Amyloid goes way back, and scientific writing about has had various zigs and zags starting with Virchow (1821 – 1902) who named it because he thought it was made out of sugar. For a long time it was defined by the way it looks under the microscope being birefringent when stained with Congo red (which came out 100 years ago, long before we knew much about protein structure (Pauling didn’t propose the alpha helix until 1951).
Birefringence itself is interesting. Light moves at different speeds as it moves through materials — which is why your legs look funny when you stand in shallow water. This is called the refractive index. Birefringent materials have two different refractive indexes depending on the orientation (polarization) of the light looking at it. So when amyloid present in fixed tissue on a slide, you see beautiful colors — for pictures and much more please see — https://onlinelibrary.wiley.com/doi/full/10.1111/iep.12330
So there has been a lot of confusion about what amyloid is and isn’t and even the exemplary Derek Lowe got it wrong in a recent post of his
“It needs to be noted that tau is not amyloid, and the TauRx’s drug has failed in the clinic in an Alzheimer’s trial.”
But Tau fibrils are amyloid, and prions are amyloid and the Lewy body is made of amyloid too, if you subscribe to the current definition of amyloid as something that shows a cross-beta pattern on Xray diffraction — https://www.researchgate.net/figure/Schematic-representation-of-the-cross-b-X-ray-diffraction-pattern-typically-produced-by_fig3_293484229.
Take about 500 dishes and stack them on top of each other and that’s the rough dimension of an amyloid fibril. Each dish is made of a beta sheet. Xray diffraction was used to characterize amyloid because no one could dissolve it, and study it by Xray crystallography.
Now that we have cryoEM, we’re learning much more. I have , gone on and on about how miraculous it is that proteins have one or a few shapes — https://luysii.wordpress.com/2010/08/04/why-should-a-protein-have-just-one-shape-or-any-shape-for-that-matter/
So prion strains and the fact that alpha-synuclein amyloid aggregates produce different clinical disease despite having the same amino acid sequence was no surprise to me.
But it gets better. The prion strains etc. etc may not be due to different structure but different decorations of the same structure by protein modifications.
The same is true for the different diseases that tau amyloid fibrils produce — never mind that they’ve been called neurofibrillary tangles and not amyloid, they have the same cross-beta structure.
A great paper [ Cell vol. 180 pp. 633 – 644 ’20 ] shows how different the tau protofilament from one disease (corticobasal degeneration) is from another (Alzheimer’s disease). Figure three shows the side chain as it meanders around forming one ‘dish’ in the model above. The meander is quite different in corticobasal degeneration (CBD) and Alzheimers.
It’s all the stuff tacked on. Tau is modified on its lysines (some 15% of all amino acids in the beta sheet forming part) by ubiquitination, acetylation and trimethylation, and by phosphorylation on serine.
Figure 3 is worth more of a look because it shows how different the post-translational modifications are of the same amino acid stretch of the tau protein in the Alzheimer’s and CBD. Why has this not been seen before — because the amyloid was treated with pronase and other enzymes to get better pictures on cryoEM. Isn’t that amazing. Someone is probably looking to see if this explains prion strains.
The question arises — is the chain structure in space different because of the modifications, or are the modifications there because the chain structure in space is different. This could go either way we have 500+ enzymes (protein kinases) putting phosphate on serine and/or threonine, each looking at a particular protein conformation around the two so they don’t phosphorylate everything — ditto for the enzymes that put ubiquitin on proteins.
Fascinating times. Imagine something as simple as pronase hiding all this beautiful structure.
Chemiotics II 
Comments
“So prion strains and the fact that alpha-synuclein amyloid aggregates produce different clinical disease despite having the same amino acid sequence was no surprise to me.”
Convincing evidence has yet to appear that the diseases that are accompanied by amyloid deposits are caused by those deposits.
The most straightforward interpretation of the failure of Lilly’s solanezumab is that amyloid does not cause Alzheimers, since preventing its buildup does not inhibit further development of the disease among those in its early stages.
It’s not the only interpretation of the failure, but nor has it ever been anything more than a hypothesis that amyloid formation is causative. Billions of dollars and many years of truly noble effort later, it’s still nothing more than a hypothesis.
Of course, even if amyloid production is merely an accompanying symptom, one would expect that drugs that do successfully prevent progression of Alzheimers will also prevent amyloid production, which is interesting and perhaps even a useful indicator for drug development, since drugs that do end up inhibiting the disease(s) for some other reason will also inhibit amyloid buildup. So a drug candidate that that appears to eliminate amyloid in a phenotypic assay is certainly worth investigating.
Peter: Point well taken. The post does assume that amyloid is causative of disease (or at least doesn’t challenge the idea).
Have a look at a sermi-recent post which argues that amyloid is actually protective against disease — https://luysii.wordpress.com/2019/11/17/barking-up-the-wrong-therapeutic-tree-in-alzheimers-disease/
Hi, and thank you. I realize now that I read the post you quoted back when you first posted it.