Early Steps in C-Type Inactivation of the hERG Potassium Channel

Figures

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  Figure 1. Experimental (a) conductive and (b) closed structures of the KcsA selectivity filter (SF). Residues Thr75 to Gly79 of two opposite subunits from PDBs 1K4C and 1K4D are shown in licorice representation. Labels indicating the position of binding sites S0–S4 are shown in the conductive structure. Distances between opposite Cα atoms of residues Gly77 are shown in pink. (c) Experimental structure of the hERG SF. Residues Thr623 to Asn629 of two opposite subunits from PDB 5VA2 are shown in licorice representation, with labels indicating the position of binding sites S0–S4. (d) Root-mean-square deviation (RMSD) of the SF in simulations of hERG-N629D, wild-type hERG, and hERG-F627Y. The RMSD is defined as the distance of the backbone atoms of residues Thr623 to Asn629 from the corresponding atoms in the conductive structure of KcsA (PDB 1K4C). The RMSD distributions are estimated using cumulative data from eight independent 1 μs trajectories for each model system.

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  Figure 2. The silhouette score as a function of the number of clusters is shown for hERG-N629D (a), wild-type hERG (b), and hERG-F627Y (c). The red arrow indicates the maxima of the silhouette score used to define the optimal number of clusters. Clustering of the SF in hERG-N629D (d), wild-type hERG (e), and hERG-F627Y (f). The K+ occupancy of binding sites S0–S4 and the cavity is represented by green bars. The number of oxygen atoms contributed from either the protein or water molecules at binding sites S0–S4, and the cavity is represented by blue bars. For green and blue bars, black lines indicate the first and third quartiles of the corresponding features in the cluster. The probability of each cluster is reported below each plot. A representative snapshot of each cluster is shown illustrating residues 624–629 and water molecules closer than 3 Å to the protein oxygen atoms defining binding sites S0–S4 in licorice representation. K+ ions are shown as green spheres.

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  Figure 3. Lack of continuous hydration in the channel cavity of hERG-F627Y. Representative snapshot from cluster f2 of Figure 2 where a gap in hydration is observed at the center of the cavity. Only two opposite subunits in cartoon representation in orange and blue are shown for clarity. Residues of the SF are shown in licorice representation. K+ ions (green) and water molecules are shown in VdW representation.

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  Figure 4. Experimental structures of the SF in NaK2CNG-D (a) and Shaker with mutation W434F (b). The residues corresponding to S624 to N629 of hERG are shown in licorice representation for two opposing subunits of the experimental structure PDB code 3K0R (a) and 7SJ1 (b). Labels are included in the binding sites that preserve the same structure observed in the conductive state.