Abstract

The human ether-a-go-go-related gene (hERG) encodes the voltage gated potassium channel (KCNH2 or Kv11.1, commonly known as hERG). This channel plays a pivotal role in the stability of phase 3 repolarization of the cardiac action potential. Although a high-resolution cryo-EM structure is available for its depolarized (open) state, the structure surprisingly did not feature many functionally important interactions established by previous biochemical and electrophysiology experiments. Using Molecular Dynamics Flexible Fitting (MDFF), we refined the structure and recovered the missing functionally relevant salt bridges in hERG in its depolarized state. We also performed electrophysiology experiments to confirm the functional relevance of a novel salt bridge predicted by our refinement protocol. Our work shows how refinement of a high-resolution cryo-EM structure helps to bridge the existing gap between the structure and function in the voltage-sensing domain (VSD) of hERG. Statement of SignificanceCryo-EM has emerged as a major breakthrough technique in structural biology of membrane proteins. However, even high-resolution Cryo-EM structures contain poor side chain conformations and interatomic clashes. A high-resolution cryo-EM structure of hERG1 has been solved in the depolarized (open) state. The state captured by Cryo-EM surprisingly did not feature many functionally important interactions established by previous experiments. Molecular Dynamics Flexible Fitting (MDFF) used to enable refinement of the hERG1 channel structure in complex membrane environment re-establishing key functional interactions in the voltage sensing domain.