On the Effect of Binding on Ubiquitin Dynamics

by Jan Henning Peters
Doctoral thesis
Date of Examination:2013-04-02
Date of issue:2014-03-26
Advisor:Prof. Dr. Bert de Groot
Referee:Prof. Dr. Bert de Groot
Referee:Prof. Dr. Christian Griesinger
Persistent Address: http://dx.doi.org/10.53846/goediss-4429

 

 

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Abstract

English

Protein-protein interactions play an important role in all biological processes. But the principles underlying these interactions are not yet fully understood. Ubiquitin is a small signalling protein that non-covalently interacts with and is recognised by a multitude of other proteins. I have conducted molecular dynamics simulations of ubiquitin in complex with 12 different binding partners and compared ensembles of bound and unbound ubiquitin to 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 characteristic 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, I introduce a model of conformational restriction, extension and shift, which describes the full range of observed effects. The observation of characteristic restrictions of the main mode dynamics in complexes, lead me to develop the hypothesis that ubiquitin binding can be modulated by changing main mode behaviour, for example by mutation of residues in the hydrophobic core. Using a screening protocol based on non-equilibrium free energy simulations, eleven mutations of ubiquitin were identified that shift the equilibrium population of unbound ubiquitin along the main mode. I calculated the effect of these mutations on the free energy of binding to different binding partners that require ubiquitin to be a characteristic state, observing a significant shift in binding affinity.
Keywords: Ubiquitin; Molecular Dynamics; Protein-Protein Interaction; Binding; Conformational Dynamics
 
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