ADVERTISEMENT
2 /3 FREE ARTICLES LEFT THIS MONTH Remaining
Chemistry matters. Join us to get the news you need.

If you have an ACS member number, please enter it here so we can link this account to your membership. (optional)

ACS values your privacy. By submitting your information, you are gaining access to C&EN and subscribing to our weekly newsletter. We use the information you provide to make your reading experience better, and we will never sell your data to third party members.

ENJOY UNLIMITED ACCES TO C&EN

Awards

2020 Priestley Medalist JoAnne Stubbe digs deep into the details of enzymes

The MIT biochemist’s intense focus has helped her solve some of biochemistry’s important puzzles

by Celia Henry Arnaud
March 23, 2020 | APPEARED IN VOLUME 98, ISSUE 11

 

09811-cover1-opener.jpg
Credit: Gretchen Ertl

Since retiring 4 years ago, JoAnne Stubbe has cut way back on work. She now goes to her office at the Massachusetts Institute of Technology only 6 days a week.

In brief

This year’s Priestley Medalist, JoAnne Stubbe, has spent much of her career puzzling over the details of complicated enzyme mechanisms. She is a pioneer in understanding how radicals play a role in enzyme chemistry. She has devoted much of her 4-decade career to figuring out the inner workings of the enzymes that help create the building blocks of DNA. Read on to find out more about the winding path her career took from Williams College to the Massachusetts Institute of Technology, with other stops in between.

COVER STORY

2020 Priestley Medalist JoAnne Stubbe digs deep into the details of enzymes

It’s safe to say that over her more than 50-year career in chemistry, the emeritus professor has lived for science. Solving nature’s puzzles is what kept her coming to lab every day of the week and, at age 73, is what occupies her mind even now.

And she did solve many puzzles during her long career in biochemistry—so many that she’s now being awarded the 2020 Priestley Medal, the highest honor bestowed by the American Chemical Society. (ACS publishes C&EN.) The award citation demonstrates just how broad Stubbe’s scientific interests have been. She is being recognized for “pioneering studies of enzymatic radical chemistry, long-range proton-coupled electron transfer, DNA cleavage by anti-cancer drugs, enzymatic formation of polyesters and purine biosynthesis.”

She was able to accomplish those things, according to the former students and postdocs that C&EN talked with, because of her drive and passion.

Getting started

Many people of a certain generation say that they fell in love with chemistry because of a chemistry set. Not Stubbe. As a child she enjoyed the outdoors and hiking. Chemistry wasn’t really in the picture.

Stubbe first got interested in chemistry during a summer research job with Edward Trachtenberg, a physical organic chemist at Clark University. Her father was a mathematician at the university and made the connection with Trachtenberg. As a high school student in Worcester, Massachusetts, she didn’t know much chemistry before that summer in 1964, but she quickly saw its allure.

cover1-medal-logo.jpg

“What I liked was working in the lab,” Stubbe says. “It didn’t matter what I worked on. I like seeing the colors change. I like detective stories. I like having some question, doing experiments and making observations, and then putting the pieces of the puzzle together.”

As an undergraduate at the University of Pennsylvania, athletic pursuits sometimes took priority over chemistry. Stubbe played tennis on the junior varsity team. She remembers skipping a lecture by famed organic chemist Robert B. Woodward, who was visiting from Harvard University, to play tennis.

She even came close to quitting chemistry because she didn’t like the fires and explosions that would sometimes happen in labs. Safety practices in those days were nowhere near what they are now. Students would dispose of solvents in the labs in long troughs, which would sometimes ignite accidentally because of nearby Bunsen burners.

At Penn, Stubbe worked with another physical organic chemist, Edward Thornton, who encouraged her to go to graduate school. She applied to the University of California, Berkeley, and got in.

09811-cover1-obama.jpg
Credit: AP/Gerald Herbert
JoAnne Stubbe receives a 2008 National Medal of Science from President Barack Obama.

“It was an interesting time to have been in Berkeley,” she says. Student protests against the Vietnam War were at their height. Choosing a graduate mentor at Berkeley was stressful. One person Stubbe considered working with didn’t accept women graduate students because he thought they would leave to get married, she remembers. Another potential mentor offered her a project that would provide good training for a technician position. But she wanted more than that.

