Characterization of Pre-Dissociative Structures of the E6AP Trimer by All-atom Unbiased Molecular Dynamics

The activity of the E6AP protein, a member of the ubiquitin transfer system, is regulated through the association-dissociation of its homo-trimeric structure. Under physiologic conditions, this protein is in a mixture of mono, di and tri-mere complexes, where the D543A mutation further destabilize the complex. These featured render this protein as an excellent model for a study of pre-dissociation events that can be detected by applying a cluster analysis of the ∼200 ns long trajectories. The analysis of the WT complex revealed inherent divergence of the subunits, each exhibiting multiplicity of configurations that differ in their energy. Surprisingly, the trimer is more stable than the subunits. The D543A mutation caused the trimer complex to assume many equi-potential configurations, rendering it more flexible than the subunits. The trimeric destabilization is not observed in a mutant that affects only the structure of the active site. We propose that the pre-dissociation configurations can be identified much earlier than the structural disintegration of a proteinous complex.