Energy Landscape for Fold-Switching in Regulatory Protein RfaH

The C-terminal domain (CTD) of bacterial regulatory protein RfaH undergoes a dramatic structural rearrangement from an α-helical hairpin to a β-barrel. We employ a quasi-continuous interpolation scheme and geometry optimization techniques to construct a kinetic transition network for this process. The computed free energy landscape at 310 K is multifunneled, and the predicted free energy ensembles are in good agreement with experiment and other simulation studies. We find that rearrangement from the α-helical conformer to the β-sheet proceeds via an essentially unstructured state. The techniques refined for the present system should be transferable to other protein conformational switches, with the potential to advance our understanding of such systems.