Pauling and Corey's alpha-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease

Abstract

Transthyretin, beta(2)-microglobulin, lysozyme, and the prion protein are four of the best-characterized proteins implicated in amyloid disease. Upon partial acid denaturation, these proteins undergo conformational change into an amyloidogenic intermediate that can self-assemble into amyloid fibrils. Many experiments have shown that pH-mediated changes in structure are required for the formation of the amyloidogeneic intermediate, but it has proved impossible to characterize these conformational changes at high resolution using experimental means. To probe these conformational changes at atomic resolution, we have performed molecular dynamics simulations of these proteins at neutral and low pH. In low-pH simulations of all four proteins, we observe the formation of alpha-pleated sheet secondary structure, which was first proposed by L. Pauling and R. B. Corey [(1951) Proc. Natl. Acad. Sci. USA 37, 251-256]. In all beta-sheet proteins, transthyretin and beta(2)-microglobulin, alpha-pleated sheet structure formed over the strands that are highly protected in hydrogen-exchange experiments probing amyloidogenic conditions. In lysozyme and the prion protein, alpha-sheets formed in the specific regions of the protein implicated in the amyloidogenic conversion. We propose that the formation of alpha-pleated sheet structure may be a common conformational transition in amyloidosis.

Fig. 1.

MD-generated α-sheet intermediate structures for four amyloidogenic proteins: transthyretin (a), β₂m (b), D67H lysozyme (c), and bovine PrP (d). (Left) The native structure. (Right) α-Sheet intermediates from unfolding simulations. Regions shown in red convert to α-extended chain conformations.

Fig. 2.

Average local secondary structure by residue. (a) Average over the first nanoseconds of the native simulation of TTR at 310 K. (b) Average over the α-sheet unfolding intermediate of TTR. (c) β₂m at 310 K. (d) α-Sheet intermediate of β₂m. (e) α-Sheet intermediate of WT lysozyme. (f) α-Sheet intermediate of D67H lysozyme. (g) Bovine PrP at 298 K. (h) α-Sheet intermediate of bovine PrP. A residue was classified in a particular conformation if its (φ,ψ) angles were within ± 30° of the average values that follow: α_R = (45°, 92°); α_L = (–87°, –49°); β-structure (both parallel and antiparallel) = (–165° ≤ φ ≤ –83°) and (89° ≤ ψ ≤ 169°); and P_II = (–79°, 149°). Using these definitions there is some overlap between β and P_II.

Fig. 3.

Peptide plane flip in the transition from β-to α-sheet structure in TTR. Blue points represent the distribution of (φ,ψ) angles for the entire chain in the TTR α-sheet intermediate. Red dots are the angles sampled for Lys-15 on the A strand during the transition from theβ to theα_R conformation. Green dots are for the adjacent residue, Val-16, during the same transition as it converts from β to α_L. These residues pass through the right-handed P_II and the left-handed P_II conformations, respectively. Black dots represent average (φ,ψ) values for: β_par (–119, 113), β_anti (–139, 135), α_R-helix (–57, –47), α_R-extended (–87, –49), α_L-helix (47, 57), α_L-extended (45, 92), P_II(R) (–149, 79), and P_II(L) (–79, 149).

Fig. 4.

Average local secondary structure for poly(l-lysine). (a) At 276 K. (b) At 323 K. Definitions are provided in the legend for Fig. 2.

Fig. 5.

α-Sheet intermediate model for self-assembly into amyloid. A main-chain model for an α-sheet is shown with partial charges on the interface (red for negative, blue for positive charges).