Modeling study of the HlyBD-TolC hemolysin secretion system using the AI-based structural prediction and molecular dynamics simulation

Modeling study of the HlyBD-TolC hemolysin secretion system using the AI-based structural prediction and molecular dynamics simulation

The HlyBD-TolC complex, belonging to the type I secretion system (T1SS), is found in many pathogenic Gram-negative bacteria. This complex comprises three components: the ABC-type inner membrane transporter HlyB, the periplasmic adaptor HlyD, and the outer membrane channel TolC. Recent crystal and cryo-EM structures have shed light on the stoichiometry of the HlyB hexamer and HlyD hexamer in the functional complex. In this study, we performed a modeling study using the AI-based structure prediction program Alphafold-multimer to gain a deeper understanding of the assembly of the T1SS system. The program predicted a funnel-like hexameric model of the HlyD, which was stable in a molecular dynamics simulation, and the HlyD hexamer would intermesh with the TolC trimer in a cogwheel structure. Combining the modeled and docked structures, we built an assembly model of HlyBD-TolC, showing a central channel spanning the complex. These observations suggest a mechanism reminiscent of the DNA helicase.