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Sandbox GGC3

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Spike glycoprotein

 3D structure representation of the Spike glycoprotein related to the SARS-CoV-2 ^[1]  ^[2].

1 Introduction
2 The Spike Protein
3 Domains
4 Activation of S-protein
5 The Mechanism of the Spike Protein
6 Mutation
7 Structural highlights

Introduction

The Spike protein is related to the novel coronavirus pandemic discovered in 2019. The virus is named as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and it belongs to the β coronavirus family. The SARS-CoV-2 is a single stranded RNA with 29,881bp length, which encodes for 9860 amino acids. It is compose of two proteins: the structural and non-structural proteins. The structural proteins are S,E,M and N ; whiles as the non-structural proteins are encoded on the ORF regions^[3].

The Spike Protein

The S-protein is a structural protein extends from the viral membrane and it is uniformly arranged as a trimer on the surface to give the crown-like appearance of the SARS-Co V-2. The Spike protein is 14-1255bp long, which mediates a receptor binding and fusion of the virus and a cellular membrane ^[4]. Is also gives the virus its name in Latin as "Corona".

Domains

The S-protein of the SARS-CoV-2 has two main subunits , an S1 and S2 subunits. The S1 subunit is located on residue #14–685 ( contains the NTD) and interact with human AEC2 by attaching its virion to the cell membrane by interacting with host receptor. The S2 subunit is located on residue #686–1273 ( contains the CT) which serves as the fusion protein of the virus ^[5].

Activation of S-protein

Before the Spike protein can be activated , it has to be cleaved by the protease Furin protein. This 2D image below shows the schematic cleavage of the S-protein before and after it enters the host cell

^[6]

The Mechanism of the Spike Protein

^[7]

Mutation

The most studied mutation site of the S-protein is at residue 614 which encodes for the amino acid Aspartic acid (D) and is normally changed to Glycine (G). And this form of mutation causes the enhancement of the viral transmission ^[8].

Structural highlights

These are the structural 3D representations of the s-protein showing the two subunits , the binding regions to its receptor human ACE2 , Mutation site , RBD site and cleavage site respectively NTD -CT .Val367 . D614 . LYS 187 .ALA 668

References

↑ 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
↑ 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
↑ Huang, Y., Yang, C., Xu, X., Xu, W., & Liu, S. (2020). Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacologica Sinica, 41(9), 1141-1149. doi:10.1038/s41401-020-0485-4
↑ 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
↑ 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
↑ Shang, J., Wan, Y., Luo, C., Ye, G., Geng, Q., Auerbach, A., & Li, F. (2020, May 26). Cell entry mechanisms of SARS-CoV-2. Retrieved November 14, 2020, from https://www.pnas.org/content/117/21/11727
↑ Huang, Y., Yang, C., Xu, X., Xu, W., & Liu, S. (2020). Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacologica Sinica, 41(9), 1141-1149. doi:10.1038/s41401-020-0485-4
↑ 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

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Sandbox GGC3

From Proteopedia

Spike glycoprotein

Contents

Introduction

The Spike Protein

Domains

Activation of S-protein

The Mechanism of the Spike Protein

Mutation

Structural highlights

References

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