Locked on one side only: ground state dynamics of the outer membrane efflux duct TolC

Playing a major role in the expulsion of antibiotics and the secretion of cell toxins in conjunction with inner membrane transporters of three protein superfamilies, the outer membrane channel TolC occurs in at least two states blocking or permitting the passage of substrates. The details of the underlying gating mechanism are not fully understood. Addressing the questions of extracellular access control and periplasmic gating mechanism, we conducted a series of independent, unbiased 150-300 ns molecular dynamics simulations of wild-type TolC in a phospholipid membrane/150 mM NaCl water environment. We find that TolC opens and closes freely on the extracellular side, suggesting the absence of a gating mechanism on this side in the isolated protein. On the periplasmic side, we observe the outer periplasmic bottleneck region adopting in all simulations a conformation more open than the TolC wild-type crystal structures until in one run the successive binding of two sodium ions induces the transition to a conformation more closed than any of the available TolC X-ray structures. Concurrent with a heightened sodium residence probability near Asp374, the inner periplasmic bottleneck region at Asp374 remains closed throughout the simulations unless all NaCl is removed from the system, inducing a reopening of the outer and inner bottleneck. Our findings suggest that TolC is locked only on the periplasmic side in a sodium-dependent manner.