and S7). Recently reported chemical shift assignments of two brain seed–derived Ab(1– 42) fibril
preparations ( 18) differ from our chemical shifts
(table S7), suggesting different polymorphs.
Three hydrophobic clusters stabilize the subunit conformation: (i) Ala2, Val36, Phe4, and Leu34;
(ii) Leu17, Ile31, and Phe19; and (iii) Ala30, Ile32,
Met35, and Val40. Because the hydrophobic clusters expand in the stacked subunits along the
fibril axis, they essentially contribute to fibril
structure stability (Fig. 4B).
Combined analysis of NMR and cryo-EM data
suggests salt bridges between Asp1 and Lys28;
Asp7 and Arg5; and Glu11 and His6 and His13 ( 16).
The salt bridges of Glu11 stabilize the kink in the
N-terminal part of the b sheet around Tyr10 (fig.
S8D). This structural feature has also been reported
for fibrils of the Osaka mutant E22D of Ab(1– 40)
( 12). In rat and mouse, which are animal species that are known not to develop Alzheimer’s
disease, His13 is replaced by arginine, which
possibly prevents the formation of the kink
Compared with previous Ab42 fibril structures
( 11, 13, 14), substantial structural differences are
observed in the turn region of residues 20 to 25—
for example, here only Phe19, but not Phe20, is
facing the hydrophobic core (Fig. 2 and fig. S12).
This region, which forms two of the four edges
of the Ab(1– 42) fibril, contains the sites of pathogenic familial mutations of Ab: Flemish (A21G),
Arctic (E22G), Dutch (E22Q), Italian (E22K), and
Iowa (D23N). Furthermore, the effect of two
mutants in the N terminus at Ala2 can now be
rationalized based on the fibril structure: A2T
(Icelandic) might be protective against Alzheimer’s
disease, because threonine is more polar than
alanine and could destabilize the fibril by disrupting the hydrophobic cluster Ala2, Val36, Phe4,
and Leu34 (Fig. 2). In contrast, A2V is pathogenic,
which could be related to the fact that valine
is more hydrophobic than alanine and would
strengthen the hydrophobic interaction leading
to increased fibril stability.
The staggered arrangement of the subunits
has direct implications for fibril growth. Each
monomer that binds to a certain fibril end sees
the same interface, in contrast to a true dimeric
interface (in the case of a C2 symmetry), where
added monomers would alternatingly see either
two identical binding sites or a curb preformed
by the preceding subunit. The binding sites presented by the two fibril ends are different from
each other (Fig. 4, C and D), which leads to different binding pathways with possibly different
energy barriers and likely results in polarity of
amyloid fibril growth ( 19, 20). The binding energy, however, has to be identical on both ends.
The subunits are not planar; instead, the chain
rises along the fibril axis from the N to the C
terminus, forming grooves and curbs at the binding interface (Fig. 4, C and D). We refer to the
fibril ends as “groove” and “ridge” because b
strand 27 to 33 forms a ridge on the surface of
one end of the protofilament and a groove on the
other end. The b strands are staggered with relation to one another in a zipper-like manner (Fig.
4A and fig. S11C). For example, Phe4 of subunit
i is in contact with Leu34 and Val36 from the
subunit i-2 directly below. At both fibril ends,
the binding site for the addition of subunit i
contains contributions of subunits i-1, i-2, i- 3,
i- 4, and i- 5, or i+1, i+2, i+ 3, i+ 4, and i+ 5, respectively, and very small, likely insignificant
contributions from i- 7 and i+ 7 (fig. S11D). Therefore, five Ab(1– 42) subunits are required to provide the full interface for monomer addition. For
Fig. 1. Ab(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 b strands. (B) Atomic model of
the fibril with parallel cross-b 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
a contour level of 1.5 s; additional contour levels of 1 s and 2 s are shown in fig. S4). (B) Detailed view of
the interactions between the N and C terminus and the side chain of Lys28 (at a contour level of 1 s).
(C) Side view of the same two opposing subunits showing the relative orientation of the nonplanar subunits.
The large peripheral cross-b sheets are tilted by 10° with respect to the plane perpendicular to the fibril axis.