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Playing games online is fun but generally regarded as a waste of time. That is, unless online gaming happens to help scientists cure AIDS.

Structure of Molecule Critical for HIV to Multiply Decoded by Gamers

Biochemists have been working for years to determine the structure of a molecule known as an HIV-1 protease. A protease is an enzyme that "snips" long chains of amino acids made by a virus into smaller chains of amino acids known as virions. The virions are capable of infecting new cells and acquiring new proteins there. If the virus is never "snipped" by protease, it remains coiled into a long, inert chain that cannot infect new cells.

Protease inhibitors, as you might imagine, are a key goal of AIDS treatment. Scientists have been trying to ascertain the geometry of the HIV-1 protease for almost 15 years. Online gamers decoded the structure of the molecule in just three weeks.

Scientists already knew that the placement of the HIV-1 protease was something like a dumbbell, with two larger, folded ends connected by a more or less straight chain of amino acids in the middle. They knew that the "snipper" in both ends of the dumbbell was aspartic acid. But they did not know how the enzyme positioned itself so that the aspartic acid would break the long dormant virus into smaller active pieces.

Read more: Green Glowing Cats Will Help in HIV Research

To gain insight into the geometry of the enzyme, researchers in the laboratory of University of Washington AIDS researcher Dr. David Baker developed a game called Foldit. Their idea was to tap into the enormous intellectual energy online gamers put into their games.

Foldit is a series of games (or tutorials) about how proteins coil and uncoil inside a cell. They start with "One Small Clash" and work their way up to "Rubber Band Reversal."

Gamers are given basic information about how the individual amino acids in the protein may attract or repel each other, and then they are presented with amino acid sequences in real proteins of known geometry to "fold." They are invited to try to make a protein depicted on the screen loop or wiggle. They can double the length of the protein to form a helix. They can shake the protein, work on just segments of the protein, freeze and unfreeze segments, and introduce cross links to hold the protein together. They can make the protein more or less compact and use a voiding tool to see which areas of the protein could be worked on more.

The game generates a score based on how well the protein is folded compared to what scientists already know, and the site maintains a list of high scoring gamers. Foldit gamers may share solutions and form groups, or compete against each other individually. Scientists then use analyze how gamers made decisions about folding proteins to write new computer algorithms to explain the structure of still-unknown proteins.

Foldit has been online since 2008. The structure of the protease enzyme is the fourth scientific breakthrough made with the help of online gamers. When brute computing power is not enough for scientists to figure out a problem, Foldit and similar tools make scientific discovery possible through the use of crowdsourcing.
Continue reading after recommendations

  • Alex Wright, "Managing Scientific Inquiry in a Laboratory the Size of the Web," New York Times, 27 December 2010, accessed 26 September 2011.
  • Photo courtesy of Trygveu on Flickr:

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