9. Figure legends
Figure 1: Diversity in structural network and backbone topology
upon transient association. (A) The structure deviation
information obtained by computing Cα-RMSD (Å) is compared against
network dissimilarity score (NDS) information obtained by comparing
structural networks based on atom contacts. The RMSD is plot on the
x-axis and the NDS is plot on the y-axis. The variability observed in
46% of the cases is lower than the mean comparison scores. About 194
cases (21.65%) show strong dissimilarity in network even though there
is no significant change in their topology, the alteration of the
network in these cases is analysed in detail. The control data shown in
yellow dots correspond to similar information obtained from structure
variability of single chain single domain proteins that do not associate
transiently. The mean of the working dataset is significantly greater
than the mean of the control. (B) Those cases with high network
dissimilarity without much structural deviation found on the top left
region of the scatter plot as listed. Only the top 12 cases out of which
four interesting cases are picked for detailed case studies are
highlighted. Their corresponding datapoints are marked on the scatter
plot shown on the left. The list of 197 cases that fall in this region
are tabulated in Supplementary Figure 4.
Figure 2: Alteration of structural network in case studies
analysed from change in basic network parameters. The observed changes
are illustrated on cartoon diagram of the structure networks. Edges that
are gained and lost are shown as orange and blue lines respectively.
Those hubs that are gained and lost are shown as orange and blue spheres
respectively. (A) rearrangement of edges in the pore domain of
the chain A in AcrB protein is shown, where most of the edges around the
pore are lost and those within the pore are gained. (B) Loss of
hubs in the C-terminal domain of the amylase protein is observed.(C) Several edges and hubs are gained around the binding site
of the Iota toxin component upon interaction with actin protein.(D) Loss of edges far form the binding site is observed in
human DLD protein.
Figure 3: Absolute difference between Fiedler vectors (Fv) of
DLD protein. Fv components cluster the nodes of the PSN into groups.(A) shows the aligned Fv components of the bound and unbound
PSN of DLD protein. The clustering of most sites look almost similar
since the topological change in the backbone is not much. (B)The absolute difference between the vectors point to those nodes whose
local clustering have changed due to variation of edge weights. When the
absolute difference between these vectors is taken, it is found that
there are spikes at specific sites which have been perturbed by being
clustered differently. (C) these specific sites are mapped onto
the cartoon diagram of the bound protein. The binding partners are shown
as surface. The sidechains of identified sites in the bound and unbound
structures are shown as yellow and red spheres respectively.