Date of Award

12-8-2025

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Bioinformatics

First Advisor

Robert Smookler Reis

Second Advisor

Srinivas Ayyadevara

Abstract

Protein aggregation within mitochondria emerges early in both aging and Alzheimer’s disease (AD) and contributes to progressive loss of proteostasis. Insoluble mitochondrial aggregate fractions from Caenorhabditis elegans revealed extensive enrichment of metabolic and translational proteins that also appear in human Alzheimer hippocampal aggregates. Comparative analysis across age and genotype identified a conserved subset of aggregation-prone proteins, several of which cluster around elongation factor 2 (eEF-2), a regulator of ribosomal translocation and energy coupling. Cross-species integration defined a network in which eEF-2 links chaperones, metabolic enzymes, and RNA-binding proteins that co-aggregate in both human Alzheimer material and nematode models. Functional tests such as RNAi-mediated knockdowns in C. elegans demonstrated that selective disruption of eEF-2–centered interactions reduced detergent-insoluble protein aggregate burden. It also showed improvement in physiological traits associated with proteostasis in tau-expressing strains, whereas Aβ models respond differently under identical conditions. Small-molecule binding at a defined surface pocket of eEF-2 remodels AD-specific interactions without altering its catalytic or ribosomal functions. Mitochondrial reporters showed increased TOMM-20 signal and diminished activation of the mitochondrial unfolded-protein response following treatment with the eEF-2 binding drug or small molecule, indicating restoration of mitochondrial integrity. These convergent findings from proteomics, network reconstruction, and experimental validation suggest that eEF-2 operates as a structural hub through which mitochondrial and cytosolic aggregates reinforce one another. Pharmacologic engagement of a non-catalytic interface weakens this reinforcement while sparing essential translation, providing a mechanistic framework for targeting proteostasis failure in AD and related neurological disorders.

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