The physicochemical and phylogenetic properties of twelve spike glycoprotein models for SARS-CoV-2 from China, Iran, and Tunisia

Abstract

Background The coronavirus spike glycoprotein is a trimeric structural surface protein that facilitates the viral adhesion through attaching receptors on the human cell surface. This study aims to analyse and compare the genomic and phylogenetic properties of these spike glycoproteins from China, Iran, and Tunisia. Methods This is a descriptive cross-sectional comparative study for the different properties of S glycoprotein from 12 SARS-CoV-2 specimens from GenBank. Clustal Omega was used to study model sequences alignment, residual conservation, phylogeny, and identity matrix. SWISS-MODEL developed and validated the 3D models for three protein sequences with the highest model quality. The different physicochemical characteristics of different models were assessed by ExPASy proteomics. Results The Chinese and the Iranian sequences share 100% identity, although they have a different amino acids number, and 25-29.27% identity to the Tunisian sequences. The 12 models are monophyletic, with varying stages of evolutionary divergence. There are six fully, three highly, and five lowly conserved residues across the sequences. The resulting three highly reliable 3D models were of different global qualities, being the lowest for the Tunisian, and the highest for the Iranian models. All the models are highly hydrophilic. The Tunisian models were unstable in comparison to the relatively stable other models with different physicochemical characteristics. Conclusion The models had different N-terminal residues and side groups polarity and charge. The S glycoproteins are not identical nor unique in model structure nor the physicochemical profiles in different parts of the world. The Tunisian models are drastically biodiverse from the Chinese and Iranian models.

Pathogenesis of COVID‐19 described through the lens of an undersulfated and degraded epithelial and endothelial glycocalyx

“…33 We hypothesize that the degree of HS sulfation, thus, the net negative charge of the GL, is the initial deterrent to SARS-CoV-2 viral attachment. Various researchers found the SARS-CoV-2 SP and net GRAVY score to be highly negative, [121][122][123][124] categorizing the SP as a stable, hydrophilic molecule capable of establishing hydrogen bonds. 121 Most viral particles have a net negative charge at neutral pH because they have an isoelectric point below 7.…”

N-Acetylcysteine and Other Sulfur-Donors as a Preventative and Adjunct Therapy for COVID-19

“…Most viral particles have a net negative charge at neutral pH, and SARS-CoV-2 is no exception. Various research reports confirmed the SARS-CoV-2 spike protein (SP) and net GRAVY score to be highly negative [74][75][76][77]. Nonetheless, if the GL is undersulfated and 3-O-sulfotransferase 3B (3OST-3B) is overexpressed, as is the case during chronic inflammatory conditions, the GL may facilitate SARS-CoV-2 entry [3].…”