SARS-CoV-2 protein NSP4
From Proteopedia
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| - | < | + | <StructureSection load='' size='340' side='right' caption='Caption for this structure' scene='90/903539/Alphafold2_nsp11/1'> |
| - | {{Theoretical_model}} | + | {{Theoretical_model}} {{Template:ModelConfidence}} |
| + | To the right is an '''[[AlphaFold]]2''' 3D model of SARS CoV-2 Protein NSP4 (length = 500 amino acids, i.e. YP_009725300.1, color coded by the pLDDT scores. It corresponds to the highest ranked model in terms of the pLDDT confidence scores, ''i.e.'', model 1<ref name="MIT_ColabFold">[https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb MIT ColabFold]</ref>. | ||
| + | [[Image:NSP4_AlphaFold2_Movie.gif|250px|left|thumb|'''Morph''' of the top 5 ranked [[AlphaFold]]2 models of '''SARS-CoV-2 Protein NSP4''', ''rainbow'' color coded N-C (blue to red)<ref name="MIT_ColabFold"/>.]] | ||
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== Function == | == Function == | ||
'''Non-structural protein 4 (nsp4)''' | '''Non-structural protein 4 (nsp4)''' | ||
Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.<ref>[https://zhanglab.ccmb.med.umich.edu/COVID-19/ Modeling of the SARS-COV-2 Genome]</ref><ref>pmid 32200634</ref> | Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.<ref>[https://zhanglab.ccmb.med.umich.edu/COVID-19/ Modeling of the SARS-COV-2 Genome]</ref><ref>pmid 32200634</ref> | ||
| + | '''Non-structural protein 11 (NSP11)''' is the short peptide at the C-term of the large SARS-CoV-2 polyprotein ORF1ab (pp1a). it is the cleavage product of pp1a polyprotein by 3CLpro/Mpro protease at the nsp10/11 junction. NSP11 overlaps a portion of the RNA that codes for NSP12, so whether NSP11 is actually expressed as well as its putative function is not known<ref name="NY Times COVID-19">[https://www.nytimes.com/interactive/2020/04/03/science/coronavirus-genome-bad-news-wrapped-in-protein.html ''NY Times'' (3-Apr-2020) Bad News Wrapped in Protein: Inside the Coronavirus Genome]</ref>. | ||
| - | == Disease == | ||
| - | == | + | == Structural Highlights == |
| - | + | Giri's lab<ref>PMID: 34119626</ref> studied NSP11 in solution and by molecular dynamics. Based on CD, they found that NSP11 shows characteristics of an intrinsically disordered protein (IDP). They further studied the its conformational behavior in the presence of negatively charged and neutral liposomes, and found that it remains disordered. However, in SDS micelle, NSP11 adopts an α-helical conformation, suggesting the helical propensity of NSP11, which is very similar to what [AlphaFold[2 predicts. Based on MD simulations NSP11 appears to to have the behavior of an IDP. | |
== See also == | == See also == | ||
[[Coronavirus_Disease 2019 (COVID-19)]] | [[Coronavirus_Disease 2019 (COVID-19)]] | ||
__NOTOC__ | __NOTOC__ | ||
| - | </ | + | </StructureSection> |
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 13:33, 14 February 2022
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References
- ↑ 1.0 1.1 MIT ColabFold
- ↑ 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:http://dx.doi.org/10.1021/acs.jproteome.0c00129
- ↑ NY Times (3-Apr-2020) Bad News Wrapped in Protein: Inside the Coronavirus Genome
- ↑ Gadhave K, Kumar P, Kumar A, Bhardwaj T, Garg N, Giri R. Conformational dynamics of 13 amino acids long NSP11 of SARS-CoV-2 under membrane mimetics and different solvent conditions. Microb Pathog. 2021 Sep;158:105041. doi: 10.1016/j.micpath.2021.105041. Epub 2021, Jun 10. PMID:34119626 doi:http://dx.doi.org/10.1016/j.micpath.2021.105041
