tetano
Editor, Senior Moderator
Rep Biochem Mol Biol
. 2024 Apr;13(1):124-136.
doi: 10.61186/rbmb.13.1.124. Investigation of the Mutations in the SARS-CoV-2 Envelope Protein and Its Interaction with the PALS1 by Molecular Docking
Maryam Ajel[SUP] 1 2 [/SUP], Seyed Mohammad Jazayeri[SUP] 3 [/SUP], Emad Behboudi[SUP] 4 [/SUP], Mansour Poorebrahim[SUP] 5 [/SUP], Mahin Ahangar Oskouee[SUP] 1 2 [/SUP], Hossein Bannazadeh Baghi[SUP] 1 2 [/SUP], Alka Hasani[SUP] 2 [/SUP], Mojtaba Varshochi[SUP] 1 [/SUP], Ali Akbar Shekarchi[SUP] 6 [/SUP], Mohammad Sabbaghian[SUP] 2 [/SUP], Vahdat Poortahmasebi[SUP] 1 2 [/SUP]
Affiliations
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).
Conclusions: 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.
Keywords: COVID-19; Envelope; Immunogenicity; Mutation; SARS CoV 2.
. 2024 Apr;13(1):124-136.
doi: 10.61186/rbmb.13.1.124. Investigation of the Mutations in the SARS-CoV-2 Envelope Protein and Its Interaction with the PALS1 by Molecular Docking
Maryam Ajel[SUP] 1 2 [/SUP], Seyed Mohammad Jazayeri[SUP] 3 [/SUP], Emad Behboudi[SUP] 4 [/SUP], Mansour Poorebrahim[SUP] 5 [/SUP], Mahin Ahangar Oskouee[SUP] 1 2 [/SUP], Hossein Bannazadeh Baghi[SUP] 1 2 [/SUP], Alka Hasani[SUP] 2 [/SUP], Mojtaba Varshochi[SUP] 1 [/SUP], Ali Akbar Shekarchi[SUP] 6 [/SUP], Mohammad Sabbaghian[SUP] 2 [/SUP], Vahdat Poortahmasebi[SUP] 1 2 [/SUP]
Affiliations
- PMID: 39582830
- PMCID: PMC11580137
- DOI: 10.61186/rbmb.13.1.124
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).
Conclusions: 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.
Keywords: COVID-19; Envelope; Immunogenicity; Mutation; SARS CoV 2.