Fibril structure of amyloid-β(1-42) by cryo-electron microscopy

Abstract

Amyloids are implicated in neurodegenerative diseases. Fibrillar aggregates of the amyloid-β protein (Aβ) are the main component of the senile plaques found in brains of Alzheimer's disease patients. We present the structure of an Aβ(1-42) fibril composed of two intertwined protofilaments determined by cryo-electron microscopy (cryo-EM) to 4.0-angstrom resolution, complemented by solid-state nuclear magnetic resonance experiments. The backbone of all 42 residues and nearly all side chains are well resolved in the EM density map, including the entire N terminus, which is part of the cross-β structure resulting in an overall "LS"-shaped topology of individual subunits. The dimer interface protects the hydrophobic C termini from the solvent. The characteristic staggering of the nonplanar subunits results in markedly different fibril ends, termed "groove" and "ridge," leading to different binding pathways on both fibril ends, which has implications for fibril growth.

Fig. 1. Aβ(1-42) fibril structure.

(A) 3D reconstruction from cryo-EM images showing density of two protofilaments (brown and blue) and the clear separation of the β-strands. (B) Atomic model of the fibril with parallel cross-β structure. (C) and (D) Tilted views of the cross-section of the EM density and the backbone model.

Fig. 2. Atomic model and superimposed EM density of the fibril cross-section.

(A) Two subunits, one from each protofilament, are shown (blue and brown) together with the masked EM density map (at contour level of 1.5 σ, additional contour levels of 1 σ and 2 σ are shown in fig. S4). (B) Detailed view of the interactions between the N- and C-terminus and the sidechain of Lys28 (at contour level of 1 σ). (C) Side view of the same two opposing subunits showing the relative orientation of the non-planar subunits. The large peripheral cross-β sheet is tilted by 10º with respect to the plane perpendicular to the fibril axis.

Fig. 3. NMR and X-ray diffraction experiments.

(A) 2D Proton-Driven Spin Diffusion (PDSD) spectrum of fibrillar Aβ(1-42). The spectrum was recorded at a magnetic field strength of 18.8 T corresponding to a proton Larmor frequency of 800 MHz, a sample temperature of T = 0 ± 5 °C and a spinning speed of 12.5 kHz. For homonuclear ¹³C/¹³C mixing, PDSD with a mixing time of 20 ms was employed. A squared and shifted sine bell function was used for apodization (shift of 0.3·π). (B) Secondary chemical shifts calculated from assigned resonance shifts and random coil values predicting β-strand regions (difference exceeds -2 ppm) (dark blue). For Gly residues, only the Cα secondary chemical shifts are plotted. Additionally, β-strands calculated by TALOS-N and β-sheets from the cryo-EM derived atomic model are displayed (assigned by DSSP and Stride). (C) X-ray diffraction image of un-oriented Aβ(1-42) fibrils.

Fig. 4. Details of the Aβ(1-42) fibril architecture.

(A) Side view of the atomic model showing the staggered arrangement of the non-planar subunits. (B) Surface representation of a fragment of the atomic fibril model. Surface is colored according to hydrophobicity (Kyte-Doolittle scale) (gradient from brown (hydrophobic, 4.5) to white (neutral, 0.0)). View of the "ridge" (C) and "groove" (D) fibril ends. Only the contact surfaces of the subunits with the respective capping monomer (i+3 in (C) and i-4 in (D), shown as ribbon) are colored (color coding according to layer number, see (A)).