Two sets of cyan and yellow fluorescent proteins, monomeric analogues, and analogues with a weak affinity for dimerization were functionalized with supramolecular host-guest molecules by expressed protein ligation. The host-guest elements induce selective assembly of the monomeric variants into a supramolecular heterodimer. For the second set of analogues, the supramolecular host-guest system acts in cooperation with the intrinsic affinity between the two proteins, resulting in the induction of a selective protein-protein heterodimerization at a more dilute concentration. Additionally, the supramolecular host-guest system allows locking of the two proteins in a covalent heterodimer through the facilitated and selective formation of a reversible disulfide linkage. For the monomeric analogues this results in a strong increase of the energy transfer between the proteins. The protein heterodimerization can be reversed in a stepwise fashion. The trajectory of the disassembly process differs for the monomeric and dimerizing set of proteins. The results highlight that supramolecular elements connected to proteins can both be used to facilitate the interaction between two proteins without intrinsic affinity and to stabilize weak protein-protein interactions at concentrations below those determined by the actual affinity of the proteins alone. The subsequent covalent linkage between the proteins generates a stable protein dimer as a single species. The action of the supramolecular elements in concert with the proteins thus allows the generation of protein architectures with specific properties and compositions.