Investigation of the Inactivation of HERG using Molecular Dynamics Simulations of New cryo-EM Structures

Abstract

The human ether á-go-go related gene (hERG) encodes the delayed rectifier potassium channel (Kv11.1), best known for mediation of the repolarising current in the cardiac action potential. Loss of function of hERG can lead to long QT-syndrome which causes cardiac arrhythmias and sudden cardiac arrest. hERG is susceptible to a wide range of drugs which can lead to drug induced long QT-syndrome. Here, the recent cryo-EM structure of hERG in an activated state, together with newly-solved structures that are open or inactivated serve as the basis to investigate the structural determinants of hERG inactivation. We used molecular dynamics flexible fitting to refine and relax these new structures in micelles consisting of detergents, lipids and cholesterol. A combination of long simulations and libraries of short simulations were performed with a variety of ion concentrations to study different conformational states. These simulations highlighted the amino acids important for maintaining each state of the selectivity filter and therefore may be involved in hERG inactivation. Furthermore, we have used replica exchange with solute tempering to enhance sampling of the exchange of ions in the hERG selectivity filter. We observe correlations between channel conformation and ion occupancy that shed light on the coupling of ions to inactivation. Together with mutagenesis experiments, these simulations provide molecular-level understanding of hERG inactivation, with considerable clinical and pharmacological potential.