2.3 Random coil Oligomers with alpha-helical content
The AlphaFold2 machine-learning approach is based on protein data bank
(PDB) templates, sequence alignments, co-evolution rules and multiple
algorithms to design a protein-specific potential of mean force.
AlphaFold2 success stories include the prediction of single domain
protein structures,55 and most transmembrane protein
structures.56 AlphaFold2 limitations to predict very
accurately the structures of protein – protein (peptide)
complexes57,58 and generate conformational
heterogeneity59 were reported.
At the date of the present study, the PDB contained about 200,000
structures.60 The most striking AlphaFold2 result for
the structures of Aβ42 dimers up to hexamers is the prediction of
α-helix topologies for all species in addition to β-rich
topologies.54 The AlphaFold2 structures are shown in
Figure 1. While the dimer displays an antiparallel helix bundle spanning
the C-terminus (Figure 1A), all higher aggregates display parallel helix
bundles spanning the C-terminal residues 29-39. (Figures 1B-E). These
α-rich oligomers are supported indirectly by numerous experiments on Aβ
and many other amyloid polypeptides.
CD experiments on Aβ42 and Aβ40 peptides in pure buffer give 19% and
32% of α-helix structure after 4 days of
incubation.61 Addition of trifluoroethanol suggested
α-helical intermediates during Aβ assembly,62 and
addition of low solvent polarity stabilized partial α-helical structures
and accelerated Aβ40 amyloid fibrillation.63Pyroglutamate-modified pEAβ(3-42) aggregation also pointed to α-helical
intermediates, stabilized by parallel C-terminus interactions, each
monomer forming a helix-turn-helix spanning residues 10-23 and
30-36.64
Slow nucleation of short polyglutamine-containing Huntingtin fragments
via α-helix-rich oligomers and inhibition of amyloid structure in a
Huntingtin fragment by targeting α-helix-rich oligomers were also
reported experimentally.65,66 Using computational and
experimental approaches, human islet amyloid polypeptide (hIAPP)
fragment 8-20 fibril formation starts from isolated helical monomers,
helical dimers to hexamers, followed by the conversion to β at the
hexamer level.67 PolyQ-Aβ30-42 peptides at µM
concentration suggested an aggregation triggered by a rapid formation of
α-helical oligomers mediated by the C-terminal residues, as assessed by
CD and FTIR (Fourier Transformed Infrared)
spectroscopies.68 Infrared nanospectrometry monitored
a α-to-β transition during the self-assembly of the N-terminal Josephin
domain of ataxin 3.69 The conversion of rationally
designed α-helical peptides to amyloid fibrils and the oligomerization
of natural hexapeptides into amyloid fibrils through α-helical oligomers
are also well established.70,71 Overall, there are
many experiments reporting a minor population of partially folded
helical oligomers during amyloid fibril
formation.72,73
Additionally, a rational design of α-helical peptide inhibitors
targeting Aβ40 surface reduces the generation of toxic Aβ toxic
oligomers.74 Helical peptide foldamers and
peptidometics were found dual inhibitors of Aβ and hIAPP
fibrillization.75 Alpha-helix mimetics, which induce
α-helicity in Aβ using NMR and CD, inhibit the seed-catalyzed
aggregation of Aβ.76 Based on ion mobility
spectrometry – mass spectrometry combined to MD simulations, it was
suggested that Aβ C-terminal interactions play a key role in their
inhibitory activity.77 Finally, it was found that
Aβ25-35 peptide forms early stage helical conformations by CD and Raman
spectroscopic techniques, and carvedilol inhibits Aβ25-35
fibrillation.78
Computationally, AlphaFold2 α-helical tetramer and hexamer structures
are very stable using CHARMM36m-TIP3P modified and AMBER99SB-DISP for
0.3 µs MD simulations at 310 K.54 Transient formation
of helical conformations differing from helix bundles was reported by
numerous simulations of Aβ40 and Aβ42
oligomers,7,28,46,79 but a recent simulation proposed
that conformations with α-helical structure have a high propensity to
initiate Aβ42 aggregation.80 Finally, it should be
noted that the helix propensity of amyloid peptides is a fundamental
requirement to fulfill the lipid-chaperon model,81 and
helical intermediates during amyloid formation are catalysed by
membranes.36,72