The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation

Abstract

The transcription antiterminator RfaH has been shown to undergo major structural rearrangements to perform multiple functions. Structural determination of the C-terminal domain (CTD) of RfaH showed that it can exist as either an α-helix bundle when interfacing with the N-terminal domain (NTD) or as a β-barrel conformation when it is not interfacing with the NTD. In this paper, we investigate the full RfaH with both CTD and NTD using a variety of all-atom molecular dynamics (MD) simulation techniques, including targeted molecular dynamics, steered molecular dynamics, and adaptive biasing force, and calculate potentials of mean force. We also use network analysis to determine communities of amino acids that are important in transferring information about structural changes. We find that the CTD-NTD interdomain interactions constitute the main barrier in the CTD α-helix to β-barrel structural conversion. Once the interfacial interactions are broken, the structural conversion of the CTD is relatively easy. We determined which amino acids play especially important roles in controlling the interdomain motions and also describe subtle structural changes that may be important in the functioning of RfaH.

Interdomain salt‐bridges in the Ebola virus protein VP40 and their role in domain association and plasma membrane localization

“…VP40 exists in various conformations depending on the required function: a butterfly shaped dimer is involved in the transport of the protein to a membrane, a hexamer to form the viral matrix, and an octamer ring structure to bind to RNA and regulate viral transcription . As with other recently identified transformer proteins such as the RfaH transcription factor, the structural basis and mechanisms of large‐scale structural transformation in VP40 are not well understood.…”

Differential local stability governs the metamorphic fold-switch of bacterial virulence factor RfaH

“…Since the trigger for RfaH metamorphosis is the complete ops-paused TEC (13,14,16), it is challenging to study this process experimentally. Instead, most of the thermodynamic and kinetic studies have used computational approaches to directly explore this fold-switch by simulating either the isolated CTD (18)(19)(20) or the entire RfaH protein (21,22). Although the RfaH CTD is composed of only 51 residues (residues 112-162), its transition from alpha to beta has not been observed through conventional molecular dynamics (19), but through the use of enhanced sampling techniques (18,20,22) or reduced system granularity (21,23).…”

“…Instead, most of the thermodynamic and kinetic studies have used computational approaches to directly explore this fold-switch by simulating either the isolated CTD (18)(19)(20) or the entire RfaH protein (21,22). Although the RfaH CTD is composed of only 51 residues (residues 112-162), its transition from alpha to beta has not been observed through conventional molecular dynamics (19), but through the use of enhanced sampling techniques (18,20,22) or reduced system granularity (21,23). A way to circumvent such computing barriers is the use of confinement simulations, which rely on a discontinuous thermodynamic integration to estimate the absolute free energy of a clearly defined energy well (24).…”

Plasma membrane association facilitates conformational changes in the Marburg virus protein VP40 dimer

“…4 VP40 is involved in multiple functions during the viral life-cycle 5 and protein multifunctionality often requires proteins to undergo conformational changes. 6–8 It has been shown that, depending on the function, EBOV VP40 (eVP40) exists in different conformations such as a butterfly shaped dimer involved in the transport of the protein to the membrane, a hexamer to form the viral matrix beneath the lipid-envelope, and an octamer ring structure to bind RNA and regulate viral transcription. 5 The X-ray crystal structure determination of the dimeric, hexameric and octameric forms of eVP40 has provided a great deal of information about the structural transformation of the protein into various oligomeric states for performing different functions.…”