Mutagenesis of the NaChBac sodium channel discloses a functional role for a conserved S6 asparagine

Characterizing fenestration size in sodium channel subtypes and their accessibility to inhibitors

Voltage-gated sodium channels (Nav) underlie the electrical activity of nerve and muscle cells. Humans have nine different subtypes of these channels, which are the target of small-molecule inhibitors commonly used to treat a range of conditions. Structural studies have identified four lateral fenestrations within the Nav pore module that have been shown to influence Nav pore blocker access during resting-state inhibition. However, the structural differences among the nine subtypes are still unclear. In particular, the dimensions of the four individual fenestrations across the Nav subtypes and their differential accessibility to pore blockers is yet to be characterized. To address this, we applied classical molecular dynamics simulations to study the recently published structures of Nav1.1, Nav1.2, Nav1.4, Nav1.5, and Nav1.7. Although there is significant variability in the bottleneck sizes of the Nav fenestrations, the subtypes follow a common pattern, with wider DI-II and DIII-IV fenestrations, a more restricted DII-III fenestration, and the most restricted DI-IV fenestration. We further identify the key bottleneck residues in each fenestration and show that the motions of aromatic residue sidechains govern the bottleneck radii. Well-tempered metadynamics simulations of Nav1.4 and Nav1.5 in the presence of the pore blocker lidocaine also support the DI-II fenestration being the most likely access route for drugs. Our computational results provide a foundation for future in vitro experiments examining the route of drug access to sodium channels. Understanding the fenestrations and their accessibility to drugs is critical for future analyses of diseases mutations across different sodium channel subtypes, with the potential to inform pharmacological development of resting-state inhibitors and subtype-selective drug design.

The T1-tetramerisation domain of Kv1.2 rescues expression and preserves function of a truncated NaChBac sodium channel

Cytoplasmic domains frequently promote functional assembly of multimeric ion channels. To investigate structural determinants of this process, we generated the ‘T1‐chimera’ construct of the NaChBac sodium channel by truncating its C‐terminal domain and splicing the T1‐tetramerisation domain of the Kv1.2 channel to the N terminus. Purified T1‐chimera channels were tetrameric, conducted Na⁺ when reconstituted into proteoliposomes, and were functionally blocked by the drug mibefradil. Both the T1‐chimera and full‐length NaChBac had comparable expression levels in the membrane, whereas a NaChBac mutant lacking a cytoplasmic domain had greatly reduced membrane expression. Our findings support a model whereby bringing the transmembrane regions into close proximity enables their tetramerisation. This phenomenon is found with other channels, and thus, our findings substantiate this as a common assembly mechanism.

An open state of a voltage-gated sodium channel involving a π-helix and conserved pore-facing asparagine

Voltage-gated sodium (Nav) channels play critical roles in propagating action potentials and otherwise manipulating ionic gradients in excitable cells. These channels open in response to membrane depolarization, selectively permeating sodium ions until rapidly inactivating. Structural characterization of the gating cycle in this channel family has proved challenging, particularly due to the transient nature of the open state. A structure from the bacterium Magnetococcus marinus Nav (NavMs) was initially proposed to be open, based on its pore diameter and voltage-sensor conformation. However, the functional annotation of this model, and the structural details of the open state, remain disputed. In this work, we used molecular modeling and simulations to test possible open-state models of NavMs. The full-length experimental structure, termed here the α-model, was consistently dehydrated at the activation gate, indicating an inability to conduct ions. Based on a spontaneous transition observed in extended simulations, and sequence/structure comparison to other Nav channels, we built an alternative π-model featuring a helix transition and the rotation of a conserved asparagine residue into the activation gate. Pore hydration, ion permeation, and state-dependent drug binding in this model were consistent with an open functional state. This work thus offers both a functional annotation of the full-length NavMs structure and a detailed model for a stable Nav open state, with potential conservation in diverse ion-channel families.

Regulation and drug modulation of a voltage-gated sodium channel: Pivotal role of the S4-S5 linker in activation and slow inactivation

Voltage-gated sodium channels initiate electric signals in cell communications. The S4–S5 linker between the voltage-sensing and pore modules transmits depolarization signals to trigger channel activation. The mechanisms of this action, however, remain elusive. By combining biophysical and computational approaches, we identify a critical residue, T140, in the S4–S5 linker of the bacterial sodium channel NaChBac, which plays a pivotal role in channel activation and drug modulation of slow inactivation. Specifically, we discovered conformation-dependent drug binding at this site and unveiled a toggling mode of action by T140, which switches interaction partners with different S6 residues to regulate channel activation and slow inactivation. These observations suggest the possibility of conformation-specific drugs targeting the gating machinery of voltage-gated ion channels.

Voltage-gated sodium (Na_V) channels control excitable cell functions. While structural investigations have revealed conformation details of different functional states, the mechanisms of both activation and slow inactivation remain unclear. Here, we identify residue T140 in the S4–S5 linker of the bacterial voltage-gated sodium channel NaChBac as critical for channel activation and drug effects on inactivation. Mutations at T140 either attenuate activation or render the channel nonfunctional. Propofol, a clinical anesthetic known to inhibit NaChBac by promoting slow inactivation, binds to a pocket between the S4–S5 linker and S6 helix in a conformation-dependent manner. Using ¹⁹F-NMR to quantify site-specific binding by saturation transfer differences (STDs), we found strong STDs in inactivated, but not activated, NaChBac. Molecular dynamics simulations show a highly dynamic pocket in the activated conformation, limiting STD buildup. In contrast, drug binding to this pocket promotes and stabilizes the inactivated states. Our results provide direct experimental evidence showing distinctly different associations between the S4–S5 linker and S6 helix in activated and inactivated states. Specifically, an exchange occurs between interaction partners T140 and N234 of the same subunit in activation, and T140 and N225 of the domain-swapped subunit in slow inactivation. The drug action on slow inactivation of prokaryotic Na_V channels seems to have a mechanism similar to the recently proposed “door-wedge” action of the isoleucine-phenylalanine-methionine (IFM) motif on the fast inactivation of eukaryotic Na_V channels. Elucidating this gating mechanism points to a possible direction for conformation-dependent drug development.

