A Novel Gating Mechanism of the NaVMs Selectivity Filter Suggested by Molecular Dynamics Simulations

Rapid and selective ion transport is essential for the generation and regulation of electrical signaling pathways in living organisms. Here, we use molecular dynamics (MD) simulations with applied membrane potential to investigate the ion flux of bacterial sodium channel NaVMs (Mccusker et al., 2012). 4-microsecond simulations with 500mM NaCl suggest different mechanisms for inward and outward flux.The predicted inward conductance rate of ∼26 pS agrees with experiment (∼33 pS, Ulmschneider et al., 2013). The estimated outward conductance rate is 14 pS, which is considerably slower. The mean ion dwell time of the selectivity filter is prolonged from 14.8±0.8 ns to 21.4±1.1 ns. Analysis of the Na+ distribution revealed distinct patterns for influx and efflux events.During influx, site-HFS (High Field Strength) (Payandeh et al., 2012) is the dominant site with highest ion density. Ions are directly coordinated by GLU53 and SER54 sidechains in an off-axis manner. Site-CEN and Site-IN are less populated. In contrast to site-HFS, ions are distributed in the middle of the selectivity filter.The distribution of the outward current displays a different pattern: site-CEN and site-IN are instantaneously occupied with Na+, while site HFS is populated less frequently.Examining the structural fluctuation of the trajectories suggests subtle differences at the selectivity filter. Translocation of ions from cytoplasma to periplasma induces structural changes of the GLU53 sidechains from an out-facing to a lumen-facing conformation. Thereby, it slows down the flux rate by creating a narrower constriction “mouth”. During influx this residue remains rigid and potentially energetically more favorable for ion passage. We hypothesize that these structural changes at the selectivity filter glutamic acids represent a novel gating mechanism decreasing outward current.