Modeling intermediates of BamA folding an outer membrane protein

Area of Science:

• Biochemistry
• Structural Biology
• Microbiology

Background:

• BamA is a crucial outer-membrane protein in Gram-negative bacteria, essential for the assembly of other outer-membrane proteins (OMPs).
• BamA features a lateral gate, critical for its function in catalyzing OMP folding and insertion.
• The asymmetric-hybrid-barrel model proposes BamA's mechanism, involving the opening of its lateral gate.

Purpose of the Study:

• To investigate the physical consequences of the asymmetric-hybrid-barrel model of BamA function.
• To explore the folding intermediates of BamA in complex with a substrate OMP, EspP.
• To elucidate the role of sequence in determining the shape of substrate OMPs during and after folding.

Main Methods:

• Construction and simulation of multiple hybrid-barrel folding intermediates.
• Intermediates comprised the BamA β-barrel and POTRA5 domain with varying numbers of EspP β-hairpins (1-6).
• Analysis of simulation data to determine conformational changes and interactions.

Main Results:

• Simulation results support the asymmetric-hybrid-barrel model, with stronger BamA N-terminal β-strand interactions with the substrate.
• A consistent "B"-shaped conformation was observed for the final folding intermediate.
• The shape of the substrate β-barrel within the hybrid intermediate matched the fully folded substrate.
• Inward-facing glycines were identified at sharp bends in both hybrid and fully folded β-barrels.

Conclusions:

• The study provides evidence supporting the asymmetric-hybrid-barrel model for BamA function.
• The findings suggest that sequence dictates the shape of the substrate β-barrel during the folding process.
• The influence of sequence on barrel shape persists in the final, fully folded OMP.