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.