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Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy (PhD)

Degree Program

Molecular and Cellular Biology

Year Degree Awarded

2016

Month Degree Awarded

February

First Advisor

Lila M. Gierasch

Subject Categories

Biochemistry | Molecular Biology | Systems Biology

Abstract

The three-dimensional (3D) native structure of most proteins is crucial for their functions. Despite the complex cellular environment and the variety of challenges that proteins experience as they fold, proteins can still fold to their native states with high fidelity. The reason for this is the presence of the cellular proteostasis network (PN), consisting of molecular chaperones and degradation enzymes, that collaborates to maintain proteostasis, in which the necessary levels of functional proteins are optimized. Although extensive research has been carried out on the mechanisms of individual components of the proteostasis network, little is known about how these components contribute to the functioning of the network as a whole. A new protein can have three folding fates: natively folded, aggregated, or degraded. The fate is determined by both a protein’s intrinsic biophysical properties and the cellular proteostasis network through kinetic partitioning. To understand the interplay between a protein’s intrinsic biophysical properties and the cellular proteostasis network, an integrated computational and experimental approach was used. The folding fates of model proteins with different intrinsic biophysical properties under varying conditions of the proteostasis network were determined. Using FoldEco, the effects of the kinetic and thermodynamic properties of proteins on their folding fates were investigated systematically, and predictions were consistent with wet lab experiments. The folding fate of a protein is under a thermo-kinetic limitation, which indicates that the fate depends on either the kinetics or thermodynamics, but (for the most part) not on both at the same time. Different proteins behave according to the values of their limiting properties. Furthermore, up-regulation of the entire proteostasis network through the σ32 transcription factor has beneficial effects on model proteins with low stabilities and high aggregation propensities. However, the effects of up-regulation of individual chaperones or the major degradation enzyme, Lon are substrate-dependent and are related to their biophysical properties. Furthermore, KJE, GroELS, and Lon form an efficacious triad for maintaining proteostasis, and their contributions depend on the biophysical properties of their substrates, and on the concentrations of these PN components and substrates at any given time.

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