Mapping the importance of four factors in creating monovalent ion selectivity in biological molecules

Computational methods and theory for ion channel research

Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.

Conductance selectivity of Na+ across the K+ channel via Na+ trapped in a tortuous trajectory

Ion selectivity of the potassium channel is crucial for regulating electrical activity in living cells; however, the mechanism underlying the potassium channel selectivity that favors large K⁺ over small Na⁺ remains unclear. Generally, Na⁺ is not completely excluded from permeation through potassium channels. Herein, the distinct nature of Na⁺ conduction through the prototypical KcsA potassium channel was examined. Single-channel current recordings revealed that, at a high Na⁺ concentration (200 mM), the channel was blocked by Na⁺, and this blocking was relieved at high membrane potentials, suggesting the passage of Na⁺ across the channel. At a 2,000 mM Na⁺ concentration, single-channel Na⁺ conductance was measured as one-eightieth of the K⁺ conductance, indicating that the selectivity filter allows substantial conduit of Na⁺ Molecular dynamics simulations revealed unprecedented atomic trajectories of Na⁺ permeation. In the selectivity filter having a series of carbonyl oxygen rings, a smaller Na⁺ was distributed off-center in eight carbonyl oxygen-coordinated sites as well as on-center in four carbonyl oxygen-coordinated sites. This amphipathic nature of Na⁺ coordination yielded a continuous but tortuous path along the filter. Trapping of Na⁺ in many deep free energy wells in the filter caused slow elution. Conversely, K⁺ is conducted via a straight path, and as the number of occupied K⁺ ions increased to three, the concerted conduction was accelerated dramatically, generating the conductance selectivity ratio of up to 80. The selectivity filter allows accommodation of different ion species, but the ion coordination and interactions between ions render contrast conduction rates, constituting the potassium channel conductance selectivity.

Direct proof of soft knock-on mechanism of ion permeation in a voltage gated sodium channel

Sodium channels selectively conduct Na⁺ ions across cellular membrane with extraordinary efficiency, which is essential for initiating action potentials. However, how Na⁺ ions permeate the ionic channels remains obscure and ambiguous. With more than 40 conductance events from microsecond molecular dynamics simulation, the soft knock-on ion permeation mediated by water molecules was observed and confirmed by the free energy profile and electrostatic potential calculation in this study. During the soft knock-on process, the change of average distance between four oxygen atoms in Glu177-Glu177 plays a very important role for the permeation of Na⁺ ion. Exploration of the ionic conductance mechanism could provide a guideline for designing ion channel targeted drug.

Molecular strategies to achieve selective conductance in NaK channel variants

A recent crystallization of several ion channels has provided strong impetus for efforts aimed at understanding the different strategies employed by nature for selective ion transport. In this work, we used two variants of the selectivity filter of NaK channel to explore molecular mechanisms that give rise to K(+)-selectivity. We computed one-dimensional (1D) and two-dimensional (2D) potentials of mean force (PMFs) for ion permeation across the channel. The results indicate that the energies for Na(+) and K(+) permeation across the selectivity filter display significant differences in positions of the binding sites and barriers. One characteristic signature of a K(+)-selective channel is the apparent preservation of the site analogous to that of S2 in KcsA. The S2-bound ion can be almost ideally dehydrated and coordinated by 6 to 8 carbonyls. In a striking contrast, the PMFs controlling transport of ions in a nonselective variant show almost identical profiles for either K(+) or Na(+) and significant involvement of water molecules in ion coordination across the entire selectivity filter. An analysis of differences in 1D PMFs for Na(+) and K(+) suggests that coordination number alone is an insufficient predictor of site selectivity, while chemical composition (ratio of carbonyls and water molecules) correlates well with preference for K(+). Multi-ion effects such as dependence of the barriers and wells for permeant ion on the type of copermeant ion were found to play a significant role in the selectivity signature of the channel as well.

Bioinspired graphene nanopores with voltage-tunable ion selectivity for Na(+) and K(+)

Biological protein channels have many remarkable properties such as gating, high permeability, and selectivity, which have motivated researchers to mimic their functions for practical applications. Herein, using molecular dynamics simulations, we design bioinspired nanopores in graphene sheets that can discriminate between Na(+) and K(+), two ions with very similar properties. The simulation results show that, under transmembrane voltage bias, a nanopore containing four carbonyl groups to mimic the selectivity filter of the KcsA K(+) channel preferentially conducts K(+) over Na(+). A nanopore functionalized by four negatively charged carboxylate groups to mimic the selectivity filter of the NavAb Na(+) channel selectively binds Na(+) but transports K(+) over Na(+). Surprisingly, the ion selectivity of the smaller diameter pore containing three carboxylate groups can be tuned by changing the magnitude of the applied voltage bias. Under lower voltage bias, it transports ions in a single-file manner and exhibits Na(+) selectivity, dictated by the knock-on ion conduction and selective blockage by Na(+). Under higher voltage bias, the nanopore is K(+)-selective, as the blockage by Na(+) is destabilized and the stronger affinity for carboxylate groups slows the passage of Na(+) compared with K(+). The computational design of biomimetic ion-selective nanopores helps to understand the mechanisms of selectivity in biological ion channels and may also lead to a wide range of potential applications such as sensitive ion sensors, nanofiltration membranes for Na(+)/K(+) separation, and voltage-tunable nanofluidic devices.

