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Carpe Datum

By Karen Hopkin Carpe Datum Embracing new tools and ideas—even a switch from literature to science—Gregory Petsko has seized every opportunity to understand enzyme function and to make science matter. © Leah Fasten A Rhodes scholarship changed Gregory Petsko’s life—before he even set foot in England. Petsko, now a professor of biochemistry and chemistry at Brandeis University, majored in classical literature as an under-g

Karen Hopkin

Carpe Datum

Embracing new tools and ideas—even a switch from literature to science—Gregory Petsko has seized every opportunity to understand enzyme function and to make science matter.

© Leah Fasten

A Rhodes scholarship changed Gregory Petsko’s life—before he even set foot in England. Petsko, now a professor of biochemistry and chemistry at Brandeis University, majored in classical literature as an under-graduate at Princeton in the early 1970s. “By the time I was a senior, I had applied to law school, medical school, and graduate school—in both the humanities and science. So that’ll give you an idea of how set on my career path I was,” he says. “I didn’t have a clue what I wanted to do.” But he thought that spending some time in Oxford might help him decide.

With his heart set on the study of epic poetry, Petsko arranged to work with Maurice Bowra, a preeminent classicist,...

Phillips took him in and showed him the ropes. “I learned all about protein structure and function. Everything about it was great. But it wasn’t something I’d planned,” says Petsko. “It was something I did because I was open to what came along”—a philosophy he’s stuck with ever since. “I’ve really never planned anything in my life,” says Petsko. “I’ve just gone along and seen what opportunities were available, and then done what seemed most interesting.”

The approach has served him well. An elected member of both the National Academy of Sciences and the Institute of Medicine, Petsko—along with his long-time colleague Dagmar Ringe—has made pioneering contributions to the field of structural enzymology: proving that crystallographic techniques can be exploited to observe protein function in atomic detail.

He “made crystallography accessible to biologists,” says geneticist Jan Westpheling of the University of Georgia. “Greg was instrumental in connecting those dots.”

“Greg has always been at the cutting edge when it comes to new technologies,” says HHMI investigator Axel Brunger of Stanford University. “His success in using a variety of crystallographic methods to study protein function and enzyme reaction mechanisms has advanced the fields of enzymology and structural biology.”

“And he made crystallography accessible to biologists,” adds geneticist Jan Westpheling of the University of Georgia. “That was important because it clarified the relationship between structure and function, and demonstrated that structure could be used to predict function. Greg was instrumental in connecting those dots. He didn’t do it single-handedly, but he led the charge.”

A COOL CATCH

During his days at Oxford, Petsko worked with a handful of fellow students to solve the structure of triose phosphate isomerase, an enzyme central to glycolysis. “It was the fifth protein structure ever done, so we were inventing the science as we went along,” he says. “You can’t imagine how difficult everything was. The computer we were working on would fill this room, and it had less computational power than a cell phone. And there wasn’t any canned software. If you wanted a program to do something, you had to write it yourself. I wrote the first computer program to draw electron density maps with a pen plotter.” Before that, he says, electron density values were printed out on huge sheets of paper like a data-driven version of paint-by-numbers. “Then you’d put acetate film over that and draw the contour lines by hand,” he says. “It was absolutely ridiculous.”

But the effort led to the discovery of the so-called TIM barrel—a cylindrical structure that turns out to be “the most common protein fold maybe in the universe,” says Petsko. “Ten percent of the proteins encoded in the genome seem to have a TIM barrel of one type or another.” They may do different things in different proteins—but they all do something.

“It’s like an alpha helix or a beta-pleated sheet: the TIM barrel is a protein fold that basically implies function,” says Westpheling. “And Greg discovered it. This was a profound contribution in the days when people were just beginning to understand the three-dimensional structure of proteins.”

Petsko would continue to probe the workings of triose phosphate isomerase when he returned to the States. But first, he made a brief detour to Paris to spend a year in the lab of Pierre Douzou, who had invented low-temperature biochemistry. “He’d figured out how to cool solutions to really low temperatures without the solution freezing or the protein denaturing,” says Petsko. “I wanted to do that in a crystal, so I could trap real intermediates in enzyme reactions.”

His earliest success came with an enzyme called elastase. “I remember the paper,” says New York University’s Ned Seeman of the 1976 Nature report. “It had been postulated that this [enzyme’s] reaction would have a certain intermediate whose dissociation would really be slowed down at low temperature. So he cooled things down, did the structure, and, wow—there it was. That was really exciting.” The structure represented a fleeting moment in catalysis, the enzyme caught in the act and frozen mid-stride.

