Biomedical Engineering Reference
In-Depth Information
Graph of
k
-significant contacts in
S
(
k>
10)
0
.
65
Fig. 1.14
for
λ
max
=1
.The
red
and
blue
sub-graphs
respectively correspond to the
Y
-complex and
T
-complex. The nodes contained in each of the five
dashed
regions define a complete sub-graph, i.e., a clique of size 4
•
Topological stability.
In Sect.
1.3.3
, the stability of a complex has been defined as
the difference between its birth and death dates. This information is particularly
relevant when a given complex collides with another to form a larger complex.
For an assembly involving a prescribed number of complexes, one expects the
variation of the number of complexes as a function of
λ
to exhibit a plateau.
Also, for an assembly with symmetries, the homogeneity of the model can be
inferred from the stability of complexes featuring the same types, but located in
different places.
•
Geometric accuracy.
A complex may involve the correct protein instances, but
may have a loose geometry. Comparing its volume to that occupied by its
constituting instances is the goal of the volume ratio of Eq. (
1.11
).
These analysis are illustrated in Fig.
1.15
, which is concerned with a tuple
T
corresponding to the seven types of the
Y
-complex. That is, the protein instances
painted in red correspond to the seven types involved in the
Y
-complex. Interest-
ingly, eight isolated copies of the
Y
-complex are observed in the Hasse diagram,
out of 16 expected. This observation shows that contacts between protein instances
belonging to several copies of the
Y
-complex can prevail over contacts within
the isolated copies. Equally importantly, the variation of the number of connected
components shows that, upon termination, the growth process leaves two red
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