Comparative molecular dynamics reveal the conformational dynamics of the IrtAB-cMBT complex in mycobacterial iron uptake

The IrtAB transporter in Mycobacterium tuberculosis (Mtb) is essential for iron acquisition through the import of iron-bound carboxymycobactin (cMBT), yet the molecular mechanisms governing substrate recognition and transport remain unresolved. Here, we employed 450-ns molecular dynamics simulations to elucidate the conformational dynamics of IrtAB in substrate-free (apo) and substrate-bound (holo) states, revealing key structural rearrangements and residue-specific interactions underpinning its transport cycle. Comparative analyses demonstrated enhanced conformational flexibility in the holo state, with asymmetric domain movements in IrtA and IrtB subunits facilitating cMBT translocation. Three histidine residues (His356, His402, His407) in IrtA undergone significant positional shifts (6–10 Å) upon substrate binding, forming a dynamic coordination network critical for cMBT recognition. The ligand exhibited complex behavior, including a 3.5–4.0 Å downward movement within the binding pocket and RMSD fluctuations (0.5–5.0 Å), indicative of multiple energetically favorable binding modes. Substrate-induced stabilization of the transmembrane domains correlates with progressive dehydration of the binding cavity, while RMSF profiles highlighted asymmetric flexibility in transmembrane helices during transport. These findings reveal how IrtAB's exporter-like architecture is repurposed for iron-siderophore import, balancing structural rigidity with conformational plasticity to enable efficient nutrient uptake. By delineating the mechanistic basis of IrtAB-mediated iron acquisition, this study provides a framework for targeting this pathway in Mtb, offering potential avenues for therapeutic intervention against tuberculosis.