Veratridine binding to a transmembrane helix of sodium channel Na v 1.4 determined by solid-state NMR

Bioorg Med Chem. 2018 Nov 15;26(21):5644-5653. doi: 10.1016/j.bmc.2018.10.012. Epub 2018 Oct 17.

Abstract

The multi-step ligand action to a target protein is an important aspect when understanding mechanisms of ligand binding and discovering new drugs. However, structurally capturing such complex mechanisms is challenging. This is particularly true for interactions between large membrane proteins and small molecules. One such large membrane of interest is Nav1.4, a eukaryotic voltage-gated sodium channel. Domain 4 segment 6 (D4S6) of Nav1.4 is a transmembrane α-helical segment playing a key role in channel gating regulation, and is targeted by a neurotoxin, veratridine (VTD). VTD has been suggested to exhibit a two-step action to activate Nav1.4. Here, we determine the NMR structure of a selectively 13C-labeled peptide corresponding to D4S6 and its VTD binding site in lipid bilayers determined by using magic-angle spinning solid-state NMR. By 13C NMR, we obtain NMR structural constraints as 13C chemical shifts and the 1H-2H dipolar couplings between the peptide and deuterated lipids. The peptide backbone structure and its location with respect to the membrane are determined under the obtained NMR structural constraints aided by replica exchange molecular dynamics simulations with an implicit membrane/solvent system. Further, by measuring the 1H-2H dipolar couplings to monitor the peptide-lipid interaction, we identify a VTD binding site on D4S6. When superimposed to a crystal structure of a bacterial sodium channel NavRh, the determined binding site is the only surface exposed to the protein exterior and localizes beside the second-step binding site reported in the past. Based on these results, we propose that VTD initially binds to these newly-determined residues on D4S6 from the membrane hydrophobic domain, which induces the first-step channel opening followed by the second-step blocking of channel inactivation of Nav1.4. Our findings provide new detailed insights of the VTD action mechanism, which could be useful in designing new drugs targeting D4S6.

Keywords: Neurotoxin; Protein-ligand interaction; Solid-state NMR; Transmembrane peptide; Voltage-gated sodium channel.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Carbon-13 Magnetic Resonance Spectroscopy / methods
  • Dimyristoylphosphatidylcholine / chemistry
  • Lipid Bilayers / chemistry
  • Molecular Docking Simulation
  • Muscle Proteins / chemistry
  • Muscle Proteins / metabolism*
  • Nuclear Magnetic Resonance, Biomolecular / methods
  • Peptide Fragments / chemical synthesis
  • Peptide Fragments / chemistry
  • Peptide Fragments / metabolism
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Domains
  • Rats
  • Sodium Channels / chemistry
  • Sodium Channels / metabolism*
  • Veratridine / chemistry
  • Veratridine / metabolism*

Substances

  • Lipid Bilayers
  • Muscle Proteins
  • Peptide Fragments
  • Scn4a protein, rat
  • Sodium Channels
  • Veratridine
  • Dimyristoylphosphatidylcholine