A binding-block ion selective mechanism revealed by a Na/K selective channel

Abstract

Mechanosensitive (MS) channels are extensively studied membrane protein for maintaining intracellular homeostasis through translocating solutes and ions across the membrane, but its mechanisms of channel gating and ion selectivity are largely unknown. Here, we identified the YnaI channel as the Na+/K+ cation-selective MS channel and solved its structure at 3.8 Å by cryo-EM single-particle method. YnaI exhibits low conductance among the family of MS channels in E. coli, and shares a similar overall heptamer structure fold with previously studied MscS channels. By combining structural based mutagenesis, quantum mechanical and electrophysiological characterizations, we revealed that ion selective filter formed by seven hydrophobic methionine (YnaIMet158) in the transmembrane pore determined ion selectivity, and both ion selectivity and gating of YnaI channel were affected by accompanying anions in solution. Further quantum simulation and functional validation support that the distinct binding energies with various anions to YnaIMet158 facilitate Na+/K+ pass through, which was defined as binding-block mechanism. Our structural and functional studies provided a new perspective for understanding the mechanism of how MS channels select ions driven by mechanical force.Electronic supplementary materialThe online version of this article (doi:10.1007/s13238-017-0465-8) contains supplementary material, which is available to authorized users.

The MscS-like channel YnaI has a gating mechanism based on flexible pore helices

“…The overall structure of YnaI is conserved in comparison with the closed MscS described above with the cytosolic vestibule domain, pore-forming helix TM3, and the paddle (Fig. 1B), in agreement with an earlier EM map of YnaI (24).…”

“…5A). Mutational analysis of YnaI showed that M158 is responsible for the potassium/sodium selectivity and an M158A mutation leads to a substantially higher conductance (24). In all three types of channels the side chains of these residues point toward the pore axis and define the narrowest part of the pore.…”

“…5C). The mutation F209A in the portal of YnaI, which is likely to change the open cross-section of the portals, almost quadruples the conductance while a substituted β-barrel for the T. tengcongensis MscS region does not change conductance (24).…”

“…On the basis of a low-resolution cryo-EM structure of YnaI it was speculated that the additional TM helices coalign to and extend the paddles (23). Another cryo-EM structure of YnaI at higher resolution did not resolve the additional TM helices and only could be modeled from helix TM2 (24).…”

Repertoire of morphable proteins in an organism

“…In Fig. 5A semi-log main plot is shown for the cryo-EM entry (PDB ID: 5Y4O) of low conductance mechanosensitive channel YnaI (Yu et al, 2018). This entry contains seven chains of identical length (223 residues, 65% of the full length).…”