Annular and tubular protofibrils
Amyloid oligomers typically form protofibrils which in turn morph into fibrils. In some conditions annular protofibrils of α-Syn and mutant A30P and A53P α-Syn form first then combine to form tubular protofibrils [4]. We have developed Type 2P hexamer, octamer, decamer, and dodecamer models of annular protofibrils with diameters consistent with EM images of annular protofibrils (Fig. 12).
The general folding pattern for the A30P mutant hexamer (Fig 12 a-c) resembles the Type 2P tetramer of Fig.10 except that Sy7 forms a continuous β-strand that is a component of the middle barrel. There should be few side-chain clashes between the barrels. The gap distances between the barrels are 0.85 and 0.9 nm and the pitches of the pleats are similar for the three β-barrels so the pleats should intermesh well. One central inward pleat of the Ct domain has six consecutive glycines that should fit between pleats on Sy7 and Sy8 of the middle barrel that are composed of alanines. The central inward pleat of the middle barrel is composed of glycines, alanines and valines and should fit between pleats of the inner barrel.
The folding patterns for the A53T mutant octamers, decamers, and octamers are similar; Sy6 and Sy8 each contribute an additional β-strand/monomer to the inner and middle barrels; i.e., Sy2,4,6 comprise the inner β-barrel, Sy1,3,5,8 comprise a middle β-barrel, and the Ct domains that comprise an outer β-barrel of these models do not include Sy6 (Fig. 12 e-g). The number of strands per monomer increases by one for each concentric barrel. Sy7 is proposed to form a β-hairpin, but its location in the illustration is somewhat arbitrary; constrained primarily by the assumption that the folding pattern should be viable for β-Syn that has no Sy7 segment. The gap distances between barrels ranges from 0.6 to 0.9 nm for the four models. All three barrels of the octamer would have S/N values of 1.0 with gap distances of ~0.76 nm between barrels. Tight packing between barrels can be maintained by reducing S/N values of the 2ndand 3rd barrels to 0.75 and 0.60 for the decamer (Fig. 12 a-c) and dodecamer models; yielding gap distances ranging from 0.65 to 0.84 nm between barrels. Tight packing between barrels of the decamer and dodecamer may be facilitated by intermeshing pleats because the pitches of the three barrels are almost the same and most side-chains of the interacting pleats are small (glycine and alanine for the central region of the central pleat). The proposed structure of the outer Ct barrel resembles those in Figs. 10 and 11.
The 2-fold perpendicular symmetry of Type 2 models is consistent with the end-to-end interactions proposed for how annular protofibrils form tubular protofibrils. Interactions among the putative Sy7 β-hairpins may facilitate interactions among the annular protofibrils to form the tubular protofibrils; β-Syn that lacks Sy7 does not form fibrils and the Sy7 segment appears to be essential to fibril formation [60].