Molecular dynamics study on folding and allostery in RfaH

Area of Science:

• Protein folding and dynamics
• Molecular biophysics
• Structural biology

Background:

• RfaH protein regulates transcription and translation.
• Its function involves a conformational switch between alpha-helix and beta-barrel structures.
• This switch is crucial for its dual role.

Purpose of the Study:

• Investigate the thermal folding of RfaH's domains (NTD and CTD).
• Analyze the allosteric transition from alpha-helix to beta-barrel in CTD.
• Understand the stabilizing effect of NTD on CTD folding.

Main Methods:

• Coarse-grained off-lattice molecular dynamics simulations.
• Analysis of specific heat profiles to determine melting temperatures.
• Characterization of transition pathways using a Tanford beta-like parameter.

Main Results:

• Beta-barrel conformation of CTD is significantly more stable than its alpha-helix form.
• NTD interaction greatly stabilizes CTD and enhances folding cooperativity.
• The alpha-to-beta transition in CTD follows a two-state model with three parallel pathways.

Conclusions:

• RfaH's conformational change is an allosteric transition driven by thermal stability differences.
• NTD plays a critical role in stabilizing CTD for proper function.
• The transition pathways reveal complex dynamics in protein conformational changes.