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.