To survive low pH conditions in the stomach, some bacterial pathogens have elaborated different adaptive mechanisms. Among them, amino acid dependent systems consist in two components: an antiporter that facilitates the exchange of external substrate for internal product and a cytoplasmic decarboxylase that catalyzes a proton-consuming decarboxylation of the substrate amino acid. AdiC and GadC were identified as the pH-dependent and electrogenic antiporters involved in the arginine-agmatine and glutamate-GABA exchange respectively. Their 3D structures have revealed a fold typical of the amino acid-polyamine-organocation (APC) superfamily of transporters, the second largest family of secondary transporters. Using integrated computational approaches including molecular dynamics simulations, molecular and quantum mechanics calculations, we have investigated the recognition of the substrates and the pH-regulated transport of AdiC and GadC. To achieve transitions between alternating structural states along the translocation pathway, global rearrangements of a few transmembrane segments were necessary but needed to be coupled to local structural changes, involving mainly aromatic residues, to regulate access to both the outward- and inward-facing states. Also, AdiC and GadC must, among the multiple protonation forms they encounter in their surroundings, select their substrate so as to achieve an exchange that produces a net proton movement from the cytosol to the periplasmic side. For AdiC, the weaker binding of the divalent compound, Arg2+, was shown to result, in agreement with an experimental study, from a greater tendency to remain hydrated than the monovalent Arg+ substrate, and the binding of the latter was demonstrated to be impacted by changes in the protonation forms of a conserved acidic residue upon substrate binding. Furthermore, structural models of eukaryotic amino acid transporters built using AdiC structures were successfully exploited to unveil their mechanisms of amino acid recognition and translocation showing that AdiC is a good paradigm for the APC amino acid transporters.

Exploring the acid resistance mechanism of electrogenic amino acid antiporters in food-borne pathogens using computational experiments

2019 Fall National Meeting

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