Molecular Dynamics Simulations of Ion Permeation in Human Voltage-Gated Sodium Channels

J Chem Theory Comput. 2023 May 23;19(10):2953-2972. doi: 10.1021/acs.jctc.2c00990. Epub 2023 Apr 28.


The recent determination of cryo-EM structures of voltage-gated sodium (Nav) channels has revealed many details of these proteins. However, knowledge of ionic permeation through the Nav pore remains limited. In this work, we performed atomistic molecular dynamics (MD) simulations to study the structural features of various neuronal Nav channels based on homology modeling of the cryo-EM structure of the human Nav1.4 channel and, in addition, on the recently resolved configuration for Nav1.2. In particular, single Na+ permeation events during standard MD runs suggest that the ion resides in the inner part of the Nav selectivity filter (SF). On-the-fly free energy parametrization (OTFP) temperature-accelerated molecular dynamics (TAMD) was also used to calculate two-dimensional free energy surfaces (FESs) related to single/double Na+ translocation through the SF of the homology-based Nav1.2 model and the cryo-EM Nav1.2 structure, with different realizations of the DEKA filter domain. These additional simulations revealed distinct mechanisms for single and double Na+ permeation through the wild-type SF, which has a charged lysine in the DEKA ring. Moreover, the configurations of the ions in the SF corresponding to the metastable states of the FESs are specific for each SF motif. Overall, the description of these mechanisms gives us new insights into ion conduction in human Nav cryo-EM-based and cryo-EM configurations that could advance understanding of these systems and how they differ from potassium and bacterial Nav channels.

MeSH terms

  • Bacteria / metabolism
  • Humans
  • Ions / metabolism
  • Lysine
  • Molecular Dynamics Simulation*
  • Voltage-Gated Sodium Channels* / chemistry
  • Voltage-Gated Sodium Channels* / metabolism


  • Voltage-Gated Sodium Channels
  • Ions
  • Lysine