Date of this Version
Shabaltiy, Boris. 2023. Predicted Structure and Analysis of the Glycoprotein from SARS-CoV-2 Variants of Interest. Honors Theses, University of Nebraska-Lincoln.
SARS-CoV-2 has had a devastating effect on the world, and while the public concern and severity of the diseased caused by it have decreased, it is still crucial to monitor the virus for mutations so we can rapidly identify new variants of concern, and then rapidly prepare new vaccines and treatments. The SARS-CoV-2 spike (S) protein from the first isolates of the virus (root variant) was structurally characterized in early 2021. The spike protein structure, designated 7CZW, was uploaded to RCSB Protein Data Bank (RCSB PDB). All subsequent mutations the S protein has accumulated are based on the amino acid sequence of the original root variant, and so the variants of interest (VOI) identified by the CDC as of Fall 2023 are compared to it. Currently SARS-CoV-2 lineages are differentiated using the Pangolin Pango Lineage. The variants examined in this work are EG.5, FL.1.5.1, and XBB.1.16.6, which at the time of writing were responsible for the largest number of infection cases. The amino acid changes against the root variant were retrieved from nextstrain.org, and structural models of the S glycoprotein monomer were simulated using the ColabFold AlphaFold2 model. Then the key amino acids of the receptor-binding domain (RBD) were compared using UCSF Chimera 1.16, and their characteristics were examined. Understanding the structural relationships of the current VOI is important to predict the virulent and pathologic qualities of these lineages.