A Dynamic Sugar-Selective Bacterial Nanopore for Targeted Antibiotic Transport

Bacterial porins are essential for molecule transport, yet their functionality in pathogens remains underexplored. Here, a monomeric porin CymAKp is identified and characterized from a pathogen Klebsiella pneumoniae, featuring a specialized constricted segment (1-25 residues) in the pore. Single-channel recordings reveal the formation of fluctuating CymAKp nanopores that exhibit gating in symmetrical and asymmetrical lipid bilayers. The movement of the constricted segment drives these gating events, and the deletion of this segment results in stable nanopores establishing dynamic functionality of the pores. Furthermore, it is shown that CymAKp functions as a sugar-selective nanopore, facilitating the permeation of cyclic hexasaccharide while excluding larger cyclic sugars. Aminoglycoside antibiotics, structurally similar to cyclic sugars, exploit this sugar-selective pathway for translocation, and their translocation kinetics is quantified. Remarkably, molecular dynamics simulations reveal two distinct translocation pathways: one for cyclic hexasaccharides, where the constricted segment is displaced, and another for antibiotics, where the constricted segment remains within the pore. Studies establish the charged affinity site and constricted segment role in the porin as key regulators of dynamic molecular transport in pathogenic porins and provide new insights for developing nanopore-based drug delivery systems.