Multi-Funnel Landscape of the Fold-Switching Protein RfaH-CTD

Abstract

Proteins such as the transcription factor RfaH can change biological function by switching between distinct three-dimensional folds. RfaH regulates transcription if the C-terminal domain folds into a double helix bundle, and promotes translation when this domain assumes a β-barrel form. This fold-switch has been also observed for the isolated domain, dubbed by us RfaH-CTD, and is studied here with a variant of the RET approach recently introduced by us. We use the enhanced sampling properties of this technique to map the free energy landscape of RfaH-CTD and to propose a mechanism for the conversion process.

High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme

“…5b ). Unlike the previous studies using targeted MD 56 , 58 or assisted GO model with replica exchange tunneling 57 , the REHT method does not embed in itself any information of the target state. In spite of that, the simulations spontaneously transform the RFA-H CTD from helical structure to the β-barrel conformation.…”

Energy Landscape for Fold-Switching in Regulatory Protein RfaH

“…The FEL was computed from the PEL at 300 K (not shown) and 310 K (Figure 5b). These two temperatures were chosen to allow for direct comparison with previous simulations (MSM construction at 300 K; 18 replica exchange approaches at 310 K 17,19 ) and the original NMR experiment (at 310 K). 14 There was no significant difference between the two the landscapes, and so further analysis refers to the FEL at 310 K. Each branch on the free energy disconnectivity graph corresponds to a free energy group.…”

“…The refolding of RfaH-CTD has been probed using several computational approaches, including replica exchange molecular dynamics (REMD), 17 construction of Markov state models (MSMs), 18 and replica-exchange-with-tunnelling (RET). 19 REMD has been used to investigate the refolding of the isolated RfaH-CTD in implicit solvent. 17 A free energy surface was constructed by projecting the replicas simulated at 310 K onto the root-mean-square deviation (rmsd) from the all-α state and the end-to-end distance.…”

“…Recently, Bernhardt and Hansmann applied RET to decipher the refolding mechanism for RfaH-CTD. 19 In RET, 20,21 replicas evolve in the microcanonical ensemble for a short period, and are then provisionally exchanged, while simultaneously rescaling their velocities to ensure that the total energy is invariant. The replicas are then allowed to evolve again at constant energy, and the final structures are accepted or rejected based on a Metropolis criterion.…”

“…Using RET, a significant free energy barrier (approximately 10 RT) separating the all-α and all-β states of RfaH-CTD was identified, and the transition was reported to occur via a disordered conformer. 19 In the present work, the potential energy landscape (PEL) framework and kinetic transition network (KTN) analysis are combined to probe the refolding of RfaH-CTD. In particular, discrete path sampling (DPS) [22][23][24] is used to construct the PEL (which encompasses lowlying minima and the corresponding transition states that connect them) for the structural transition at full atomistic resolution.…”