Computer modeling of the hexameric channel of VacA from H. pylori.

Abstract

Helicobacter pylori (H. pylori) infects over half of the human population in the world and is a main cause of stomach ulcers. As one of the major virulence factors secreted by H. pylori, Vacuolating toxin (VacA) molecules can insert into lipid bilayers and oligomerize to form a hexameric membrane channel. It has been proposed that cell vacuolation results primarily from the formation of such channels. However, structural and functional studies of VacA transmembrane (TM) channel have been hindered by the challenge of resolving the structure of this TM domain experimentally. Here, we report a computational protocol for modeling symmetric TM helical bundles and propose a structural model of the hexameric VacA channel. In our model, van der Waals packing and Cα-H···O hydrogen bonding of small residues Gly14 and Gly18 stabilize the association of adjacent helical pairs, consistent with the frequent occurrence of GxxxG motif observed in TM helix-helix interface. Through performing molecular dynamics (MD) simulations iteratively, we refine and validate our model, demonstrating that the resulting channel is stable and supports continuous pore water flow. Additionally, we simulate the single VacA TM helix, capturing the spontaneous partial insertion of the VacA N-terminal hydrophobic region into a lipid bilayer. Our results provide molecular details of how VacA participates in vacuolating the cell and inducing cell apoptosis. The computational protocol thus established may be employed to model other pore-forming toxins without a known structure.