Unilateral access regulation: ground state dynamics of the Pseudomonas aeruginosa outer membrane efflux duct OprM

Acting as an efflux duct in the MexA-MexB-OprM multidrug efflux pump, OprM plays a major role in the antibiotic resistance capability of Pseudomonas aeruginosa, trafficking substrates through the outer cell membrane. Whereas the available crystal structures showed restricted OprM access on both ends, the underlying gating mechanism is not yet fully understood. To gain insight into the functional mechanism of OprM access regulation, we conducted a series of five independent, unbiased molecular dynamics simulations, computing 200 ns dynamics samples of the wild-type protein in a phospholipid membrane/150 mM NaCl water environment. On the extracellular side, OprM opens and closes freely under the simulated conditions, suggesting the absence of a gating mechanism on this side of the isolated protein. On the periplasmic side, we observe an opening of the tip regions at Val408 and to a lesser degree Asp416 located 1.5 nm further into the channel, leading to OprM end conformations being up to 3 and 1.4 times, respectively, more open than the asymmetric crystal structure. If our simulations are correct, our findings imply that periplasmic gating involves only the Asp416 region and that in vivo additional components, absent in our simulation, might be required for periplasmic gating if the observed opening trend near Asp416 is not negligible. In addition to that ,we identified in each monomer a previously unreported sodium binding site in the channel interior coordinated by Asp171 and Asp230 whose functional role remains to be investigated.