SARS cov2 spike trimer with antibodies

An antibody has to know its target exactly, else there may be catastrophical side effects. Therefore target structures are mainly proteins; sugar, fat and membranes are too similar to each other to discern them. The only proteins sticking out of the membrane of corona viruses are the spike trimers. An antibody fighting corona has several possibilities to attack a target: occupation of the binding region to the receptor - no more docking possible; prevention of the upturning of the binding domain - also no more docking; stiffening of the whole structure - that prevents structural changes of the spikes neccessary for entering the target cell.

In the spike trimer shown here one binding domain is in the "up" position . To investigate the binding pattern researchers don't use whole antibodies, but only the binding parts (that eases the experiments). If an antibody is sufficient to prevent an infection, it is called neutralizing. Here the binding of a nAb (only binding part) is shown . The antibody fragment binds to the spike protein similar to the receptor ACE2. Let's have a closer look:

. With a translucent antibody we recognize the antibody to snuggle to the spike surface. We may now mark the footprint of the antibody on the spike (binding amino acids) . Imagining the receptor ACE2 to bind, we find the ACE2 pootprint . With a close watch you recognize an overlap . With the old physical wisdom "where one body is there can't be another" binding of the antibody excludes binding of the spike to the receptor. If the antibody holds fast enough to the virus there may be no infection.

What does the antibody to the spike binding region in the down position? The antibody will cling to its binding region also here . All good things are three (for us, not the virus) . If there are enough antibodies abundant to neutralize all emerging spikes the virus is doomed.

this demonstration.

Literature:
H Yao et al, Cell Res 31, 25-36 (2021), DOI 10.1038/s41422-020-00444-y

for binding other antibodies:
C O Barnes et al, Cell 182, 828 (2020), DOI 10.1016/j.cell.2020.06.025
N C Wu et al., Cell Reports 33, 108274 (2020), DOI 10.1016/j.celrep.2020.108274