Fig 1.
Basic overview of pyProGA functionality.
Input requirements are on the left, data structure in the centre and various analytical and output options are shown. The subsystem analysis requires the same kind of files to be loaded for the monomers as was for the super-system (dimer).
Fig 2.
The PRN of the supersystem consisting of monomers A and B and the protein-protein interface (PPI): G = GA ∪ GB ∪ GPPI. GA and GB contain all nodes and edges within protein A and B, respectively. a) GPPI contains vertices from both monomers, but only those vertices, which have at least one edge connecting it to a vertex from the other monomer. The edges in GPPI are only those which connect the subgraphs GA and GB (dashed lines) and no edges within the subgraphs GA, GB. Hence, GPPI is a bipartite graph. Part b) shows how blocks in the adjacency matrix A correspond to parts of G and the adjacency matrix APPI of GPPI (circles indicating edges in GPPI).
Fig 3.
Network Differential Analysis (NDA).
The protein structure coloured to represent the magnitude of the centrality for each residuum. The PyMOL colour palette rainbow is used (red colour for high centrality, blue for low values). In a) is shown and in b) we show
results. Selected high scoring residues are labelled.
Fig 4.
a) The attractive GPPI. Green monomer A, blue B. Thickness of edge corresponds to interaction strength, colour to character; red for prevailing electrostatic, blue for dispersion, see [85]. b) First four most dominant principal coordinates (interaction motifs in the PPI) as identified by the SVD analysis of GPPI. Colour coded assignment of residues to PC. Factor f(r) is defined by Eq 3. c) 3D-SPIE plot helps to identify strongest attractive and repulsive interactions between monomers A and B. More details in S1 File.
Fig 5.
NDA predictions and experimental data.
The NDA scores for the residues in the UL141…TRAIL-R2 complex based on an FMO/DFTB calculation. The top panel shows the scores of residues in both proteins (the border is depicted by the dashed line) and the bottom is a detailed plot for the residues of the TRAIL-R2 protein. The table contains experimental SPR (surface plasmon resonance) data published elsewhere [87]. Specific site mutations in the TRAIL-R2 protein to alanine (so called alanine scan), resulted in altered stability of the complex. The NDA bars corresponding to the residues that were mutated in the SPR experiments are labelled.