She ended up joining George Kenyon’s lab, one of the first in the Berkeley Chemistry Department working at the interface of chemistry and biology. In his lab, she synthesized analogs of phosphoenolpyruvate, a molecule important to glycolysis, which is a process in the body that breaks down glucose and produces energy. She also studied the specificity and stereochemistry of the last step of the glycolysis reaction, in which the enzyme pyruvate kinase catalyzes the transfer of phosphate from phosphoenolpyruvate to adenosine diphosphate.

Although Stubbe had taken biology as an undergraduate at Penn, she had found the class’s reliance on memorization boring. A biochemistry class at Berkeley sparked renewed interest in the subject. She learned about how enzymes can catalyze reactions with tremendous rate accelerations and by mechanisms that looked like magic to a chemist. That class also awakened a fascination with how reaction mechanisms could be applied to solve biological problems.

Stubbe graduated from Berkeley in 3 years. After that, she headed to the University of California, Los Angeles, for a postdoctoral position with Julius Rebek. While there, Stubbe met William R. Moomaw, who was on sabbatical from Williams College, a small liberal arts college in Massachusetts. He encouraged her to apply for a position at Williams, where she would be able to teach and do research. She came from a family of teachers, so the promise of teaching was alluring.

Her time at Williams, Stubbe says, gave her a chance to build her confidence as both a teacher and a researcher. She taught biochemistry and physical chemistry, neither of which she had prior experience with. And she was the first person in the Chemistry Department to get a US National Institutes of Health R01 grant, which she partly used to study mechanism-based inhibitors. These are molecules that bind to an enzyme and block it from doing its job.

But at Williams, Stubbe felt her research moved too slowly: undergraduates have limited time in the lab. She wanted to do more.

A path presented itself when she met Christopher T. Walsh at a Gordon Research Conference in 1975. At that time, Walsh was a chemistry professor at MIT studying enzymes and enzyme inhibition. Stubbe had a thirst for research, he thought. “It seemed to me that she was not going to be satisfied teaching chemistry in an undergraduate-only institution where her desire to do groundbreaking research was not going to be easy to satisfy,” Walsh says. He told her about his positive experiences as a postdoc with Robert Abeles at Brandeis University.

Stubbe procured funding and took a leave of absence to work with Abeles, who was a pioneer in mechanistic enzymology. Her experiences there changed the course of her career and affected the rest of her academic career, including what she studied and how she ran her own research group.

A new direction

“Brandeis was orders of magnitude better than any other place in the country in terms of enzymology and biochemistry,” Stubbe says. “I was surrounded by people who were thinking about all these problems that I thought were exciting and important.”

After her time in Abeles’s lab, Stubbe decided not to return to Williams. She wanted to do more research, so she accepted a position in the Department of Pharmacology at the Yale School of Medicine. Her aim was to gain knowledge of how enzymes worked in order to design, make, and study therapeutics.

The Pharmacology Department at Yale hosted only a handful of graduate students because its main function was to teach pharmacology to medical students. So in the beginning, Stubbe says, she did a lot of her own lab work. But she soon had funding that allowed her to hire technicians.

She also launched a fruitful collaboration with John W. Kozarich, a fellow pharmacology professor at Yale with whom she shared a lab and a tiny office. “We figured if we don’t collaborate with each other, we’ll probably kill each other in this little office,” recalls Kozarich, who is now a distinguished scientist emeritus at biopharmaceutical firm ActivX Biosciences. The pair studied bleomycin and other cancer therapeutics that bind to DNA.

Stubbe’s work ethic was already evident. “I consider myself a workaholic,” Kozarich says. “But she’s in a different stratosphere. If there was a choice of going home and having dinner or working more, she’d work more.”

Still, Stubbe wanted to do even more research at the interface between chemistry and biology, and she wanted to work with graduate students. So in 1980, she moved to the Biochemistry Department at the University of Wisconsin–Madison, which she says was a haven for mechanistic enzymology.

Graduate students at last

09811-cover1-lobsterfest.jpg
Credit: Courtesy of JoAnne Stubbe
Each summer, JoAnne Stubbe hosted a lobster fest for her group at her house in Maine. This photo was taken in 2006.

