Structural Characterization of Proteasome Inhibition

Abstract

The proteasome plays a major role in non-lysosomal protein degradation pathways and inhibition of proteasomes became a valid therapeutic strategy for anti-cancer therapy in the recent years. Current efforts focus on the identification and development of second generation inhibitors with enhanced pharmacological properties. For this, improved structural knowledge and an advanced biochemical characterization of proteasome inhibition is necessary. In this work, I present a reproducible and robust pipeline that enables the purification, crystallization, crystal handling and structure determination of the native 20S proteasome and 20S-inhibitor complexes. Crystal structures including four previously uncharacterized inhibitor complexes with clinically relevant inhibitors were elucidated at resolutions between 1.8 and 2.1 Å. The improved resolutions allow to define the inhibition chemistry at atomic resolution. This led to revised descriptions of binding modes for epoxyketone and ketoaldehyde inhibitors, a redefinition of the proteasome active site, and a concept for future drug design. Single particle electron cryomicroscopy (cryo-EM) was the method of choice when studying the influence of 20S core particle inhibition on the dynamic 26S holoenzyme. We determined structures of the 26S proteasome with and without inhibitor and report for the first time structural changes of 26S proteasomes upon inhibition. Drug binding limits the conformational space of the 19S regulatory particle and we identified an energy barrier that stabilizes the proteasome in a non-productive state. Here, we describe that core particle inhibition triggers a structural long-range allosteric regulation of the human 26S proteasome. This thesis offers insights into the exact catalytic mechanism of peptide cleavage and proteasome inhibition in the human 20S proteasome and a detailed description of the proteolytic site. In addition, the structural impact of 20S inhibition on the human 26S proteasome was studied for the first time and the findings allow for a new way to screen and develop future allosteric proteasome inhibitors. A reproducible workflow to structurally study inhibitor-proteasome complexes by advanced protein complex purification combined with X-ray crystallography or single particle cryo-EM is presented.