Former chemistry graduate student, Hayley Knox, collaborates on paper in Nature
Former chemistry graduate student, Hayley Knox, collaborated with Penn State chemists Amie Boal and Squire Booker, along with researchers at Johns Hopkins University, to publish a paper in the scientific journal Nature. The paper, titled “Structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis,” was published on February 2, 2022. We talked to Knox, Boal, and Booker about the research and the collaborative process to get some insight into her experience.
The researchers study “carbapenems,” which are antibiotics of last resort owing to their potency and broad-spectrum activity. The clinically used carbapenems are distinguished from other classes of ß-lactam antibiotics by their C6 hydroxyethyl side chain, which confers their therapeutic usefulness. This side chain is constructed sequentially by a cobalamin-dependent radical S-adenosylmethionine (SAM) enzyme. In this paper, the team of researchers presented the crystal structures of TokK, a cobalamin-dependent radical SAM enzyme that performs three sequential methylations in the biosynthesis of asparenomycin A, a carbapenem antibiotic. The structures provide insight into the mode of methylation and the stereochemical control of the enzyme.
Credit: Knox et al., 2022
Boal, associate professor of chemistry, described her experience working with graduate student Knox as exciting.
“Hayley worked hard to collect beautiful datasets for this project,” said Boal. “It was a lot of fun to help craft the story with her and our other collaborators. I thought it was particularly exciting to think about how her contribution fits into what we know about biological radical catalysis. Hayley’s structure is one of the first of an important class of C-C coupling enzymes and her work shows that this platform is both very simple and versatile.”
Some of Knox’s specific contributions to the research involved solving the crystal structures of TokK in the absence and presence of its carbapenem substrate as well as performing the spectroscopy work. In her graduate work, Knox focused on structurally characterizing cobalamin-dependent radical SAM enzymes. In 2021, she was part of another publication in Nature Chemical Biology on the structure of a distinct cobalamin-dependent radical SAM enzyme that does not perform any radical chemistry. With TokK, the collaborators were finally able to see the active site of a cobalamin-dependent radical SAM enzyme that performs radical chemistry and further our understanding of this diverse class of enzymes.
According to Booker, Evan Pugh University Professor of Chemistry and of Biochemistry and Molecular Biology and Holder of the Eberly Distinguished Family Chair in Science at Penn State, Knox became one of the world’s experts at purifying and manipulating cobalamin-dependent radical SAM enzymes, which were considered almost impossible to study for quite some time. She determined X-ray crystal structures of two distinct members of the cobalamin-dependent radical SAM methylase subfamily, which operate by two distinct mechanisms of catalysis.
“It has been a real privilege to see Hayley blossom into the exceptional scientist that she is,” said Booker, who is also an investigator with the Howard Hughes Medical Institute. “It took a lot of guts for her to take on these kinds of projects. Hayley has many great assets, but my favorites are her fearlessness and passion for research. She has a very low activation energy for doing experiments.”
When asked how it felt to represent the Penn State Department of Chemistry by having her work published as a graduate student, Knox said: “I am very happy to have this work published! The last few months of my Ph.D. were focused on writing this paper up and it’s great to see it out.”
On collaborating with Booker, Boal and the researchers at Johns Hopkins, Knox said it was “a fantastic experience from which I learned a lot!”
You can read more about Knox’s collaborative research in a press release written about the research.
Knox was a member of the Booker Lab at Penn State and defended her thesis in July 2021. She is currently a postdoctoral associate in the Allen Lab at Boston University.