And elastase was just the beginning. Over the next 25 years, Petsko continued to perfect the cool-and-capture approach—along with other cutting-edge crystallographic tricks—to examine enzyme activities up close. As a faculty member at MIT in the 1980s, Petsko joined forces with Ringe, who at the time was working a nontenure-track position as an instructor running the undergraduate chemistry labs. Together, the two learned how to freeze crystals without damaging them and how to coax reactions into producing a homogeneous crop of enzymes caught holding their intermediates, structures that reveal exactly how the catalysts work their chemical magic. That work culminated in a spectacular series of structures representing the entire catalytic pathway of cytochrome P450, an enzyme Petsko describes as the biological equivalent of a blow torch. “It can take oxygen from the air and insert an oxygen atom into a CH bond in a substrate—a reaction that normally you’d need a temperature of 400 or 500 or 700 degrees to do. And the enzyme does it at room temperature,” he says. “It’s a remarkable catalyst” that allows organisms to metabolize drugs and detoxify harmful compounds.

That study—published in Science in 2000—employed half a dozen different techniques to isolate the structures of all the reaction intermediates. And it managed to shed light on how the enzyme actually accomplishes its astonishing task, which for Petsko is the bottom line. “For me, structure is just a means to an end. That end is function. I care about function,” he says. “I want to know how things work.”

“Greg never loses sight of the big picture. For him, it’s ultimately about the biology,” says former postdoc Ann Stock, an HHMI investigator at the University of Medicine and Dentistry of New Jersey–Robert Wood Johnson Medical School. “In the field of structural biology, that hasn’t always been true. In the early years, many structural biologists focused mostly on the nuts-and-bolts technical aspects of solving three-dimensional structures.” Petsko is proficient when it comes to nuts and bolts, she says, “but he sees them as tools that allow him to explore the biology of proteins.”

And using crystal structures to sequester ephemeral enzyme reaction intermediates was not entirely intuitive. “Biochemists were suspicious of the approach,” says Ringe. “They knew that biological molecules are flexible entities. And then along came these structural biologists with their rock solid crystals, well, it seemed that something was amiss.” Just proving that the enzymes in crystals were active, she says, “was a major breakthrough. It validated for biochemists that looking at structure was going to be a useful thing.”

A PERFECT PAIR

For Petsko, it’s his scientific partnership with Ringe that has been the most useful thing. “I am the luckiest son of a bitch who’s ever lived,” he says. “Because every day I go to work I know that in the next office there is an incredible scientist who cares about exactly the same things that I care about. The best day I’ve ever had in science was the day I met Dagmar Ringe.”

“They’re just wonderfully intellectually compatible,” says George Kenyon of the National Science Foundation. “So the relationship is remarkably synergistic.”

The pair are now putting their heads together to study the proteins, pathways, and processes that go awry in neurological disorders, such as Parkinson’s and Alzheimer’s diseases. The change in direction stems from a mutual decision to “get more biological,” says Petsko, who did his part by learning some yeast genetics during a 1995 sabbatical in the late Ira Herskowitz’s lab at the University of California, San Francisco. In looking for genes whose expression changes when yeast cells are quiescent, Petsko and company discovered a gene whose human homolog was later found to be mutated in families with a rare form of Parkinson’s. By then, his group had already crystallized the gene’s protein product. “And we realized that we had, sitting in our lab, the first three-dimensional structure of a protein involved in neurologic disease,” he says. After a few months of discussion, Petsko and Ringe decided to “jump in with both feet”—the lab is now using a combination of genetics and structural biology to try to get to the heart of these debilitating diseases.

“He’s fearless about heading into completely new areas,” notes Stock. And in moving between crystallography, genetics, and eukaryotic biology, Westpheling adds, “he’s had a real impact on each of these fields.”

More important, Petsko continues to have a broad impact through his teaching. “He gives talks that you think about and talk about for days afterward,” says Stock. His classes and seminars are “well worth the price of admission,” laughs Westpheling.

“Greg is really one of the most powerful people in American science,” adds Westpheling. “People listen when he speaks. Not everyone agrees with him about everything. But they applaud the fact that he opens the discussion so thoughtfully.”

Petsko is proud of his writing—but not half as proud as he is of his scientific progeny. “When I think about the legacy of my years in the lab, it’s not the published papers, it’s not the solved structures, it’s not this accomplishment or that one,” he says. “It’s the people who have come through the lab. It’s all about the people. And the older I get, the more I realize, it was always about the people. That’s what matters the most.”

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