Structure of the C-terminal domain of the prokaryotic sodium channel orthologue NsvBa

Eur Biophys J. 2016 Dec;45(8):807-814. doi: 10.1007/s00249-016-1125-2. Epub 2016 Apr 22.

Abstract

Crystallographic and electrophysiological studies have recently provided insight into the structure, function, and drug binding of prokaryotic sodium channels. These channels exhibit significant sequence identities, especially in their transmembrane regions, with human voltage-gated sodium channels. However, rather than being single polypeptides with four homologous domains, they are tetramers of single domain polypeptides, with a C-terminal domain (CTD) composed of an inter-subunit four helix coiled coil. The structures of the CTDs differ between orthologues. In NavBh and NavMs, the C-termini form a disordered region adjacent to the final transmembrane helix, followed by a coiled-coil region, as demonstrated by synchrotron radiation circular dichroism (SRCD) and double electron-electron resonance electron paramagnetic resonance spectroscopic measurements. In contrast, in the crystal structure of the NavAe orthologue, the entire C-terminus is comprised of a helical region followed by a coiled coil. In this study, we have examined the CTD of the NsvBa from Bacillus alcalophilus, which unlike other orthologues is predicted by different methods to have different types of structures: either a disordered region adjacent to the transmembrane region, followed by a helical coiled coil, or a fully helical CTD. To discriminate between the two possible structures, we have used SRCD spectroscopy to experimentally determine the secondary structure of the C-terminus of this orthologue and used the results as the basis for modeling the open and closed conformations of the channel.

Keywords: Bioinformatics; Coiled coil; Structure prediction; Synchrotron radiation circular dichroism spectroscopy; Voltage-gated sodium channels.

MeSH terms

  • Amino Acid Sequence
  • Bacillus*
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Computational Biology
  • Models, Molecular
  • Protein Domains
  • Sequence Homology, Amino Acid*
  • Sodium Channels / chemistry*
  • Sodium Channels / metabolism

Substances

  • Bacterial Proteins
  • Sodium Channels