title: Intrinsically disordered regions stabilize the helical form of the C-terminal domain of RfaH: A molecular dynamics study.
abstract: 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 α-helical hairpin (two-helix bundle) in full-length RfaH, despite the intrinsically favored β-barrel structure. Here, we carried out μs-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 α4 helix in CTD to α3 helix in NTD. In the absence of the IDR1, destabilization of key interdomain contacts and unfolding of the CTD α5 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.
authors.affiliation: Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
authors.forename: Sangni
authors.initials: S
authors.lastname: Xun
authors.affiliation: Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China. Electronic address: jiangfan@pku.edu.cn.
authors.forename: Fan
authors.initials: F
authors.lastname: Jiang
authors.affiliation: Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China. Electronic address: wuyd@pkusz.edu.cn.
authors.forename: Yun-Dong
authors.initials: YD
authors.lastname: Wu
mesh_terms: D029968:Escherichia coli Proteins / Q000737:chemistry*; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D010445:Peptide Elongation Factors / Q000737:chemistry*; D015534:Trans-Activators / Q000737:chemistry*
chemical_list: D029968:Escherichia coli Proteins; D010445:Peptide Elongation Factors; C106401:RfaH protein, E coli; D015534:Trans-Activators
keywords: Intrinsic disorder; MD simulation; Protein; RfaH; Salt-bridge; α-Helix