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Although proteins have been recognized as small-world networks and their small-world network properties of clustering and short paths have been exploited computationally to produce biologically relevant information, they have not been truly explored as such, that is as navigable small-world networks in the original spirit of Milgram’s work. This research seeks to fill this gap by exploring local search on a network representation of proteins and to probe the source of navigability in proteins. Previously, we confirmed that proteins are navigable small-world networks and observed that local search paths exhibit different characteristics from global search paths. In this paper, we investigate the biological relevance of the differences in path characteristics on a type III receptor tyrosine kinase (KIT). A chief difference that works in favour of local search paths as intra-protein communication pathways is their weaker proclivity, compared to global search paths, for traversing longrange edges. Longrange edges tend to be less stable and their inclusion tends to decrease the communication propensity of a path. The source of protein navigability is traced to clustering provided by shortrange edges. The majority of a protein’s shortrange edges reside within structures deemed important for longrange energy transport and modulation of allosteric communication in proteins. Therefore, the disruption of intra-protein communication as a result of the destruction of these structures via random rewiring is expected. A local search perspective leads us to this expected conclusion while a global search perspective does not. These findings initiate the compilation of a list of path properties that are characteristic of intra-protein pathways and could suggest fresh avenues for evolving and regulating navigability in small-world networks.

Comparing local search paths with global search paths on protein residue networks: allosteric communication