Previous tests relied on proteins that had been modified extensively but were still based on naturally occurring protein structures. These variants also folded rapidly, suggesting that cooperative folding might be intrinsic to any protein of a certain size and final stability.
The Washington group thought, however, that Top7 would make a more rigorous test substrate. They had computationally designed Top7 to be stable despite its completely novel fold and structure. Its folding, they now report, involves at least three distinct kinetic phases and one or more intermediate structures. A rapid collapse is followed by a slower process of internal rearrangement.
Top7, the authors suggest, may be too stable for its own good. It lacks the buried polar interactions that often destabilize nonnative conformations. Top7 also uses a lot of local interactions, explaining why fragments of Top7 are individually stable. These local structures may complicate or slow the folding of the protein as a whole, whereas natural proteins favor long-range interactions that lock the native structure into place.
The group's conclusions are based on one protein, which is why the paper “is in the theory section of the journal,” says Baker. “It is definitely a speculation. One won't know until one sees further examples.” It may be other groups that provide those examples, however, as Baker is now focusing on altering existing proteins to generate new functions.