References
1. 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.
https://doi.org/10.1038/s41586-020-2286-9
2. Clark, L. K., Green, T. J., & Petit, C. M. (2020). Structure of
Nonstructural Protein 1 from SARS-CoV-2. Journal of Virology ,95 (4). https://doi.org/10.1128/jvi.02019-20
3. Egorova, T., & Alkalaeva, E. (2020). Nsp1 of SARS-CoV-2
Stimulates Host Translation Termination .
4. Kamitani, W., Narayanan, K., Huang, C., Lokugamage, K., Ikegami, T.,
Ito, N., Kubo, H., & Makino, S. (2006). Severe acute respiratory
syndrome coronavirus nsp1 protein suppresses host gene expression by
promoting host mRNA degradation. Proceedings of the National
Academy of Sciences of the United States of America , 103 (34),
12885–12890. https://doi.org/10.1073/pnas.0603144103
5. Vankadari, N., Jeyasankar, N. N., & Lopes, W. J. (2020). Structure
of the SARS-CoV-2 Nsp1/5′-Untranslated Region Complex and Implications
for Potential Therapeutic Targets, a Vaccine, and Virulence. The
Journal of Physical Chemistry Letters , 9659–9668.
https://doi.org/10.1021/acs.jpclett.0c02818
6. Tohya, Y., Narayanan, K., Kamitani, W., Huang, C., Lokugamage, K., &
Makino, S. (2009). Suppression of Host Gene Expression by nsp1 Proteins
of Group 2 Bat Coronaviruses. Journal of Virology , 83 (10),
5282–5288. https://doi.org/10.1128/jvi.02485-08
7. Pandala, N., Cole, C. A., McFarland, D., Nag, A., & Valafar, H.
(2020). A Preliminary Investigation in the Molecular Basis of Host
Shutoff Mechanism in SARS-CoV. Proceedings of the 11th ACM
International Conference on Bioinformatics, Computational Biology and
Health Informatics, BCB 2020 , August .
https://doi.org/10.1145/3388440.3412483
8. Semper, C., Watanabe, N., & Savchenko, A. (2021). Structural
characterization of nonstructural protein 1 from SARS-CoV-2.IScience , 24 (1), 101903.
https://doi.org/10.1016/j.isci.2020.101903
9. Schubert, K., Karousis, E. D., Jomaa, A., Scaiola, A., Echeverria,
B., Gurzeler, L. A., Leibundgut, M., Thiel, V., Mühlemann, O., & Ban,
N. (2020). SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit
translation. Nature Structural and Molecular Biology ,27 (10), 959–966. https://doi.org/10.1038/s41594-020-0511-8
10. Kumar, A., Kumar, A., Kumar, P., Garg, N., & Giri, R. (2020).
SARS-CoV-2 NSP1 C-terminal region (residues 130-180) is an intrinsically
disordered region. BioRxiv .
https://doi.org/10.1101/2020.09.10.290932
11. 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., & Beckmann, R. (2020). Structural
basis for translational shutdown and immune evasion by the Nsp1 protein
of SARS-CoV-2. Science , 369 (6508), 1249–1256.
https://doi.org/10.1126/SCIENCE.ABC8665
12. Lokugamage, K. G., 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 (24),
13598–13608. https://doi.org/10.1128/jvi.01958-12
13. 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 (20), 11128–11137. https://doi.org/10.1128/jvi.01700-12
14. Bouayad, A. (2020). Innate immune evasion by SARS-CoV-2: Comparison
with SARS-CoV. Reviews in Medical Virology , 30 (6), 1–9.
https://doi.org/10.1002/rmv.2135
15. Vankadari, N., Jeyasankar, N. N., & Lopes, W. J. (2020). Structure
of the SARS-CoV-2 Nsp1/5′-Untranslated Region Complex and Implications
for Potential Therapeutic Targets, a Vaccine, and Virulence.Journal of Physical Chemistry Letters , 11 (22), 9659–9668.
https://doi.org/10.1021/acs.jpclett.0c02818
16. Almeida, M. S., Johnson, M. A., Herrmann, T., Geralt, M., &
Wüthrich, K. (2007). Novel β-Barrel Fold in the Nuclear Magnetic
Resonance Structure of the Replicase Nonstructural Protein 1 from the
Severe Acute Respiratory Syndrome Coronavirus. Journal of
Virology , 81 (7), 3151–3161.
