  The proteasome is a large biomolecular complex responsible for protein
degradation. It is under intense research due to its fundamental role in
cellular homeostasis, and tremendous potential for medicinal applications.
Recent data from X-ray crystallography and cryo-electron microscopy have
suggested that there is a large-scale structural change upon binding of an
inhibitor. We carried out atomistic molecular dynamics simulations of the
native and inhibited proteasomes to understand the molecular details of the
inhibition. Here we describe the technical details of the simulations and
assess the quality of the trajectories obtained. The biochemical aspects of the
proteasome are under further investigation and will be published elsewhere.
This work was a part of the GCS-Prot project at the HLRS, run on the Cray XC40
supercomputing system.
