A 20-Year Research Quest

In 1989, the Exxon Valdez supertanker spilled 11 millions gallons of crude oil into Alaska’s Prince William Sound; oil lingered at the site for decades. Though the disaster continues to affect wildlife generations later, remediation occurred naturally. As of 2015, only 0.6% of the spill remained, with much of the cleanup credit going to natural processes.

For the past 20 years, chemistry professor Rachel Narehood Austin has worked with students in her lab to examine how nature managed to clean up our mess. One of her primary research goals at Barnard has been to reveal an oil-degrading enzyme, alkane monooxygenase (AlkB), in its 3-D active state. The resulting paper, “Structure and mechanism of the alkane-oxidizing enzyme AlkB,” was published this past April in Nature Communications.

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Austin says the primary reason for solving the structure of the enzyme was to understand its structure and function. It’s particularly important because the enzyme functions in the global carbon cycle, which is critical to the planet’s habitability. The enzyme carries out the first step in metabolizing one form of organic carbon into carbon dioxide. The goal of the work is not to inhibit the enzyme to prevent carbon dioxide from going into the atmosphere, rather it’s to gain a better understanding of the carbon cycle itself. How AlkB influences the cycle’s functions is subtle and not fully understood. She says the active 3-D version is an important element in the scientists’ toolkit for fully deciphering the carbon cycle.

“There’s this whole question mark of what’s actually happening in our environment. And if we don’t understand the process of what’s happening, then it’s really hard for us to predict how human activities can change it,” she says.

Several students worked with Austin on the project, but she credits three former Barnard students who worked alongside her in the lab with helping her bring this structure to fruition and serving as co-authors of the recent paper. All three are pursuing a Ph.D. in chemistry. Juliet Lee ’21 and Shoshana C. Williams ’20, both of whom were Beckman Scholars, are continuing their studies at Caltech and Stanford, respectively, and Allison Forsberg ’20 went off to USC. The students’ professional achievements underscore Austin’s parallel priority, teaching students how to become scientists, which includes how to handle the successes alongside rolling with failed experiments, resisting outside pressures, and maintaining the long view.

THE HEART OF THE MATTER

“For years, people have known that [AlkB] is a critical enzyme in the carbon cycle. If you go to a conference of environmental microbiologists, and you talk to people after the Deepwater Horizon oil spill, or the Exxon Valdez oil spill, they’re all talking about this enzyme,” says Austin. “They’ve known it’s a key ingredient in the bioremediation of oil [for 80 years], but nobody has known about the three-dimensional structure. So, 20 years seems like nothing to figure that out.”

Austin has always been intrigued by the interface between the environment and chemistry. While scores of scientists work on the environment in countless capacities, Austin’s niche in this area is that of an inorganic chemist interested in the role of metals in biological systems.
 

PACING THE SCIENCE

Shortly after Austin moved to Barnard, a mutual colleague introduced her to Liang Feng, a professor of molecular and cellular physiology at Stanford. A postdoctoral fellow in Feng’s lab, Xue Guo, had solved the three-dimensional structure of a protein she thought might be AlkB. This protein was out of Feng’s area of expertise, and the mutual colleague thought Austin could help, and she did. 

The protein that Guo had purified was crystallized in an inactive form. Eventually, Austin was able to show that the protein Guo had purified was active, it just wasn’t crystallizing in its active form — and it was indeed AlkB. Feng, now fully invested in the research, joined Austin’s long-held quest to determine the structure of active AlkB. “We were holding out to get the active form, because that’s the most important thing [for the environment],” Austin says.

For seven years, the two worked together with several students in Austin’s lab. Juliet Lee spent two summers at Stanford working side by side with Guo to find a form of AlkB that was easier to characterize in its active form. Finally, more than 20 years into Austin’s research, Feng concluded that the structural data was ready to publish. Austin began writing, and there was much to say. It was, she believed, top journal material.

To get the word out, the team told a simple story, one that could be easily followed, without any superfluous complications, unnecessary caveats, or clarifications. “We just cut out anything that wasn’t essential. And I think that’s partly why it ended up being so easy to review, because it was a simple story,” she says.

NEXT STEPS

During the seven years Austin was examining the inactive structure of AlkB, she had a sense of when she might find the active form. Nevertheless, the discovery has opened up a host of questions. She compared the experience to rock climbing, when a piece of protection is placed in a crevice to secure a climber while she moves up to the next level.

“Without having [the paper] out, I was always torn in multiple directions about how to spend my energy,” she says. “And now it’s really clear what we should do next. So it’s kind of exciting. I feel like I’m ready for the next 20 years for sure.”

Austin says the active site of the enzyme, the place where two iron ions are, is “mind blowing.”

“Normally if you have two metal ions in an active site, it is really obvious to see how they work together,” she says. “In AlkB, the two iron ions are too far apart to directly work together. So the next thing is to better understand how the active site works.”

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LESSONS LEARNED

Austin acknowledged the setbacks over the years. Though she doesn’t revel in them, she doesn’t hide them from her students either. “Science is hard, and young students make a ton of mistakes, and there’s certainly a temptation for students to say, ‘I want to prove something,’” she says. “I sit them down [and say], ‘You know, that’s really not the point.’”

She says if they do four experiments and they get four different results, that is the reality. Rushing is not an option, she says. In light of recent cheating scandals in the scientific community, she believes that upholding standards like peer reviews and respecting colleagues is just as critical in teaching science as finding the 3-D active state of alkane monooxygenase.

“The end never justifies the means — it’s how you live your life that is always, in my experience, more important than any endpoint,” she says. “I think if I can help my students see that we can do really good and fun science and that we can do it carefully and ethically, that’s probably more important than anything else I’m going to do in my life.”

On September 7, 2023, Rachel Narehood Austin won the ACS Award for Research at an Undergraduate Institution from the American Chemical Society.

Photos by Tom Stoelker