investigation of the mutations in the sars-cov-2 envelope protein and its interaction with the pals1 by molecular docking

Background: the envelope (e) protein of globally circulating severe acute respiratory syndrome coronavirus 2 (sars‑cov‑2) is highly conserved. this study aimed to find the mutation rate of the e genes in covid-19 patients, and also to evaluate the conformational characteristics of viral e protein.methods: in this study, 120 patients with sars-cov-2 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 3d 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 120 covid-19 patients were included (57.5% were male and 42.5% female), with an overall mean age of 55.70±10.61 years old. of 10 nucleotide changes, 8 (80%) were silent. also, 2 (20%) missense mutations (amino acid altering) were found in the e gene (l73f and s68f).conclusion: these mutations insert some new helix structures in the e mutants. also, the results of molecular docking studies indicated that both s68f and l73f mutations could notably enhance the stability and binding affinity of protein e’s c-terminal motif to the protein associated with lin7 1, maguk p55 family member (pals1) which may probably increase local viral spread, and infiltration of immune cells into lung alveolar spaces.