A recent grant from Westminster’s Drinko Center for Undergraduate Research gave senior biochemistry major Morgan Shine the tools necessary to streamline the work on her data-heavy seniors honors research project.
Shine began working on her project, “Characterizing Binding Interactions of a Uridylated Intermediate and a Truncated Stem-loop through Molecular Dynamics (MD) Simulations,” the summer after her sophomore year as part of a National Science Foundation-Research Experience for Undergraduates (NSF-REU) program at Duquesne University.
Her research—understanding the role of the most prominent uridylated intermediate in degradation by characterizing its binding interactions with key degradation proteins—expanded during the fall of her junior year when she started studying a truncated stem-loop to better understand the role of uridylation in this process. Just last summer, Shine participated in another chemistry NSF-REU program at Duquesne to learn how to study RNA-protein complexes with molecular dynamics simulations.
With more than a year of research conducted, her final honors project integrates both experimental and computational techniques to characterize the binding interactions of the uridylated intermediate and the truncated stem-loop.
Since necessary computer simulations and the gathering of important data have been key to her research, the Drinko grant helped Shine purchase an external hard drive to store her molecular dynamics data.
“For the computational side of my research, I have been performing extensive molecular dynamics simulations with three different stem-loops—the wild-type stem-loop, the uridylated intermediate, and the truncated stem-loop—in six different systems. This adds up to over 1 TB of data, which is roughly five times more than I can store on my laptop,” she said. The grant allowed her to streamline years of data and focus on her research rather than computer storage.
Shine plans to pursue a Ph.D. in biochemistry following graduation.
Westminster’s Drinko Center for Undergraduate Research financially supports undergraduate research through various grants aimed at either the undertaking of research and creative projects at Westminster College or the external presentation and dissemination of research and creative works at conferences.