Intrinsic Ion Selectivity of Narrow Hydrophobic Pores

We show that narrow hydrophobic pores have an intrinsic ion selectivity by using single-walled carbon nanotube membranes as a model. We examined pores of radius 3.4−6.1 Å, and conducted molecular dynamics simulations to show that Na+, K+, and Cl− face different free energy barriers when entering hydrophobic pores. Most of the differences result from the different dehydration energies of the ions; however, changes in the solvation shell structure in the confined nanotube interior and van der Waals interactions in the small tubes can both play a role. Molecular dynamics simulations conducted under hydrostatic pressure show that carbon nanotube membranes can act as ion sieves, with the pore radius and pressure determining which ions will permeate through the membrane. This work suggests that the intrinsic ion selectivity of biological pores of differing radii might also play a role in determining their selectivity, in addition to the more common explanations based on electrostatic effects. In addition, “hydrophobic gating” can arise in continuous water-filled pores

Free energy of binding, and dissociation constants relative to bulk water for phenytoin and benzocaine at two sites in the NavAb central cavity.

<p>Free energy of binding, and dissociation constants relative to bulk water for phenytoin and benzocaine at two sites in the NavAb central cavity.</p

Locating the Route of Entry and Binding Sites of Benzocaine and Phenytoin in a Bacterial Voltage Gated Sodium Channel

<div><p>Sodium channel blockers are used to control electrical excitability in cells as a treatment for epileptic seizures and cardiac arrhythmia, and to provide short term control of pain. Development of the next generation of drugs that can selectively target one of the nine types of voltage-gated sodium channel expressed in the body requires a much better understanding of how current channel blockers work. Here we make use of the recently determined crystal structure of the bacterial voltage gated sodium channel NavAb in molecular dynamics simulations to elucidate the position at which the sodium channel blocking drugs benzocaine and phenytoin bind to the protein as well as to understand how these drugs find their way into resting channels. We show that both drugs have two likely binding sites in the pore characterised by nonspecific, hydrophobic interactions: one just above the activation gate, and one at the entrance to the the lateral lipid filled fenestrations. Three independent methods find the same sites and all suggest that binding to the activation gate is slightly more favourable than at the fenestration. Both drugs are found to be able to pass through the fenestrations into the lipid with only small energy barriers, suggesting that this can represent the long posited hydrophobic entrance route for neutral drugs. Our simulations highlight the importance of a number of residues in directing drugs into and through the fenestration, and in forming the drug binding sites.</p></div

Mechanism of Ion Permeation and Selectivity in a Voltage Gated Sodium Channel

The rapid and selective transport of Na⁺ through sodium channels is essential for initiating action potentials within excitable cells. However, an understanding of how these channels discriminate between different ion types and how ions permeate the pore has remained elusive. Using the recently published crystal structure of a prokaryotic sodium channel from <i>Arcobacter butzleri</i>, we are able to determine the steps involved in ion transport and to pinpoint the location and likely mechanism used to discriminate between Na⁺ and K⁺. Na⁺ conduction is shown to involve the loosely coupled “knock-on” movement of two solvated ions. Selectivity arises due to the inability of K⁺ to fit between a plane of glutamate residues with the preferred solvation geometry that involves water molecules bridging between the ion and carboxylate groups. These mechanisms are different to those described for K⁺ channels, highlighting the importance of developing a separate mechanistic understanding of Na⁺ and Ca²⁺ channels

Lipid and water in the fenestrations as a function of drug position.

<p>(A) A representative snapshot showing lipid occupying the lateral fenestrations while benzocaine sits at its minimum energy position in the activation gate. The position of F203 (orange) and T138 (yellow surface) are also shown. (B) The extent to which lipid penetrates into the fenestration is plotted as a function of the position of each drug. Low values indicate extension further into the fenestration. (C) A snapshot showing an extreme example of a water chain extending from the channel lumen to phenytoin on the exterior surface of the protein. In most cases the water chain does not extend this far. (D) The probability that a continuous water chain extends from each drug back to the channel lumen as a function of drug position (solid lines). Also shown is the probability that a water chain extends from the drug directly to bulk water (dashed lines). In B and D the data for individual windows are shown in points and a moving average of 5 data points is indicated by the line.</p

Free energy surfaces for (A,C) benzocaine and (B,D) phenytoin in the NavAb central cavity viewed along the pore axis (A,C) and from the membrane (B,D) obtained from metadynamics simulations.

<p>Contours are shown at 1/mol intervals.</p

Drug positions in unbiased simulations.

<p>20 Equally spaced snapshots from three unbiased simulations of benzocaine (A and C) and phenytoin (B and D) in the closed (A and B) and inactivated (C and D) NavAb. Each colour represents snapshots from a different simulation, while a single protein conformation is shown in each case.</p

Snapshots of the most commonly sampled binding poses.

<p>The drug and surrounding residues are shown. The residues with the strongest interactions with the drug are named in bold. (A) benzocaine in the activation gate with amine pointing at the central cavity. (B) benzocaine in the activation gate with amine pointing down. (C) benzocaine in a fenestration with amine pointing to the central cavity. (D) Benzocaine in a fenestration with amine pointing toward the lipid. (E) Phenytoin in the activation gate. (F) Phenytoin in a fenestration.</p

Drug-protein interactions in each site.

<p>The interaction energies for (A) benzocaine and (B) phenytoin with residues lining the channel lumen when the drug is in one of the commonly occupied clusters. Four significantly different cluster are shown for benzocaine, corresponding to those pictured in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003688#pcbi-1003688-g001" target="_blank">Fig. 1</a> & <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003688#pcbi-1003688-g003" target="_blank">3</a>. Two clusters are shown for phenytoin corresponding to binding at the activation gate (green) and fenestration (blue). Residues from regions not having significant interactions with the drugs are omitted.</p