Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection

Protein-protein interactions play an important role in all biological processes. However, the principles underlying these interactions are only beginning to be understood. Ubiquitin is a small signalling protein that is covalently attached to different proteins to mark them for degradation, regulate transport and other functions. As such, it interacts with and is recognised by a multitude of other proteins. We have conducted molecular dynamics simulations of ubiquitin in complex with 11 different binding partners on a microsecond timescale and compared them with ensembles of unbound ubiquitin to investigate the principles of their interaction and determine the influence of complex formation on the dynamic properties of this protein. Along the main mode of fluctuation of ubiquitin, binding in most cases reduces the conformational space available to ubiquitin to a subspace of that covered by unbound ubiquitin. This behaviour can be well explained using the model of conformational selection. For lower amplitude collective modes, a spectrum of zero to almost complete coverage of bound by unbound ensembles was observed. The significant differences between bound and unbound structures are exclusively situated at the binding interface. Overall, the findings correspond neither to a complete conformational selection nor induced fit scenario. Instead, we introduce a model of conformational restriction, extension and shift, which describes the full range of observed effects. Author Summary: Due to their importance in biological processes, the investigation of protein-protein interactions is of great interest. Experimental structures of protein complexes provide a wealth of information but are limited to a static picture of bound proteins. Ubiquitin is a signalling protein that interacts with a wide variety of different binding partners. We have used molecular dynamics simulations to compare the dynamic behaviour of bound and unbound ubiquitin in complex with different binding partners. Our observations suggest that the conformations accessible to bound ubiquitin, while often restricted in comparison to unbound ubiquitin, still occupy a subspace of the conformational space as those of unbound ubiquitin. This corresponds to the “conformational selection” binding model. Only on a local level near the binding interface, differences between bound and unbound structures were found in specific regions of the bound ensemble. To account for the different types of behaviour observed, we extend the currently available binding models by distinguishing conformational restriction, extension and shift in the description of binding effects on conformational ensembles.