ANALYSIS OF ATP-DEPENDENT CHAPERONE PROTEIN INTERACTIONS WITH MISFOLDED PROTEINS, AMYLOIDS, AND AGGREGATED PROTEINS

Abstract

Protein aggregation occurs when proteins adopt non-native conformations, exposing hydrophobic surfaces due to misfolding. The exposed regions of two or more proteins associate to form amorphous deposits or highly ordered, stable fibrillar structures called amyloid aggregates. Within the cell, a robust network of proteins safeguard against protein misfolding and aggregation. This network is referred to as the proteostasis network and includes molecular chaperone proteins, co-chaperone proteins, and the ubiquitin proteasome system. Molecular chaperone proteins function in various cellular processes including intracellular transport, oligomeric assembly, and efficient protein folding. Moreover, molecular chaperones are required for folding denatured, misfolded, and de novo proteins into their native conformation. It is thought that neurodegenerative diseases may be the result of a derailed proteostasis network in response to aging, mutations, and environmental stress, among other factors that contribute to protein aggregation. The neurodegenerative diseases Alzheimer’s disease, Huntington’s disease, and Parkinson’s disease are characterized by protein misfolding and accumulation into aggregates composed of amyloid fibrils. In each of these protein misfolding diseases, the roles of chaperone proteins are complex and not well understood. Given that these diseases share a common theme of protein misfolding and aggregation, researchers have questioned whether molecular chaperone proteins are involved in disease pathology, which has led to investigations into the possible use of chaperone-based strategies as treatment options. It is thought that protein aggregation in neurodegenerative diseases results from disturbances in pathways that regulate protein quality control. This thesis investigates the role of ATP-dependent chaperone proteins in disaggregating and resolubilizing protein aggregates, including model aggregates, amyloids of Sup35 in yeast and hyperphosphylated tau in human cells. Here, we investigated the biochemical properties of the Hsp100/Clp chaperone protein family, which couples ATP binding and hydrolysis to unfold and reactive aggregated and misfolded polypeptides. We studied the role of molecular chaperone proteins in the progression of protein aggregation in a model of Alzheimer’s disease and developed novel chaperone tools for targeting amyloid proteins for protein clearance. Furthermore, we investigated the mechanism of substrate recognition and amyloid disassembly by Hsp104 in a yeast [PSI+] prion model of amyloid assembly. Moreover, we identified a novel function of the chaperone protein ClpX in protein disaggregation in vitro and in vivo. We observed that ClpX can bind and reactivate native and engineered protein aggregates in the absence of ATP. Lastly, in an Alzheimer’s disease model of hyperphosphylated tau, we monitored changes in chaperone protein levels in response