Nakama T, Tadokoro M, Liu H. K, Ebihara R, Yagi-Utsumi M, Kato K, Fujita M.

chemRxiv (2026)

Weak interactions between proteins and ligands drive essential biological processes. However, structural insights into these transient complexes remain elusive due to the limitations of analytical techniques in capturing them at atomic resolution. Here, we report the isolation of a transient protein–ligand complex by confinement in a coordination cage to study its structure. When cutinase-like-enzyme (CLE) and its lipid ligand were co-encapsulated, their enforced proximity mimicked the densely packed cellular environments, enhancing binding at CLE’s active site. This confinement enabled nuclear magnetic resonance (NMR) analysis of the protein–lipid complex, revealing interactions at the catalytic site and adjacent loops that are undetectable by standard NMR in bulk solutions. Our approach using coordination cages offers a novel avenue for resolving otherwise inaccessible, transient protein–ligand interactions.