Naturally and synthetically linked lys48 diubiquitin: a QM/MM study

Site-specific chemical conjugates of proteins with ubiquitin-like modifiers are a powerful tool for biochemists to probe the function of these post-translational modifications. As a prominent example, the seven native isopeptide-linked diubiquitins serve as models to study polyubiquitin chains, but not all of them can be prepared by enzymatic means. To date, several approaches to access synthetically conjugated diubiquitins have been reported, however, an experimental structure of such a molecule with an unnatural linker remains elusive. Therefore, here we present structural models of the Lys48-connected diubiquitin with the natural isopeptide and a synthetic triazole linker using hybrid quantum mechanical and molecular mechanical (QM/MM) methods. Despite differences in the flexibility of the linkers, the systems with the synthetic and natural linker were found to be very similar in regard to the analyzed geometric features. This provides computational support for the use of the synthetically linked conjugate as a mimic of the natural isopeptide bonded diubiquitin.