Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel

Abstract

The crystal structure of the open conformation of a bacterial voltage-gated sodium channel pore from Magnetococcus sp.(NaVMs) has provided the basis for a molecular dynamics study defining the channel's full ion translocation pathway and conductance process, selectivity, electrophysiological characteristics, and ion-binding sites. Microsecond molecular dynamics simulations permitted a complete time-course characterization of the protein in a membrane system, capturing the plethora of conductance events and revealing a complex mixture of single and multiion phenomena with decoupled rapid bidirectional water transport. The simulations suggest specific localization sites for the sodium ions, which correspond with experimentally determined electron density found in the selectivity filter of the crystal structure. These studies have also allowed us to identify the ion conductance mechanism and its relation to water movement for the NavMs channel pore and to make realistic predictions of its conductance properties. The calculated single-channel conductance and selectivity ratio correspond closely with the electrophysiology measurements of the NavMs channel expressed in HEK 293 cells. The ion translocation process seen in this voltage-gated sodium channel is clearly different from that exhibited by members of the closely related family of voltage-gated potassium channels and also differs considerably from existing proposals for the conductance process in sodium channels. These studies simulate sodium channel conductance based on an experimentally determined structure of a sodium channel pore that has a completely open transmembrane pathway and activation gate. V oltage-gated cation channels are proteins that produce electrical signals in neurons and other excitable cells to regulate muscle contraction, gene expression, and release of hormones and neurotransmitters among other functions. In response to a change in transmembrane electrical potential, the channels open pores through which ions move passively across the membrane. The large family of cation channels includes those selective for sodium, potassium, or calcium. The opening and closing of these ion-specific channels is carefully choreographed to produce the electrical signals required by the nervous system for rapid signal transduction (1).Voltage-gated sodium channels have been causally linked with a wide range of neurological and cardiovascular diseases and hence are important pharmaceutical drug-development targets (2, 3). Eukaryotic voltage-gated sodium channels are large, singlechain polypeptides, consisting of 24 transmembrane (TM) helices that form four homologous repeats, each contributing both a voltage sensor and a pore domain; the latter are arranged to form a central Na + -selective transmembrane pathway. Bacterial voltagegated sodium channels are far simpler, consisting of four polypeptide chains, each of which is composed of six TM segments, with segments TM1-TM4 forming the voltage sensors and TM5-TM6 forming the pore domains. The TM5-TM6 segment...

Catalysis of Na + permeation in the bacterial sodium channel Na V Ab

“…Several simulation studies have recently examined the energetics and the dynamics of Na + , Ca 2+ , and K + in the SF of Na V Ab (18)(19)(20)(21)(22)(23)(24)(25). Consistent with the above results, some of these studies described coordination of Na + by the carboxyl group of E177 (18,20,21,24) and a two-ion knock-on mechanism (19,20,23,24) involving low free energy barriers (19,22,23).…”

Molecular basis of ion permeability in a voltage‐gated sodium channel

“…The NavMs channel has previously been shown to exhibit a significant selectivity for Na + over K + (Ulmschneider et al , 2013). In this study, whole‐cell patch clamping was used to determine the relative permeabilities of additional monovalent and divalent cations (Li + , Cs + , Ca 2+ , Mg 2+ and Ba 2+ ) in the NavMs channel (Fig 1 and Appendix Fig S1A, Table 1A).…”

“…Sodium ions from the AB tetramer are depicted as cyan spheres, those from the CD tetramer as teal spheres. Predicted sodium ion binding sites from Ulmschneider et al (2013) are indicated as small black spheres and labelled on the right of the spheres according to the nomenclature (S 0 –S 4 ) in that study. Predicted sodium ion binding sites from Payandeh et al (2011), based on a closed channel structure of the close orthologue NavAb, are indicated on the far right and labelled as per the nomenclature of that study (Site HFS , Site CEN and Site IN ).…”

“…The resolution of the first such structure (3.5 Å), however, was too low to determine the details of the sites of the ions in the SF, whilst the latter structures contained channel blocker ligands which interfered with ion binding. The sodium ion binding site locations and mechanisms for ion selectivity have also been predicted by a number of molecular dynamics (MD) studies, although they differ considerably in their details (Amaral et al , 2012; Chakrabarti et al , 2013; Stock et al , 2013; Ulmschneider et al , 2013; Xia et al , 2013; Zhang et al , 2013; Boiteux et al , 2014; Furini et al , 2014). …”

Prokaryotic NavMs channel as a structural and functional model for eukaryotic sodium channel antagonism

“…Nevertheless, although these findings are encouraging for using the NavMs as a model for mammalian sodium channel pharmacology, it should be kept in mind that there are also likely to be differences in the effects of drugs that block mammalian Na v channels in the fast inactivated state, which is not found in prokaryotic channels. The density in the center of the SF corresponds to sodium ions (28). (E and F) In silico docking results using the apo NavMs-pore structure and PI1.…”