Figure 1. The effective opening radius in two K-channel structures.

Shown are ~5 Å slabs of the molecular surface of the large conductance bacterial channel MthK (PDB: 4HYO) and the chimeric Kv1.2/2.1 voltage gated K-channel (PDB: 2R9R). The molecular surfaces were calculated as indicated in the main text. The probe radius (in Å) is shown above each representation. The top row shows the molecular surfaces for a 4 Å-radius probe (about the size of a hydrated K⁺). The middle row (with underlined radii values) shows the size of the largest spheres able to pass through the pore (r_E). The lower row shows that probes 0.1 Å bigger cannot pass. With SURF, these probes leave a dimple or a bump at the pore entrance, depending on whether the rolling trajectory began outside or inside the cavity, respectively (radius = 5.7 Å and 4.6 Å, for MthK and Kv1.2/2.1, respectively). Meanwhile, with HOLLOW, the non-permeating probes (radius = 5.9 Å and 5.3 Å, for MthK and Kv1.2/2.1, respectively) leave the cavity full of virtual O atoms (red spheres). Two opposite pore-helices and K⁺ ions in selectivity filter (in green) are shown for reference. The T1, the β-subunit, and the voltage sensing domains are not represented in 2R9R for clarity. Figure prepared with VMD (http://www.ks.uiuc.edu/Research/vmd/).