5. Conclusion
The alteration of the structure network upon transient interactions
between the structure of a protein complex of interacting partners is
analysed by comparing it against an available unbound structure as a
reference. Studying the effect of perturbations using a network graph of
residue-residue interactions within the protein is a beneficial and
robust tool in the analysis of structural excursions. Comparing several
basic network parameters and using advanced graph spectral approaches a
local and global difference between the unbound and the bound form of
protein chains is identified. It is understood that even when there is
no significant change in the overall fold of a given protein the network
of interactions may rearrange themselves to yield a preferred function
or phenotype. Change of protein function can be analysed by studying the
change in network parameters at the active site. The protein binding
event is found to increase the connectivity within a protein in the case
of a non-enzymatic toxin inhibitor. A significant loss of connectivity
in the case of DLD protein is associated with the formation of a strong
hydrophobic patch in the bound form of this homodimer enzyme. Probing
the spectral properties of the protein structural network yielded
Fiedler vectors which are compared to find nodes which jump from one
cluster to another. The path of communication from the site of binding
to the highest perturbed site is obtained by building the shortest path
between the nodes. These methods of studying the effect of perturbations
throw light on understanding the allostery mechanisms.