Molecular simulations of ion permeation and selectivity in sodium selective ion channels
Creators: name: Flood, Emelie
Publisher: name: RMIT University
Year: 2024
Subjects: classificationCode: 510501
subject: Biological physics

description: Na+-selective ion channels play key roles in a wide range of both physiological bodily functions and pathological disease processes including propagation of nervous signals, cardiac function and pain sensation. Different channels achieve Na+ selectivity despite differences in structure, function and evolutionary origin. For example, voltage gated sodium channels (Navs) are tetramers that open and close in response to cell membrane depolarisation, whereas acid sensing ion channels (ASICs) are trimeric channels that respond to a change in extracellular pH. A key function of Na+ channels is their ability to select for Na+ while discriminating against other ions. To achieve this selectivity, Navs makes use of a highly flexible selectivity filter (SF) where ion coordination is facilitated by the side chains of the amino acids. In contrast, ASICs have been proposed to rely on a size-constriction mechanism. However, the utilisation of size-constriction for ion selectivity has not been proven.<br><br> Furthermore, the amino acids of the SF present diverse chemistries to achieve selectivity in these channels, with the mammalian Nav using a DEKA ring (Glu, Asp, Lys and Ala), the bacterial Nav an EEEE ring (four Glus), and ASIC a GAS-belt (Gly, Ala and Ser). Therefore it has been proposed that different Na+-selective channels employ different mechanisms to achieve Na+ selectivity. There are a number of recently solved atomic scale Na+ channel structures of Navs and ASICs which presents an opportunity to elucidate these mechanisms and understand the origins of ion selectivity at the molecular level. Computer simulations are becoming increasingly useful to complement physical experiments in the investigation of biological systems. Molecular Dynamics (MD) simulations can be used to study the properties of macromolecules at the atomic scale. In this thesis, we use MD to explore the mechanisms of ion selectivity in sodium-selective channels. To provide insight into the ion-protein interactions relevant to ion discrimination, we require that these interactions are described with a high level of accuracy. We have therefore investigated the parameters defining the interactions between ions and the chemical groups of interest, and tested them against quantum mechanical calculations and experimental data to determine accurate models for use in our simulations. We have explored ion permeation in Navs and ASICs using multi-μs fully atomistic simulations, as well as enhanced sampling methods. <br><br>Our results demonstrate that low free energy multi-Na+/multi-carboxylate complexes facilitate selective ion permeation in a similar fashion in all of these channels. In the bacterial Navs, these complexes are formed with carboxylates from the EEEE ring. To investigate conduction and selectivity in mammalian Nav channels, we have constructed a model of the human Nav1.2 channel by grafting core functional sequences into a structurally well-defined bacterial channel scaffold. We report that Na+ ion conduction in Nav1.2 relies on the formation of energetically stable multi-Na+/multi-carboxylate complexes formed by both the DEKA and vestibular EEDD rings. These stable complexes facilitate a knock-on conduction mechanism. Furthermore, we have observed that the positively charged DEKA Lys forms a similar Na++Lys/multi-carboxylate complex deep in the pore to facilitate low barrier ion pass-by permeation for Na+, but not K+.<br><br> In contrast Lys acts as an electrostatic plug that partially blocks the channel, leading to discrimination. In the ASIC channel, we have found that Na+ and K+ are equally favoured around the GAS constriction, not supporting its previously postulated role in Na+ selectivity. Instead, we have identified a preference for Na+ at the lower end of the pore where a ring of Glu and Asp side chains participate in multi-Na+/multi-carboxylate complexes, with similar K+ ion complexes disfavoured, suggesting a SF at the intracellular end of the ASIC pore. These results are supported by mutagenesis and novel unnatural amino acid substitution experiments performed by collaborators. Our studies of these evolutionarily, structurally and functionally different ion channels have revealed essential high-field strength carboxylate binding events that underscore selective permeation. These key carboxylates form tight multi-ion/multi-carboxylate complexes that thermodynamically select for Na+ over K+. This suggests a common mechanism for the selection of Na+ ions in membrane ion transport. These studies reveal the principles governing Na+ selectivity across several ion channels, with the potential to extend to the whole family of Na+-selective ion channels and pumps in nature.