A computational model for lipid-anchored polysaccharide export by the outer membrane protein GfcD

Area of Science:

• Bacterial outer membrane protein structure and function
• Molecular dynamics simulations
• Bacterial capsule biogenesis

Background:

• Polysaccharide capsules protect bacteria, with group 4 capsules in Escherichia coli encoded by the gfcABCDE-etp-etk operon.
• GfcE is implicated in free polysaccharide export, but export of lipid-anchored chains remains uncharacterized.
• GfcD, an outer membrane beta-barrel protein, is a candidate for exporting lipid-anchored group 4 capsules.

Purpose of the Study:

• Investigate the function of GfcD in exporting lipid-anchored group 4 capsules.
• Determine the structural basis for GfcD's role in lipid A anchor export.
• Utilize molecular dynamics to simulate GfcD's interaction with the bacterial membrane and lipid A.

Main Methods:

• AlphaFold prediction of GfcD structure, revealing two beta-barrel domains.
• Unsteered molecular dynamics simulations of GfcD embedded in a bacterial outer membrane model.
• Insertion of lipid A into the C-terminal barrel of GfcD to mimic polysaccharide anchoring.

Main Results:

• GfcD possesses a unique C-terminal beta-barrel with a large lateral aperture.
• The lateral aperture remains stable during simulations, suggesting a functional exit gate.
• Lipid A's hydrophobic chains readily exit the GfcD C-terminal barrel into the surrounding membrane.

Conclusions:

• GfcD's C-terminal barrel likely acts as a lateral exit gate for lipid A anchors.
• This mechanism facilitates the export of lipid-anchored group 4 capsules in Escherichia coli.
• The findings provide structural insights into bacterial capsule biogenesis and outer membrane transport.