Defense Date

7-10-2024

Graduation Date

Summer 8-2024

Availability

One-year Embargo

Submission Type

dissertation

Degree Name

PhD

Department

Chemistry and Biochemistry

School

School of Science and Engineering

Committee Chair

Jeffrey D. Evanseck

Committee Member

Mihaela Rita Mihailescu

Committee Member

Michael Cascio

Committee Member

Lakshmi Rumkamar

Keywords

RNA, C9orf72, SARS-CoV-2, molecular dynamics, docking, ALS, FTD, amyotrophic lateral sclerosis, frontotemporal dementia

Abstract

The research described in this dissertation focuses on the investigation of the structure and dynamics of regions of RNA implicated in two diseases: COVID-19 and amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). Both studies sought to create experimentally corroborated models that were used to characterize the structure and dynamics of the C9orf72 repeat expansion and the s2m region in coronaviruses, respectively and provided the foundation for future work. In our work involving the s2m region of SARS-CoV-2, the virus responsible for COVID-19, we determined that the homology modeling approach commonly used to derive atomistic structures when no coordinates are available yields a structure that differs from published 2D NMR findings despite high sequence homology and previously high conservation of the region in coronaviruses. Utilizing 2D predicted structure data, we developed an atomistic representation of SARS-CoV-2 s2m and observed greater flexibility and more variation in dynamics not observed in the SARS-CoV s2m simulations, relating the change in sequence and structure to the dynamics of the region. This project laid the foundation for subsequent work that studied the evolution of the s2m region in SARS-CoV-2 variants and other regions of interest within the genome and provides a basis for studying the motif in other viral families in which it is conserved.

Utilizing similar computational techniques, our second study modeled G-quadruplex and hairpin structures associated with the hexanucleoide repeat expansion of C9orf72, a genetic mutation associated with the development of ALS and FTD and sought to characterize trends in structure, dynamics, and interactions as the number of repeats increased. We observed structural changes in the G-quadruplex structures containing 16 or more repeats, which may be an indication that there is an upper limit for quadruplex stacking within an intramolecular quadruplex. Additionally, as repeat number increased, we observed a base-pairing pattern that grew in prevalence in the hairpin structures. This may be a pattern that could be used to target hairpins in peptide nucleic acid therapeutics. We began enhanced sampling studies to better understand the relative energy of binding to an RNA binding protein, fragile-x ribonucleoprotein, speculated to be involved in the development of ALS/FTD. This foundational work provides steppingstones for future projects to determine structural or dynamic characteristics to leverage for future therapeutics targeting the repeat expanded RNA.

Language

English

Additional Citations

Kensinger, A. H.; Makowski, J. A.; Pellegrene, K. A.; Imperatore, J. A.; Cunningham, C. L.; Frye, C. J.; Lackey, P. E.; Mihailescu, M. R.; Evanseck, J. D. Structural, Dynamical, and Entropic Differences between SARS-CoV and SARS-CoV-2 S2m Elements Using Molecular Dynamics Simulations. ACS Physical Chemistry Au 2023, 3 (1), 30–43. https://doi.org/10.1021/acsphyschemau.2c00032.

Download

Share

COinS