COVID-19 AlphaFold2 Models

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At present, there are still a number of proteins from the SARS CoV-2 virus whose 3D structures have not yet been experimentally determined. [[AlphaFold]]2 was used to predict these structures using the MIT ColabFold server<ref name="MIT_ColabFold">[https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb MIT ColabFold]</ref>, which was developed by [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb Sergey Ovchinnikov, Milot Mirdita and Martin Steinegger].. For each prediction, five 3D models were predicted, ranked from 1 to 5 (with 1 being the best). Views of these AlphaFold2 predictions can be seen on the Proteopedia pages:<br>
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At present, there are still a number of proteins from the SARS CoV-2 virus whose 3D structures have not yet been experimentally determined. [[AlphaFold]]2 was used to predict these structures using the MIT ColabFold server<ref name="MIT_ColabFold">[https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb MIT ColabFold]</ref>, which was developed by [https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb Sergey Ovchinnikov, Milot Mirdita and Martin Steinegger]. For each prediction, five 3D models were predicted, ranked from 1 to 5 (with 1 being the best). Views of these AlphaFold2 predictions can be seen on the Proteopedia pages:<br>

Revision as of 08:40, 8 February 2022

SARS-CoV-2 Protein Organization, from Gordon et al. & Krogan (2020) )
SARS-CoV-2 Protein Organization, from Gordon et al. & Krogan (2020)[1] )
Organization of SARS-CoV-2 virus (from Holmes & Enjuanes (2003))
Organization of SARS-CoV-2 virus (from Holmes & Enjuanes (2003)[2])


The quality of SARS-CoV-2 experimentally determined structures varies widely (Grabowski et al., 2021). Validated and corrected structures can be obtained from COVID19.BioReproducibility.Org.


At present, there are still a number of proteins from the SARS CoV-2 virus whose 3D structures have not yet been experimentally determined. AlphaFold2 was used to predict these structures using the MIT ColabFold server[3], which was developed by Sergey Ovchinnikov, Milot Mirdita and Martin Steinegger. For each prediction, five 3D models were predicted, ranked from 1 to 5 (with 1 being the best). Views of these AlphaFold2 predictions can be seen on the Proteopedia pages:


SARS-CoV-2 protein M - Component of the viral envelope that plays a central role in virus morphogenesis and assembly via its interactions with other viral proteins[3][4][5].

SARS-CoV-2 protein N - The primary function of the Nucleocapsid protein (N-protein) is to package the viral genome into a helical ribonucleoprotein (RNP) complex[3][4][5].

SARS-CoV-2 protein NSP6 - Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic[3][4][5].

SARS-CoV-2 protein ORF10 - It is currently unclear whether this region translates into a functional protein[3][4][5]. </StructureSection>

References

  1. ↑ Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Huttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, Garcia-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020 Mar 22. doi: 10.1101/2020.03.22.002386. PMID:32511329 doi:http://dx.doi.org/10.1101/2020.03.22.002386
  2. ↑ Holmes KV, Enjuanes L. Virology. The SARS coronavirus: a postgenomic era. Science. 2003 May 30;300(5624):1377-8. doi: 10.1126/science.1086418. PMID:12775826 doi:http://dx.doi.org/10.1126/science.1086418
  3. ↑ 3.0 3.1 3.2 3.3 3.4 MIT ColabFold
  4. ↑ 4.0 4.1 4.2 4.3 Modeling of the SARS-COV-2 Genome
  5. ↑ 5.0 5.1 5.2 5.3 Zhang C, Zheng W, Huang X, Bell EW, Zhou X, Zhang Y. Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. J Proteome Res. 2020 Apr 3;19(4):1351-1360. doi: 10.1021/acs.jproteome.0c00129., Epub 2020 Mar 24. PMID:32200634 doi:http://dx.doi.org/10.1021/acs.jproteome.0c00129

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