Neurologists and drug chemists pretty much view amyloid as a bad thing. It is the major component of the senile plaque of Alzheimer’s disease, and when deposited in nerve causes amyloidotic polyneuropathy. A recent paper and editorial casts amyloid in a different light [ Cell vol. 173 pp. 1068 – 1070, 1244 – 2253 ’18 ]. However if amyloid is so bad why do cytomegalovirus, herpes simplex viruses and E. Coli make proteins to prevent a type of amyloid from forming.
Cell death isn’t what it used to be. Back in the day, they just died when things didn’t go well. Now we know there are a variety of ways that cells die, and all of them have rather specific mechanisms. Apoptosis (aka programmed cell death) is a mechanism of cell death used widely during embryonic development. It allows the cell to die very quietly without causing inflammation. Necroptosis is entirely different, it is another type of programmed cell death, designed to cause inflammation — bringing the immune system in to attack invading pathogens.
Two proteins (Receptor Interacting Protein Kinase 1 — RIPK1, and RIPK3) bind to each other forming amyloid, that looks for all the world like typical amyloid –it binds Congo Red, shows crossBeta diffraction and has a filamentous appearance. Fascinating chemistry aside, the amyloid formed is crucial for necroptosis to occur, which is why various bugs try to prevent it.
The paper above describes the structure of the amyloid formed — unusual in itself, because until now amyloid was thought to involve the aggregation of a single protein.
The proteins are large: RIPK1 contains 671 amino acids, and RIPK3 contains 518. They both contain RHIMs (Receptor interacting protein Homotypic Interaction Motifs) which are fairly large themselves (amino acids 496 – 583 of RIPK1 and 388 – 518 of RIPK3). Yet the amyloid the two proteins form use a very small stretches (amino acids 532 – 543 from RIPK1 and 451 – 462 from RIPK3). How the rest of these large proteins pack around the beta strands of the 11 amino acid stretches isn’t discussed in the paper. Even within these stretches, it is two consensus tetrapeptides (IQIG from RIPK1, and VQVG from RIPK3) that do most of the binding.
Even if you assume that I (Isoleucine) Q (glutamine) G (glycine) V (valine) occur at a frequency of 5%, in our proteome of 20,000 proteins assuming a length of amino acids IQIG and VQVG should occur 10 times each. This may explain why 300/20,000 of our proteins contain a 100 amino acid segment called BRICHOS which acts as a chaperone preventing amyloid formation. For details see — https://luysii.wordpress.com/2018/04/01/a-research-idea-yours-for-the-taking/.
Just another reason to take up the research idea in the link and find out just what other things amyloid is doing within our cells in the course of their normal functioning.
Chemiotics II 