The mechanism of Na⁺/K⁺ selectivity in mammalian voltage-gated sodium channels based on molecular dynamics simulation

Voltage-gated sodium (Nav) channels and their Na⁺/K⁺ selectivity are of great importance in the mammalian neuronal signaling. According to mutational analysis, the Na⁺/K⁺ selectivity in mammalian Nav channels is mainly determined by the Lys and Asp/Glu residues located at the constriction site within the selectivity filter. Despite successful molecular dynamics simulations conducted on the prokaryotic Nav channels, the lack of Lys at the constriction site of prokaryotic Nav channels limits how much can be learned about the Na⁺/K⁺ selectivity in mammalian Nav channels. In this work, we modeled the mammalian Nav channel by mutating the key residues at the constriction site in a prokaryotic Nav channel (NavRh) to its mammalian counterpart. By simulating the mutant structure, we found that the Na⁺ preference in mammalian Nav channels is collaboratively achieved by the deselection from Lys and the selection from Asp/Glu within the constriction site.

An entropic mechanism of generating selective ion binding in macromolecules

Several mechanisms have been proposed to explain how ion channels and transporters distinguish between similar ions, a process crucial for maintaining proper cell function. Of these, three can be broadly classed as mechanisms involving specific positional constraints on the ion coordinating ligands which arise through: a “rigid cavity”, a ‘strained cavity’ and ‘reduced ligand fluctuations’. Each operates in subtly different ways yet can produce markedly different influences on ion selectivity. Here we expand upon preliminary investigations into the reduced ligand fluctuation mechanism of ion selectivity by simulating how a series of model systems respond to a decrease in ligand thermal fluctuations while simultaneously maintaining optimal ion-ligand binding distances. Simple abstract-ligand models, as well as simple models based upon the ion binding sites in two amino acid transporters, show that limiting ligand fluctuations can create ion selectivity between Li⁺, Na⁺ and K⁺ even when there is no strain associated with the molecular framework accommodating the different ions. Reducing the fluctuations in the position of the coordinating ligands contributes to selectivity toward the smaller of two ions as a consequence of entropic differences.

Differentiating between Na⁺ and K⁺ ions is important for many cellular processes, such as nerve conduction and the regulation of membrane potentials. Different biological molecules utilise different methods to discriminate between ions. In this work, the reduced ligand fluctuation mechanism of ion selectivity is described. This entropy-driven mechanism is due to the limited thermal fluctuations of the atoms in some macromolecular ion binding sites. The elucidation of this mechanism offers a more complete picture of the ways in which the fundamental process of ion selectivity can be achieved.

How does overcoordination create ion selectivity?

Some biological molecules can distinguish between ions of similar nature, which may be achieved by enforcing specific coordination numbers on ions in the binding site. It is suggested that when this number is favourable for one ion type, but too large for another, this creates ion selectivity through the proposed mechanism of 'overcoordination'. Much debate has occurred about the role overcoordination plays, and suggestions made as to how molecules can enforce particular coordination numbers, but there has not been an examination of the microscopic underpinning of ion selectivity by overcoordination. Here we use molecular-dynamics to systematically investigate how the number of ligands affects the ion-ligand and ligand-ligand interaction energies, and thus the thermodynamic ion selectivity, of a combination of model systems: three ions (Li(+)/Na(+)/K(+)) with three different ligands (water/formaldehyde/formamide). We find that the ligand-ligand repulsion controls the changes in geometry of each system with changing ligand number. Ion selectivity by overcoordination is achieved as smaller ions exhibit anomalous geometrical changes with the addition of extra ligands, whilst larger ions do not.

Role of spatial ionic distribution on the energetics of hydrophobic assembly and properties of the water/hydrophobe interface

We present results from all-atom molecular dynamics simulations of large-scale hydrophobic plates solvated in NaCl and NaI salt solutions. As observed in studies of ions at the air-water interface, the density of iodide near the water-plate interface is significantly enhanced relative to chloride and in the bulk. This allows for the partial hydration of iodide while chloride remains more fully hydrated. In 1 M solutions, iodide directly pushes the hydrophobes together (contributing -2.51 kcal mol(-1)) to the PMF. Chloride, however, strengthens the water-induced contribution to the PMF by ~-2.84 kcal mol(-1). These observations are enhanced in 3 M solutions, consistent with the increased ion density in the vicinity of the hydrophobes. The different salt solutions influence changes in the critical hydrophobe separation distance and characteristic wetting/dewetting transitions. These differences are largely influenced by the ion-specific expulsion of iodide from bulk water. Results of this study are of general interest to the study of ions at interfaces and may lend insight to the mechanisms underlying the Hofmeister series.

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 Arcobacter butzleri, 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 Ca(2+) channels.