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.