Introduction
The quest to determine precise molecular mechanisms by which amyloid
beta (Aβ) peptides wreak havoc on the human brain can appear hopeless.
These peptides are shapeshifters; they assume countless forms that are
often present simultaneously and likely have partially occupied
secondary structures (see Deleanu et al.1 and Urban et
al.2 for recent reviews). Numerous factors affect Aβ
assemblies; e.g., ions and heavy cations, lipids, concentration, time,
method of isolation and preparation, location in the body, initial seed
conformation, length of the peptide, and oxidation. Also, they appear to
interact with up to twenty receptors3, and with
several other types of amyloid-forming peptides.
It remains unclear which of their many guises and interactions are the
culprits. Much attention has focused on the most visible and stable
forms: fibrils within the amyloid plaques that are the hallmark of
Alzheimer’s Disease (AD). Their stability has allowed the molecular
structure of some forms to be determined experimentally. However,
fibrils come in multiple forms: some have U-shaped
monomers4-7; others have S-shaped
monomers5,8, some have two-fold symmetry along their
long axis and others have three-fold symmetry5,8; and
most have in-register parallel β-sheets, one has an elongated plus a
β-hairpin conformation9, and at least one highly toxic
mutant forms antiparallel β-sheets4-7,10. However,
evidence is increasing that much smaller assemblies, called oligomers,
are more detrimental (reviewed in11-13) and that the
longer of the two major forms, Aβ42, is the most
toxic12. A subset of the oligomer school contends that
Aβ oligomers perturb neuronal signaling and eventually kill neurons by
forming transmembrane ion channels13-20.
Many, perhaps most, large Aβ assemblies reflect their origin: i.e., the
final structure depends upon the ‘seed’ structure from which it has
grown21. Previously we attempted to address these
issues by developing atomically explicit models of the structures of
Aβ42 hexamers, dodecamers, annular protofibrils, and an ion
channel22,23. The starting point for our models was
the hypotheses that Aβ42 hexamers can adopt a concentric antiparallel
β-barrel structure with a hydrophobic core β-barrel, formed by the last
third of the sequence (S3), surrounded by a more hydrophilic β-barrel
formed by the first third (S1) and middle third (S2) of the sequence. In
these models all monomers have well defined identical conformations and
interactions with other monomers.
Several aspects of our hexamer model were unprecedented: (1)
six-stranded antiparallel beta-barrels had never been reported. However;
Laganowsky et al. 24 have since found that a
segment from an amyloid-forming protein, alpha B crystalline, indeed has
the six-stranded antiparallel β-barrel motif (which they call
Cylindrin), and Do et al. 25 found that several
eleven-residue peptides with the sequences of portions of S3 that
includes methionine also form this motif. Their calculations confirm our
findings that the presence of glycine facilitates packing of aliphatic
side chains (especially methionine) in the interior of the barrel. The
importance of these residues is supported by findings that mutation of
Gly33 to Ala26 or oxidation of
Met3527 reduces toxicity and alters oligomerization of
Aβ42. (2) Our β structures were antiparallel whereas all known Aβ fibril
β-structures were parallel. However, since then an Iowa mutant
responsible for some forms of early onset AD has been shown to form
fibrils with antiparallel β-sheets10. More important,
recent experiments indicate that some Aβ42 oligomers do have an
antiparallel β secondary structure that is similar to that of OMPA (an
antiparallel β-barrel channel)28-30, and NMR studies
of tetramers,
octamers31, and
150 kDa oligomers32 indicate that S3 β-strands are
antiparallel. Also, antiparallel oligomers are more toxic than those
with parallel structures28,30. (3) Concentric
β-barrels had never been observed when we proposed the structures. But
recent studies have found that the channel-forming toxins
Areolysin33 and Lysenin34 do, in
fact, contain concentric β-barrels. (4) There was no experimental
evidence supporting our proposal that the S1 segments form a β-strand or
possibly a β-hairpin. However, subsequently two fibril structures with
S-shaped monomers that include S1 have been solved (one with 3-fold
symmetry5,8 and one with two-fold
symmetry4). In both, the S1 and S2 segments comprise a
parallel β-sheet with a bend near the center of S1. We model S1 in two
basic conformations: as a continuous β-strand from residues 2-13, and as
a β-hairpin with residues A2-H6 forming the first strand (S1a) and
residues Y10-H13 forming the second strand (S1b). The β-turn of the
hairpin occurs at residues with a high propensity for turn and coil
conformations (D7-S8-G9)35, but the exact location and
direction of the turn varies among the models. Although often ignored by
modelers, numerous findings indicate that alterations within S1 segments
affect the toxicity of Aβ and that some mutations within S1 are
pathogenic (see 8 and 36 for
reviews). Banchelli et al.37 found that
Cu++ causes formation of dimers by binding between
His6 and His13 or His14 of two Aβ monomers. They concluded that at least
portions of adjacent S1 segments are antiparallel (consistent with some
of our models) rather than in-register parallel. Also, Tyr10 side chains
can cross-link under oxidizing conditions to form
dimers38, indicating that they are proximal in some
oligomers. (5) There was no experimental evidence that Aβ42 forms
β-barrels. However, Serra-Batiste et al. 19 have
recently discovered membrane-mimicking conditions under which Aβ42, but
not Aβ40 peptides, form a well-defined β-barrel composed of only two
monomeric conformations. These results support our proposal that Aβ42
channels contain well-ordered β-barrels resembling those we proposed for
oligomers and annular protofibrils.
Experimental constraints used in developing the models presented here
were derived primarily from negatively stained electron micrographs of
annular protofibrils. Two types of Annular ProtoFibrils have been
reported: beaded APFs (bAPFs) that resemble necklaces formed by a string
of beads, and smooth APFs (sAPF) that resemble smooth
rings39. Portions of electron micrographs used in this
study are shown in Fig. 1. These APFs form in the presence of hexane,
with bAPFs forming initially from oligomers, then gradually transforming
into sAPFs. Also, we have incorporated results of recent solid-state NMR
studies of oligomers31,32 in our latest models.