Alexander Duckworth joined the Integrated Program in Biochemistry (IPiB) with the goal of learning more about how scientists ‘solve biomolecular structures’ — that is, how they figure out what essential components to life, such as proteins, look like.
Duckworth’s research as a member of the Keck Lab revolves around genome maintenance proteins, which bind to DNA that’s been damaged and attempt to repair it. But his project took a turn when an advanced biomolecular imaging technology called cryo-electron microscopy (cryo-EM) arrived on the UW–Madison campus in 2020. Importantly, around the same time biochemistry assistant professor and Morgridge Institute investigator Tim Grant started his cryo-EM lab, and the Keck and Grant labs began a collaboration focused on Duckworth’s project.
Duckworth’s work using cryo-EM revealed something unexpected: PriA, the protein that he and the Keck Lab had been studying for years, appears to have a switching mechanism that turns ‘on’ only when the protein binds to the right piece of damaged DNA. If the protein switch doesn’t activate, other proteins aren’t recruited to help repair the DNA.
“When we saw the cryo-EM structure of PriA bound to damaged DNA, we saw that one region of the protein had moved to a completely different location relative to its position without DNA,” Duckworth says. “We weren’t expecting to see a switch-like mechanism at all, but that is what we saw with cryo-EM. The cryo-EM results really got us thinking about how PriA structural changes are regulated and how the protein knows it’s bound to the correct thing.”
Along with publications in PLOS One and Methods in Enzymology, Duckworth’s experiments have resulted in a first-author publication that is under review. Duckworth and his advisor, biomolecular chemistry professor Jim Keck, have continued to collaborate with Tim Grant’s lab to build their understanding of the protein.
“Our view of how this protein works has just exploded into several different directions. We’re looking at it bound to not just DNA now, but to other proteins as well,” Duckworth says. “We’re doing more controlled, dynamic experiments to see how that switch-like mechanism happens in solution. Cryo-EM has really opened several new avenues of research, I’d say. It’s just been super fun.”
During his time in IPiB, Duckworth has been active in the Graduate Leadership & Development Committee (GLDC). He is also a trainee in the Biotechnology Training Program. After defending his Ph.D., he plans to start a postdoctoral researcher position in the Grant Lab to learn even more about using cryo-EM to solve complex biological problems.
To learn more about Duckworth’s research, attend his Ph.D. defense on Tuesday, March 21 at 11:00 a.m. CT in Room 1211 of the DeLuca Biochemical Sciences Building.