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