Vaccine design
The spike protein in its trimeric form induces our immune system to defending reactions. To achieve a thorough vaccination protection it must be prevented that the spikes used can change their structure as in the course of an infection into a less immunogenic shape. The building plan - the genetic information - for the spike protein is well known as there are enough molecular engineering tools to change the plan. So let's get to work!
The vaccine NVAX-CoV2373 contains the complete spike protein (3x all 1273 amino acids) of the original sars-cov2. It is produced in insect cell cultures and will be administered with Tween80 (=polysorbate 80), which (as nonionic tensid) functions as emulgator and enables the formation of micelles.
A word on the molecular models presented in this series of demonstrations: Proteins are kept in shape by internal bonds between amino acids, but they are not completely rigid. Also they are not in a vacuum, but in a water based solution (either in the mucosal lining of our respiratory tract or in laboratories in special salt solutions as neccessary for the individual experiment). The investigation of the atomic coordinates by cryo electron microscopy used here to depict the molecules require special conditions to see anything at all. Proteins "feel" their surroundings and may react with conformational changes to different surroundings. The spike proteins demonstrated here are from preparations in different laboratories and may differ in detail. Furthermore, besides "rigid" parts proteins harbor stretches in ther chains with some degree of mobility. These parts cannot be shown in the models.Out of the 1273 amino acids in the vaccination spike only aa 14 to 1146 are visible, in between the regions 619-631 and 678-688 are invisible because of too great mobility. So of these loops only start and end points may be seen. But the "red" loop is of special importance: it contains the recognition sequence for cleavage of the spike protein into the subunits. In the original spike the sequence proline-arginine-arginine-alanine-arginine-serine (PRRARS) is cleaved after the third arginine, so the S1 part is removed and S2 can refold. In the vaccination spike all three arginines are replaced by genetic engineering by glutamine (PQQAQS). The cleaving protease won't recognize this as cleavage site, so the spike stays unharmed.
Another (standard-)mutation is at positions 986 and 987: amino acids lysine and valine are replaced both by proline. Proline differs from other amino acids by its ring structure involving the protein chain backbone atoms . In the "blue" spike structure also the neighboring amino acids are shown with their atoms; sequence -leucine-asparagic acid-proline-proline-glutamic acid-alanine- . At the junction of the helices proline renders the protein chain rigid and prevents thus a refolding to the S2 structure.
Many viruses contain a fattic acid molecule. It is provided by the host cell and may vary according to host. In this spike preparation linolic acid was found . What may that be good for? Besides forces between amino acids originating from electric charges there are hydrophobic interactions (fat likes fat). The completely uncharged part of the fatty acid is stuck in a hydrophobic pocket formed by amino acids without any charged side chains . These amino acids form the , fixing the "greasy" part of the linolic acid. The carboxylic group of the linolic acid is engaged too: it binds to charged amino acids by hydrogen bonds - but in the neighboring spike protein . So there is a connection keeping the spike trimer together in the receptor binding region.
Back to the spike trimer . The spike preparation is emulgated in polysorbate before vaccination. The sorbitol part of this tensid was found in the spike protein . Let's have a look at the surroundings: . Besides interaction with uncharged amino acids there are hydrogen bridges to side chains of histidine and arginine . The tensid molecule influences the structure of the spikes: the receptor domain is tilted by 14° from the symmetry axis to the viral surface compared to "normal" spikes.
Also in this spike preparation the protein is glycosylated .
this demonstration.
Literature:
S Bangaru et al., Science 370, 1089-1094 (2020) DOI: 10.1126/science.abe1502
R N Kirchdoerfer et al, Nature Sci Rep 8, 1587 (2018) DOI: 10.1038/s41598-018-34171-7