For Sam Epstein ‘19, his senior thesis was an opportunity for the chemistry major with a biochemistry concentration to cap four years of lab experience in a project that was published in science journal Nature Communications—an extraordinary feat for an undergraduate.
Epstein’s thesis, “Probing Chain Sequestration in Carrier Proteins Using Raman Spectroscopy,” pioneered an innovative and more affordable manner to analyze acyl carrier proteins, molecules so difficult to trace that the full nuances of their structure and interaction with each other have eluded scientists.
“I independently designed, conducted, and analyzed the results of my own experiments.” said Epstein. The senior, who is on his way to NYU for a Ph.D. in chemistry this fall, was also happy to acknowledge the assistance he received on the way towards his achievement.
“My thesis advisor was [Assistant Professor] Lou Charkoudian,” said Epstein. “We would meet often to help guide the direction of my future experiments and lab progress. Additionally, our lab group has a weekly meeting where I would frequently present my research progress and ask other students in our lab for help troubleshooting or planning next steps of our research.”
The biochemical process at the heart of Epstein’s work, which received an Honorable Mention at the 2019 NSF Graduate Research Fellowship Program, has implications for the field of pharmacology, and his work points towards a more sustainable means of producing antibiotics.
What did you learn from working on your thesis?
The goal of my project was to attach a site-specific Raman-active probe to the acyl carrier protein (ACP) in place of its natural substrate to effectively report on whether it is sequestered within the protein’s hydrophobic cavity. This technique would provide a quick method for resolving structural information about the ACP and is crucial for elucidating protein-substrate interactions. I independently designed, conducted, and analyzed the results of my own experiments. I learned how to express and purify proteins, perform chemoenzymatic reactions to attach a probe to the ACP, and use Raman spectroscopy to analyze how the probe can be leveraged to report on its own electrostatic environment. As a Biochemistry Superlab teaching assistant, I also trained my peers to perform these methods. I not only attained my goal of completing the proof-of-concept experiment to validate our proposed novel method but I also expanded the scope of our analysis to incorporate probes of different sizes and include “novel ACPs,” for which their structure had never previously been characterized by any technique. I also incorporated site-directed mutagenesis into this work to gain a better understanding of which parts of the protein govern the chain sequestration mechanism.
What are the implications for your thesis research?
As ACPs are central to polyketide biosynthesis, a clear implication of this work is to facilitate the engineering of the biological systems that are used to produce complex molecules, including pharmaceuticals. This new technique, when published, will introduce a new method for producing data on chain sequestration and protein conformation that is less resource, sample and time intensive than conventional methods.
“What They Learned” is a blog series exploring the thesis work of recent graduates.