UW’s Protein Guru, David Baker, Eyes Alternative Biofuels, Vaccines in New 3-D Structures

4/2/09Follow @xconomy

David Baker’s parents were both scientists at the University of Washington, and growing up, he figured that was the last thing he’d ever want to be. Yet after a couple of intriguing detours, his life path has led him right back to the UW campus. It’s there that he has carved out his own path as a world leader in understanding proteins, and how these complex 3-D structures carry out all the biological functions that DNA tells them to do in the body.

“I wasn’t really interested in science much as a kid because my parents were in science,” Baker says. “I didn’t really listen to people very much.”

Baker, 46, now has a lot of people who want to listen to him, like graduate students, faculty, big drugmakers, industrial corporations, and venture capitalists. Baker, a UW biochemistry professor and investigator for the Howard Hughes Medical Institute, is leading an effort to design new enzymes on computers from scratch that Mother Nature never created through evolution. His dream, which is beginning to take shape in a pair of Seattle-based startup companies—Arzeda and Bio Architecture Lab—is to craft enzymes that might break down stubborn proteins so entire plants can be used for biofuels, or crops can be made resistant to herbicides.

This is all gaining momentum in the wake of the Human Genome Project, as scientists have gained access to the sequence of the entire 3-billion-letter string of human DNA, and many other organisms. But the genes are really just an instruction manual, or a parts list, for the real work in biology that gets done by proteins. And while DNA comes in a linear, digital string of chemical units known as A,C, G, and T, proteins that arise from the code are chaotic, spaghetti-like 3-D structures that carry out all the business in the body, forming everything from muscles, nerves, and blood, to the stomach enzymes you produce to digest your meals.

Scientists have long used tedious, expensive crystallography or nuclear magnetic resonance spectroscopy technologies to characterize proteins. Over the past 15 years, Baker’s lab has pioneered new ways to make it so distributed computer networks can be used to perform complex calculations that predict how a gene sequence will turn into a precisely folded protein structure. Now that Baker’s team has made significant strides there—and gotten more than 200,000 people around the world to contribute their computer downtime to the cause—Baker is pursuing the kinds of applications that get entrepreneurs and VCs excited. He says it’s now becoming possible to create new proteins from scratch to do all kinds of useful things.

“David possesses the rare combination of having a strong scientific mind with the creativity and foresight to stay on the cutting edge of significant trends in terms of the Internet and networked computing,” says Nikesh Parekh, CEO of Bio Architecture Lab and an angel investor. “He has vision in terms of pushing the envelope of science.”

Daniela Grabs, a former student of Baker’s and co-founder of Arzeda, adds: “David is very smart and he is genuinely interested in understanding science (and not in becoming rich or famous). He truly believes that only by sharing and exchanging ideas and experiences we can advance the most.”

I sought to learn more about how Baker got on this track during a visit to his UW lab a couple of weeks ago.

He showed up like a man in a hurry, a little after 10 am, when he usually gets to the lab each day. Baker has brown eyes, and brown curly hair that fans out over his ears. He has a slight, wiry, and athletic frame that is a giveaway of one of his favorite hobbies—hiking and climbing … Next Page »

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  • Chad Waite

    About time some one wrote about the awesome work that David is doing.
    We are excited about starting a company with soem of David’s followers.