Aquaporins (AQPs) are a family of transmembrane proteins known for their role in selective water transport across cell membranes. The AQP family has 13 members in mammalian cells that localize in different tissues. Aquaporin 6 (AQP6), which localizes in the intracellular vesicle membrane of epithelial cells and in kidney, vagina, and benign ovarian tumors, has a unique ability to function as an anion channel, allowing ions to pass through under certain cellular conditions. The presence of this anion permeability property in AQP6, despite its primary sequence matching closely with water channel proteins of the aquaporin family, makes it more intriguing. Although the structure of AQPs has been well resolved experimentally, the precise mechanism by which AQP6 carries out anion transport has remained elusive to date. In recent research, Yamamoto and co-workers, using molecular dynamics (MD) simulations, shed light on the fascinating process of anion permeation through AQP6. The simulations model the behavior of molecules in response to environmental conditions, thereby providing a vibrant picture of chloride ions traversing the AQP6 channel.

One of the key results in the study is that chloride ions permeate through the central pore formed by the homotetrameric formation of AQP6. Under low pH conditions, the structure of AQP6 is significantly modulated to facilitate the movement of chloride ions. Specifically, the simulations revealed that the low pH allows subtle opening and wetting of the hydrophobic selectivity filter (SF) within the central pore, permitting the chloride ions to pass through. The low pH is sensed by two histidines (H184 and H189) that get protonated and trigger the gating of the SF region.

This result is particularly interesting because it suggests that AQP6 operates differently from other AQPs that typically allow water molecules to pass through their pores. Further insights were gained by examining the effects of mutations in AQP6 to conduct anions. The study focused on the N63G mutation in human AQP6, which corresponds to a similar mutation (N60G) in rat AQP6 known to eliminate anion permeation. The MD simulations confirmed that this mutation eliminated chloride ion permeation through the central pore, in line with previous experimental observations. This loss of function occurs because N63 is located in the middle of the central pore and may form the crucial component of the SF.

The findings from these MD simulations provide a deeper understanding of the molecular mechanism behind anion permeation in AQP6. The research not only explains how pH levels influence the gating of the AQP6 channel but also highlights the central pore's critical role in this process. Moreover, this study opens up new avenues for exploring similar mechanisms in other ion channels, particularly those formed by multisubunit assemblies, which may share analogous pH-dependent behaviors.