I dealt with ICU cases of covid19 patients over a year and I'm still trying to understand this myself as so complicated like...... Don't know if this helps.
Spike protein functions breaks up into this -
The S protein is a highly glycosylated and large type I transmembrane fusion protein that is made up of 1,000's of amino acids, depending upon the type of virus.
As compared to the M and E proteins that are primarily involved in virus assembly, the S protein plays a crucial role in penetrating host cells and initiating infection.
Notably, the presence of S proteins on the coronaviruses is what gives rise to the spike-shaped protrusions found on their surface.
S proteins of coronaviruses can be divided into two important functional subunits, which include the N-terminal S1 subunit, which forms the globular head of the S protein, and the C-terminal S2 region that forms the stalk of the protein and is directly embedded into the viral envelope.
How S protein allows coronaviruses to enter cells
Once the S1 subunit binds to host cell receptors, two major conformational changes must occur for the S2 subunit to complete the fusion of the virus to the cell membrane. The two components of the S2 subunit that are involved in the coronavirus fusion include heptad repeat (HR) regions one and two, otherwise referred to as HR1 and HR2.
The first conformation otherwise referred to as pre-hairpin, involves the transformation of an unstructured linker within the S2 subunit to become helical. The second conformational change to occur involves the inversion of this subunit’s C-helix to the coil, resulting in the formation of a six-helix bundle.
Once these conformations are completed, the fusion peptide is anchored to the membrane of the host cell to allow the virus to move closer towards the cell membrane and eventually deliver the nucleocapsid to the target cell.
From some of the research I have seen is that 1 of the reasons people are having issues after vaccination is that the spike protien isn't staying in the deltoid muscle and is breaking free and going to different areas of the body. I would say it is mildly concerning, however the immediate overall risk to most people is very low, will it remain low after a period of time ? That is something that is yet to be determined.
No, I am not sure of all the "ins" and "outs" of this process but according to 1 of the people that worked on one of the vaccines the spike protein is supposed to stay stuck on something else and not go roaming about the body.