Analyzing protein-protein interaction (PPI) networks has been a crucial prerequisite for understanding the molecular
basis for most of the diseases. Although several investigations have been carried out on PPI network analysis, none
of them explicitly considered binding affinity as a criterion for the analysis. In this work, we have performed a systematic
analysis of protein-protein interaction networks in five organisms based on the binding affinity of interacting partners. We
observed that eukaryotes are marginally dominated with high affinity complexes and an opposite trend was observed in
prokaryotes. In addition, hub-hub interactions have the highest percentage of “high affinity” interactions followed by hubnonhub
and nonhub-nonhub interactions. Further, all organisms contain hubs, which are enriched specifically with high or
low affinity complexes irrespective of the dominance of these interactions. Sub network analysis indicates that the closed
triad motifs with high and low affinity complexes are more significant than the open motifs. The analysis of clustering coefficient
and amino acid properties showed specific preferences in different organisms. These findings deepen the knowledge
of PPI networks and provide useful insights for target identification in drug discovery.
Keywords: Binding affinity, network analysis, network motif, protein-protein interaction.
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