Department or Program

Biology

Abstract

All living cells contain membrane proteins called ion channels. Ion channels regulate the diffusion of ions across both sides of the membrane, allowing for vital functions such as the regulation of cellular content and the transmission of electrical signals between cells. Viroporins are ion channels that are encoded by viruses. Viroporins are found in devastating viral pathogens such as COVID-19, HIV, and rotavirus. NSP4 is a rotavirus viroporin that disrupts cellular Ca2+homeostasis, leading to host cell lysis and the proliferation of more virions. Though the structure of some domains of NSP4 have been determined, the full-length structure of this viroporin is unknown. Until recently, only in vitro methods of structure determination, such as x-ray crystallography, were considered to be accurate. However, two recently published algorithms demonstrated a high degree of accuracy when determining the structure of membrane proteins from their amino acid sequences. These algorithms are known as AlphaFold and trRosetta. The goal of this project is to use AlphaFold to predict the molecular structure of the full-length NSP4 from SA11 rotavirus and compare this structure to a recently determined structure from the Banks lab generated via trRosetta, as well as its established crystal structure. This project also includes comparisons between predicted and experimental structures for AlphaFold’s intended targets: eukaryotic and prokaryotic proteins.

Level of Access

Restricted: Embargoed [Open Access After Expiration]

First Advisor

Banks, Lori

Date of Graduation

5-2022

Degree Name

Bachelor of Arts

Number of Pages

36

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