Biology Reference
In-Depth Information
FIGURE 3.1
Flowchart of the PSN analysis approach.
fromMD trajectories or ENM-NMA. Outcome of this stage is the total pool of paths
for the system under study. Meta paths made of the most recurrent nodes and links in
the path pool (i.e., global meta paths) are worth computing to infer a coarse/global
picture of the structural communication in the considered system. More resolved in-
formation on the most likely communication pathways can be additionally inferred
from cluster analysis of the path pool. Path clusters can be analyzed through cluster
meta paths, cluster centers, and computational descriptors of path features. All pa-
rameters defined for the PSN and PSN-PATH analyses in the case study shown
herein are summarized in
Table 3.1
.
3.2.2
Building the PSG
Building of the PSG is carried out by means of the PSN module implemented in the
Wordom software (
Seeber et al., 2011
). PSN analysis is a product of graph theory
applied to protein structures (
Vishveshwara, Brinda, & Kannan, 2002
). A graph is
defined by a set of vertices (nodes) and connections (edges) between them. In a
PSG, each amino acid residue is represented as a node and these nodes are connected
by edges based on the strength of noncovalent interactions between residues
(
Vishveshwara et al., 2009
). The strength of interaction between residues
i
and
j
(
I
ij
) is evaluated as a percentage given by the following equation:
n
ij
p
N
i
N
j
I
ij
ΒΌ
100
where
I
ij
is the percentage interaction between residues
i
and
j
;
n
ij
is the number of
atom-atom pairs between the side chains of residues
i
and
j
within a distance cutoff
