Molecular Structure of Piwi–Arx Noncovalent Interactions in Drosophila melanogaster

Abstract

This thesis investigates how the Piwi protein regulates germline stem cells in the ovary of Drosophila melanogaster, with a focus on how its activity is shaped by direct protein–protein interactions. Genetic evidence has shown that Piwi's functionality mainly relies on RNA-guided chromatin repression and interactions with other proteins. To better understand this mechanism, Piwi’s interaction with Arx was analyzed and compared to the Piwi–Papi interaction, which served as a control. Structurally several protein-protein interactions were examined using tools such as AlphaFold, ChimeraX, and Mol*. The Piwi–Arx interaction was modeled and assessed for stability and binding confidence, while Piwi mutants (S606W and R679A) were designed to disrupt predicted amino acids and noncovalent interactions to test their importance in binding. The results suggest that Piwi's function depends strongly on its binding partners. The Piwi–Arx interaction showed high predicted interaction confidence, supporting the idea that Arx may contribute to activation or stabilization of Piwi-mediated silencing. Overall, this work highlights that Piwi’s role in genome regulation is not determined by Piwi alone, but by a network of protein interactions that help regulate silencing roles in the germline.