Mechanism of K+ transport along the intersubunit tunnel of kdpFABC

Prokaryotes such as E. coli employ a unique channel-pump protein complex called kdpFABC to import K+ into the cell in low external K+ environments. KdpA is an ion channel subunit and kdpB is a P-type ATPase. Current research indicates that transport of K+ ions occur by diffusion of K+ ions from the kdpA ion-binding site to the kdpB ion-binding site through a ∼40 Å long tunnel that passes through the channel-pump interface. However, there is no clear consensus on whether K+ ions or water molecules populate the tunnel in the cryo-EM studies. Through molecular dynamics simulations, we find that K+ ions and water molecules co-exist in the tunnel. Furthermore, we notice that not more than two K+ ions can coexist in the tunnel after the S3 site of the selectivity filter and before the channel-pump interface. We employ well-tempered metadynamics simulations to calculate the free energy of ion transport along the intramembrane tunnel, and preliminary data show that a large barrier prevents spontaneous diffusion of a K+ ion from the channel to the pump subunit in the E1-ATP state. Further investigations are ongoing.