SARS Cov2 spike trimer with nanobodies

The model to the left shows the meanwhile familiar aspect of the spike trimer. All three binding domains are in the down position. In the experiments described by Schoof and colleagues several nanobodies derived from alpaca antibodies were found, exhibiting different working mechanisms. One of these (Nb6) is desribed here.

Nb6 binds to the receptor binding domain of the spike protein in a special way , to two proteins at the same time. Let's have a look at the contact region of nanobody and binding domain (in order to prevent a ravenous yearning for chocolate, we eliminate the sugar molecules ). In the round about view we recognize the indentation with the blue binding domain; spots for binding of the receptor ACE2 are occupied by the nanobody. The neighboring domain (violet) is also held tight.

Back to the complete spike trimer . Because of the inherent symmetry there are two more binding spots . The result: all binding spots to the receptor are occupied, by binding of one nanobody to two spikes simultaneously the uplifting of the binding domains into the active position is prevented .

At room- or bodytemperature all molecules are in constant movement in all spacial directions. A binding of molecules (like between nanobody and spike) occurs after accidential kicks. Not every kick results in a bond, direction and orientation have to be proper. By more kicks from other molecules a bond may be unhooked, if the pushing energy is larger than the bonding energy. All this is in a temperature dependent balance depending also on the concentrations of the reaction partners. The authors of this study used a trick to enhance the local concentration of the nanobodies: by genetic engineering they connected three nanobodies with two "rubber bands", resulting in a tight fit of three nanobodies to three spike proteins simultaneously. In cell culture this construction showed a manyfold better protection against cov2 infection.
Nanobodies are resistant to high temperature (50°C), dryness (freeze drying) and aerosol formation (nasal spray!).

this demonstration.

Literature:
M Schoof et al, Science 370, 1473-1479 (2020), DOI 10.1126/science.abe3255

and:
P A Koenig et al, Science (2021), DOI 10.1126/science.abe6230
G V Nieto et al., Nature Scientific Reports 11, 3318 (2021), DOI 10.1038/s41598-021-82833-w