Protein folding: Matching theory and experiment

The impact of folding funnels and folding simulations on the way experimentalists interpret results is examined. The image of the transition state has changed from a unique species that has a strained configuration, with a correspondingly high free energy, to a more ordinary folding intermediate, whose balance between limited conformational entropy and stabilizing contacts places it at the top of the free energy barrier. Evidence for a broad transition barrier comes from studies showing that mutations can change the position of the barrier. The main controversial issue now is whether populated folding intermediates are productive on-pathway intermediates or dead-end traps. Direct experimental evidence is needed. Theories suggesting that populated intermediates are trapped in a glasslike state are usually based on mechanisms which imply that trapping would only be extremely short-lived (e.g., nanoseconds) in water at 25 degrees C. There seems to be little experimental evidence for long-lived trapping in monomers, if folding aggregates are excluded. On the other hand, there is good evidence for kinetic trapping in dimers. alpha-Helix formation is currently the fastest known process in protein folding, and incipient helices are present at the start of folding. Fast helix formation has the effect of narrowing drastically the choice of folding routes. Thus helix formation can direct folding. It changes the folding metaphor from pouring liquid down a folding funnel to a train leaving a switchyard with only a few choices of exit tracks.