Batrachotoxin acts as a stent to hold open homotetrameric prokaryotic voltage-gated sodium channels

Batrachotoxin (BTX), an alkaloid from skin secretions of dendrobatid frogs, causes paralysis and death by facilitating activation and inhibiting deactivation of eukaryotic voltage-gated sodium (Nav) channels, which underlie action potentials in nerve, muscle, and heart. A full understanding of the mechanism by which BTX modifies eukaryotic Nav gating awaits determination of high-resolution structures of functional toxin-channel complexes. Here, we investigate the action of BTX on the homotetrameric prokaryotic Nav channels NaChBac and NavSp1. By combining mutational analysis and whole-cell patch clamp with molecular and kinetic modeling, we show that BTX hinders deactivation and facilitates activation in a use-dependent fashion. Our molecular model shows the horseshoe-shaped BTX molecule bound within the open pore, forming hydrophobic H-bonds and cation-π contacts with the pore-lining helices, leaving space for partially dehydrated sodium ions to permeate through the hydrophilic inner surface of the horseshoe. We infer that bulky BTX, bound at the level of the gating-hinge residues, prevents the S6 rearrangements that are necessary for closure of the activation gate. Our results reveal general similarities to, and differences from, BTX actions on eukaryotic Nav channels, whose major subunit is a single polypeptide formed by four concatenated, homologous, nonidentical domains that form a pseudosymmetric pore. Our determination of the mechanism by which BTX activates homotetrameric voltage-gated channels reveals further similarities between eukaryotic and prokaryotic Nav channels and emphasizes the tractability of bacterial Nav channels as models of voltage-dependent ion channel gating. The results contribute toward a deeper, atomic-level understanding of use-dependent natural and synthetic Nav channel agonists and antagonists, despite their overlapping binding motifs on the channel proteins.

A hypothetical molecular mechanism for TRPV1 activation that invokes rotation of an S6 asparagine

TRPV1 channels comprise four subunits containing six transmembrane segments (S1–S6) that surround a central pore. Kasimova et al. hypothesize that channel opening involves rotation of an S6 asparagine residue toward the pore, as well as associated pore hydration and external cavity dehydration.

The transient receptor potential channel vanilloid type 1 (TRPV1) is activated by a variety of endogenous and exogenous stimuli and is involved in nociception and body temperature regulation. Although the structure of TRPV1 has been experimentally determined in both the closed and open states, very little is known about its activation mechanism. In particular, the conformational changes that occur in the pore domain and result in ionic conduction have not yet been identified. Here we suggest a hypothetical molecular mechanism for TRPV1 activation, which involves rotation of a conserved asparagine in S6 from a position facing the S4–S5 linker toward the pore. This rotation is associated with hydration of the pore and dehydration of the four peripheral cavities located between each S6 and S4–S5 linker. In light of our hypothesis, we perform bioinformatics analyses of TRP and other evolutionary related ion channels, evaluate newly available structures, and reexamine previously reported water accessibility and mutagenesis experiments. These analyses provide several independent lines of evidence to support our hypothesis. Finally, we show that our proposed molecular mechanism is compatible with the prevailing theory that the selectivity filter acts as a secondary gate in TRPV1.

CDtoolX, a downloadable software package for processing and analyses of circular dichroism spectroscopic data

Circular dichroism (CD) spectroscopy is a highly used method for the examination and characterization of proteins, including, amongst other features, their secondary and tertiary structures, thermal stability, comparisons of wildtype and mutant proteins, and monitoring the binding of small molecules, folding/unfolding pathways, and formation of macromolecular complexes. This article describes CDtoolX, a new, user-friendly, free-to-download-and-use software program that enables processing, displaying, archiving, calibrating, comparisons, and analyses of CD and synchrotron radiation circular dichroism spectroscopic data.

Mutational analysis of state-dependent contacts in the pore module of eukaryotic sodium channels

Voltage-gated sodium channels have residues that change or may change contacts upon gating. Contributions of individual contacts in stability of different states are incompletely understood. Pore-lining inner helices contain exceptionally conserved asparagines in positions i20. Here we explored how mutations in positions i20 and i29 affect electrophysiological properties of insect sodium channels. In repeat interfaces I/IV, III/II and IV/III, alanine substitutions caused positive activation shifts in positions i20 and i29, negative shifts of slow inactivation in positions i20 and positive shifts of slow inactivation in positions i29. The results support the hypothesis on open state inter-repeat H-bonding of residues i20 and i29. The shift magnitudes vary between interfaces, reflecting structural asymmetry of the channels. Mutations in positions i20 of repeats III and IV caused much longer recovery delay from the slow and fast inactivation than other mutations. In repeat IV, alanine substitution of tyrosine i30 rescued positive activation shift of mutation in position i29. Our data suggest that polar residues in positions i29 are involved in stabilization of both the open and slow-inactivated states. Transition between the states may involve switching of H-bonding partners of residues i29 from the conserved asparagines to currently unknown residues.