Monomer Isolation from Oligomeric Proteins within Coordination Cages to Study Interface Ligand Binding

Isolating native monomers of oligomeric proteins offers a promising yet underexplored approach to elucidating their functions and identifying drugs that target oligomerization interfaces. Here, we present a strategy for isolating monomers from oligomeric proteins by confinement within spherical Pd²⁺-coordination cages. Upon encapsulation of a stable dimeric protein, superoxide dismutase 1 (SOD1), a well-defined cavity of the metallo-cage selectively captured its monomer, retaining the same structure as in the native dimer. This size-selective isolation enabled direct analysis of monomeric properties, particularly interfacial ligand binding. Saturation transfer difference (STD) NMR revealed that flavonoids, such as quercetin, bind specifically to the encapsulated SOD1 monomer but not to the dimer, indicating interactions at the exposed dimer interface. These findings establish monomer isolation within coordination cages as a strong platform for studying oligomeric proteins.