Many Gram-negative bacteria are highly virulent and are becoming increasingly resistant to modern antibiotics due to improper use. Drug uptake in Gram-negative bacteria is challenging due to the presence of an asymmetric outer membrane (OM) that hinders uptake and numerous efflux pumps in the cytoplasmic membrane, which expel antibiotics that do enter the cell. While small molecules (< ~600 Da) can diffuse through OM porins, large molecules, nutrients and antibiotics require the inner membrane’s proton motive force and integral membrane proteins to facilitate their active transport. Potential antibiotic targets on the OM include the TonB-dependent transporters (TBDTs) that, true to their name, employ the periplasm-spanning TonB protein to import large, rare nutrients such as ferric iron siderophores, nickel chelates, and cobalamins into the periplasm. Characteristic of all TBDTs is a luminal domain, which prevents the passive diffusion of molecules into the periplasmic space, but needs to be unfolded to permit nutrient import. Through the use of molecular dynamics simulations, we seek to understand the OM import pathway of TBDTs from nutrient binding to luminal domain opening and eventually nutrient import and luminal domain refolding.
