Intrinsically disordered regions stabilize the helical form of the C-terminal domain of RfaH: A molecular dynamics study

RfaH protein functions as both transcription anti-terminator and translation enhancer in bacteria. Recent studies have shown that the C-terminal domain (CTD) is an alpha-helical hairpin (two-helix bundle) in full-length RfaH, despite the intrinsically favored beta-barrel structure. Here, we carried out mu s-timescale molecular dynamics (MD) simulations for the wild-type (WT) RfaH, its E48S mutant and an established model without the intrinsically disordered region (IDR1) linking the CTD and the N-terminal domain (NTD). Our simulations showed that the WT can be well stabilized by our RSFF1 force field, while the E48S mutant and the model without IDR1 undergo considerable structural change, which is in good agreement with experimental observations. The IDR1 plays important roles in stabilizing the hydrophobic environment near the crucial E48-R138 salt-bridge as well as in tethering alpha 4 helix in CTD to alpha 3 helix in NTD. In the absence of the IDR1, destabilization of key interdomain contacts and unfolding of the CTD alpha 5 helix were observed in the simulation. In addition, the intrinsically disordered tail of the CTD (IDR2) is also of great significance to stabilize the bound conformation of CTD. These findings provide important implications for consideration of simulations in revealing the functions of residues invisible in a crystal structure. (C) 2016 The Author(s). Published by Elsevier Ltd.