Virtual Quasi-2D Intermediates as Building Blocks for Plausible Structural Models of Amyloid Fibrils from Proteins with Complex Topologies: A Case Study of Insulin

Conformational transitions
of globular proteins into amyloid fibrils
are complex multistage processes exceedingly challenging to simulate
using molecular dynamics (MD). Slow monomer diffusion rates and rugged
free energy landscapes disfavor swift self-assembly of orderly amyloid
architectures within timescales accessible to all-atom MD. Here, we
conduct a multiscale MD study of the amyloidogenic self-assembly of
insulin: a small protein with a complex topology defined by two polypeptide
chains interlinked by three disulfide bonds. To avoid kinetic traps,
unconventional preplanarized insulin conformations are used as amyloid
building blocks. These starting conformers generated through uniaxial
compression of the native monomer in various spatial directions represent
6 distinct (out of 16 conceivable) two-dimensional (2D) topological
classes varying in N-/C-terminal segments of insulin’s A- and
B-chains being placed inside or outside of the central loop constituted
by the middle sections of both chains and Cys7A–Cys7B/Cys19B–Cys20A
disulfide bonds. Simulations of the fibrillar self-assembly are initiated
through a biased in-register alignment of two, three, or four layers
of flat conformers belonging to a single topological class. The various
starting topologies are conserved throughout the self-assembly process
resulting in polymorphic amyloid fibrils varying in structural features
such as helical twist, presence of cavities, and overall stability.
Some of the protofilament structures obtained in this work are highly
compatible with the earlier biophysical studies on insulin amyloid
and high-resolution studies on insulin-derived amyloidogenic peptide
models postulating the presence of steric zippers. Our approach provides in silico means to study amyloidogenic tendencies and viable
amyloid architectures of larger disulfide-constrained proteins with
complex topologies.