Bacteria's most well-studied chaperone is the GroEL nano-cage, which encapsulates a folding substrate within its walls. This cage was thought to be little more than a way to isolate substrates to prevent aggregation of slow-folding proteins. But the new findings suggest an active role, as folding rates inside the cage were up to 15-fold faster than in solution.
Folding is hastened by several cage features, including cage size. For small proteins, GroEL mutants with a smaller cavity further accelerated folding, until a point at which necessary rearrangements were spatially restricted. Confinement hastens folding by preventing those misfolded intermediates that would not fit within the cage. “The number of possible conformations,” says Hartl, “is astronomically large. The cage reduces it to a subfraction of that.”
For large proteins, both smaller and larger cavities slowed folding. The cage thus seems to be evolutionarily optimized to suit its ∼250 in vivo substrates. “You can improve folding rates for some with GroEL mutations,” says Hayer-Hartl, “but only at the expense of other substrates.”
Flexible, finger-like extensions at the bottom of the cavity were necessary for some proteins to fold quickly. The authors speculate that these mildly hydrophobic sequences gently massage misfolded states, increasing the substrate's fluidity and easing rearrangements.
Some proteins also required clusters of negative charges on the cavity wall for optimal folding. Proteins most impeded by the loss of these clusters were themselves negatively charged, so perhaps the clusters help by keeping these proteins from sticking to the cage walls.
The authors would next like to identify intermediates in spontaneous and GroEL-mediated folding events to see just how the folding landscape changes inside the cage.