COVID-19 AlphaFold2 Models: Difference between revisions
No edit summary |
No edit summary |
||
| (12 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
[[Image:SARS-Cov-2-genome.jpg| | [[Image:SARS-Cov-2-genome.jpg|1000px|center|thumb|SARS-CoV-2 Protein Organization, from Gordon | ||
et al. & Krogan (2020)<ref>PMID: 32353859</ref> )]] | et al. & Krogan (2020)<ref>PMID: 32353859 </ref> )]] | ||
[[Image:VirusImage.jpg| | [[Image:VirusImage.jpg|left|330px|thumb|Organization of SARS-CoV-2 virus (from Holmes & Enjuanes (2003)<ref>pmid 12775826</ref>)]] | ||
==Background== | ==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> | 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== | ==AlphaFold2 Predicted Structures== | ||
{{Template:COVID Validation}} | {{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=" | '''[[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>. | ||
'''[[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. | '''[[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>.. | ||
'''[[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]]''' - '''''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_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]]''' - '''''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 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"/>. | ||
| Line 21: | Line 21: | ||
[[Coronavirus_Disease 2019 (COVID-19)]]<br> | [[Coronavirus_Disease 2019 (COVID-19)]]<br> | ||
[[SARS-CoV-2_virus_proteins]]<br> | [[SARS-CoV-2_virus_proteins]]<br> | ||
__NOTOC__ | |||
== References == | == References == | ||
<references/> | <references/> | ||