Shown holding a 3-D protein model, David Baker, UW Medicine professor of biochemistry and adjunct professor of bioengineering, is grateful for the anonymous contribution his lab received last year to support protein-folding research. “[Gifts are] very useful in pushing the research ahead,” says Baker. “Usually you can only write grants for things you’ve already done, so gifts are good for exploring brand-new areas.”
“That’s awful, isn’t it?” asks David Baker.
Baker, UW Medicine professor of biochemistry and adjunct professor of bioengineering, likes to keep his Rosetta@home project volunteers up to date on the program. Today, though, he’s a little chagrined; he sees that he hasn’t written them — the 270,000 people providing him with computer power — in more than a month.
When scientists like Baker deal with proteins — specifically, with predicting how strands of amino acids will fold up into proteins — they need to be able to do a lot of calculations. Even the folding of smaller proteins, consisting of a few hundred amino acids, involves tens of thousands of chemical interactions.
As a result, studying the folding of proteins takes a lot of computing power. And because proteins are involved in the body’s chemical reactions, cell structure and intercellular communication (not to mention diseases), understanding how proteins fold — and what function their folded form will fulfill — is crucial to advancing medical research.
Rosetta@home, designed by Baker, is a computer program that takes advantage of downtime on home computers and PlayStations. Participants download the program, and when their device is not in use, Rosetta@home begins its calculations, displaying what one advocate calls “spiffy” protein-folding graphics.
Although they enjoy the nifty graphics, Rosetta’s volunteers participate for other reasons. Writing on a web-based message board, they mention the possibility of finding protein-fueled cures for pressing health issues like AIDS, Alzheimer’s and cancer. For some of them, the desire to advance medical research is intensely personal. One user writes, “Chemotherapy isn’t a kind treatment. To see it used on a young child is heartbreaking. I’d never felt so helpless.”
In 2009, an anonymous donor chose a different way to support Baker’s work — by making a financial contribution to Rosetta@home in support of research and outreach. And Rosetta’s research findings are impressive.
“We’ve been able to predict structures of proteins from their amino acid sequences,” says Baker. “Lately, we’ve been able to show that using very limited amounts of experimental data — not enough data to normally determine the structure of a protein — we can get quite accurate structures using Rosetta@home.”
Although they’re not yet close to a clinical application, says Baker, he and his colleagues are using Rosetta to create new proteins. One of their targets is malaria. “We’re designing proteins for gene therapy approaches and for attacking pathogens,” he says.
If Baker, a leader in the field of protein-folding research, sounds like he must be busy, he is. But he still feels a little guilty about letting his Rosetta@home journal lapse.
“I’m going to try to write something tonight or this weekend,” Baker says.