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Network theory-based approaches provide valuable insights into the variationsin global structural connectivity between differing dynamical states ofproteins. Our objective is to review network-based analyses to elucidate suchvariations, especially in the context of subtle conformational changes. Wepresent technical details of the construction and analyses of protein structurenetworks, encompassing both the non-covalent connectivity and dynamics. Weexamine the selection of optimal criteria for connectivity based on thephysical concept of percolation. We highlight the advantages of usingside-chain based network metrics in contrast to backbone measurements. As anillustrative example, we apply the described network approach to investigatethe global conformational change between the closed and partially open statesof the SARS-CoV-2 spike protein. This conformational change in the spikeprotein is crucial for coronavirus entry and fusion into human cells. Ouranalysis reveals global structural reorientations between the two states of thespike protein despite small changes between the two states at the backbonelevel. We also observe some differences at strategic locations in thestructures, correlating with their functions, asserting the advantages of theside-chain network analysis. Finally we present a view of allostery as a subtlesynergistic-global change between the ligand and the receptor, theincorporation of which would enhance the drug design strategies.

Surveying the side-chain network approach to protein structure and dynamics: The SARS-CoV-2 spike protein as an illustrative case