Conservation and specialization in PAS domain dynamics

The PAS (Per-ARNT-Sim) superfamily is presented as a well-suited study case to demonstrate how comparison of functional motions among distant homologous proteins with conserved fold characteristics may give insight into their functional specialization. Based on the importance of structural flexibility of the receptive structures in anticipating the signal-induced conformational changes of these sensory systems, the dynamics of these structures were analysed. Molecular dynamics was proved to be an effective method to obtain a reliable picture of the dynamics of the crystal structures of HERG, phy3, PYP and FixL, provided that an extensive conformational space sampling is performed. Other reliable sources of dynamic information were the ensembles of NMR structures of hPASK, HIF-2α and PYP. Essential dynamics analysis was successfully employed to extract the relevant information from the sampled conformational spaces. Comparison of motion patterns in the essential subspaces, based on the structural alignment, allowed identification of the specialized region in each domain. This appears to be evolved in the superfamily by following a specific trend, that also suggests the presence of a limited number of general solutions adopted by the PAS domains to sense external signals. These findings may give insight into unknown mechanisms of PAS domains and guide further experimental studies. © The Author 2005. Published by Oxford University Press. All rights reserved

Inhibition of the hERG potassium channel by phenanthrene:a polycyclic aromatic hydrocarbon pollutant

The lipophilic polycyclic aromatic hydrocarbon (PAH) phenanthrene is relatively abundant in polluted air and water and can access and accumulate in human tissue. Phenanthrene has been reported to interact with cardiac ion channels in several fish species. This study was undertaken to investigate the ability of phenanthrene to interact with hERG (human Ether-à-go-go-Related Gene) encoded Kv11.1 K(+) channels, which play a central role in human ventricular repolarization. Pharmacological inhibition of hERG can be proarrhythmic. Whole-cell patch clamp recordings of hERG current (I(hERG)) were made from HEK293 cells expressing wild-type (WT) and mutant hERG channels. WT I(hERG1a) was inhibited by phenanthrene with an IC(50) of 17.6 ± 1.7 µM, whilst I(hERG1a/1b) exhibited an IC(50) of 1.8 ± 0.3 µM. WT I(hERG) block showed marked voltage and time dependence, indicative of dependence of inhibition on channel gating. The inhibitory effect of phenanthrene was markedly impaired by the attenuated inactivation N588K mutation. Remarkably, mutations of S6 domain aromatic amino acids (Y652, F656) in the canonical drug binding site did not impair the inhibitory action of phenanthrene; the Y652A mutation augmented I(hERG) block. In contrast, the F557L (S5) and M651A (S6) mutations impaired the ability of phenanthrene to inhibit I(hERG), as did the S624A mutation below the selectivity filter region. Computational docking using a cryo-EM derived hERG structure supported the mutagenesis data. Thus, phenanthrene acts as an inhibitor of the hERG K(+) channel by directly interacting with the channel, binding to a distinct site in the channel pore domain. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00018-021-03967-8

Voltage-gating and assembly of split Kv10.1 channels

Voltage-gated ion channels allow ions to pass cell membrane upon changes of transmembrane electrical potential. Conformational changes in the voltage-sensing domain of the channel (VSD) are assumed to be transmitted to the pore domain (PD) through an alpha-helical linker between them (S4-S5 linker). We have previously shown that expression of VSD and PD as separate fragments results in functional Kv10.1 channels that retain voltage-dependence. Here we used such ‘split’ channels to investigate functional interactions between VSD and PD. We found that their electrophysiological properties greatly depend on where the S4-S5 linker is interrupted. Remarkably, wild-type-like channel behavior could be fully or largely restored by mutations of crucial linker amino acids, indicating that precise functional interactions between VSD and PD remain when they are not covalently bound. Voltage-Clamp Fluorometry measurements revealed that VSD motion is alerted in specific split channels, but these changes were subtler. Finally, the increased separation between VSD activation and channel opening in the split channel carrying a large deletion in the S4-S5 linker, as well as the failure of the PD expressed alone to give currents, suggest that the role of the VSD in the is to open the channel pore and prevent it from closing

Voltage-gating and assembly of split Kv10.1 channels

Voltage-gated ion channels allow ions to pass cell membrane upon changes of transmembrane electrical potential. Conformational changes in the voltage-sensing domain of the channel (VSD) are assumed to be transmitted to the pore domain (PD) through an alpha-helical linker between them (S4-S5 linker). We have previously shown that expression of VSD and PD as separate fragments results in functional Kv10.1 channels that retain voltage-dependence. Here we used such ‘split’ channels to investigate functional interactions between VSD and PD. We found that their electrophysiological properties greatly depend on where the S4-S5 linker is interrupted. Remarkably, wild-type-like channel behavior could be fully or largely restored by mutations of crucial linker amino acids, indicating that precise functional interactions between VSD and PD remain when they are not covalently bound. Voltage-Clamp Fluorometry measurements revealed that VSD motion is alerted in specific split channels, but these changes were subtler. Finally, the increased separation between VSD activation and channel opening in the split channel carrying a large deletion in the S4-S5 linker, as well as the failure of the PD expressed alone to give currents, suggest that the role of the VSD in the is to open the channel pore and prevent it from closing

Differential Association between HERG and KCNE1 or KCNE2

The small proteins encoded by KCNE1 and KCNE2 have both been proposed as accessory subunits for the HERG channel. Here we report our investigation into the cell biology of the KCNE-HERG interaction. In a co-expression system, KCNE1 was more readily co-precipitated with co-expressed HERG than was KCNE2. When forward protein trafficking was prevented (either by Brefeldin A or engineering an ER-retention/retrieval signal onto KCNE cDNA) the intracellular abundance of KCNE2 and its association with HERG markedly increased relative to KCNE1. HERG co-localized more completely with KCNE1 than with KCNE2 in all the membrane-processing compartments of the cell (ER, Golgi and plasma membrane). By surface labeling and confocal immunofluorescence, KCNE2 appeared more abundant at the cell surface compared to KCNE1, which exhibited greater co-localization with the ER-marker calnexin. Examination of the extracellular culture media showed that a significant amount of KCNE2 was extracellular (both soluble and membrane-vesicle-associated). Taken together, these results suggest that during biogenesis of channels HERG is more likely to assemble with KCNE1 than KCNE2 due to distinctly different trafficking rates and retention in the cell rather than differences in relative affinity. The final channel subunit constitution, in vivo, is likely to be determined by a combination of relative cell-to-cell expression rates and differential protein processing and trafficking