New Protein Design

[Nicholas1992]

Hi fellow folders,

I was wondering if it is possible to design a protein that rearranges the carbon atoms
in graphite to form diamond(s)? If so, I wouldn't mind to assist in the design process.

[DoctorSockrates]

It'd be really cool to do that and such, but the mechanisms of the reactions needed would probably need to be studied first. With Foldit's capabilities, it's moreso a game about predicting structure if we don't know how we would go about with a reaction.

Take the Aflatoxin Challenge puzzles for instance. In those puzzles, we are designing an enzyme to do a function, but we already have key residues locked down that we already know should carry the reaction forward. The idea that we're harnessing in these puzzles is the notion that if we create a more stable modeled transition state, the reaction doesn't need as much activation energy.

Without a guiding reaction that we know is going to work yet, Foldit isn't really geared to "simulate" enzymatic reactions with substrates, at least not yet (that would be freakin' cool, I concur, and I'd probably spend hours in this enzymatic sandbox making molecular factories.)

Foldit's main focus is moreso predicting the structures of proteins that we have the sequence for but don't know the structure of (of which there is A LOT, thanks DNA sequencing). This can include hypothetical proteins that are designed by players to explore what kinds of structures are actually viable in real life, but these player designed proteins don't necessarily have functions, and it's very difficult to test what a player designed protein would actually do unless you had some sort of reference, like in the Aflatoxin Challenge.