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Friday 18 June 2021

Complete Mechanism of Spike protein for integration of COVID-19


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Complete Mechanism of Spike protein for integration of COVID-19

                               Spike protein is a wide-ranging group I transmembrane protein that ranges in length between 1,160 amino acid residues for an avian respiratory syncytial viral infection to 1,400 amino acid residues for feline coronavirus1.  This molecule is also heavily glycosylated, between around 21 and 35 N-glycosylation domains2. Spike proteins contain consequences on the virion surface, giving it its unique "corona," or crown-like structure3. The congregations, including all CoV spike proteins, are organized into two domains: an S1 domain at the N-terminus, which is essential for specific receptors, and an S2 domain at the C-terminus necessary for fusion4. The spike proteins of various respiratory viruses are distinguished by whether or not they are cleaved during virions' formation and exocytosis. With a few exclusions, most alpha coronaviruses and the beta coronavirus SARS-CoV have an uncleaved spike protein. Still, certain β - and all gamma coronaviruses have the protein fragmented between the S1 and S2 domain names, most likely by furin, a Golgi-resident host protease5.

                 Furthermore, various strains of the betacoronavirus mouse hepatitis virus (MHV) have varied cleavage requirements, such as MHV-2 and MHV-A59. The S2 component is the most consistent part of the proteins, but the S1 component can differ by sequencing even amongst covid species6. The N-terminal domain (NTD) and the C-terminal domain (CTD) are two subdomains of the S1 (CTD)5. These are receptor-binding domains (RBDs) that can bind a wide range of proteins and carbohydrates5.

The spike protein of the coronavirus is a group I fusing protein. The creation of alpha-helical coiled-coil structure is a distinctive property of this group of fusion proteins that have anticipated -helical secondary structures and the ability to form coiled coils in their C-terminal portion areas7. The influenza hemagglutinin protein HA is the most well-studied member of the class I fusion protein family. As an HA0 forerunner, HA is produced and then assembled into trimers. By cleaving HA0 into the HA1 and HA2, the protein becomes fusion-ready. The fusing peptide is found at the N-terminus of HA2 and is a highly conserved hydrophobic motif. Three long helices produce the center coiled-coil of the trimer, with three shorter helices arranged around them in the pre-fusion configuration8. The fusion peptide is protected in this conformation because it is immersed inside the trimer junction. Endosomal acidification causes the unstructured linker to become helical, allowing for the creation of a long helix in the N-terminal region during fusion. In this form, characterized as a hairpin, the fusion peptide is directed towards the target membrane, where it is integrated, connecting the infected and target cell membranes. The inversion of the C-helix, which compresses into the slots of the N-terminal trimeric coiled coils to create a six-helix bundle, is the second conformational change (6HB)5. The transmembrane region and the fusion peptide embedded through into target membrane are placed closer together in the resultant configuration, allowing the virulent and cell membranes to merge4.

Covid spike proteins have two heptad repetitions in their S2 region, which is a common characteristic of group I infectious fusion proteins9. Heptad repeats are a repeated heptapeptide with hydrophobic residues a and d that engage in the fusion process and thus indicate the production of coiled-coil. The post-fusion structures of the HR for SARS-CoV and MHV were resolved and comprised the typical six-helix pack. By altering critical positions and conducting blocking tests with HR2 peptides, the functional role of MHV and SARS-CoV HR was validated10.

               Chimeric viruses have proven the importance of the spike protein in cell tropism11. Mouse hepatitis virus (MHV) comes in various types that mostly infected the cerebellum and liver. Even though multiple varieties of MHV induce diverse disease patterns, the role of its spike protein in tissue tropism has been widely explored. JHM is a very virulent strain that produces life-threatening encephalitis but is not hepatotropic11. The MHV-A59 strain causes hepatitis and mild meningitis. MHV-2 is a hepatotropic virus. The S protein has been related to the tropism and pathogenesis of MHV by utilizing chimeric viruses across these various strains. JHM or MHV-2 S genes introduced into the MHV-A59 background boost neurovirulence and hepatotropism of the recombinant virus, respectively. However, in the JHM context, replacing the JHM S protein sequence with the MHV-A59 S gene does not produce hepatotropism, indicating that additional factors control viral tropism. From continuously infected microglial cells, a mutant MHV-A59 strain with altered tropism was identified. The single mutation Q159L in the S1 region is accountable for the virus's poor hepatotropism and decreased replication in the liver12. Other coronaviruses have also demonstrated the importance of the spike protein in tropism. IBV is an ordinary domestic poultry infection that multiplies epithelial cells from the renal, oviduct, stomach, and respiratory systems. Medical strains of IBV only infect and develop on chicken embryo kidney cells and embryonated eggs in vitro. The IBV Beaudette strain is an abbreviated strain developed by serially passing IBV through eggs. IBV Beaudette infects CEF, BHK-21, and Vero cells in addition to chicken embryo kidney cells. The virus's tropism is restricted to primary chicken cells when the S gene in the Beaudette background is replaced with that of the IBV M41 strain13. This hybrid virus, on the other hand, has the attenuated phenotype of Beaudette in vivo. These findings suggest that the S protein is primarily responsible for Beaudette's shift in tropism in cell culture, albeit damping mutations in other genes also cause avirulence.