At Wisconsin, Stubbe was finally able to recruit graduate students. “It was not a warm and fuzzy place,” says Scott Salowe, who was a graduate student with Stubbe at Wisconsin and is now a team leader in discovery biology at Venenum Biodesign. “The science was outstanding in everything we did. But it was intense.”

Stubbe says she expected her team to work hard, but she also wanted them to have fun doing science. She eventually received tenure in Wisconsin’s Biochemistry Department, the first woman to do so.

Throughout her career, Stubbe would spend sabbaticals learning about various topics, including yeast genetics, electron paramagnetic resonance spectroscopy, and X-ray crystallography. In this way, she would teach herself—or get others to teach her—techniques and science that she needed so she could answer questions she was interested in.

The most creative ideas come from young people.

One sabbatical that Stubbe took while at Wisconsin likely paved the way for her later move to MIT. She wanted to learn more about how metals functioned in biology. Bleomycin used iron to help cleave DNA, and a type of enzyme she was fascinated by—a ribonucleotide reductase (RNR)—used metal cofactors for catalysis. To learn more, she spent a sabbatical in Stephen J. Lippard’s lab at MIT. Lippard’s research focused on the interaction of metals with biological systems like DNA.

Lippard remembers one of Stubbe’s Wisconsin colleagues saying he hoped MIT wasn’t planning to steal Stubbe. “I walked away from that meeting and thought to myself, ‘Gee, what a good idea that would be,’ ” Lippard says.

Stubbe’s friend Walsh—the one who encouraged her experience with Abeles—was chair of the MIT Chemistry Department at the time. And he was on board with recruiting Stubbe. “I’d known her for 12 years and had observed her fierce determination and her first-rate intellect. I thought she’d be a great colleague,” Walsh says. “We needed more faculty on the biochemistry side of the department.”

Stubbe moved to MIT as a tenured faculty member in 1987. She was the first tenured woman in MIT’s Chemistry Department.

At the time, the department’s biochemistry division was small, which made recruiting students challenging. J. Martin Bollinger Jr., now a chemistry professor at the Pennsylvania State University, was Stubbe’s first grad student at MIT. He remembers his initial meeting with her to learn about her group’s research.

“JoAnne assumed you were interested in science and just started talking. Her passion was overwhelming,” Bollinger says. “She was so intense. It was a bit intimidating. I felt I needed comrades in arms.” So he convinced classmates Squire J. Booker and Michael J. Absalon to join Stubbe’s group along with him.

When Booker approached Stubbe, he says, she downplayed his limited research experience. “I figured if she was willing to teach, I was willing to learn,” Booker says. Booker is also now a professor at Penn State.

Many of Stubbe’s students and postdocs describe the atmosphere in her lab as “intense,” but they also say she made them better scientists. She taught them to tackle big problems and to dig into the details to solve them—and to be meticulous in the process.

“Every observation would be accounted for before a paper would go out,” says Wilfred A. van der Donk, a professor at the University of Illinois at Urbana-Champaign who was a postdoc with Stubbe in the 1990s. Stubbe wanted to tell the full story about a set of results before publishing.

Advertisement

Although they may have found her lab intense, many of her former group members continue to enjoy their relationships with her. “Every time I go to Boston, I have a meal with her or visit her in her office,” Bollinger says. “It’s not because I need anything. It’s just because I enjoy talking to her about science.”

“I enjoyed every second I was in the lab,” says Mohammad Seyedsayamdost, a chemistry professor at Princeton University who was a grad student at MIT with Stubbe. “I would go back any day to be a grad student in her lab.”

One group member didn’t do research but was a source of fun for the other members. That was Stubbe’s dog, Zymie.

Many students and postdocs fondly remember Zymie—Stubbe’s cairn terrier, whose full name was McEnzyme. A fixture in the MIT lab, Zymie attended group meetings. When members gave talks, Zymie would sit up front, watching the laser pointer. “If you turned it off, the dog would look at you waiting for you to turn it back on,” says Deborah Perlstein, who was a grad student with Stubbe and is now a chemistry professor at Boston University. “If you got into an extended conversation and took too long to turn the laser pointer back on, she would jump, put her paws on the screen, and start barking, trying to make the laser pointer come back.”

