Regensburg 2013 – scientific programme

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BP: Fachverband Biologische Physik

BP 8: Posters: Proteins

BP 8.20: Poster

Monday, March 11, 2013, 17:30–19:30, Poster B2

Ubiquitin dynamics in complexes investigated using Molecular Dynamics simulations — •Jan Henning Peters and Bert de Groot — Max Planck lnstitute für Biophysikalische Chemie, Göttingen, Germany

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, regulates 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 several 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.