https://doi.org/10.1128/jvi.01939-06
17. Alsulami, A. F., Thomas, S. E., Jamasb, A. R., Beaudoin, C. A.,
Moghul, I., Bannerman, B., Copoiu, L., Vedithi, S. C., Torres, P., &
Blundell, T. L. (2021). SARS-CoV-2 3D database: understanding the
coronavirus proteome and evaluating possible drug targets.Briefings in Bioinformatics , 00 (September 2020), 1–12.
https://doi.org/10.1093/bib/bbaa404
18. Needleman, S. B., & Wunsch, C. D. (1970). A general method
applicable to the search for similarities in the amino acid sequence of
two proteins. Journal of Molecular Biology , 48 (3),
443–453. https://doi.org/10.1016/0022-2836(70)90057-4
19. Rice, P., Longden, L., & Bleasby, A. (2000). EMBOSS: The European
Molecular Biology Open Software Suite. Trends in Genetics ,16 (6), 276–277. https://doi.org/10.1016/S0168-9525(00)02024-2
20. Yang, J., & Zhang, Y. (2015). I-TASSER server: New development for
protein structure and function predictions. Nucleic Acids
Research , 43 (W1), W174–W181. https://doi.org/10.1093/nar/gkv342
21. Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M.
(1993). PROCHECK: a program to check the stereochemical quality of
protein structures. Journal of Applied Crystallography ,26 (2), 283–291. https://doi.org/10.1107/s0021889892009944
22. Laskowski, R. A., Rullmann, J. A. C., MacArthur, M. W., Kaptein, R.,
& Thornton, J. M. (1996). AQUA and PROCHECK-NMR: Programs for checking
the quality of protein structures solved by NMR. Journal of
Biomolecular NMR , 8 (4), 477–486.
https://doi.org/10.1007/BF00228148
23. Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web
service for the recognition of errors in three-dimensional structures of
proteins. Nucleic Acids Research , 35 (SUPPL.2), 407–410.
https://doi.org/10.1093/nar/gkm290
24. Vriend, G., & Sander, C. (1993). Quality control of protein models:
Directional atomic contact analysis. Journal of Applied
Crystallography , 26 (pt 1), 47–60.
https://doi.org/10.1107/S0021889892008240
25. Anandakrishnan, R., Aguilar, B., & Onufriev, A. V. (2012). H++ 3.0:
Automating pK prediction and the preparation of biomolecular structures
for atomistic molecular modeling and simulations. Nucleic Acids
Research , 40 (W1), 537–541. https://doi.org/10.1093/nar/gks375
26. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S.,
Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera -
A visualization system for exploratory research and analysis.Journal of Computational Chemistry , 25 (13), 1605–1612.
https://doi.org/10.1002/jcc.20084
27. Xue, L. C., Rodrigues, J. P., Kastritis, P. L., Bonvin, A. M., &
Vangone, A. (2016). PRODIGY: A web server for predicting the binding
affinity of protein-protein complexes. Bioinformatics ,32 (23), 3676–3678. https://doi.org/10.1093/bioinformatics/btw514
28. Martin, A. J. M., Vidotto, M., Boscariol, F., Di Domenico, T.,
Walsh, I., & Tosatto, S. C. E. (2011). RING: networking interacting
residues, evolutionary information and energetics in protein structures.Bioinformatics , 27 (14), 2003–2005.
https://doi.org/10.1093/bioinformatics/btr191
29. Piovesan, D., Minervini, G., & Tosatto, S. C. E. (2016). The
RING 2 . 0 web server for high quality residue interaction networks .44 (May), 367–374. https://doi.org/10.1093/nar/gkw315
30. Singer, J., Gifford, R., Cotten, M., & Robertson, D. (2020).
CoV-GLUE: A Web Application for Tracking SARS-CoV-2 Genomic Variation.Preprints , June , 2020060225.
