Table 2. Analysis of the G-loop gate during ion permeation events
MD runØ minimum distances between opposing G-loop gate subunits when ions pass the gate (Å)Ø number of coordinating water molecules
1µs_run15.904.73
1µs_run26.475.66
1µs_run36.755.64
1µs_run46.655.54
1µs_run56.405.34
1µs_run66.375.24
1µs_run76.845.71
1µs_run8a7.195.69
1µs_run9a7.135.88
1µs_run10a7.185.77
1µs_run116.054.68
1µs_run126.055.47
1µs_run13a7.105.93
1µs_run14a 7.145.78

For this analysis, only those MD steps with a K+ ion within a certain area of the G-loop gate (cylinder with a radius and height of 4 Å placed at the center of mass of the G-loop gate forming residues G318 and M319 of all four subunits), were extracted from the MD runs and used for analysis of minimum distances and solvation. This leads to an average pore diameter of 6.4 Å (unrestrained runs) during ion permeation. For determining the extent of solvation, all oxygen atoms of water molecules within 3.5 Å of the K+ ion were counted. The optimal ion coordination number in liquid water was estimated to be 6.9–7 within 3.5 Å (Rowley and Roux, 2012). The lower values shown in the table indicate that the ions permeated in a partially solvated manner, which was facilitated by coordination with the carbonyl oxygens of G318 residues (see Figs. 5 A and S11).

  • a Harmonic restraints on G-loop gate–forming residues G318 and M319.