Lipid regulation of hERG1 channel function

Abstract

The lipid regulation of mammalian ion channel function has emerged as a fundamental mechanism in the control of electrical signalling and transport specificity in various cell types. In this work, we combine molecular dynamics simulations, mutagenesis, and electrophysiology to provide mechanistic insights into how lipophilic molecules (ceramide-sphingolipid probe) alter gating kinetics and K+ currents of hERG1. We show that the sphingolipid probe induced a significant left shift of activation voltage, faster deactivation rates, and current blockade comparable to traditional hERG1 blockers. Microseconds-long MD simulations followed by experimental mutagenesis elucidated ceramide specific binding locations at the interface between the pore and voltage sensing domains. This region constitutes a unique crevice present in mammalian channels with a non-swapped topology. The combined experimental and simulation data provide evidence for ceramide-induced allosteric modulation of the channel by a conformational selection mechanism.

PIP2-dependent coupling of voltage sensor and pore domains in Kv7.2

“…To achieve this, we employed all-atom molecular dynamics (MD) simulations. This technique has been successfully employed to provide atomic-level structural insights on lipid-protein interactions in membrane proteins with high spatiotemporal resolution [30][31][32][33][34] , in close agreement with the experimental data [30][31][32][33][34][35] . We chose to identify PIP2 binding sites in homomeric Kv7.2 channels for several reasons.…”

Insights into lipid-protein interactions from computer simulations

“…All three examples are at a relatively global level, although the GPCRs also show clear binding sites for cholesterol and PIP lipids. In other recent work, we targeted channels that play a role in cardiac arrhythmias and we identified more specific binding sites for lipid and lipid-like ligands, including ceramides that bind and modulate the HERG potassium channel (Miranda et al 2021) and poly-unsaturated fatty acid derivatives that modulate the KCNQ1 potassium channel (Yazdi et al 2021).…”

Two decades of Martini: Better beads, broader scope

“…A main limitation for proteins in Martini is the lack of an accurate description of conformational flexibility, which means most simulations use fixed secondary and tertiary structures with some flexibility for loops or specific domains, requiring specific assumptions by the investigator. Although there are several examples of proteins with relative domain motions, 383,424 including individual helices, 399,425 and proteins can sometimes be simulated in different, but fixed, conformational states, 239,262 we expect a major improvement to be made with the further fine-tuning of G o-type potentials. 177 Such potentials can be efficiently incorporated into Martini models using virtual sites.…”

“…In some cases, Martini simulations can also directly provide a link to the mechanism and function of membrane proteins. Recent examples include the lipid scrambling by TMEM16K 238 and the modulation of the hERG potassium channel by ceramides (Figure 5a, left panel), where a combination of Martini, atomistic simulations, and electrophysiology enabled a detailed functional model 239 . Another example is the mechanism of partitioning between raft and nonraft‐like domains in membranes depending on the preferential interaction with specific lipids (PIP2 240 or polyunsaturated chains 241 ) or on palmitoylation 240,242 .…”

“…Elements of the structure are shown in cartoon representation, purple for the pore domain and green for the voltage‐sensor domains. Reproduced with permission from Miranda et al 239 Right : State‐dependent remodeling of the local membrane environment by the transporter GltPh. Top panel shows all‐outward state, bottom panel all‐inward state.…”