Who says you need a biochemistry degree to engineer an AIDS breakthrough? As our colleague Matt Peckham wrote on Techland, a bunch of online gamers have managed to crack a puzzle that AIDS researchers have been trying to solve for years.
Online Foldit players figured out the structure of a retroviral protease, a type of protein that is crucial to the replication of HIV. In this case, gamers worked on the protein that allows the Mason-Pfizer monkey virus (M-PMV) to progress into simian AIDS in rhesus monkeys. Legitimate scientists have tried unsuccessfully to model the protein; Foldit players working in concert were able to “solve” the structure in a matter of weeks.
So, what is Foldit, you ask? It’s basically an online game that asks players to figure out the complex three-dimensional structures of proteins. Proteins consist of long chains of amino acids, which fold into various, convoluted shapes. The way a protein is folded says a lot about how it works, but solving its intricate structure is the tricky part.
Foldit’s website provides a nice little primer on protein folding and what is medically useful about it:
[K]nowing the structure of a protein is key to understanding how it works and to targeting it with drugs. A small protein can consist of 100 amino acids, while some human proteins can be huge (1000 amino acids). The number of different ways even a small protein can fold is astronomical because there are so many degrees of freedom. Figuring out which of the many, many possible structures is the best one is regarded as one of the hardest problems in biology today and current methods take a lot of money and time, even for computers. Foldit attempts to predict the structure of a protein by taking advantage of humans’ puzzle-solving intuitions and having people play competitively to fold the best proteins.
Gamers on Foldit, which was unveiled by University of Washington researchers in 2008, are asked to manipulate the structure of proteins. The more stable their structure, the higher their score. It sounds complicated, but you don’t need any scientific training to play Foldit. As science writer Ed Yong wrote on Discover‘s Not Exactly Rocket Science blog last year:
The controls are intuitive, tutorial levels introduce the game’s mechanics, colourful visuals provide hints, and the interface is explained in simple language. While protein scientists concern themselves with “rotating alpha-helices and “fixing degrees of freedom,” Foldit players simply “tweak,” “freeze,” “wiggle” and “shake” their on-screen shapes. It’s telling that barely an eighth of the players work in science, and two-thirds of the top scorers have no biochemistry experience beyond high school.
The solution to the M-PMV protein was published [PDF] in the journal Nature. This is Foldit’s second paper in Nature — the first was a review of how online gaming can be useful to this particular area of medical research. Ongoing Foldit projects are focused on solving structural challenges in proteins involved with cancer, Alzheimer’s and other major diseases.