Figure 5. Octadecamer model. (a) Wedge representation of strand
positions in the central cross-section; the twelve peripheral subunits
are stippled. (b-e) Flattened representation of (b) the core 6-stranded
S3 β-barrel, (c) the middle 18-stranded S2-S3 β-barrel; the poorly
conserved S1a interacts with the poorly conserved portion near the end
of S2 and its structure is likely more disordered than depicted, (d) the
outer 24-stranded S1-S2 β-barrel, and (e) two peripheral S1a-S1b
β-hairpins. Residues are colored according to the number of residue
types at each position of a multi-sequence alignment. (f-i) Atomic-scale
models. (f) Top view and (g) side view cross-section of backbone ribbon
representation colored by rainbow. (h & i) Model with conserved side
chains colored by degree of conservation as in b-e; (h) middle
cross-section, (i) side view cross-section.
We suspect that the second largest oligomer (bead) is an octamer.
Identification and development of a best model was complicated. An
NMR-based model of an Aβ42 structure has been proposed for both
tetramers and octamers31. For those, each tetramer
forms a six-stranded antiparallel β-sheet with 2-fold perpendicular
symmetry and two different subunit conformations. Two central S3 strands
resemble those of our model; they are antiparallel with a perpendicular
2-fold axis at V36. The remaining portion of these subunits was
classified as disordered. S3’s of these subunits are flanked by S3
strands that are oriented in the opposite direction relative to the
plane of the β-sheet; e.g. side chains of odd numbered residues
of the flanking S3 strands are on the opposite side as those of the
central S3 strands. S2 strands of these subunits comprise edge strands
as part of a β-hairpin with S3. The structure of the S1 region was
undetermined. The octamer structure was proposed to be a β-sandwich in
which two tetramers related by 2-fold symmetry pack back-to-back. These
structures were developed in the presence of detergents, and thus may
differ from the APFs analyzed here that were developed in the presence
of hexane.
We used atomic-scale modeling to explore the feasibility of octamer
structures with concentric β-barrels. After developing numerous models,
we concluded that the structure illustrated in Fig. 6 is the soundest
that is also consistent with the size of the next to smallest beads,
those circled in red in Fig. 2 (See Fig. S3 of the supplement for
alternative models). Some aspects of this model resemble those of the
hexamer model; all monomers have the same conformation due to radial and
2-fold perpendicular symmetry, and an antiparallel S3 β-barrel with S/N
= 1.0 that forms the hydrophobic core. There are however substantial
differences in addition to the number of subunits: (1) S3 strands of the
8-stranded core barrel are oriented radially in the opposite direction;
i.e., G33, M35, and G35 are on the exterior instead of on the interior.
(2) The β-turn linking S1b to S2
centers at H14-Q15 instead of H13-H14 and turns in the opposite
direction. (3) S1 is a single continuous β-strand instead of a S1a-S1b
β-hairpin, and thus each subunit contributes only two instead of three
strands to the outer barrel. (4) The S1 and S2 strands of the outer
β-barrel are more tilted; i.e., S/N = 1.5 instead of 1.0. These changes
result in the outer barrel having 16 strands and a diameter of 3.6 nm.
The gap distance between the two barrels is about the same as for the
hexamer model. The pleats intermesh at the perpendicular 2-fold axes:
i.e., the outwardly-oriented M35 side chains fit into the pleats behind
the outwardly-oriented D7 residues, and the inwardly-oriented F19 side
chains fit in the pleats of inwardly-oriented V36 residues. Aromatic
side chains of inwardly-oriented F4, Y10, and F19 are adjacent on the
same pleat and interact (interactions between aromatic groups tend to be
energetically favorable57). Locations of G33 and G37
on the exterior of the S3 barrel allow F4, Y10, and F19 side chains to
pack next to S3 without major side chain clashes; note that the only
outwardly-oriented S3 side chains in the middle cross-section are those
of M35 (Fig. 6f). The outer barrel has several inwardly-oriented side
chains with polar atoms: i.e., the hydroxyl groups of S8 and Y10, the
imidazole ring of H6, and the carboxyl group of D23. These are near
enough to one another to form H-bonds and salt-bridges. All positively
and negatively charged side chains on the exterior of the outer barrel
form salt-bridges. β-barrels in proteins often have eight
strands58,59. The interior of the 8-stranded S3 barrel
is large enough to accommodate the alkyl side chains of I32, L34, V36,
and V40 and still leave a narrow pore lined with alkyl groups through
its center. Portions of this pore may be occupied by hexane.