COVID-19 AlphaFold2 Models: Difference between revisions

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JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref>.
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>
</StructureSection>
== References ==
== References ==
<references/>
<references/>

Revision as of 17:29, 4 February 2022

Your Heading Here (maybe something like 'Structure')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.


Caption for this structure

Drag the structure with the mouse to rotate

ReferencesReferences

  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:http://dx.doi.org/10.1002/ijch.201300024
  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:http://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:http://dx.doi.org/10.1021/acs.jproteome.0c00129

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Joel L. Sussman
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