THE ROLE OF CORONAVIRUS - HOST CELL MEMBRANE INTERACTIONS DURING VIRAL ENTRY AS MEDIATED BY CONSERVED REGIONS OF THE FUSION PEPTIDE

The global impact of coronavirus outbreaks such as SARS CoV-1 in 2002, MERS CoV in 2012, and the ongoing SARS-CoV-2 COVID19 pandemic, has highlighted the urgent need for a deeper understanding of coronavirus entry mechanisms to better predict and prevent future variants and pandemics. Central to viral entry is the binding and fusion of the virus with the host cell membrane, a process orchestrated by the Spike (S) protein. Within the S, the fusion peptide (FP) is a short, highly conserved domain that inserts into the host membrane, initiating membrane fusion, genome release and subsequent infection. Due to its critical role in viral entry and high sequence conservation across coronaviruses, the FP has been previously studied and characterized. However, several of its conserved residues and their precise interactions with host cell membrane components such as lipids remains underexplored. My dissertation addresses this gap by using biochemical and biophysical approaches to dissect the interactions between the FP and the host cell membrane. Specifically, I examine the functional role of two key residues: a hydrophobic phenylalanine and a conserved tyrosine. The first part of my research reveals how phenylalanine mediates interactions with membrane cholesterol, a component known to enhance viral entry. We also develop an atomic force microscopy based tool to study unnatural and naturally occurring mutations in the FP. The second part uncovers how the conserved tyrosine modulates FP structure during interactions with the membrane, impacting fusion and transduction outcomes. Together, these findings show that molecular chemical affinity between amino acids and water-membrane interface or membrane lipids is a critical parameter, more so than secondary structural changes in determining FP mediated coronavirus membrane fusion. By identifying and understanding conserved mechanistic features of the FP we can identify targets for the design of broad-spectrum antivirals, vaccines and screening or prediction tools. This work advances our fundamental understanding of coronavirus biology and supports the long-term goal of pandemic preparedness.

Name thesis:degree_name

Ph. D., Biomedical Engineering

Level thesis:degree_level

Doctor of Philosophy

Discipline thesis:degree_discipline

Biomedical Engineering

Grantor

Cornell University

Year dc:date.issued

2025

Author dc:creator

• Pachaury, Ambika

Committee members dc:contributor.committeemember

• Abbott, Nicholas
• Whittaker, Gary

• biochemistry
• cholesterol
• coronavirus
• fusion peptide
• membrane

Statement dc:rights

• Attribution 4.0 International

Licence dc:rights.uri

• https://creativecommons.org/licenses/by/4.0/

Language dc:language.iso

en

DOI

https://doi.org/10.7298/hhka-0270

Dc Identifier Other

ProQuest Submission ID: 15296
ProQuest Publication ID: 32245601

OAI identifier oai:identifier

oai:ecommons.cornell.edu:1813/121098