Chemistry Professor Sheds Light on Mechanisms of Key Enzyme Reaction
By Ben Panko
New research from Assistant Professor of Chemistry Yisong (Alex) Guo breaks down the complex and fascinating chemical processes comprising an important enzyme reaction that is found in many natural processes. The study was a close collaborative work with Associate Professor of Chemistry Maria Kurnikova, Wei-chen Chang from North Carolina State University, and Nei-Li Chan from National Taiwan University, and was featured as a supplementary cover on a recent issue of the Journal of the American Chemical Society, with artwork by Rachel Keeney, Mellon College of Science publications manager and graphic designer.
Enzymes are proteins that act as catalysts in organisms, accelerating chemical reactions so they're fast enough to be practical and sustainable. Guo's research looked specifically at a non-heme-iron oxygenase enzyme called AsqJ. As its name implies, this type of enzyme is critical in using molecular oxygen to perform chemical transformations that are related to biological pathway regulations, and research into their mechanisms helped British physician Peter Ratcliffe garner last year's Nobel Prize in Physiology or Medicine.
"A lot of study has been directed to how these enzymes work because hopefully people can use it as a catalyst to design and synthesize natural products in the pharmaceutical environment," Guo said.
A key chemical reaction these enzymes catalyze is epoxidation, a process that involves installing a three-atom ring containing oxygen, called an epoxide, onto a molecule. This epoxide acts as a functional group for the molecule, allowing it to participate in a variety of chemical reactions.
"Epoxides have very versatile chemistry," Guo noted. "Although there's a lot of organic chemistry research about this epoxidation reaction, in this non-heme-iron enzyme there has never been a detailed mechanistic study."
Using Mössbauer spectroscopy, kinetic measurements, x-ray crystallography and theoretical calculations, Guo's team scrutinized the reactions behind epoxidation catalyzed by AsqJ. The efforts from his lab was joined by Kurnikova for the molecular dynamics simulations, by Chang from North Carolina State University for the organic synthesis and Chan from National Taiwan University for the x-ray crystallography.
"This enzyme by itself is fundamentally important to understanding this group of enzymes that is involved in all these important chemical reactions or biological pathways in nature," Guo said.
A major finding of the study was discovering the existence of an intermediate species in the epoxidation reaction. This intermediate species, which exists briefly during the catalysis, had been hypothesized to exist but evidence of it had never been experimentally observed.
Another subtler finding of the research concerned a co-substrate of the enzyme called 2-oxoglutarate. By observing the mechanisms of AsqJ, Guo and his collaborators concluded that this co-substrate likely "flips" in the solution so that a water molecule can leave the enzyme, creating room for an oxygen molecule to bind to the enzyme's iron center. This finding was made possible via the molecular dynamics simulations led by Research Professor Igor Kurnikov and Kurnikova.
In future research, Guo and his team plan to look at other enzymes that have been previously studied and see whether they might use this flipping motion as a gating mechanism to regulate or trigger the addition of an oxygen molecule.
This research was funded by grants from the National Institutes of Health (GM125924), National Taiwan University and Taiwan's Ministry of Science and Technology (106-2113-M-002-021-MY3). Other authors on the study were: Jikun Li, Yijie Tang and Justin Lee from Carnegie Mellon's Department of Chemistry; Hsuan-Jen Liao and Te-Sheng Lin from National Taiwan University; and Jhih-Liang Huan and Lide Cha from North Carolina State University.