The C-terminal domain of transcription factor RfaH: Folding, fold switching and energy landscape

Abstract

We study the folding and fold switching of the C-terminal domain (CTD) of the transcription factor RfaH using a hybrid sequence-structure based model. We show that this model captures the essential thermodynamic behavior of this metamorphic domain, i.e., a switch in the global free energy minimum from an -helical hairpin to a 5-stranded {beta}-barrel upon separating the CTD from the rest of the protein. Using this model and Monte Carlo sampling techniques, we analyze the energy landscape of the CTD in terms of progress variables for folding towards the two folds. We find that, below the folding temperature, the energy landscape is characterized by a single, dominant funnel to the native {beta}-barrel structure. The absence of a deep funnel to the -helical hairpin state reflects a negligible population of this fold for the isolated CTD. We observe, however, a significantly higher -helix structure content in the unfolded state compared to results from a similar but fold switch-incompetent version of our model. Moreover, in folding simulations started from an extended chain conformation we find transient -helix structure that disappears as the chain progresses to the thermally stable {beta}-barrel state.