Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection.

ABSTRACT: 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

SUBMITTER: Peters JH 

PROVIDER: S-EPMC3464204 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature