Selective ion permeation involves complexation with carboxylates and lysine in a model human sodium channel

Bacterial and human voltage-gated sodium channels (Navs) exhibit similar cation selectivity, despite their distinct EEEE and DEKA selectivity filter signature sequences. Recent high-resolution structures for bacterial Navs have allowed us to learn about ion conduction mechanisms in these simpler homo-tetrameric channels, but our understanding of the function of their mammalian counterparts remains limited. To probe these conduction mechanisms, a model of the human Nav1.2 channel has been constructed by grafting residues of its selectivity filter and external vestibular region onto the bacterial NavRh channel with atomic-resolution structure. Multi-μs fully atomistic simulations capture long time-scale ion and protein movements associated with the permeation of Na+ and K+ ions, and their differences. We observe a Na+ ion knock-on conduction mechanism facilitated by low energy multi-carboxylate/multi-Na+ complexes, akin to the bacterial channels. These complexes involve both the DEKA and vestibular EEDD rings, acting to draw multiple Na+ into the selectivity filter and promote permeation. When the DEKA ring lysine is protonated, we observe that its ammonium group is actively participating in Na+ permeation, presuming the role of another ion. It participates in the formation of a stable complex involving carboxylates that collectively bind both Na+ and the Lys ammonium group in a high-field strength site, permitting pass-by translocation of Na+. In contrast, multiple K+ ion complexes with the DEKA and EEDD rings are disfavored by up to 8.3 kcal/mol, with the K+-lysine-carboxylate complex non-existent. As a result, lysine acts as an electrostatic plug that partially blocks the flow of K+ ions, which must instead wait for isomerization of lysine downward to clear the path for K+ passage. These distinct mechanisms give us insight into the nature of ion conduction and selectivity in human Nav channels, while uncovering high field strength carboxylate binding complexes that define the more general phenomenon of Na+-selective ion transport in nature.Author summary: Ion channels can rapidly and selectively conduct an ionic species, essential for the firing of neurons, where sodium and potassium channels respond to changes in membrane potential to release stores of sodium and potassium ions in succession. The ability of a protein pore to discriminate between these two nearly identical ions has remained an intriguing problem for decades. In particular, the origins of sodium selectivity have been obscured by diverse protein chemistries that exhibit sodium-selective conduction in prokaryotes and eukaryotes. Here we use multi-microsecond atomistic simulations to observe and contrast the permeation mechanisms of sodium and potassium ions in model human and bacterial sodium channels. These channels exhibit shared features of conduction, centered on the involvement of charged protein groups that form complexes with the smaller sodium ion. In the human channel model, we observe a special role for the signature lysine that allows sodium to pass, but partially blocks potassium. As sodium channels are vital to heartbeat, sensation, muscle contraction and brain activity, these insights could assist developments in improved therapeutics for disorders such as epilepsy and chronic pain, with mechanisms relevant to a range of ion transport processes in biology and materials.