Dynamical Nonequilibrium Molecular Dynamics Simulations Reveal Atomistic Steps of C-Type Inactivation in Cardiac hERG Channels

hERG is a voltage-gated potassium channel whose malfunction is associated with cardiac pathologies. Unlike other potassium channels, hERG exhibits a peculiarly fast C-type inactivation at the level of the selectivity filter (SF), which has complicated our understanding of its structural dynamics. Molecular Dynamics (MD) simulations offer powerful tools to probe ion channel gating, but conventional equilibrium MD simulations are often unable to capture fast transitions. Despite their potential, Dynamical Nonequilibrium MD simulations (D-NEMD) have rarely been applied to understand ion channel mechanisms. Here, we combine equilibrium MD simulations, D-NEMD simulations, and electrophysiology assays to atomistically characterize a possible pathway of hERG C-type inactivation. First, we show that the ion occupancy within the SF influences hERG propensity to spontaneously inactivate. Then, we reveal three possible major steps that underlie hERG inactivation: (i) the disruption of contacts between residues of the SF, P-helix, and S5–P helix, (ii) the flipping of V625, which ultimately (iii) constricts the SF, leading to the final nonconductive state of the channel. Mutagenesis and electrophysiological recordings confirm the functional relevance of the computationally identified residues. Overall, our results demonstrate the utility of D-NEMD in investigating rapid nonequilibrium transitions in physiologically relevant complex proteins, such as ion channels, which remain a challenge for conventional equilibrium simulations and structural methods, such as X-ray crystallography and cryo-EM.