We drew a couple of figures to illustrate our thoughts about mutation Y453F. We used our models of the "canonical" SARS-CoV-2 RBD bound to human and ferret ACE2 as a base, and use ferret ACE2 because it is virtually identical to European mink in this region of the protein.
In all figures, we show only 3 amino acids important to understand this mutation: ACE2 position 34 (white) and RBD positions 453 (orange) and 455 (pink). Some special atoms of each amino acid are colored red (oxygen) or blue (nitrogen) when necessary.
Human ACE2 bound to SARS-CoV-2. Y453 makes a hydrogen bond with H34 (red/blue spheres) and hydrophobic contacts with L455. All three amino acids stabilize each other through these bonds/contacts and contribute to a stronger interaction between the two proteins.
Ferret ACE2 bound to SARS-CoV-2. Y453 and Y34 are bulky and push each other away. Y453's oxygen (red sphere) doesn't have a partner to bond to (no nitrogen/blue sphere nearby), which is a destabilizing factor for the interaction. Y34 makes other bonds of its own (not drawn here).
Ferret ACE2 bound to SARS-CoV-2 Y453F. The difference between Y and F is the lack of that oxygen atom. So, without it, F453 happily makes stabilizing hydrophobic contacts with both ACE2 Y34 and RBD L455, contributing to a stronger interaction between the two proteins.
Finally, human ACE2 bound to SARS-CoV-2 Y453F. H34 is smaller and makes stabilizing contacts with both F453 and L455. As a result, the Y453F mutation *coincidentally* seems to work out for binding both our ACE2 and the ferret's (and likely mink's too).
Figures are licensed under CC-BY 4.0, so feel free to use them if you want (with proper attribution). Happy to provide higher resolution versions too. All done in #Pymol. Obligatory reminder that these are models, not actual atomic structures.
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1/ One of the mutations reported in the new variant of SARS-CoV-2 found in minks in Denmark - Y453F - sits right in the middle of the interface with the ACE2 receptor, interacting with H34, a residue we and others marked as an important "hotspot" for the interaction.
2/ Unfortunately, we only have a partial sequence of ACE2 for the American mink (Neovison vison), which is the species that is bred for its fur, according to Wikipedia. But if we look at its European cousin (Mustela lutreola), we find interesting mutations in their ACE2 variant:
3/ There is D30E, which we & others predict enhances affinity since it stabilizes a salt-bridge w SARS-CoV-2 Spike K417. Then, we have H34Y, which is particularly interesting in the context of this new viral variant. Here's the relevant part of the aln with our ACE2: