Spike binding region and receptor
In this model you see only the receptor binding domain (RBD) of the spike protein of sars-cov2. The atoms of the amino acids are depicted as yellow spheres. Of the receptor, angiotensin converting enzyme2 (ACE2), only the relevant part for binding is shown in pale blue (click for a . It is a good idea to to click everthing in consecutive order and only once, because of my programming laziness and ignorance, otherwise very funny views may result).
The topic here is the binding of the spike protein to the receptor. Structural investigators trapped 17 amino acids of the spike protein to be involved in binding to the receptor . In the receptor ACE2 even 20 amino acids are involved . In these amino acids (colored green) the main bonding power is from electrically charged atoms: red = oxygen (negative charge), blue = nitrogen (positive charge). Now you may wonder why you don't see anything? A covalent chemical bond within a molecule has a length of about 1.5 Å (that equals to 150 pm, 1 pm = 10-12 m = 1 billionth mm). Bonds between spike and ACE2 are hydrogen bridges with dimensions between 2.6 and 3.7 Å. They are not covalent bonds, but they are short enough to obstruct the view between the proteins. To have a proper view to the bonds in the interface we separate the proteins and have a view on the bonding surfaces . What looks like rubber strings between the proteins symbolizes the hydrogen bonds keeping sars-cov2 tied to ACE2. The investigation method used here is unable to locate the hydrogen atoms involved because of their too minute size.
In 2003 there was a previous sars-coronavirus which didn't spread as fast and furious as cov2. What makes cov2 more rigorous? In a "reagent tube" you may measure the strength of binding of the spike protein to its receptor. The affinity of cov2 to ACE2 is about 15 times stronger than cov1. A reason for this is a different arrangement of hydrogen bridges in the contact area . What about the more catching variants of cov2 termed now α, β, γ, δ? In these mutants the electrical properties of the binding motiv are changed by replacements of amino acids . The mutations E484K (meaning glutamic acid at position 484 in the protein chain is replaced by lysine) , N501Y (asparagine replaced by tyrosine) and K417N/T (lysine replaced by asparagine or threonine) influence the strength of binding. In other regions of the spike protein are more mutations influencing the course of infection.
this demonstration.
Literature:
J Lan et al, Nature 581, 215-220 (2020), DOI: 10.1038/s41586-020-2180-5
The structure file used for this demonstration was created from 2ajf.pdb and 6m0j.pdb.
N R Faria et al, https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586