An atomistic view of the YiiP structural changes upon zinc(II) binding

Background: YiiP is a bacterial zinc-for-proton antiporter belonging to the cation diffusion facilitator family. The zinc(II) ions are transported across the cell membrane, from the cytosol to the extracellular space. Methods: We performed atomistic molecular dynamics simulations of the YiiP dimer with zinc(II) ions in solution to elucidate how the metal ions interact with the protein while moving from the cytosol to the transport site. Results: We observed that of the two cavities of the dimer, only one was accessible from the cytosol during transport. Zinc(II) binding to D49 of the transport site triggered a rearrangement of the transmembrane domain that closed the accessible cavity. Finally, we analyzed the free-energy profiles of metal transit in the channel and observed the existence of a high barrier preventing release from the transport site. Conclusions: The observed dynamics is consistent with the dimer-dimer interface forming a stable scaffold against which the rest of the trans-membrane rearranges. General significance: Zinc(II) transporters are present in all kingdoms of life. The present study highlights structural features that might be of general relevance.