Structural Dynamics and Topology of Human KCNE3 in Lipid Bilayers Studied by Site-Directed Spin Labeling and Electron Paramagnetic Resonance Spectroscopy

KCNE3 is a member of the KCNE family and consists of a single-pass transmembrane segment that is vital for cellular function. It plays a role in modulating both activities and the function of voltage-gated potassium ion channels, including KCNQ1. KCNE3 interacts with voltage-gated potassium channels to form a complex that regulates the channel’s biophysical and physiological properties. KCNE3 is found in the colon, small intestine, and certain stomach cell types. Dysfunction and hereditary mutations in KCNE3 have been linked to a number of human disorders. The structural dynamics of KCNE3 in a native membrane environment are not yet fully understood. Here, we employed electron paramagnetic resonance (EPR) spectroscopy in connection with site-directed spin labeling to study the structural dynamics of KCNE3 in a lipid bilayer membrane. Fifty residue sites of the KCNE3 amino acid sequence were scanned using spin-labeling and CW-EPR spectral line shape analysis to determine the site-specific motions of KCNE3. The sites included 19 predicted transmembrane domain (TMD) sites and 31 residue sites of the N- and C-termini of KCNE3. The analysis of CW-EPR spectra revealed that sites residing within the predicted transmembrane domain (TMD) of KCNE3 exhibit reduced mobility in comparison to those of the KCNE3 N- and C-termini sites. Power saturation EPR measurements were then performed to obtain the topology of KCNE3 with respect to the POPC/POPG lipid bilayers. The results mapped the location of the membrane-spanning domain of the protein to residues 57–82. Power saturation EPR data further showed that the KCNE3 extracellular N-terminus is largely solvent-exposed, with some segments weakly or partially associated with the surface of the membrane. These results are in good agreement with the earlier solution NMR structure of KCNE3 in isotropic bicelles.