1.     Basu, A., Sarkar, A., & Maulik, U. (2020). Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2. Scientific reports10(1), 1-15.

2.     Bernardi, A., Huang, Y., Harris, B., Xiong, Y., Nandi, S., McDonald, K. A., & Faller, R. (2020). Development and simulation of fully glycosylated molecular models of ACE2-Fc fusion proteins and their interaction with the SARS-CoV-2 spike protein binding domain. PloS one15(8), e0237295.

3.     Pal, M., Berhanu, G., Desalegn, C., & Kandi, V. (2020). Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): an update. Cureus12(3).

4.     Sanchez, C. M., Pascual-Iglesias, A., Sola, I., Zuñiga, S., & Enjuanes, L. (2020). Minimum determinants of transmissible gastroenteritis virus enteric tropism are located in the N-terminus of spike protein. Pathogens9(1), 2.

5.     Kuznetsov, A., & Järv, J. (2020). Mapping of ACE2 binding site on SARSCoV2 spike protein S1: docking study with peptides. Proceedings of the Estonian Academy of Sciences69(3), 228-234.

6.     Prajapat, M., Shekhar, N., Sarma, P., Avti, P., Singh, S., Kaur, H., ... & Medhi, B. (2020). Virtual screening and molecular dynamics study of approved drugs as inhibitors of spike protein S1 domain and ACE2 interaction in SARS-CoV-2. Journal of Molecular Graphics and Modelling101, 107716.

7.     Cheng, J., Zhao, Y., Xu, G., Zhang, K., Jia, W., Sun, Y., ... & Zhang, G. (2019). The S2 subunit of QX-type infectious bronchitis coronavirus spike protein is an essential determinant of neurotropism. Viruses11(10), 972.

8.     Tan, T. K., Rijal, P., Rahikainen, R., Keeble, A. H., Schimanski, L., Hussain, S., ... & Townsend, A. R. (2021). A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses. Nature communications12(1), 1-16.

9.     Pawłowski, P. H. (2021). Charged amino acids may promote coronavirus SARS-CoV-2 fusion with the host ce. AIMS Biophysics8(1), 111-120.

10.  Ling, R., Dai, Y., Huang, B., Huang, W., Yu, J., Lu, X., & Jiang, Y. (2020). In silico design of antiviral peptides targeting the spike protein of SARS-CoV-2. Peptides130, 170328.

11.  Bickerton, E., Maier, H. J., Stevenson-Leggett, P., Armesto, M., & Britton, P. (2018). The S2 subunit of infectious bronchitis virus Beaudette is a determinant of cellular tropism. Journal of virology92(19), e01044-18.

12.  Xue, F., Yu, X., Shang, Y., Peng, C., Zhang, L., Xu, Q., & Li, A. (2020). Heterologous overexpression of a novel halohydrin dehalogenase from Pseudomonas pohangensis and modification of its enantioselectivity by semi-rational protein engineering. International journal of biological macromolecules146, 80-88.

Jiang, Y., Gao, M., Cheng, X., Yu, Y., Shen, X., Li, J., & Zhou, S. (2020). The V617I substitution in avian coronavirus IBV spike protein plays a crucial role in adaptation to primary chicken kidney cells. Frontiers in Microbiology11.

Credits: Dr. Mohd Ashraf Rather, Asst. Prof. Fish Genetics and Biotechnology, SKUAST-K 

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