Structural and molecular insight into the pH-induced low-permeability of the voltage-gated potassium channel Kv1.2 through dewetting of the water cavity

Abstract

Understanding the gating mechanism of ion channel proteins is key to understanding the regulation of cell signaling through these channels. Channel opening and closing are regulated by diverse environmental factors that include temperature, electrical voltage across the channel, and proton concentration. Low permeability in voltage-gated potassium ion channels (Kv) is intimately correlated with the prolonged action potential duration observed in many acidosis diseases. The Kv channels consist of voltage-sensing domains (S1-S4 helices) and central pore domains (S5-S6 helices) that include a selectivity filter and waterfilled cavity. The voltage-sensing domain is responsible for the voltage-gating of Kv channels. While the low permeability of Kv channels to potassium ion is highly correlated with the cellular proton concentration, it is unclear how an intracellular acidic condition drives their closure, which may indicate an additional pH-dependent gating mechanism of the Kv family. Here, we show that two residues E327 and H418 in the proximity of the water cavity of Kv1.2 play crucial roles as a pH switch. In addition, we present a structural and molecular concept of the pH-dependent gating of Kv1.2 in atomic detail, showing that the protonation of E327 and H418 disrupts the electrostatic balance around the S6 helices, which leads to a straightening transition in the shape of their axes and causes dewetting of the water-filled cavity and closure of the channel. Our work offers a conceptual advancement to the regulation of the pH-dependent gating of various voltage-gated ion channels and their related biological functions.

Protons in gating the Kv1,2 channel: a calculated conformational change in response to addition of a proton, and a proposed path from voltage sensing domain to gate

“…The distances are from the X-ray structure, not the optimization, but for the open state these agree fairly well. Note the key roles of H418 and E327; these have been identified experimentally by Lee et al as critical for gating[33]. However, all of the labeled residues are important in the paths; the R226 – K312 pair can be seen at the top; the N412 and N414 are probably the last step in transmitting the proton to the gate, if needed to close the channel.…”

“…While the parts of the wire that have not been calculated are, for this reason, at present hypotheses, they are consistent with everything we know, and consistent with the calculation that has been completed. This gating model includes the effects of certain known mutations (H418 and E327 are of particular importance [33]) as well as the fact that the T1 segment is involved with gating, something not accounted for in essentially any version of the standard model. The standard models have some difficulty in showing just how the S4-S5 linker manages to transmit the force of an S4 motion to the gate, although it must do so in some manner.…”

Water, Protons, and the Gating of Voltage-Gated Potassium Channels

“…Here, we will be concerned with certain mutations of residues that are conserved and ionizable, so that they are possibly relevant to the presence and transmission of protons. These include the finding of Lee et al [120] that a glutamate in the S4-S5 linker is required for the channel to function. Lee and coworkers found that in addition to E327, a histidine, H418 (in the 3Lut numbering from the pdb), played a key role in the pH gating of the K v 1.2 channel, both near the junction of the S4-S5 linker (i.e., the linker between the VSD and the gate) where the linker joins the pore below the gate.…”

Protons in Gating the Kv1.2 Channel: A Calculated Set of Protonation States in Response to Polarization/Depolarization of the Channel, with the Complete Proposed Proton Path from Voltage Sensing Domain to Gate

“…As far as we can see, the proton path interpretation is consistent with all these data. Furthermore, there are other mutation experiments that point to specific residues as being crucial, including (using the 3Lut numbering) E327 [ 50 ] and H418 [ 24 , 32 ]. If either of these is deleted, or in most cases even mutated, the channel fails.…”