Probing the Binding Modes of a Multidomain Protein to Lipid-based Nanoparticles by Relaxation-based NMR

The interactions of two model multidomain proteins-covalently linked diubiquitins, Ub₂-with lipid-based nanoparticles have been quantitatively probed by the measurements of NMR lifetime line broadening, ΔR₂. By combined analysis of ΔR₂ profiles arising from interactions with liposomes of varying sizes, an approach recently developed for the characterization of interactions of monoubiquitin with liposomes, we determine how the parameters of exchange (liposome binding) and dynamics of each individual domain of Ub₂ on the surface of liposomes change when the domains are covalently attached to one another by a flexible linker. Two different covalent linkages were used: K63-linked and K48-linked Ub₂. The possibility of three distinct modes of binding of Ub₂ to liposomes requires the introduction of simple but important modifications to the strategy of analysis originally developed for monoubiquitin.