COVID-19 AlphaFold2 Models: Difference between revisions

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==Your Heading Here (maybe something like 'Structure')==
[[Image:SARS-Cov-2-genome.jpg|1000px|center|thumb|SARS-CoV-2 Protein Organization, from Gordon
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
et al. & Krogan (2020)<ref>PMID: 32353859 </ref> )]]
JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref>.
[[Image:VirusImage.jpg|left|330px|thumb|Organization of SARS-CoV-2 virus (from Holmes & Enjuanes (2003)<ref>pmid 12775826</ref>)]]
==Background==
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 [http://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>
==AlphaFold2 Predicted Structures==
{{Template:COVID Validation}}
'''[[SARS-CoV-2 protein NSP6]]''' - '''''AlphaFold2 Theoretical Model''''' - Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic<ref name="MIT_ColabFold"/><ref name="Zhang Lab">[https://zhanglab.ccmb.med.umich.edu/COVID-19/ Modeling of the SARS-COV-2 Genome]</ref><ref name="Zhang"> pmid 32200634</ref>.


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)
'''[[SARS-CoV-2_protein_NSP11]]''' - '''''AlphaFold2 Theoretical Model''''' - is the 13 amino acid peptide at the C-term of the large SARS-CoV-2 polyprotein ORF1ab (pp1a). Neither its functions, nor if it is expressed ''in vivo'' is clear<ref name="MIT_ColabFold"/><ref name="Zhang Lab">[https://zhanglab.ccmb.med.umich.edu/COVID-19/ Modeling of the SARS-COV-2 Genome]</ref><ref name="Zhang"> pmid 32200634</ref>..
These are:


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>]
'''[[SARS-CoV-2 protein M]]''' - '''''AlphaFold2 Theoretical Model''''' - Component of the viral envelope that plays a central role in virus morphogenesis and assembly via its interactions with other viral proteins<ref name="MIT_ColabFold"/><ref name="Zhang Lab">[https://zhanglab.ccmb.med.umich.edu/COVID-19/ Modeling of the SARS-COV-2 Genome]</ref><ref name="Zhang"> pmid 32200634</ref>.


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>]
'''[[SARS-CoV-2_protein_ORF6]]''' - '''''AlphaFold2 Theoretical Model''''' : Could be a determinant of virus virulence<ref name="MIT_ColabFold"/><ref name="Zhang Lab">[https://zhanglab.ccmb.med.umich.edu/COVID-19/ Modeling of the SARS-COV-2 Genome]</ref><ref name="Zhang"> pmid 32200634</ref>.


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.
'''[[SARS-CoV-2 protein N]]''' - '''''AlphaFold2 Theoretical Model''''' - The primary function of the Nucleocapsid protein (N-protein) is to package the viral genome into a helical ribonucleoprotein (RNP) complex<ref name="MIT_ColabFold"/><ref name="Zhang_Lab"/><ref name="Zhang"/>.


'''[[SARS-CoV-2 protein ORF10]]''' - '''''AlphaFold2 Theoretical Model''''' - It is currently unclear whether this region translates into a functional protein<ref name="MIT_ColabFold"/><ref name="Zhang_Lab"/><ref name="Zhang"/>.


</StructureSection>
== See also ==
[[Coronavirus_Disease 2019 (COVID-19)]]<br>
[[SARS-CoV-2_virus_proteins]]<br>
__NOTOC__
== References ==
== References ==
<references/>
<references/>
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