COVID-19 AlphaFold2 Models: Difference between revisions

Revision as of 14:29, 4 February 2022

Your Heading Here (maybe something like 'Structure')

JSmol in Proteopedia ^[1].

For a number of proteins in the SARS-CoV-19 Virus, there are not experimentally etermiend 3D structures. AlphaFold2 was used to create 3D models using the MIT ColabFold^[2]. server of these proteins. For each of them 5 3D models were predicted ranked 1 to 5 (with 1 being the best)

These are:

SARS-CoV-2 protein ORF10 - It is currently unclear whether this region translates into a functional protein.^[3]^[4]]

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.^[5]^[6]]

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.

↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:https://dx.doi.org/10.1002/ijch.201300024
↑ MIT ColabFold https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb
↑ Modeling of the SARS-COV-2 Genome
↑ 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:https://dx.doi.org/10.1021/acs.jproteome.0c00129
↑ Modeling of the SARS-COV-2 Genome
↑ 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:https://dx.doi.org/10.1021/acs.jproteome.0c00129

References

Proteopedia Page Contributors and Editors (what is this?)

Joel L. Sussman

[1] Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:https://dx.doi.org/10.1002/ijch.201300024

[MIT_ColabFold-2] MIT ColabFold https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb

[3] Modeling of the SARS-COV-2 Genome

[4] 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:https://dx.doi.org/10.1021/acs.jproteome.0c00129

[5] Modeling of the SARS-COV-2 Genome

[6] 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:https://dx.doi.org/10.1021/acs.jproteome.0c00129

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@@ Line 3: / Line 3: @@
 JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref>.
-== Function ==
+For a number of proteins in the SARS-CoV-19 Virus, there are not experimentally etermiend 3D structures. AlphaFold2 was used to create 3D models using the MIT ColabFold<ref name="MIT_ColabFold"> MIT ColabFold https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb </ref>. server  of these proteins. For each of them 5 3D models were predicted ranked 1 to 5 (with 1 being the best)
+These are:
-== Disease ==
+SARS-CoV-2 protein ORF10 - It is currently unclear whether this region translates into a functional protein.<ref>[https://zhanglab.ccmb.med.umich.edu/COVID-19/ Modeling of the SARS-COV-2 Genome]</ref><ref>pmid 32200634</ref>]
-== Relevance ==
+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.<ref>[https://zhanglab.ccmb.med.umich.edu/COVID-19/ Modeling of the SARS-COV-2 Genome]</ref><ref>pmid 32200634</ref>]
-== Structural highlights ==
+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.
-This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
 </StructureSection>
 == References ==
 <references/>

COVID-19 AlphaFold2 Models: Difference between revisions

Revision as of 14:29, 4 February 2022

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