PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape

Ubiquitin (Ub) can generate versatile molecular signals and lead to different celluar fates. The functional poly-valence of Ub is believed to be resulted from its ability to form distinct polymerized chains with eight linkage types. To provide a full picture of ubiquitin code, we explore the binding landscape of two free Ub monomers and also the functional landscapes of of all eight linkage types by theoretical modeling. Remarkably, we found that most of the compact structures of covalently connected dimeric Ub chains (diUbs) pre-exist on the binding landscape. These compact functional states were subsequently validated by corresponding linkage models. This leads to the proposal that the folding architecture of Ub monomer has encoded all functional states into its binding landscape, which is further selected by different topologies of polymeric Ub chains. Moreover, our results revealed that covalent linkage leads to symmetry breaking of interfacial interactions. We further propose that topological constraint not only limits the conformational space for effective switching between functional states, but also selects the local interactions for realizing the corresponding biological function. Therefore, the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity. The simulation results also provide several predictions that qualitatively and quantitatively consistent with experiments. Importantly, the K48 linkage model successfully predicted intermediate states. The resulting multi-state energy landscape was further employed to reconcile the seemingly contradictory experimental data on the conformational equilibrium of K48-diUb. Our results further suggest that hydrophobic interactions are dominant in the functional landscapes of K6-, K11-, K33- and K48 diUbs, while electrostatic interactions play a more important role in the functional landscapes of K27, K29, K63 and linear linkages.Author Summary: Ubiquitination, as an important post-translational modification of proteins, provides a versatile cellular signaling mechanism. This is mostly contributed by the possibility of ubiquitin units to form different polyUb chains through eight different linkages. However, it is still unclear how these linkage types determine the different functions of polyUb chains. In this study, we address this question via the theoretical modeling and molecular dynamics simulation. This allows us to obtain a full picture of topology-function relationship of polyUb chains. The theoretical results led us to propose that topology of polyUb chains selects the functional landscapes from its binding landscape and the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity.