The Systems Biology of the Protein Quality Control

Abstract

The 26S proteasome, an ATP-dependent protease, is the main powerhouse for protein degradation in all eukaryotic cells. Proteostasis is maintained by the ubiquitin-proteasome system (UPS) targeting aberrant proteins whose accumulation and aggregation are hallmarks of aging and neurodegenerative disorders. Previous studies demonstrated complex regulations of the formation and clearance of protein aggregates in eukaryotic cells, to minimize their damage to cellular activities. However, the mechanism of how protein aggregates are processed, as well as which factors are involved, are mostly elusive. In this dissertation, I investigate how aberrant proteins are selectively degraded by the proteasome and how the cell processes the aggregates of misfolded proteins. First, I develop a novel approach to simulate the ATPase's conformational dynamics using its empirical free-energy landscape (FEL). The FEL model successfully predicts the proteasome behaviors under a variety of conditions both in this and in previous studies and provides important insights into the molecular events and transitions underlying proteasomal activities. Damaged or misfolded proteins, if survive proteasomal degradation, may aggregate and form a macroscopic cellular structure called "aggresome". Aggresome can arise in various stress conditions and may nucleate the formation of pathological aggregates in neurodegenerative diseases. In the second study, I establish the first in vitro model system to recapitulate the process of aggresome formation and clearance, which provides unprecedented opportunities to investigate the mechanism of the complex regulation of processing aggregated proteins in the cell. With this system, I divide the aggresome pathway into multiple stages including nucleation, centrosome targeting, and clearance, and identify the key players and their mechanistic activities in each stage separately. These findings are expected to reveal the link between the toxicity of protein aggregates and their ability to be targeted to the aggresome and undergo further clearance. Together, by integrating molecular mechanistic studies and live-cell phenotypic observations, this dissertation advances the understanding of how different components in the protein quality control systems collaborate to mount an effective defense against protein aggregation, which may inspire novel therapeutics to ameliorate disease-related protein aggregates.