Smooth Annular Protofibrils.
Beaded APFs gradually morph into smooth APFs. Most sAPFs in the upper portion of Fig. 1b exhibit concentric rings: an outer dark ring, followed by a light ring, followed by a second dark ring which surrounds a circular light center. These sAPFs resemble cog gears or cog wheels due to evenly spaced dark dots on the perimeter of the outer ring; thus, we call these dots cogs. White-centered cog APFs (WCsAPFs) are densely packed in the top region of the micrograph of Fig. 1b, which appears to be enclosed or covered by a film. Many dark centered sAPFs (DCsAPFs) in other portions of Fig. 1b and in Fig. 1c also have cogs on their perimeters, but they have only an outer dark ring and an adjacent light ring. The micrograph of Fig. 1d is dominated by super smooth APFs (SsAPFs) that have few or no cogs and relatively dark centers.
The concentric rings of WCsAPFs EM images provide the strongest pictorial evidence that Aβ42 peptides can assemble into concentric β-barrel structures (Fig. 7). Radial image averaging should be used cautiously because it can produce the appearance of radial symmetry even when none exists. Selected unaveraged images were included to illustrate that some WCsAPFs, especially the larger ones, exhibit radial symmetry without radial averaging.
WCsAPFs can be classified into seven sizes. Each image was first averaged radially and then all images of the same size and radial symmetry were aligned and averaged (Fig. 1e). The number of images used for each size is indicated in the upper right corner of Fig. 7. We hypothesize that the outer white ring corresponds to a S3 β-barrel, that the number of strands in this barrel is the same as the number of monomers in the assembly, and that the S/N value is either 1.0 or 1.5. These assumptions permit the number of monomers in the assembly to be calculated from the diameter of the white ring (see parameters below the images). Our calculations suggest that the number of monomers increase by four for each size increase. Also, the number of cogs in the outer dark ring increases by one for each size increase. Assuming one radial unit-cell per cog, each radial unit-cell contains four monomers. Thus, these sAPFs may develop and grow from mergers of tetramers. If the tetramer structure of Aβ42 proposed by Cuidad et al.31for S3 strands is approximated in the S3 barrel of the white-centered sAPFs, then the radial unit-cell would be composed of four monomers and contain two subunit conformations. Although an α-helical motif for S1b-S2 of Cin may be viable for 36mers and possibly 28mers, size restrictions make it less likely for other white-centered sAPFs. We suspect that Cin subunits of the other WCsAPFs form antiparallel inner β-barrels with the strand tilts and involvement of S1 segment changing as the size of the assembly changes, in a manner that keeps the gap distance between the barrels near 1.0 nm.
The final image and schematic of Fig. 7 illustrates the most extreme example of multiple concentric β-barrels. The unaveraged image has a relatively hexagonal shape. Averaging with 6-fold symmetry reveals multiple concentric rings. Fig. S5 of the supplement compares images of putative 24mers and a 72mer to this image, and illustrates details of a model in which a 72mer sAPF surrounds a 24mer sAPF. The central rings of the image resemble the first of the WCsAPF images, the putative 24mers. The outer diameter of the image is consistent with a 72mer sAPF with S/N = 0.5 for the S3 barrel. The model has six concentric β-barrels, but this type of assembly is rare; this is the only image that we observed with these properties.