09811-cover1-zymie.jpg
Credit: Courtesy of JoAnne Stubbe
JoAnne Stubbe's dog, Zymie, spent lots of time with her research group.

Radical research

Over her many years of research, Stubbe helped unravel the mechanism of how the cancer drug bleomycin cleaves DNA; provided insights into how certain bacterial enzymes make huge polyoxoester molecules, which are biodegradable polymers with the properties of thermoplastics; and contributed to the scientific community’s understanding of metal cofactors’ structures, biosyntheses, and roles in catalysis.

But Stubbe is best known for her work unraveling the mechanism of RNRs. People had a tough time believing the mechanism she proposed in the late 1970s, but it has stood the test of time.

RNRs, which occur in all organisms, catalyze the conversion of ribonucleotides to deoxyribonucleotides, the building blocks of DNA. Through an intricate process, the enzymes remove the hydroxyl group from the 2′ carbon on a ribonucleotide’s sugar ring, reducing the molecule into a deoxyribonucleotide. RNRs therefore play a central role in nucleic acid metabolism, controlling the pools of deoxyribonucleotide molecules available for DNA replication and repair. Stubbe proposed a radical-based mechanism for this reduction process. To test this hypothesis, she started with a ribonucleoside 5′-diphosphate (NDP) that was isotopically labeled at specific proton positions in the ribose ring. Through experiments with this substrate, she showed that the C–H bond at the 3′ position of the sugar ring in NDPs is cleaved by RNR to initiate loss of water from the 2′ position.

09811-cover1-rnr.jpg
Credit: Courtesy of JoAnne Stubbe
Ribonucleotide reductases (RNRs) catalyze the transformation of ribonucleotides to deoxyribonucleotides (top). The ribbon structure is based on a docking model of RNR from Escherichia coli. Effectors that control substrate specificity are shown in yellow, and the substrates are shown in green. The inset shows the amino acids involved in the proton-coupled electron transfer (PCET) pathway that is involved in moving a radical from a tyrosine to a cysteine 35 Å away.

Stubbe and others further cemented the radical-based mechanism of RNRs by establishing that a tyrosyl radical in the enzyme was essential to the process. They determined that its role was to generate a thiyl radical an incredible 35 Å away, in the site in the enzyme where the NDP was held. Stubbe and collaborators spent years figuring out how the unpaired valence electron on the tyrosyl radical could make its way across that 35 Å divide to reach the active site. They demonstrated that the process involves many highly oxidizing radical intermediates: the electron would pass from intermediate to intermediate, hopping across the enzyme via processes like proton-coupled electron transfer to catalyze the removal of the hydroxyl group on the ribonucleotide.

“Why would nature ever design something where you had six really hot oxidants as stepping stones to get to the chemistry you cared about?” Stubbe asks, marveling at the chemistry of RNRs. “Moreover, radical transfer over this very long distance was unprecedented and reversible,” she says.

Many experiments went into uncovering the full RNR pathway, and the techniques that Stubbe and her team used to run them were often at the cutting edge of science. For example, the researchers pioneered the use of unnatural amino acids to trap radicals within an enzyme. Initially they spliced the modified residues into RNRs using native protein ligation methods. And when Peter Schultz’s group at Scripps Research Institute developed a more sophisticated method for incorporating unnatural amino acids into proteins using a cell’s translational machinery, Stubbe sent a student to Schultz’s lab to learn how to do it.

In all the work that Stubbe’s lab has done, the team primarily used spectroscopic methods and kinetics to observe radicals in biological molecules. No one had solved a structure of an active RNR—until recently.

Stubbe’s MIT colleague Catherine Drennan, with whom she has collaborated, recently used constructs of RNRs with site-specifically incorporated unnatural amino acids to capture a cryo-electron microscopy image of an intermediate of the enzyme. “We’ve been after this so long,” Stubbe says. “We can now put all the biochemical and biophysical information into structural context. I am so excited. I wish I had enough energy to work in Cathy’s lab to see and design experiments to understand the complex dynamics of these proteins.”

