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Updated: Nov 1, 2025
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Published on: April 21, 2022
Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study
Hadi Sedigh Ebrahim-Saraie1, Behzad Dehghani2, Ali Mojtahedi3
1Razi Clinical Research Development Unit, Razi Hospital, Guilan University of Medical Sciences, Rasht, Iran.
Background:
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the global outbreak of coronavirus disease 2019 (Covid-19), which has been considered as a pandemic by WHO. SARS-CoV-2 encodes four major structural proteins, among which spike protein has always been a main target for new vaccine studies. This in silico study aimed to investigate some physicochemical, functional, immunological, and structural features of spike protein using several bioinformatics tools.
Method:
We retrieved all SARS-CoV-2 spike protein sequences from different countries registered in NCBI GenBank. CLC Sequence Viewer was employed to translate and align the sequences, and several programs were utilized to predict B-cell epitopes. Modification sites such as phosphorylation, glycosylation, and disulfide bonds were defined. Secondary and tertiary structures of all sequences were further computed.
Results:
Some mutations were determined, where only one (D614G) had a high prevalence. The mutations did not impact the B-cell and physicochemical properties of the spike protein. Seven disulfide bonds were specified and also predicted in several N-link glycosylation and phosphorylation sites. The results also indicated that spike protein is a non-allergen.
Conclusion:
In summary, our findings provided a deep understanding of spike protein, which can be valuable for future studies on SARS-CoV-2 infections and design of new vaccines.
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