Complete Mechanism of Spike protein for integration of COVID-19

                 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.

References

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 reports, 10(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 one, 15(8),
e0237295.

3.    
Pal, M., Berhanu, G., Desalegn, C., & Kandi, V. (2020). Severe acute
respiratory syndrome coronavirus-2 (SARS-CoV-2): an update. Cureus, 12(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. Pathogens, 9(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 Sciences, 69(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 Modelling, 101,
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. Viruses, 11(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
communications, 12(1), 1-16.

9.    
Pawłowski, P. H. (2021). Charged amino acids may promote coronavirus
SARS-CoV-2 fusion with the host ce. AIMS Biophysics, 8(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. Peptides, 130,
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 virology, 92(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 macromolecules, 146, 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 Microbiology, 11.

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