Abstract
This survey for mathematicians summarizes several works by the author on protein geometry and protein function with applications to viral glycoproteins in general and the spike glycoprotein of the SARS-CoV-2 virus in particular. Background biology and biophysics are sketched. This body of work culminates in a postulate that protein secondary structure regulates mutation, with backbone hydrogen bonds materializing in critical regions to avoid mutation, and disappearing from other regions to enable it.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
E-mail address: rpenner{at}ihes.fr
Date: August 18, 2022. It is a pleasure to thank Minus van Baalen, Misha Gromov, Pablo Guardado-Calvo, Konstantin Khrapko and Nadya Morozova for helpful discussions.
Refined final conjectural last page.
6 It is slightly more subtle. The spike is comprised of two domains, S1 mediating binding and S2 mediating fusion. Our finding about BHBs applies to S1 and not to S2. Two likely explanations are first that S2 is active at much lower pH along the endosomal pathway, as discussed before, and second that S1 sits atop S2 fastening it in place before the two are cleaved by host proteins, also in the endosome.