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.