Investigation of the Mutations in the SARS-CoV-۲ Envelope Protein and Its Interaction with the PALS۱ by Molecular Docking

Background: The envelope (E) protein of globally circulating severe acute respiratory syndrome coronavirus ۲ (SARS‑CoV‑۲) is highly conserved. This study aimed to find the mutation rate of the E genes in COVID-۱۹ patients, and also to evaluate the conformational characteristics of viral E protein. Methods: In this study, ۱۲۰ patients with SARS-CoV-۲ positive test results were selected according to real-time PCR assay. Specific primers for conventional PCR have been used to amplify E gene; furthermore, to identify the E gene mutations, direct sequencing of the E genes was also done. Bioinformatics techniques were used to investigate the possible effects of antigenic changes and ۳D characteristics of amino acid substitutions. Also, the immunogenicity of wild-type and mutant E was analyzed utilizing a ClusPro docking server and the IEDB online platform. Results: A total of ۱۲۰ COVID-۱۹ patients were included (۵۷.۵% were male and ۴۲.۵% female), with an overall mean age of ۵۵.۷۰±۱۰.۶۱ years old. Of ۱۰ nucleotide changes, ۸ (۸۰%) were silent. Also, ۲ (۲۰%) missense mutations (amino acid altering) were found in the E gene (L۷۳F and S۶۸F). Conclusion: These mutations insert some new helix structures in the E mutants. Also, the results of molecular docking studies indicated that both S۶۸F and L۷۳F mutations could notably enhance the stability and binding affinity of protein E's C-terminal motif to the Protein Associated with LIN۷ ۱, MAGUK P۵۵ Family Member (PALS۱) which may probably increase local viral spread, and infiltration of immune cells into lung alveolar spaces.

کلیدواژه ها:

COVID-۱۹ ، Envelope ، Immunogenicity ، Mutation ، SARS‑CoV‑۲.