Discussion
Our goal has been to analyze whether most experimental results
concerning Synuclein oligomers, protofibrils, and transmembrane channels
are consistent with relatively simple β-barrel assemblies in which all
monomers have approximately identical conformations and interactions. We
are as concerned with understanding the overall assembly process as with
modeling any specific oligomer structure. Figs. 17 and 25 outline a
plausible, if somewhat speculative, series of transitions leading from
trimers and tetramers, to larger oligomers, lipoproteins, protofibrils,
fibrils, and transmembrane channels.
Although we attempt to make our models and hypotheses as simple as
possible, they are more complicated and ambiguous than we would have
preferred. Nonetheless, they are no more complex than required to
explain experimental results; if anything they are too simple. Our
models typically have a higher content of secondary structure than
reported experimentally. As previously described for the helical trimers
and tetramers of Figs. 5 and 18, we suspect that the secondary
structures of these more complex models are also only fractionally
occupied. A major point of Figs. 17 and 25 is that the assemblies are
dynamic and unlikely to be as structured as the models imply, especially
as they merge or morph into other assemblies or break down. Thus we view
our models as idealized hypothetical approximations of time-averaged
structures for some of the more stable stages of synuclein interactions;
i.e. for specific assemblies that can be identified microscopically
and/or isolated biochemically.
Tight packing between adjacent β-barrels in our models may account for
some features of synuclein sequences that, to our knowledge, have not
been explained previously: e.g., the prevalence of small apolar
side-chains, especially glycine and alanine, but also valine, and small
ambivalent threonine and serine within putative β-strands and the
preference for valine over the larger isolucine and leucine side-chains.
The high degree of conservation of these residues among the three
synuclein families suggests a vital role for these residues, but that
role is unlikely to involve fibril formation since β-Syn does not form
fibrils. A novel feature of our concentric β-barrel hypothesis is the
concept that intermeshing-pleats facilitates tight packing between
adjacent concentric β-barrels in some assemblies. The presence of
glycines may reduce steric clashes when this type of packing does not
occur; i.e., if pleates cross one another. Another striking feature of
synuclein sequences is the distribution of charged residues. Although
there is evidence that the negatively charged Ct domain is important to
some interactions and assemblies, its purpose has not been explained.
Here we suggest that its negative charges interact with positively
charged components of some zitterionic lipid headgroups, particularly in
high-density lipoproteins, but possibly in membranes as well. Highly
conserved positively charged lysines of the putative signature turn
regions are proposed to interact with negatively charged components of
lipids and fatty acids.
The major motivation for analyzing amyloid structures is to develop
effective ways to prevent, treat, and/or cure the devastating diseases
they cause. Those of us who study molecular structure want to know which
assemblies are functional, which are benign, and which are toxic. Then
perhaps we can eliminate or neutralize toxic culprits without hindering
vital functions. Low resolution EM images and hypothetical models will
not suffice; but they may help achieve these goals.
Lysenin and Aerolysin toxins share several properties with the
concentric β-barrel models we have proposed previously for Aβ42 and
propose here for synuclein amyloid oligomers: 1) they are composed of
multiple identical subunits related by radial symmetry, 2) they contain
concentric β-barrel structures, 3) diameters and tilt angles of their
β-barrels are consistent with β-barrel theory, 4) they exist both in
soluble and transmembrane channel conformations, and (5) AFM images of
the channel conformations are similar. However, amyloids are
substantially more polymorphic and less stable than the two toxins; so
much so that they are often said to be intrinsically disordered. These
factors complicate experimental determination of their oligomeric
structures. In the Appendix we list some examples of experimental
approaches suggested by our models. These include experiments to: reduce
polymorphism and disorder by stabilizing specific oligomer structures,
determine which assemblies are toxic and which portions of those
assemblies are responsible for the toxicity, to obtains additional
structural images, and to develop techniques and/or drugs to treat PD
and other Synuclein-related diseases.
We hope our hypotheses and models will assist efforts to obtain the
detailed evidence that can lead to medical breakthroughs.