University of Washington professor earns Nobel Prize for protein design

PORTLAND, Ore. (KOIN) – When University of Washington Biochemistry Professor David Baker began researching how to design proteins from scratch, he and his research team were in the "lunatic fringe." Now, he has a Nobel Prize.

Proteins are the "workhorses of biology," and are essential to cell function, UW explained in a press release announcing Baker's win on Wednesday.

For decades, Baker and his colleagues have used computing power to learn how 3-D shapes of proteins determine how they function.

“Proteins are the miniature machines that carry out all the important jobs in our bodies and in all living things,” Baker explained during a press conference. “Before our work, the only proteins that we knew about were the proteins that we discovered in nature.”

"What we’ve learned how to do is design completely new proteins that have new functions. And so now we’re working on problems like designing proteins to attack cancers and acting much more specifically and precisely in the body so it can be safer and more effective than current treatments," Baker said of his research -- noting proteins can be designed for an array of medical issues, such as attacking Alzheimer's disease or developing a universal flu shot. Proteins can also be designed for environmental issues, such as breaking down plastic or other pollutants.

Baker, a graduate of Seattle's Garfield High School, initially considered majoring in social studies or philosophy before switching to biology in his senior year as Harvard undergrad. He later earned his doctorate in biochemistry at University of California, Berkeley.

“I took a biology class and learned about proteins and how they fold up and I thought that would be a really interesting thing," Baker recalled. "But I remember you had to write a paper in the class on something. I wanted to write a paper on that and the TA said, ‘That’s too complicated, no one will ever understand it.’ So, I didn’t do that."

Baker didn't start his protein studies until he became a UW professor -- joining the institution in 1993. He's now the director for UW's Institute for Protein Design.

“Many engineers in biology have taken proteins that already existed in nature and tried to modify them a little bit to solve a problem. And what we’ve been trying to do is start completely from scratch,” Baker explained. “People said that was a crazy thing to do. It was very much on the lunatic fringe until when we started getting better at it – and really this is in the last several years – suddenly it’s in the mainstream.”

Chasing the "lunatic fringe," led Baker to his Nobel Prize in Chemistry -- announced Oct. 9 by the Royal Swedish Academy of Sciences -- for discovering how to create new proteins that do not exist in nature.

Baker shares the award with Demic Hassabis and John M. Jumper of DeepMind, who were honored for protein structure prediction.

Baker's colleagues praise his work for transforming research in biology.

"Joining the ranks of Nobel Laureates is a testament to David Baker's dedication and innovation," said University of Washington President Ana Mari Cauce. "The University of Washington is proud to be a place that fosters groundbreaking and impactful research and extends its heartfelt congratulations to David on this remarkable recognition."

UW School of Medicine CEO and Dean Dr. Timothy Dellit, added, “Protein design is paving the way for development of new and highly effective vaccines, novel therapy such as antivirals to block viral infection, treatment of celiac disease, cancer immunotheragenics. It is just phenomenal what David’s scientific innovation and discovery is leading to in terms of impact of our communities."

Among his other achievements, Baker has published more than 640 peer-reviewed research papers, co-founded 21 biotech companies, was named among the 100 most influential people in health by TIME in May, and helped create an online puzzle game, "Foldit," which helps people with no background in science solve protein structure problems.

Baker says this is just the beginning.

“We figured out how to design new proteins, we figured out how to make them bind to cancer targets, for example, and we’re getting better at learning how to make them catalyzed chemical reactions, so we’ve really learned a lot about how to design proteins with new functions," he added. "So, I think now what’s tremendously exciting is to look at the vast array of problems that we face and try to design proteins that solve these problems.”