Reports of Biochemistry and Molecular Biology

en Investigation of the Mutations in the SARS-CoV-2 Envelope Protein and Its Interaction with the PALS1 by Molecular Docking میکروب شناسی Microbiology مقالات اصلی Original Article <div class="WordSection1" style="text-align: justify;">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.</div> <div style="text-align: justify;"><div aria-label="Page Break" class="cke_pagebreak" contenteditable="false" data-cke-display-name="pagebreak" data-cke-pagebreak="1" style="page-break-after:always" title="Page Break"></div></div> COVID-19, Envelope, Immunogenicity, Mutation, SARS‑CoV‑2. 124 136 http://rbmb.net/browse.php?a_code=A-10-1500-1&slc_lang=en&sid=1 Maryam Ajel 100319475328460020335 100319475328460020335 No Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran & Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. Seyed Mohammad Jazayeri 100319475328460020336 100319475328460020336 No Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran. Emad Behboudi 100319475328460020337 100319475328460020337 No Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran. Mansour Poorebrahim 100319475328460020338 100319475328460020338 No Targeted Tumor Vaccines Group, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany. Mahin Ahangar Oskouee 100319475328460020339 100319475328460020339 No Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran & Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. Hossein Bannazadeh Baghi 100319475328460020340 100319475328460020340 No Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran & Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. Alka Hasani 100319475328460020341 100319475328460020341 No Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. Mojtaba Varshochi 100319475328460020342 100319475328460020342 No Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. Ali Akbar Shekarchi 100319475328460020343 100319475328460020343 No Department of Pathology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. Mohammad Sabbaghian 100319475328460020344 100319475328460020344 No Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. Vahdat Poortahmasebi poortahmasebiv@tbzmed.ac.ir. 100319475328460020345 100319475328460020345 Yes Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran & Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.