The Daily Bulletin

Please join the Chemistry Department for the next seminar of the fall 2024 seminar series, “Using Structure to Predict Function in Protein Biochemistry: A Combined Computational and Wet Lab Approach,” presented by Julia Koeppe, associate professor of chemistry at SUNY Oswego, on Thursday, October 24, at 12:15 p.m. in Science and Mathematics Complex 173. Coffee and donuts will be provided.

Abstract
We are using a combined computational and wet lab approach to study protein structures of unknown function. We now have access to thousands of high resolution structures and structure models of proteins for which the function is unknown. In our lab, we use both sequence and structure alignment tools to analyze selected structures with the goal of identifying possible enzymes. We also use molecular docking to predict what model substrates (or possible inhibitors) fit near a proposed active site. We then produce the target enzymes in the lab using standard wet-lab biochemistry techniques for expression and purification. Finally, we perform kinetic assays with model substrates selected from the docking studies to test the predicted function. To date, we have tested several proteins for predicted hydrolase function, and we have confirmed esterase, lipase, or mannanase activity in our most well-studied target proteins.

Speaker Bio
Julia R. Koeppe, Ph.D., earned undergraduate degrees in chemistry and Spanish from Hope College in Michigan, and her Ph.D. in biochemistry from the University of California San Diego. From there, she moved to Oxford University in England, where she did postdoctoral research in both the Biochemistry and Chemistry departments. Dr. Koeppe became a faculty member in the Chemistry Department at SUNY Oswego in 2016, and she now serves as department chair. Throughout her career, Dr. Koeppe has studied the function and interactions of various biomolecules with a specific focus on protein interactions and protein function. At SUNY Oswego, she works with both undergraduate and M.S. students in her research lab. In 2015, Dr. Koeppe began working with collaborators to develop the BASIL CURE (Biochemistry Authentic Scientific Inquiry Lab - Course-Based Undergraduate Research Experience), and she now serves on the steering committee for the project.