Molecular dynamics simulations suggest possible activation and deactivation pathways in the hERG channel

Figures

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  Fig. 1. Side view of hERG channel. A single subunit (a) and the whole protein (b) are colored by domain: in blue, the voltage sensor domain ranging from helix S1 to loop L45, including the positively charged helix S4; in red, the pore domain, composed of helix S5, P-Loop, selectivity filter, and helix S6; in gray, the carboxy-terminal domain with the C-Linker and the cyclic nucleotide-binding homology domain.

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  Fig. 2. Contact analysis and activation/deactivation hypotheses. a Contact map of the first subunit of the system with Qg = 8e during the transition from O to C state. The black dots represent the contacts in the initial O conformation not broken during the simulation while the colored symbols indicate the contacts formed or broken at different times (tf and tb, respectively) during TMD. b Illustration of the two activation/deactivation hypotheses displaying the relevant conserved interactions in the C state.

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  Fig. 3. Activation/deactivation pathways of the closed system with Qg = 8e. Paths identified in subunits I (a), II (b), III (c), and IV (d). Panel e schematizes the main families of activation/deactivation pathways identified in all systems. Arrows describe the preferred routes of motion propagation: blue arrows refer to S4→L45→S6 route; red arrows refer to the L45→S6 route; green arrows refer to S4→S1→S5→S6. Black dots correspond to residues on the path with CI > 0.15 (see Supplementary Table 1); yellow circles refer to the pathological mutation R531Q/W42 known to alter the gating of the channel inducing the LQTS. The mutations W410S, Y420C, and T421M impair both the trafficking and the gating41. Average minimal path lengths \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\langle {d}_{\min }\rangle$$\end{document}⟨dmin⟩ are also reported.

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  Fig. 4. Communication pathways in split channels. Split channels disconnected before D540 (a) and after G546 (b): dotted circles are centered on the source and sink regions used in the network analysis; these locations correspond to helices S4 and S6; red arrows schematize the S4→L45→S6 and S4→L45→S5→S6 paths while green arrows refer to S4→S1→S5→S6 path. Average minimal path lengths \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\langle {d}_{\min }\rangle$$\end{document}⟨dmin⟩ are reported in the G546-split system (b); no pathways are found for D540 (a).

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  Fig. 5. Pseudo-potential of mean force for hERG with Qg = 8e as a function of geometrical descriptors, relevant for the O→C transition. The geometrical observables are: displacement and rotation of helices S4 and bending of helices S6 (a); rotation of the cytosolic domains with respect to the transmembrane ones (b). Pseudo-PMF maps as follows: S4 rotation vs S4 displacement (c); S6 bending vs S4 displacement (d); S6 bending vs S4 rotation (e); PD-CTD rotation vs S6 bending (f); PD-CTD rotation vs S4 displacement (g); PD-CTD rotation vs S4 rotation (h). Dashed lines are a guide to the eye. Bin widths are as follows: S4 displacement: 1.0 Å; S4 rotation: 2°; S6 bending: 1°; PD-CTD rot: 1°. Free energies were expressed in kcal/mol.