The lysine side chain's swing motion in AapA1 toxin promotes water transport through transmembrane pores

The rising antibiotic resistance of Helicobacter pylori and the emergence of multi-drug-resistant strains pose significant challenges to its eradication. Understanding the molecular mechanisms driving this resistance is critical. This study investigates how AapA1, a toxin protein, may inhibit H. pylori growth and cause morphological changes by forming transmembrane pores in its inner membrane. Using experimental data and molecular dynamics simulations, we analyzed the pore structure and its formation mechanism. Results show that AapA1 forms pores on liposomes and exists stably in the membrane as α–helices through different multimers, creating hydrophilic pores of varying sizes. Dynamic oscillation of K16/23 side chains in the membrane affects water transport through these pores, and restricting their movement significantly reduces transport. AapA1 monomers adopt three distinct conformations, with the K16/23 residues showing an up–down swing motion, potentially facilitating accelerated transport of substances. This study provides a new perspective on the dynamic structure–function relationship of AapA1–membrane interaction and highlights the role of positively charged residues in AapA1. Understanding the multimeric AapA1–membrane structure and the mechanism underlying AapA1–induced transmembrane pores is particularly crucial to develop new drugs and treatment options to reduce drug resistance emergence and combat any new emergence development.