MSNBC's Thomas Roberts talks with University of Washington Center for Game Science director Seth Cooper and researcher Firas Khatib about a video game that helped unravel a protein structure in an AIDS-like virus.
By Alan Boyle
Last updated 12:45 p.m. ET Sept. 20:
Video-game players have solved a molecular puzzle that stumped scientistsfor years, and those scientists say the accomplishment could point the way to crowdsourced cures for AIDS and other diseases.
"This is one small piece of the puzzle in being able to help with AIDS," Firas Khatib, a biochemist at the University of Washington, told me. Khatib is the lead author of a research paper on the project, published today by Nature Structural & Molecular Biology.
The feat,which was accomplished using a collaborative online game called Foldit, is also one giant leap for citizen science — a burgeoning field that enlists Internet users to look for alien planets, decipher ancient texts and do other scientific tasks that sheer computer power can't accomplish as easily.
"People have spatial reasoning skills, something computers are not yet good at," Seth Cooper, a UWcomputer scientist who is Foldit's lead designer and developer, explained in a news release. "Games provide a framework for bringing together the strengths of computers and humans."
Unraveling a retrovirus
For more than a decade, an international team of scientists has been trying to figure out the detailed molecular structure of a protein-cutting enzyme from an AIDS-like virus found in rhesusmonkeys. Such enzymes, known as retroviral proteases, play a key role in the virus' spread — and if medical researchers can figure out their structure, they could conceivably design drugs to stop the virus in its tracks. The strategy has been compared to designing a key to fit one of Mother Nature's locks.
The problem is that enzymes are far tougher to crack than your typical lock. There are millionsof ways that the bonds between the atoms in the enzyme's molecules could twist and turn. To design the right chemical key, you have to figure out the most efficient, llowest-energy configuration for the molecule — the one that Mother Nature herself came up with.
That's where Foldit plays a role. The game is designed so that players can manipulate virtual molecular structures that look likemulticolored, curled-up Tinkertoy sets. The virtual molecules follow the same chemical rules that are obeyed by real molecules. When someone playing the game comes up with a more elegant structure that reflects a lower energy state for the molecule, his or her score goes up. If the structure requires more energy to maintain, or if it doesn't reflect real-life chemistry, then the score is lower.
Morethan 236,000 players have registered for the game since its debut in 2008.
The monkey-virus puzzle was one of several unsolved molecular mysteries that a colleague of Khatib's at the university, Frank DiMaio, recently tried to solve using a method that took advantage of a protein-folding computer program called Rosetta. "This was one of the cases where his method wasn't able to solve it," Khatibsaid.
Fortunately, the challenge fit the current capabilities of the Foldit game, so Khatib and his colleagues put the puzzle out there for Foldit's teams to work on. "This was really kind of a last-ditch effort," he recalled. "Can the Foldit players really solve it?"
They could. "They actually did it in less than 10 days," Khatib said.
University of Washington
A screen shot shows how the Folditprogram posed the monkey-virus molecular puzzle.
One floppy loop of the molecule, visible on the left side of this image, was particularly tricky to figure out. But players belonging to the Foldit Contenders Group worked as a tag team to come up with an incredibly elegant, low-energy model for the monkey-virus enzyme.
"Standard autobuilding and structure refinement methods showed within hours...