This was the state of the art 19 years ago in a PNAS paper (vol. 99 pp. 16742 – 16747 ’02). “Amyloid fibrils are filamentous structures with typical diameters of 10 nanoMeters and lengths up to several microns. No high resolution molecular structure of an amyloid fibril has yet been determined experimentally because amyloid fibrils are noncrystalline solid materials and are therefore incompatible with Xray crystallography and liquid state NMR.”
Well solid state NMR and cryo electron microscopy have changed all that and we now have structures for many amyloids at near atomic resolution. It’s probably behind a pay wall but look at Cell vol. 184 pp. 4857 – 4873 ’21 if you have a chance. I’ve spent the last week or so with it, and a series of posts on various aspects of the paper will be forthcoming. The paper contains far too much to cram into a single post.
So lacking an Xray machine to do diffraction, what did we have 57 years ago when I started getting seriously interested in neurology? To find amyloid we threw a dye called Congo Red on a slide, found that it bound amyloid and became birefringent when it did so.
Although the Cell paper doesn’t even mention Congo Red, the structure of amyloid they give explains why this worked.
What is birefringence anyway? It means that light moving through a material travels at different speeds in different directions. The refractive index of a material is the relative speed of light through that material versus the speed of light in a vacuum. Stand in a shallow pool. Your legs look funny because light travels slower in water than in air (which is nearly a vacuum).
Look at the structure of Congo Red — https://en.wikipedia.org/wiki/Congo_red. It’s a long thin planar molecule, containing 6 aromatic rings, kept planar with each other by pi electron delocalization.
The previous post contained a more detailed description of amyloid — but suffice it to say that instead of wandering around in 3 dimensional space, the protein backbone in amyloid is confined to a single plane 4.8 Angstroms thick — here’s a link — https://luysii.wordpress.com/2021/10/11/amyloid-structure-at-last/
Plane after plane stacks on top of each other in amyloid. So a micron (which is 10,000 Angstroms) can contain over 5,000 such planes, and an amyloid fibril can be several microns long.
It isn’t hard to imagine the Congo Red molecule slipping between the sheets, making it’s orientation fixed. Sounds almost pornographic doesn’t it? This orients the molecule and clearly light moving perpendicular to the long axis of Congo Red will move at a different speed than light going parallel to the long axis of Congo Red, hence its birefringence when the dye binds amyloid.
Well B-DNA (the form we all know and love as the double helix) has its aromatic bases stacked on top of each other every 3.4 Angstroms. So why isn’t it birefringent with Congo Red? It has a persistence length of 150 basePairs or about .05 microns, which means that the average orientation is averaged out, unlike the amyloid in a senile plaque
There is tons more to come. The Cell paper is full of fascinating stuff.
Chemiotics II 