Biomedical Engineering Reference
In-Depth Information
Fig. 7
Aggregation state network. The size of the largest aggregate N
la
and its number of
protofilaments N
pf
la
were used to cluster all simulation snapshots into states (i.e., nodes of
the network). The size and the color of nodes correspond to the statistical weight and the
number of protofilaments N
pf
la
, respectively. Links are direct transitions within 0.5 ns of Langevin
dynamics. Note the much higher heterogeneity of protofibrillar intermediates for the ˇ-unstable
(dE
D
2:5 kcal/mol,
bottom
) as compared to the ˇ-stable (dE
D
1:5 kcal/mol,
top
) model.
The
insets
show (proto)fibrillar structures that are representative of each region of the aggregation
state network. In these structures, monomers in the amyloid-competent conformer ˇ and amyloid-
protected conformer are in
red
and
blue
, respectively. Furthermore, hydrophobic spheres are
gray
and hydrophilic spheres are not shown for visual clarity. Reprinted from [
50
] with permission
by Elsevier
with its axis. The aggregation state network (Fig.
7
) is a graph in which the
states and direct transitions observed during the Langevin dynamics simulations
are displayed as nodes and links, respectively. Furthermore, the size of each
node reflects the statistical weight of the corresponding state. Micellar oligomers
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