Cumulative hydropathic topology of a voltage-gated sodium channel at atomic resolution

Proteins. 2020 Oct;88(10):1319-1328. doi: 10.1002/prot.25951. Epub 2020 Jun 13.


Voltage-gated sodium channels (NavChs) are biological pores that control the flow of sodium ions through the cell membrane. In humans, mutations in genes encoding NavChs can disrupt physiological cellular activity thus leading to a wide spectrum of diseases. Here, we present a topological connection between the functional architecture of a NavAb bacterial channel and accumulation of atomic hydropathicity around its pore. This connection is established via a scaling analysis methodology that elucidates how intrachannel hydropathic density variations translate into hydropathic dipole field configurations along the pore. Our findings suggest the existence of a nonrandom cumulative hydropathic topology that is organized parallel to the membrane surface so that pore's stability, as well as, gating behavior are guaranteed. Given the biophysical significance of the hydropathic effect, our study seeks to provide a computational framework for studying cumulative hydropathic topological properties of NavChs and pore-forming proteins in general.

Keywords: NavAb; cumulative hydropathic effects; hydrophobic gating; scaling; topology; voltage-gated sodium channels.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Arcobacter / chemistry*
  • Arcobacter / metabolism
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Hydrophobic and Hydrophilic Interactions
  • Ion Channel Gating / physiology*
  • Models, Molecular
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Sodium / chemistry*
  • Sodium / metabolism
  • Thermodynamics
  • Voltage-Gated Sodium Channels / chemistry*
  • Voltage-Gated Sodium Channels / metabolism


  • Bacterial Proteins
  • Voltage-Gated Sodium Channels
  • Sodium