The folding of a metamorphic protein

A principle of the energy landscape theory of protein folding is that amino acid sequences that fold in biologically relevant times are characterized by a funnel-shaped landscape directed towards the native state. Some proteins, however, have recently been found to reversibly switch between two entirely different folds controlled by changes in the local environment. Do these so-called metamorphic proteins exhibit rugged energy landscapes with multiple deep funnels? We used a hybrid sequence-structure based all-atom model to simulate the folding and fold switching of the C-terminal domain (CTD) of the bacterial transcription factor RfaH, a prototypical metamorphic protein. The CTD adopts an α-helical hairpin within the free RfaH structure but undergoes a structural transformation into a β-barrel fold when detached from the rest of RfaH. For the isolated CTD, we found an energy landscape characterized by a single dominant funnel to the beta-barrel state. This suggests that protein folding funnels can be robust against sequence variants that encode for more than one fold. Our results indicate, moreover, that the encoding of dual folds mainly impacts the unfolded state of the CTD, which we found exhibits residual α-helical structure.