, S. (2018). Inhibition of stress granule formation by middle east respiratory syndrome Coronavirus 4a accessory protein facilitates viral translation, leading to efficient virus replication. Journal of Virology, 92(20), e00902-18. https://doi.org/https://doi.org/10.1128/JVI.00902-18
- Narayanan, K., Kim, K. H., & Makino, S. (2003). Characterization of N protein self-association in coronavirus ribonucleoprotein complexes. Virus Research, 98(2), 131–140. https://doi.org/https://doi.org/10.1016/j.virusres.2003.08.021
- Negi, S. S., Schein, C. H., Oezguen, N., Power, T. D., & Braun, W. (2007). InterProSurf: A web server for predicting interacting sites on protein surfaces. Bioinformatics (Oxford, England)), 23(24), 3397–3399. https://doi.org/https://doi.org/10.1093/bioinformatics/btm474
- Nelson, G. W., Stohlman, S. A., & Tahara, S. M. (2000). High affinity interaction between nucleocapsid protein and leader/intergenic sequence of mouse hepatitis virus RNA. The Journal of General Virology, 81(Pt 1), 181–188. https://doi.org/https://doi.org/10.1099/0022-1317-81-1-181
- Parrinello, M., & Rahman, A. (1980). Crystal structure and pair potentials: A molecular-dynamics study. Physical Review Letters, 45(14), 1196–1199. https://doi.org/https://doi.org/10.1103/PhysRevLett.45.1196
- Prakash, A., Kumar, V., Lynn, A. M., & Haque, R. (2019). Insights into the DNA binding induced thermal stabilization of transcription factor FOXP3. Journal of Biomolecular Structure & Dynamics, 37(9), 2219–2229. https://doi.org/https://doi.org/10.1080/07391102.2018.1486228
- Prasad, K., Khatoon, F., Rashid, S., Ali, N., AlAsmari, A. F., Ahmed, M. Z., Alqahtani, A. S., Alqahtani, M. S., & Kumar, V. (2020). Targeting hub genes and pathways of innate immune response in COVID-19: A network biology perspective. International Journal of Biological Macromolecules, 163 doi:, 1–8. https://doi.org/https://doi.org/10.1016/j.ijbiomac.2020.06.228
- Raaben, M., Groot Koerkamp, M. J., Rottier, P. J., & de Haan, C. A. (2007). Mouse hepatitis coronavirus replication induces host translational shutoff and mRNA decay, with concomitant formation of stress granules and processing bodies. Cellular Microbiology, 9(9), 2218–2229. https://doi.org/https://doi.org/10.1111/j.1462-5822.2007.00951.x
- Reineke, L. C., Tsai, W. C., Jain, A., Kaelber, J. T., Jung, S. Y., & Lloyd, R. E. (2017). Casein Kinase 2 is linked to stress granule dynamics through phosphorylation of the stress granule nucleating protein G3BP1. Molecular and Cellular Biology, 37(4), e00596-16. https://doi.org/https://doi.org/10.1128/MCB.00596-16
- Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42(Web Server issue), W320–324. (Web Server issue), https://doi.org/https://doi.org/10.1093/nar/gku316
- Sarma, P., Sekhar, N., Prajapat, M., Avti, P., Kaur, H., Kumar, S., Prakash, A., Dhibar, D.P., & Medhi, B. (2020). In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain). Journal of Biomolecular Structure and Dynamics. https://doi.org/https://doi.org/10.1080/07391102.2020.1753580
- SchuÈttelkopf, A. W., & Van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica Section D: Biological Crystallography, 60(8), 1355–1363.
- Sterling, T., & Irwin, J. J. (2015). ZINC 15-ligand discovery for everyone. Journal of Chemical Information and Modeling, 55(11), 2324–2337. https://doi.org/https://doi.org/10.1021/acs.jcim.5b00559
- Surjit, M., Kumar, R., Mishra, R. N., Reddy, M. K., Chow, V. T., & Lal, S. K. (2005). The severe acute respiratory syndrome coronavirus nucleocapsid protein is phosphorylated and localizes in the cytoplasm by 14-3-3-mediated translocation. Journal of Virology, 79(17), 11476–11486. https://doi.org/https://doi.org/10.1128/JVI.79.17.11476-11486.2005
- Tarus, B., Bertrand, H., Zedda, G., Di Primo, C., Quideau, S., & Slama-Schwok, A. (2015). Structure-based design of novel naproxen derivatives targeting monomeric nucleoprotein of Influenza A virus. Journal of Biomolecular Structure & Dynamics, 33(9), 1899–1912. https://doi.org/https://doi.org/10.1080/07391102.2014.979230
- Tian, W., Chen, C., Lei, X., Zhao, J., & Liang, J. (2018). CASTp 3.0: Computed atlas of surface topography of proteins. Nucleic Acids Research, 46(W1), W363–W367. https://doi.org/https://doi.org/10.1093/nar/gky473
- Troyer, L., & Brady, W. (2020). Barriers to effective EMS to emergency department information transfer at patient handover: A systematic review. Am J Emerg Med, 38(7), 1494-1503. https://doi.org/https://doi.org/10.1016/j.ajem.2020.04.036
- Tseng, Y. T., Wang, S. M., Huang, K. J., & Wang, C. T. (2014). SARS-CoV envelope protein palmitoylation or nucleocapid association is not required for promoting virus-like particle production. Journal of Biomedical Science, 21, 34 https://doi.org/https://doi.org/10.1186/1423-0127-21-34
- Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/https://doi.org/10.1002/jcc.20291
- Wada, M., Lokugamage, K. G., Nakagawa, K., Narayanan, K., & Makino, S. (2018). Interplay between coronavirus, a cytoplasmic RNA virus, and nonsense-mediated mRNA decay pathway. Proceedings of the National Academy of Sciences of the United States of America, 115(43), E10157–E10166. https://doi.org/https://doi.org/10.1073/pnas.1811675115
- Yang, J., Roy, A., & Zhang, Y. (2013). Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics, 29(20), 2588–2595. https://doi.org/10.1093/bioinformatics/btt447
- Ye, Q., West, A. M. V., Silletti, S., & Corbett, K. D. (2020). Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein. Protein Science, 29(9), 1890–1901. https://doi.org/https://doi.org/10.1002/pro.3909
- Yu, I. M., Oldham, M. L., Zhang, J., & Chen, J. (2006). Crystal structure of the severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein dimerization domain reveals evolutionary linkage between corona- and arteriviridae. Journal of Biological Chemistry, 281(25), 17134–17139. https://doi.org/https://doi.org/10.1074/jbc.M602107200
- Zhou, B., Liu, J., Wang, Q., Liu, X., Li, X., Li, P., Ma, Q., & Cao, C. (2008). The nucleocapsid protein of severe acute respiratory syndrome coronavirus inhibits cell cytokinesis and proliferation by interacting with translation elongation factor 1alpha. Journal of Virology, 82(14), 6962–6971. https://doi.org/https://doi.org/10.1128/JVI.00133-08
- 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., & Tan, W., China Novel Coronavirus Investigating and Research Team. (2020). A Novel Coronavirus from Patients with Pneumonia in China, 2019. The New England Journal of Medicine, 382(8), 727–733. https://doi.org/https://doi.org/10.1056/NEJMoa2001017