Figure 7. Images of WCsAPFs and schematics of Aβ42 models with three concentric β-barrels. The outer orange rings of the schematics represent the outer β-barrel formed by S1 and S2, the blue ring represents a S3 β-barrel, the inner orange ring represents an inner β-barrel formed by S1 and S2, the inner yellow ring represents a β-barrel formed only by S2 strands, and the tiny red ring represents a highly tentative β-barrel formed by S1a segments. The yellow cylinders of the 32mer and 36mer models represent α-helices formed by S1b-S2 segments. Parameters of the models are listed below the images. The upper rows of images were averaged radially for the number of WCsAPF’s indicated in the upper right corner. The lower row of images are individual sAPFs. The green circles on the images indicate the proposed size and location of boundary between the outer and middle β-barrels. A small DCsAPF (the first image) was included because it also occurs frequently within the same region of the micrograph. The final schematic/EM image is larger and has more concentric rings than the others. The schematic illustrates that the assembly may have six concentric β-barrels with a three-barrel 72mer sAPF surrounding a three-barrel 24mer sAPF (also see Supplement Fig. S5).
Like the tetramers proposed by Cuidad et al.31, our WCsAPFs models have two monomeric conformations and 2-fold perpendicular symmetry. An antiparallel S3 β-barrel is sandwiched between two cylinders formed by S1-S2 segments. In our models S1a-S1b-S2 β-strands of half the monomers form an outer β-barrel with a structural motif resembling that proposed above for hexamers (Fig. 8). S2 of these monomers connects to the S3 strands for which centrally located V36 side chains are oriented outwardly. We call the conformation of these monomers Cout. The outer two barrels of Cout subunits intermesh at the axis of perpendicular 2-fold symmetry; i.e., the outwardly oriented V18 residues of S2 fit over the outwardly-oriented V36 residues of S3, and inwardly-oriented F4 residues of S1a fit over inwardly-oriented V36 residues of the other S3 conformation, Cin.
Prediction of the structure of the S1-S2 portion of Cinis more difficult. Gao et al.32 developed a method to stabilize and isolate 150-kDa Aβ42 oligomers, which they conclude are composed of 32 subunits. These oligomers may correspond to the 32mer WCsAPF of Fig. 7. Their solid-state NMR studies indicate that S3 forms antiparallel β strands centered at V36, consistent with our model and the structure of the central S3 strands of the tetramer. Their results for S2 strands are more complicated. Based on their analysis of chemical-shifts for backbone C sites, they concluded that residues 11-24 have a β secondary structure, but that these residues occupy multiple magnetically inequivalent sites. Additional NMR results indicated that proximal residues are sequentially either three or four positions apart on S1b-S2. They interpreted these data as indicative of out-of-register parallel β-sheets in which the strands are shifted three positions relative to one another. This arrangement is not possible if S2 segments form antiparallel β-barrels.
An alternative possibility is that the assembly contains two distinct S2 conformations, one that has β-secondary structure and another that has α-helical secondary structure in which residues three or four positions apart are proximal (Fig. 8e). If so, then some results may come from the β-structure while other results come from the α-conformation. We propose that S1b-S2 α-helices of Cin monomers comprise the inner ring of the 32mer sAPFs. These helices are substantially shorter than the β-strands and stack end-on inside the S3 barrel. Although Gao et al.32 concluded that S1a segments are disordered, they may form an inner, parallel β-barrel for Cin, and part of an antiparallel β-barrel for Cout. If so, the portion of the assembly inside the S3 β-barrel would resemble a TIM αβ-barrel in which eight parallel α-helices surround an eight stranded parallel β-barrel. This motif has been observed in numerous soluble proteins60 and could contribute to the stability of 150-kDa oligomers. A high stability of this structure could also explain why the putative 32mers are the most frequently observed WCsAPFs (Fig. 7).
Additional NMR results of Gao et al.32 regarding interactions between S1b-S2 residues and S3 residues are consistent with our model if one assumes some data are due to interactions with Cout and others with interactions with Cin (Fig. 8). Note that the three residues (V12, K16, and F19) proposed to interact with S3 residues near the beginning and ends of S3 strands are on the same face of the putative α-helix. In spite of the relatively consistent agreement between this model and the NMR data, we cannot be confident any of the putative 32mer APFs proposed here correspond to the 150-kDa oligomer studied by Gao et al.32 because different procedures and conditions were used to obtain the structures.