On the mechanism of GIRK2 channel gating by phosphatidylinositol bisphosphate, sodium, and the Gβγ dimer

Permeation mechanisms through the selectivity filter and the open helix bundle crossing gate of GIRK2

“…Although it has been argued that PIP 2 alone is sufficient for the activation by comparing the F192 (HBC gate) Cα-Cα as well as the minimum distances in the presence/absence of the regulator, we have found this approach to be primarily structure-dependent and insufficient to draw any conclusions from [28] . In essence, if the simulations start with a HBC-closed conformation of GIRK2, PIP 2 alone is unable to activate the channel even reaching a micro-second time scale [28] .…”

“…A two-step energy minimization protocol (steepest descent and conjugate gradient algorithm) was performed by 10,000 steps each, with FF14SB [38] , LIPID17 [39] , [40] , and GAFF2 [41] , [42] , [43] force fields for protein, lipid membrane and PIP 2 , respectively. This set of force field parameters has been shown to be capable of probing the activation and the deactivation of the GIRK2 channel reasonably, particularly the gating mechanism by the same modulators in the present study [28] . Next, heating from 0 to 300 K was achieved using the Langevin thermostat algorithm [44] , with a time step of 0.5-femtosecond (fs) to avert internal disturbance.…”

“…The equilibrium MD simulations were conducted at constant temperature and pressure ensemble (NPT) for 0.5 microseconds (µs), followed by production jobs at constant temperature and volume ensemble (NVT) for 1 µs. To accelerate the permeation events, an external voltage at 0.06 V/nm from the extra- to intracellular side was applied as outlined in previous studies [28] , [45] , [46] , under which the secondary structure of all subunits of GIRK2 was well maintained. Accordingly, transmembrane voltage was estimated to be around −200 mV based on the transmembrane thickness of around 32 Å.…”

“…However, the validity of their conclusions is being questioned by the fact that PIP 2 alone is insufficient to significantly activate GIRK2, which has been substantially tested by both electrophysiological experiments and our previous MD simulations [27] , [28] . Although it has been argued that PIP 2 alone is sufficient for the activation by comparing the F192 (HBC gate) Cα-Cα as well as the minimum distances in the presence/absence of the regulator, we have found this approach to be primarily structure-dependent and insufficient to draw any conclusions from [28] . In essence, if the simulations start with a HBC-closed conformation of GIRK2, PIP 2 alone is unable to activate the channel even reaching a micro-second time scale [28] .…”

How Plants Sense and Respond to Stressful Environments

“…In direct contrast to the case for animals, no direct role for lipids has been found in cation sensing in plants. In animals, where GIPCs are absent, all reported Na 1 sensors to date are selective ion channels (reviewed by Isayenkov and Maathuis, 2019), of which some are regulated by the composition of their membrane environment (Whorton and MacKinnon, 2011;Li et al, 2019). Besides plants, GIPCs are found in fungi and protozoans, but it has not been established whether these lipids have a conserved function in cation sensing.…”