Sandbox GGC3

From Proteopedia

Revision as of 16:15, 13 November 2020

Spike glycoprotein

This is the 3D structure representation of the Spike glycoprotein known as S-protein
[1]  [2]. The S-protein of SARS-CoV-2 expressed by the ORF1b gene is trimeric in structure, where each monomer is 180 kDa in size and has two main subunits, an S1 and an S2 subunit. S1 subunit attaches itself to the host cell angiotensin-converting enzyme 2 (ACE2) transmembrane protein. S2 subunit acts in the fusion process of the S-protein which is done by the cleavage protease transmembrane serine or furin [3]

References

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. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
3. ↑ Mohammad, A., Alshawaf, E., Marafie, S. K., Abu-Farha, M., Abubaker, J., & Al-Mulla, F. (2020). Higher binding affinity of Furin to SARS-CoV-2 spike (S) protein D614G could be associated with higher SARS-CoV-2 infectivity. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, S1201-9712(20)32237-2. Advance online publication. https://doi.org/10.1016/j.ijid.2020.10.033

   Disease

   The spike glycoprotein is associated with the noval human COV2 responsible for severe acute respiratory syndrome (SARS).The s-protein froms the sructural protein of the SARS-COV-2 virus which gives it crown-like from <ref> UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics. (2020, October 07). Spike glycoprotein. Retrieved November 13, 2020, from https://www.uniprot.org/uniprot/P59594 == Function == SARS-COV-2 utilizes s-protein to facilitate attachment to host cell surface membranes <ref>doi.org/10.1016/j.ijid.2020.10.033.

   == Relevance == The two subunits of the s-protein ; S1 and S2 interact with other proteins like the 3a and 7a on the SARS-COV-2. The s-protein has other protein modifications such as the amino acid modification in which there is a disulfide bond, Glycosylation with an N-liked to asparagine of the host cell . There is also a post-translation modification where the Spike glycoprotein is digested within host endosomes <ref> https://www.uniprot.org/uniprot/P59594.

   Aside the modifications of the s-protein, this protein is related to other porteins shown in the blast below. 
   

   [[Image:Picture1.jpg]]

   A phylogenetic tree made from the most closet proteins shown below. [[Image:Picture2.jpg]]

   == Structural highlights ==

   This is a sample scene created with SAT to NTD -CT<scene name='75/752266/Ntd_-_ct/1'>S1 subunit is in the downstream of NTD and S2 subunit is in the upsteam of CT</scene><ref>doi.org/10.1016/j.ijid.2020.10.033 .Val367<scene name='75/752266/Val367/1'>Binding region val367</scene><ref>6. China National Center for Bioinformation 2019 Novel Coronavirus Resource. (n.d.). Retrieved November 13, 2020, from https://bigd.big.ac.cn/ncov/protein?lang=en . D614 <scene name='75/752266/Asp_614/1'>The Mutation site D614 </scene><ref>doi.org/10.1016/j.ijid.2020.10.033. LYS 187 <scene name='75/752266/Lys_187/1'>The Receptor Binding Domain (RBD)</scene>.ALA 668 <scene name='75/752266/Ala_668/1'>Furin Cleavage site</scene> <ref>https://doi.org/10.1016/j.virol.2006.02.003.

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