The Wednesday Post (11/08/2010)

Looking at protein folders

A recent Nature letter looks at the properties of human protein folders and how they can design better programs to do it automatically (Photo taken by Thomas Tu)

My mother was always vaguely disdainful of me playing computer games as a child (… and as an adult). But it turns out I was just training myself to cure cancer. Some scientists have made a free online game called Foldit, where the objective is to make the most stable protein structure.

Why have they made this game? Because if we look at the DNA sequence of a gene, we are only told the amino-acid sequence of a protein. However, proteins work because of their 3D shape. Seeing as there can be more than a googol different ways of folding a particular chain of amino-acids, protein sequence can only give us so much information. The most stable structure is probably the shape that a protein takes in the body. Once we know that, we can design drugs that can alter the protein’s function. We may also understand how mutations in genes change the stucture of a protein and cause diseases ,such as cancer.

To help us, there are computer programs to fold proteins automatically. Basically, these take the protein and randomly mix it up. If it’s less stable, the new structure is thrown away; if it’s more stable, the new structure is kept and changed again. This happens over and over until no further small changes make it more stable.

But human players are willing to think forward and make huge changes to increase the stability. These changes are so drastic that the program would think it’s a road to a less stable protein. The top players get within a tenth of a nanometer of the correct known structures. The scientists have recorded their moves, looked at their strategies for making a stable protein and are starting to incorporate these techniques into their computer programs.

More than 100 000 people have created accounts for Foldit and the majority of them are not biologists, but gamers with too much time on their hands. So I wonder what my mum would say about my 9 straight hours of Super Mario Brothers 3 now. (P.S. She still thinks it was a waste of time)

Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010). Predicting protein structures with a multiplayer online game Nature, 466 (7307), 756-760 DOI: 10.1038/nature09304

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Filed under Thomas' Corner

3 responses to “The Wednesday Post (11/08/2010)

  1. Have you actually tried this? I saw something about it a few months ago and I had a shot. It’s actually really addictive and awesome, in its own way.

    • I must admit that I have tried and completely failed at it. Couldn’t get the hang of it past the later tutorial levels. Maybe if they made histidine residues ride tiny Yoshis, I’d be better at it…

      • …you idiot.
        As you mentioned FoldIt was based on existing software. It’s called Rosetta. I have used that plus a number of protein structure prediction servers so maybe I have more experience looking at the ribbon models and maybe that helps? I dont know, fun though.

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