Teamwork

MIT’s emphasis on collaboration is one of the things Stubbe most appreciates about her time there.

A poster that today sits in her office is a monument to her gratitude for collaboration. It’s an advertisement for the 2012 Killian Lecture, MIT’s highest honor for faculty, which she delivered. Whereas most recipients’ posters sport a large photo of themselves, Stubbe’s poster features a collage of photos of her collaborators, something she requested.

09811-cover1-poster.jpg
Credit: Gretchen Ertl
The poster for JoAnne Stubbe's Killian Lecture features a collage of photos of her collaborators.

“Everything I’ve done has been collaborative,” Stubbe says. She always aimed to solve the puzzle in front of her, and she knew which pieces she needed help with. “You make decisions about what you want to bring in your lab and who you’re going to collaborate with,” she says.

She’s also put that collaborative spirit to work by serving as a mentor for younger professors at MIT.

When Drennan first joined the MIT Chemistry Department, Stubbe volunteered as an editor to critique Drennan’s papers before submission. “JoAnne gave me back the manuscript all marked up, and at first I was pretty upset, thinking that I had done a terrible job, but then I realized JoAnne’s comments were exactly what the paper needed,” Drennan says. “JoAnne had clearly spent a huge amount of time reading and thinking about my work, finding every potential flaw. Who has that kind of time? No one, but JoAnne made the time.”

Many others comment on Stubbe’s penchant for being a straight shooter who tells it like it is. “I felt I never had to wonder where I stood with her,” Bollinger says. “It was clear from the first minute that you were going to get honesty.” When he was department chair, Lippard considered her one of the people he could go to for a clear and honest opinion of how the department was handling issues.

In addition to her research and mentoring, Stubbe devoted much time to her teaching.

When Stubbe first moved to MIT, the Chemistry Department didn’t have a biochemistry course. She partnered with William H. Orme-Johnson and John M. Essigmann to create a sophomore-level biochemistry class. She and Essigmann sat in on each other’s lectures. He recalls a time when she was teaching undergraduates about stereochemistry in biological molecules such as amino acids. “She looked out over a sea of faces frozen with terror, and she realized that the students were having difficulty,” Essigmann says. “She bought chemical model kits for every student in the class, and then she had a personal interview with each student” to ensure they understood the concept of stereochemistry.

If a student is interested, I’m willing to spend infinite amounts of time to get them up to speed.

Stubbe devoted so much time because she thought teaching was one of the most important things she did. “If a student is interested, I’m willing to spend infinite amounts of time to get them up to speed,” Stubbe says.

For Stubbe, teaching integrates seamlessly into how she does science. When she reads the literature, she’s on the lookout for papers with scientific concepts that would make good homework or exam problems. “The problem will incorporate the fundamentals that the students are learning in class, but then it takes things a step further,” says Elizabeth M. Nolan, who also taught a course with Stubbe at MIT.

Even though Stubbe is no longer teaching, Nolan still gets emails from her with papers that would be good for Nolan’s class. “It’s a huge contribution that she makes in terms of educating students and providing us with the next generation of highly trained and thoughtful scientists,” Nolan says.

Stubbe has received many awards over the course of her career. The Priestley Medal is just the latest in a long line of awards that has included, among others, the Arthur C. Cope Scholar Award in 1993, the F. A. Cotton Medal in 1998, the Nakanishi Prize in 2009, the National Medal of Science in 2008, and the Welch Award in Chemistry in 2010, which she shared with Walsh, her longtime friend.

Stubbe shut down her lab in 2016, when she turned 70, and relinquished her space. She says it was time for the next generation to take over.

“The most creative ideas come from young people,” Stubbe says. “They think about things completely differently from the way I think about things. That’s where you do harebrained experiments that change the world. You need young people in your department all the time.”

During the 6 days a week she still comes to campus, Stubbe mostly works on review articles and meets with collaborators and their students. True to form, the ideas keep coming. “I get up in the middle of the night with ideas. You can’t just cut it off,” she says. “It’s hard because you do science with such intensity for so long. It’s so much a part of me that letting go isn’t easy.”

X

Article:

This article has been sent to the following recipient:

Leave A Comment

*Required to comment