The permeation of potassium ions through the lipid scrambling path of the membrane protein nhTMEM16

The TMEM16 family of transmembrane proteins includes Ca2+-activated phospholipid scramblases (PLS) that can also function as non-selective ion channels. Extensive structural and functional studies have established that a membrane-exposed hydrophilic groove in TMEM16 PLS can serve as a translocation pathway for lipids. However, it is still unclear how the TMEM16 PLS conduct ions. A protein-delimited pore model suggests that ions are translocated through a narrow opening of the groove region, which is not sufficiently wide to allow lipid movement, whereas a proteolipidic pore model envisions ions and lipids translocating through an open conformation of the groove. We investigated the dynamic path of potassium ion (K+) translocation that occurs when an open groove state of nhTMEM16 is obtained from long atomistic molecular dynamics (MD) simulations, and calculated the free energy profile of the ion movement through the groove with umbrella sampling methodology. The free energy profile identifies effects of specific interactions along the K+ permeation path. The same calculations were performed to investigate ion permeation through a groove closed to lipid permeation in the nhTMEM16 L302A mutant which exhibits a stable conformation of the groove that does not permit lipid scrambling. Our results identify structural and energy parameters that enable K+ permeation, and suggest that the presence of lipids in the nhTMEM16 groove observed in the simulations during scrambling or in/out diffusion, affect the efficiency of K+ permeation to various extents.

Automated summary

The TMEM16 family of transmembrane proteins includes phospholipid scramblases (PLS) that can also function as ion channels. The mechanism of ion conduction in TMEM16 PLS is still unclear. Molecular dynamics simulations and free energy calculations were used to investigate the dynamic path of potassium ion translocation through an open groove state of nhTMEM16 and the effects of lipids on ion permeation. The results provide insight into the structural and energy parameters that enable ion permeation and the influence of lipids on the efficiency of ion permeation.