NMR studies of polyubiquitin chains: insights into structural basis of functional diversity

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Signaling by polyubiquitin (polyUb) chains mediates numerous cellular processes. All these processes involve the covalent modification of the substrate protein with a polyubiquitin chain that is itself formed by isopeptide linkages between the C-terminus of one Ub and a specific Lys residue of the next Ub. Remarkably, the outcome of the signaling event depends on the specific Lys residue that is involved in the formation of the polyUb signal. In the current model of Ub-mediated signaling, diversity in signaling arises from the ability of differently linked polyUb chains to act as functionally distinct signals. Such a model predicts that the distinct structures adopted by alternatively linked polyUb chains modulate their recognition by various effector proteins. However, direct structural evidence in support of this view has been lacking. This work is aimed at elucidating structural differences (if any) between Lys48- and Lys63-linked polyUb chains, and to investigate the structural basis of the specific recognition of Lys48-linked polyUb chains by UBA domains.

Using a combination of NMR methods, Lys48-linked Ub2 chains are shown to adopt a 'closed' conformation in solution under physiological conditions. A switch in the conformation of these chains, from 'closed' to 'open' states with decreasing pH is described. The Ub2 interface in the 'closed' conformation is shown to be dynamic, allowing functionally important hydrophobic residues sequestered at the interface to be accessible to Ub-recognition factors. In contrast, Lys63-linked Ub2 chains are shown to be characterized by an extended conformation, with no definitive interface between the Ub units. Such an extended conformation allows each Ub moiety to independently bind a UBA molecule, in a manner similar to the monoUb-UBA interaction. The results presented in this study suggest that the specific recognition of Lys48-linked Ub2, however, may not involve such a simple 'one-UBA-per-Ub' interaction. The interaction of UBA with Lys48-linked Ub2 appears to involve the primary association of the UBA domain with the proximal Ub in Ub2. The relative positioning of the distal Ub in the chain allows its simultaneous association with the same UBA domain, leading to a higher affinity UBA-Ub2 interaction. The results provide the first experimental evidence that alternately linked polyUb chains adopt distinct conformations, and suggest that specific recognition of these chains might indeed depend on differences in their structures.