摘要：Reconciling protein functional data with crystal structure is arduous because rare conformations or crystallization artifacts occur. Here we present a tool to validate the dimensions of open pore structures of potassium-selective ion channels. We used freely available algorithms to calculate the molecular contour of the pore to determine the effective internal pore radius ( r E) in several K-channel crystal structures. r E was operationally defined as the radius of the biggest sphere able to enter the pore from the cytosolic side. We obtained consistent r E estimates for MthK and Kv1.2/2.1 structures, with r E = 5.3–5.9 Å and r E = 4.5–5.2 Å, respectively. We compared these structural estimates with functional assessments of the internal mouth radii of capture ( r C) for two electrophysiological counterparts, the large conductance calcium activated K-channel ( r C = 2.2 Å) and the Shaker Kv-channel ( r C = 0.8 Å), for MthK and Kv1.2/2.1 structures, respectively. Calculating the difference between r E and r C, produced consistent size radii of 3.1–3.7 Å and 3.6–4.4 Å for hydrated K+ ions. These hydrated K+ estimates harmonize with others obtained with diverse experimental and theoretical methods. Thus, these findings validate MthK and the Kv1.2/2.1 structures as templates for open BK and Kv-channels, respectively.
