Amyloid Evolution: Antiparallel Replaced by Parallel

Abstract

Several atomic structures have now been found for micrometer-scale amyloid fibrils or elongated microcrystals using a range of methods, including NMR, electron microscopy, and X-ray crystallography, with parallel β-sheet appearing as the most common secondary structure. The etiology of amyloid disease, however, indicates nanometer-scale assemblies of only tens of peptides as significant agents of cytotoxicity and contagion. By combining solution X-ray with molecular dynamics, we show that antiparallel structure dominates at the first stages of aggregation for a specific set of peptides, being replaced by parallel at large length scales only. This divergence in structure between small and large amyloid aggregates should inform future design of molecular therapeutics against nucleation or intercellular transmission of amyloid. Calculations and an overview from the literature argue that antiparallel order should be the first appearance of structure in many or most amyloid aggregation processes, regardless of the endpoint. Exceptions to this finding should exist, depending inevitably on the sequence and on solution conditions.

Figure 1

Symmetries and SAXS/WAXS. (a) Shown is the construction of test nanocrystal structures obeying each of the eight allowed steric zipper symmetries, which are expected to give eight distinct scattering signatures. (b) Shown is the WAXS of the ILQINS peptide solution recorded after 24 h of self-assembly (black) and the calculated scattering for MD snapshots of 1296-peptide nanocrystals (6 × 12 × 18) taken at 10 ns (AP 5, blue; P 1, red). The AP lattice parameters are a = 20.6 Å, b = 19.1 Å, and γ = 82°; the peaks relevant to the lattice shape are annotated with the corresponding Bragg spacing (main and inset). (c) Overlapping regions of the SAXS/WAXS curves are annotated by the type of information that they provide (shape, structure, and solvation). The designed AP structure has extremely good agreement in the structural region with a WAXS curve taken in 2014 and also quite good agreement with these WAXS data. The designed class 1 structure also captures some features of these WAXS data. To see this figure in color, go online.

Figure 2

AP structure. (a) Two sequential planes are shown perpendicular to the c axis; the termini are in close contact on the a axis, but not across the steric zipper. (b) Given is the plane perpendicular to the b axis, showing the backbones of the peptides only. Termini are also in contact along the c axis, and hydrogen bonding is strong. (c) An MD snapshot of the two planes shown in (a) superimposed is given, with semiordered mobile water molecules shown as orange spheres. (d) A slice through the whole model aggregate (c plane) is given, showing no peptides but only the regular array of water columns. To see this figure in color, go online.

Figure 3

Replica exchange. (a–c) Shown are the extended reference peptides used for HREMD simulations; these peptides have a pleated conformation compatible with the P structure. (d) AP sheets form very quickly in the accelerated simulation systems, preventing formation of the P sheet by absorbing free monomers (the example trace for ILQINS is shown). (e–g) Representative AP single β-sheets formed in these simulations are shown. Side-chain orientation in the AP sheets initially formed is not regular; the structures (e–g) are mixed between the intrasheet orderings of classes 5 and 6 and of 7 and 8. To see this figure in color, go online.

Figure 4

MD. Classical MD over 100 ns in explicit water shows that AP single β-sheets have greater configurational stability than P. (a–f) Shown are the P and AP β-structures consistent with classes 1 or 2 (P) and 5 or 6 (AP) at 100 ns for the three sequences studied. (g–i) The backbone hydrogen bonding declines more rapidly for the P structure in each case. Thick lines indicate a moving average over a 1-ns window. To see this figure in color, go online.