Theses Doctoral

Structure and Neutralization of Viral Fusion Proteins

Casner, Ryan Gavin

Emerging infectious diseases remain persistent threats that are challenging to predict. Humanity has faced many terrible pandemics and will face more, but to pinpoint the specific time and place of an outbreak, the type of pathogen, and the consequences is effectively impossible. This point was recently highlighted by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) viral pandemic, which led to global clinical and socioeconomic damage. When confronted by such a viral threat, the biomedical research community fervently responded with unprecedented haste to reveal SARS-CoV-2 clinical information, genome sequences, spike fusion protein structures, antigenic properties, antiviral therapeutics, and new vaccine platforms all within a year.

As a small part of the tremendous collaborative research response, I used structural methods to study the SARS-CoV-2 spike fusion protein, specifically mechanisms of antibody-mediated viral neutralization. Viral fusion proteins are key components of virus particles that enable a virus to enter an animal host cell. Fusion proteins are the most common targets for neutralizing antibodies and serve a vital role as vaccine immunogens to elicit a protective immune response. To develop an understanding of SARS-CoV-2 antibody-mediated neutralization, one of my primary research interests was solving antibody structures in complex with the spike fusion protein using cryo-EM (cryogenic electron microscopy). With antibody structures I helped characterize spike epitopes, rationalize antigenic properties of emerging variants, and hypothesize viral neutralization mechanisms.

I discovered antibody structures with multiple neutralization mechanisms including receptor blocking, conformational “locking” of the RBD (receptor binding domain), and spike disassembly. Viruses are evolving pathogens, and the Omicron sub-lineages are some of the most antibody-resistant SARS-CoV-2 variants to date. I studied mechanisms of Omicron antibody neutralization, which included traditional mechanism such as receptor blocking, as well as new mechanisms involving spike disassembly and conformational locking at SD1 (subdomain 1) epitopes. I also investigated broad antibody recognition at a conserved RBD epitope which neutralized not only SARS-CoV-2 but also SARS-CoV and other sarbecoviruses. Lastly, I had the opportunity to study other classes of viral fusion proteins, including those of alphaviruses and rabies virus, which serve as representative class members of the other varieties of viral fusion proteins, broadening my research for any type of known viral pathogen.

Structural studies of antibodies highlight vulnerabilities of the spike protein when targeting SARS-CoV-2 and other fusion proteins in future vaccine design. The trials and tribulations of SARS-CoV-2 and the wealth of new research on coronaviruses offer hope of future pandemic preparedness. Understanding the structural mechanisms of viral fusion proteins and antibody neutralization gives hope of developing further therapeutic interventions. The work described in this thesis on fusion proteins SARS-CoV-2 spike (S), alphavirus envelope (E), and rabies virus glycoprotein (G) have prepared me to combat other infectious viral agents, including those already infecting humans and those at risk of spilling over into humans. When posed with such unpredictable emerging threats, we can learn from the past and position ourselves to be ready for the future.


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More About This Work

Academic Units
Biochemistry and Molecular Biophysics
Thesis Advisors
Shapiro, Lawrence S.
Ph.D., Columbia University
Published Here
April 12, 2023