Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces

Overview & Synopsis

The modeling of protein assemblies on the atomic level remains a central issue in structural biology, as protein interactions play a key role in numerous cellular processes. This problem is traditionally addressed using docking tools, where the quality of the models that are produced is based on their similarity to a single reference experimental structure. However, this approach using a static reference does not take into account the dynamic quality of the protein interface. Here, we used all-atom classical Molecular Dynamics simulations to investigate the stability of the interface for three complexes that previously served as targets in the CAPRI competition, and for each one of these targets, ten models distributed over the High, Medium and Acceptable categories. To assess the quality of these models from a dynamic perspective, we set up new criteria which take into account the stability of the reference protein interface. We show that, when the protein interfaces are allowed to evolve along time, the original ranking based on the static CAPRI criteria no longer holds as over 50% of the docking models undergo a category change (either toward a better or a lower group) when reassessing their quality using dynamic information.