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 Navpore remains limited. In this work, we performed atomistic
molecular dynamics (MD) simulations to study the structural features
of various neuronal Navchannels 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 Navselectivity 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 Navcryo-EM-based and cryo-EM configurations that could advance
understanding of these systems and how they differ from potassium
and bacterial Navchannels.