https://doi.org/10.20944/preprints202006.0225.v1
31. Rodrigues, C. H. M., Pires, D. E. V, & Ascher, D. B. (2018).DynaMut : predicting the impact of mutations on protein
conformation , flexibility and stability . 46 (April), 350–355.
https://doi.org/10.1093/nar/gky300
32. Rezaei, S., Sefidbakht, Y., & Uskoković, V. (2020). Comparative
molecular dynamics study of the receptor-binding domains in SARS-CoV-2
and SARS- CoV and the effects of mutations on the binding affinity.Journal of Biomolecular Structure and Dynamics , 0 (0),
1–20. https://doi.org/10.1080/07391102.2020.1860829
33. Zhang, N., Chen, Y., Lu, H., Zhao, F., Alvarez, R. V., Goncearenco,
A., Panchenko, A. R., & Li, M. (2020). MutaBind2: Predicting the
Impacts of Single and Multiple Mutations on Protein-Protein
Interactions. IScience , 23 (3), 100939.
https://doi.org/10.1016/j.isci.2020.100939
34. Lieutaud, P. (2016). How disordered is my protein and what is
its disorder for ? A guide through the “ dark side ” of the protein
universe . 4 (1), 1–33.
https://doi.org/10.1080/21690707.2016.1259708
35. Vinterhalter, G., Kova, J. J., Uversky, V. N., & Pavlovi, G. M.
(2021). International Journal of Biological Macromolecules
Bioinformatics analysis of correlation between protein function and
intrinsic disorder . 167 , 446–456.
https://doi.org/10.1016/j.ijbiomac.2020.11.211
36. Chand, G. B., Banerjee, A., & Azad, G. K. (2020). Identification of
novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their
implications on its protein structure. PeerJ , 2020 (7),
1–11. https://doi.org/10.7717/peerj.9492
37. Goethe, M., Fita, I., & Rubi, J. M. (2015). Vibrational entropy of
a protein: Large differences between distinct conformations.Journal of Chemical Theory and Computation , 11 (1),
351–359. https://doi.org/10.1021/ct500696p
38. Shi, M., Wang, L., Fontana, P., Vora, S., Zhang, Y., Fu, T. M.,
Lieberman, J., & Wu, H. (2020). SARS-CoV-2 Nsp1 suppresses host but not
viral translation through a bipartite mechanism. BioRxiv ,2 , 1–16. https://doi.org/10.1101/2020.09.18.302901
39. Charon, J., Barra, A., Walter, J., Millot, P., Hébrard, E., Moury,
B., & Michon, T. (2018). First Experimental Assessment of Protein
Intrinsic Disorder Involvement in an RNA Virus Natural Adaptive Process.Molecular Biology and Evolution , 35 (1), 38–49.
https://doi.org/10.1093/molbev/msx249
40. Walter, J., Charon, J., Hu, Y., Lachat, J., Leger, T., Lafforgue,
G., Barra, A., & Michon, T. (2019). Comparative analysis of mutational
robustness of the intrinsically disordered viral protein VPg and of its
interactor eIF4E. PLoS ONE , 14 (2), 1–13.
https://doi.org/10.1371/journal.pone.0211725
41. Mozzi, A., Forni, D., Cagliani, R., Clerici, M., Pozzoli, U., &
Sironi, M. (2020). Intrinsically disordered regions are abundant in
simplexvirus proteomes and display signatures of positive selection.Virus Evolution , 6 (1), 1–12.
https://doi.org/10.1093/ve/veaa028
42. Barik, S. (2020). Genus-specific pattern of intrinsically disordered
central regions in the nucleocapsid protein of coronaviruses.Computational and Structural Biotechnology Journal , 18 ,
1884–1890. https://doi.org/10.1016/j.csbj.2020.07.005
43. Sen, S., Dey, A., Bandhyopadhyay, S., & Uversky, V. N. (2012).Understanding Structural Malleability of the SARS-CoV-2 Proteins
and their Relation to the Comorbidities SARS-CoV-2 . 774 , 1–17.
44. Macraild, C. A., Richards, J. S., Anders, R. F., & Norton, R. S.
(2016). Antibody Recognition of Disordered Antigens. Structure ,24 (1), 148–157. https://doi.org/10.1016/j.str.2015.10.028