Abstract
We observe that a residue R of the spike glycoprotein of SARS-CoV-2 that has mutated in one or more of the current variants of concern or interest, or under monitoring, rarely participates in a backbone hydrogen bond if R lies in the S subunit and usually participates in one if R lies in the S subunit. A partial explanation for this based upon free energy is explored as a potentially general principle in the mutagenesis of viral glycoproteins. This observation could help target future vaccine cargos for the evolving coronavirus as well as more generally. A related study of the Delta and Omicron variants suggests that Delta was an energetically necessary intermediary in the evolution from Wuhan-Hu-1 to Omicron.
Highlights
This short note isolates a specific and elementary observation about Protein DataBank (PDB) [1] files concerning the mutated residues in the current variants of concern and of interest, plus the variants under monitoring, as per [2] 22 October 2021, of the SARS-CoV-2 spike glycoprotein S
To our knowledge, appeared in the literature other than in our own earlier work [3] in the context of specific variants of concern, and it may be material going forward in designing mRNA or other types of vaccine cargos, if necessary, as the coronavirus continues to evolve. In this highly studied example, as a potentially more general example of viral glycoprotein mutagenesis since we provide a partial explanation for our observation based upon general principles involving free energy
Some of the previous considerations can be calibrated by employing a new concept and quantity in structural biology, namely the so-called backbone free energy (BFE) from [21], which can be computed from a Protein DataBank (PDB) file to be called a structure
Summary
This short note isolates a specific and elementary observation about Protein DataBank (PDB) [1] files concerning the mutated residues in the current variants of concern and of interest, plus the variants under monitoring, as per [2] 22 October 2021, of the SARS-CoV-2 spike glycoprotein S. This observation is applied to the genesis of the Omicron variant It has not, to our knowledge, appeared in the literature other than in our own earlier work [3] in the context of specific variants of concern, and it may be material going forward in designing mRNA or other types of vaccine cargos, if necessary, as the coronavirus continues to evolve. To our knowledge, appeared in the literature other than in our own earlier work [3] in the context of specific variants of concern, and it may be material going forward in designing mRNA or other types of vaccine cargos, if necessary, as the coronavirus continues to evolve It is worth consideration, in this highly studied example, as a potentially more general example of viral glycoprotein mutagenesis since we provide a partial explanation for our observation based upon general principles involving free energy. There is, a second cleavage lying adjacent to the fusion peptide, mediated by the hostcathepsin or serine protease of a C-terminal segment S20 of S2 at residue number 815–816
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