SEATTLE — University of Washington School of Medicine professor David Baker and his biochemistry colleagues have had the audacity to think they can design complex molecules that function faster and more effectively than the ones created by Mother Nature.
It turns out they might be right.
Baker won the 2024 Nobel Prize in chemistry Wednesday for using a process known as computational protein design to turn amino acids into proteins unlike any in existence. Baker shares the prize — which includes a cut of the $1 million in award money — with Demis Hassabis and John M. Jumper of Google DeepMind. They were honored for their use of artificial intelligence in predicting protein structures from their amino acid sequences.
“Proteins are the workhorses of all living things,” Baker explained during a Wednesday news conference at UW.
His vision is to show the world how the new proteins being developed by his colleagues and students can be used to solve persistent problems in medicine, energy and technology, from creating enhanced cancer treatments to building better semiconductors.
Baker, 62, a computational biologist and an alumnus of Seattle’s Garfield High School, spent the day in soft-spoken awe and celebration.
It started with a 2 a.m. phone call from Sweden with his biochemist wife and fellow UW professor Hannele Ruohola-Baker screaming with joy in the background.
It continued throughout the day in his home and campus lab, among more than 100 well-wishing students, faculty, family and alumni. A case of sparkling wine was rolled out for the occasion — Kirkland’s best (the Signature Brut).
Baker is the eighth UW faculty member to receive a Nobel Prize. The distinction comes months after Baker was named among Time magazine’s 100 most influential people in worldwide health.
The Nobel Prize comes during what UW President Ana Mari Cauce called the “prime” of Baker’s career. The protein pioneer, who once pursued philosophy and social studies at Harvard University, now teaches biochemistry at the UW School of Medicine and directs the school’s expanding Institute for Protein Design.
Cauce calls Baker a “local kid” making “global impact” through his work and teaching.
Baker is the progeny of UW faculty members Marcia and Marshall Baker. Marcia, a geophysicist, is known for her research on cloud physics and atmospheric sciences. Physicist Marshall focused his work on string models and particle theory. Both now retired, they still live near campus and were among several family members there for Wednesday’s celebration.
David’s interest in biology and proteins didn’t ignite until his senior year of undergrad. But he hasn’t looked back since.
He studied biochemistry and biophysics at the University of California, Berkeley, and San Francisco, respectively. After graduating he joined the UW School of Medicine Faculty in 1993.
“Not everyone was a fan,” said Institute for Protein Design Executive Director Lynda Stuart.
Back then, the IPD didn’t exist. Baker’s ideas were perceived as “crazy,” she said.
But his persistence, leadership and the ability to win people over kept him in the game.
Baker’s dream is to work with people to design proteins with new functions to solve chronic problems in medicine, biology and beyond, he said.
His premise of designing and activating proteins, instead of waiting for nature to evolve over time to produce solutions, is what led to the launch of Rosetta Commons. The collaborative computational biology project has advanced numerous protein design projects worldwide, including the Nobel-winning DeepMind project. It also brought the UW Institute for Protein Design to life 12 years ago.
“This is one of the greatest things to happen to scientists,” said Trisha Davis, Baker’s former department chair, of Baker being named a Nobel laureate. “David has such potential to bring protein design into a reality.”
This will be determined by the successes of using synthetic proteins in human clinical trials.
“The number of proteins that could exist is vast, and if we can harness just a little bit of that power to solve today’s problems, it will make a difference for everybody,” Davis said.
For example, designing a protein to inhibit a virus at its start, before it becomes a pandemic.
Baker nodded to the work of his colleague and fellow biochemist, Neil King, on using new, synthetic proteins to help develop vaccines to fight flu and coronaviruses. He also highlighted the work of his students to develop proteins to help improve photosynthesis, break down plastics and other pollutants and neutralize lethal toxins delivered by snake bites.
In his afternoon remarks to students and faculty, King called Baker someone who has led them all “with no fear, with a can-do attitude, with positivity, with problem solving.”
King said because of Baker’s work, scholars who come to the institute can now gain the knowledge and tools they need to solve “real-world” problems.
“Protein design, in particular, is an extraordinarily collaborative but also extraordinarily creative endeavor. We’re inventing new things that have never been invented before and they’re exceedingly complex,” said King. “That’s why we need computers to design proteins in the first place because they’re so complex.”
For example, in their work using proteins to break down plastics, Baker’s students learn to design new proteins on the computer. They then figure out how to make new genes, which get put into bacteria that, ideally, produce the new proteins in real life. If they produce an enzyme, a type of protein, that helps break down plastic faster, the scientists then need to determine the best way to apply and distribute them in a real-world scenario.
Peik Lund-Andersen is a second-year graduate student in Baker’s lab, where he is designing novel proteins that could enhance photosynthetic systems and help with things like carbon sequestration.
He called Baker’s recognition affirming and rewarding for the years they spend working on their projects.
Baker recruited Susana Vazquez Torres to UW six years ago from Queretaro, Mexico. She’s the one working on a better antidote to venomous snake bites; such antivenoms are produced by injecting horses with small doses of venom and extracting antibodies. She’s working to find a way to leave the horse out of it and create antivenoms from synthetic proteins. Vazquez Torres said she tells her family, “This is a place where we can revolutionize treatments.”
She’s come to admire Baker not only as a mentor but as a human who is “very supportive, very smart, very creative.”
“He truly changed my life forever,” she said.
Students say Baker has been integral in recruiting so many new students into the program that there’s a new problem to solve: finding more space.
