Network organization of protein binding-site landscapes across scales

Abstract

Studying protein binding sites helps explain ligand recognition and selectivity, informing drug development and repurposing. Here, we combine protein language model embeddings with network analysis to investigate how local recognition environments organize across scales. We represented 121,673 non-redundant, experimentally identified binding sites using ProtT5 embeddings of ligand-contacting residues and constructed a mutual nearest-neighbor network. Embedding proximity was associated with local structural similarity, supporting the structural relevance of network relationships. Globally, the network exhibited ligand-related organization. At the mesoscopic scale, communities revealed heterogeneous landscapes within established protein classifications, with InterPro categories ranging from compact neighborhoods to dispersed recognition environments. Focusing on kinases, a major class of drug targets, we found that communities within individual proteins distinguished separate binding regions and resolved recurrent residue-defined microenvironments within broad structural classes. Local similarities also connected sites in proteins with low sequence identity and non-overlapping InterPro annotations, suggesting shared recognition features across distant proteins. Together, these results show how network organization captures both diversification within protein categories and local similarities across their boundaries. This multiscale framework complements conventional protein classifications and provides a basis for prioritizing structural and biochemical investigations of ligand cross-reactivity, selectivity, and repurposing opportunities.