UW biochemist wins Nobel Prize for using computers to design proteins

A biochemist at the University of Washington School of Medicine has won the Nobel Prize in Chemistry for his groundbreaking work in computational protein design.

When David Baker first set out decades ago to use computers to design completely new proteins, some questioned whether it could be done. Scientists had figured out how to alter proteins found in nature — the building blocks for all living things — but not create them from whole cloth.

“We were actually on the lunatic fringe for many, many years in trying to make proteins that could carry out very sophisticated functions starting just completely from scratch,” Baker said.

Today, the UW Institute for Protein Design, which Baker directs, is filled with researchers doing exactly that — doing amino acid origami using computer models to build novel proteins to target cancer cells, develop snake antivenom, fix carbon, speed up photosynthesis, and dissolve pollutants like microplastics.

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They’ve already helped develop a Covid-19 vaccine, Baker said, and are now tackling other viruses with pandemic potential.

“We're sort of going through the list of the greatest viruses of concern and designing proteins to block them,” he said.

After speaking with reporters, Baker was greeted at his Institute for Protein Design by dozens of giddy students and colleagues, and a whole lot of champagne.

Green Ahn, a postdoctoral researcher in Baker’s lab, is working to develop proteins that can degrade cancer-causing proteins, and on proteins that can home in on cancer but go easy on benign cells.

“Protein design has a really unique way to basically target any kinds of proteins that we want to get rid of, because there's a lot of proteins that cause disease,” Ahn said.

The immense size of the research lab, with dozens of students at computers and lab stations, initially startled Ahn.

“I was a little bit intimidated by it at first, but he really understands everyone's projects, advises everyone, and is very supportive of both grad students and postdoc career development,” Ahn said.

“I’m having a heck of a good day. I mean, this is just amazing,” said Ana Mari Cauce, UW president, who marveled at Baker receiving the Nobel Prize midcareer, at age 62, when he is still full of energy and ideas.

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“Something that I think is very special about this place is that people do come in with wild ideas, and we support them in exploring those, because you really never know,” Cauce said.

Anyone who wants to try their hand at computational protein design can play a free game Baker’s lab designed, FoldIt, which he says teaches users biochemistry while allowing them to become citizen scientists and contribute to his lab’s research.

Baker shares the award with two artificial intelligence developers at Google DeepMind in the UK, Demis Hassabis and John Jumper, who created a model to accurately predict protein structure.

“One of the discoveries being recognized this year concerns the construction of spectacular proteins. The other is about fulfilling a 50-year-old dream: predicting protein structures from their amino acid sequences. Both of these discoveries open up vast possibilities,” said Heiner Linke, chair of the Nobel Committee for Chemistry, in announcing the awards.