The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel

Abstract

Voltage-gated potassium (KV) channels are membrane proteins that respond to changes in membrane potential by enabling K+ ion flux across the membrane. Polyunsaturated fatty acids (PUFAs) induce channel opening by modulating the voltage-sensitivity, which can provide effective treatment against refractory epilepsy by means of a ketogenic diet. While PUFAs have been reported to influence the gating mechanism by electrostatic interactions to the voltage-sensor domain (VSD), the exact PUFA-protein interactions are still elusive. In this study, we report on the interactions between the Shaker KV channel in open and closed states and a PUFA-enriched lipid bilayer using microsecond molecular dynamics simulations. We determined a putative PUFA binding site in the open state of the channel located at the protein-lipid interface in the vicinity of the extracellular halves of the S3 and S4 helices of the VSD. In particular, the lipophilic PUFA tail covered a wide range of non-specific hydrophobic interactions in the hydrophobic central core of the protein-lipid interface, while the carboxylic head group displayed more specific interactions to polar/charged residues at the extracellular regions of the S3 and S4 helices, encompassing the S3-S4 linker. Moreover, by studying the interactions between saturated fatty acids (SFA) and the Shaker KV channel, our study confirmed an increased conformational flexibility in the polyunsaturated carbon tails compared to saturated carbon chains, which may explain the specificity of PUFA action on channel proteins.

Molecular Mechanisms of Resin Acids and Their Derivatives on the Opening of a Potassium Channel

“…Our research group has characterized the effects of PUFAs binding to this site at the Shaker Kv channel , Xu et al 2008, Börjesson et al 2010, Börjesson and Elinder 2011, Tigerholm et al 2012, Ottosson et al 2014, Yazdi et al 2016) and lately also at the Kv7 channels (Liin et al 2015. When bound, PUFAs modify the voltage-dependence of activation, and because both the lipophilicity and electrostatic forces are central for the effect, we have called this the lipoelectric mechanism ).…”

“…PUFAs open the Shaker Kv channel by electrostatically tuning the voltage-dependence of the final voltage-sensor movement that is closely linked to channel opening (see Introduction 1.4.3) (Börjesson and Elinder 2011). In 2011, a site of action was suggested (Börjesson and Elinder 2011) that later was validated and refined by molecular dynamics (Yazdi et al 2016).…”

“…For the docking, an open-state model of the Shaker WT channel was built from the KV1.2/2.1 chimera (PDB 2R9R) and relaxed in a pure POPC bilayer with parameters and setup as previously described (Yazdi et al 2016). The most potent compound, Wu122, was used for the docking study.…”

“…To investigate a preferred binding mode and define the binding pocket, the docked poses of Wu122 were subjected to molecular dynamics simulations of the full shaker tetramer in the POPC bilayer (Yazdi et al 2016). To enhance sampling of preferred channel-ligand poses, each Wu122 pose was copied to all subunits of the channel.…”

“…We do not fully understand the mechanism for this allosteric slowing of closing kinetics (Paper III). By modifying the molecular structure of both the channel and the compounds, combined with molecular dynamic simulations, we have found the binding site for the resin acids and derivatives on the Shaker Kv channel to a pocket formed by the S3/S4 cleft and the lipid membrane, partly overlapping the binding site for DHA (Yazdi et al 2016). However, there are subtle differences in the effects on the array of S4 mutations, suggesting that the resin acids bind deep in the S3/S4 cleft while PUFAs possibly bind more superficially.…”