Low Dimensional Topology

June 9, 2008

Folding proteins for fun and profit

Filed under: Metric geometry,Misc. — Jesse Johnson @ 10:32 am

It appears that some crafty biologists have figured out a way to trick unsuspecting internet users into helping them find minimal energy embeddings of complex proteins in R^3 (i.e. protein folding). The game fold it allows players to manipulate proteins and scores them based on how efficient an embedding they can find. The best solutions are then recorded by the main site. (There’s also a nice tutorial for players who don’t know any biology.)

Recall that a protein is a chain of amino acids linked by single-bonded carbon atoms that allow the joints to rotate. Different angles will determine different distances between atoms in the protein, so different embeddings have different amounts of potential energy. In nature, the protein will twist along the joints to take on an embedding that minimizes the energy. Scientists have figured out how to read off the sequence of amino acids in a protein, but figuring out the lowest energy embedding is not so easy, since there are infinitely many possible configurations.

There have been computer simulations of protein folding for a number of years now, but this only solves part of the problem – all the computer simulations may just just be finding local minima and missing the actual solutions. Fold it takes advantage of some of the things the human mind still does better than a computer. (I think this is called crowd sourcing.) I wonder if there are any math problems that could benefit from a similar campaign. One could probably get ropelength estimates this way, but they would still just be estimates rather than a proof.

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