Thermodynamics of ion binding and occupancy in potassium channels

Potassium channels modulate various cellular functions through efficient and selective conduction of K⁺ ions. The mechanism of ion conduction in potassium channels has recently emerged as a topic of debate. Crystal structures of potassium channels show four K⁺ ions bound to adjacent binding sites in the selectivity filter, while chemical intuition and molecular modeling suggest that the direct ion contacts are unstable. Molecular dynamics (MD) simulations have been instrumental in the study of conduction and gating mechanisms of ion channels. Based on MD simulations, two hypotheses have been proposed, in which the four-ion configuration is an artifact due to either averaged structures or low temperature in crystallographic experiments. The two hypotheses have been supported or challenged by different experiments. Here, MD simulations with polarizable force fields validated by ab initio calculations were used to investigate the ion binding thermodynamics. Contrary to previous beliefs, the four-ion configuration was predicted to be thermodynamically stable after accounting for the complex electrostatic interactions and dielectric screening. Polarization plays a critical role in the thermodynamic stabilities. As a result, the ion conduction likely operates through a simple single-vacancy and water-free mechanism. The simulations explained crystal structures, ion binding experiments and recent controversial mutagenesis experiments. This work provides a clear view of the mechanism underlying the efficient ion conduction and demonstrates the importance of polarization in ion channel simulations.

Polarization shapes the energy landscape of ion conduction in potassium channels.     

Supramolecular hydrogels based on the epitope of potassium ion channels

Imparting aromatic-aromatic interactions to the potassium binding epitope affords a supramolecular hydrogelator that responds to the K(+) concentration by self-assembly into nanofibers of different widths and crosslinking patterns, which illustrates a simple approach to generate biomimic materials based on tunable, hierarchical self-assembly of small molecules.     

Structure and ion selectivity of the open potential-dependent potassium channel

The structure and ion selectivity of the potential-dependent potassium channel is investigated. It is shown that the channel constructed by joining the α-subunit with the β-subunit concave, when the axial symmetry axes coincide, is the potential-dependent potassium channel in the open state.     

Conformational changes and gating at the selectivity filter of potassium channels

The translocation of ions and water across cell membranes is a prerequisite for many of life's processes. K(+) channels are a diverse family of integral membrane proteins through which K(+) can pass selectively. There is an ongoing debate about the nature of conformational changes associated with the opening and closing and conductive and nonconductive states of potassium (K(+)) channels. These changes depend on the membrane potential, the K(+) concentration gradient, and large scale motions of transmembrane helices and associated residues. Experiments also suggest that local structural changes in the selectivity filter may act as the dominant gate referred to as C-type inactivation. Herein we present an extensive computational study on KirBac, which supports the existence of a physical gate or constriction in the selectivity filter (SF) of K(+) channels. Our computations identify a new selectivity filter structure, which is likely associated with C-type inactivation. Specifically, the four peptide chains that comprise the filter adopt an unusual structure in which their dihedrals alternate between left- and right-handed Ramachandran angles, which also justifies the need for conservation of glycine in the K(+) selectivity filter, since it is the only residue able to play this bifunctional role.     

Highly active artificial potassium channels having record-high K+/Na+ selectivity of 20.1

Replicating extraordinarily high membrane transport selectivity of protein channels in artificial channel is a challenging task. In this work, we demonstrate that a strategic application of steric code-based social self-sorting offers a novel means to enhance ion transport selectivities of artificial ion channels, alongside with boosted ion transport activities. More specifically, two types of mutually compatible sterically bulky groups (benzo-crown ether and tert-butyl group) were appended onto a monopeptide-based scaffold, which can order the bulky groups onto the same side of a one-dimensionally aligned H-bonded structure. Strong steric repulsions among the same type of bulky groups (either benzo-crown ethers or tert-butyl groups), which are forced into proximity by H-bonds, favor the formation of hetero-oligomeric ensembles that carry an alternative arrangement of sterically compatible benzo-crown ethers and tert-butyl groups, rather than homo-oligomeric ensembles containing a single type of either benzo-crown ethers or tert-butyl groups. Coupled with side chain tuning, this social self-sorting strategy delivers highly active hetero-oligomeric K⁺-selective ion channel (5F12‧BF12)_n, displaying the highest K⁺/Na⁺ selectivity of 20.1 among artificial potassium channels and an excellent EC₅₀ value of 0.50 μmol/L (0.62 mol% relative to lipids) in terms of single channel concentration     

Remarkable potassium selectivity of ion sensors based on supramolecular gel membranes made from low-molecular-weight gelators without any ionophore

Supramolecular gels formed by low-molecular-weight gelators bearing diamide groups were used as ion-sensing membranes for the first time. Even though no special ionophore was added to the membranes, excellent ion selectivities for K(+) over alkali metal ions were realized with the sensor systems.     

Metal ion selectivity of oligopeptides

Metal binding affinity and selectivity of peptides are reviewed with a special emphasis on the high structural variety of peptide complexes. The most common structural type of these complexes is built up by the deprotonation and metal ion coordination of subsequent amide groups in the form of fused five-membered chelate rings. The metal ion selectivity of this process and the role of various anchoring groups are discussed in detail. The highest metal binding affinity of peptides is connected to the presence of two anchoring groups in appropriate location (the "double anchor"): e.g. the NH2-Xaa-Xaa-His/Cys/Asp/Met-Xaa sequence. Among the side chain donor functions, the imidazole of histidyl and thiolate of cysteinyl residues are the most effective ligating groups and their involvement in metal binding results in a great variety of different macrochelate or loop structures and/or formation of various polynuclear complexes. Examples of these structural motifs and their possible applications have been thoroughly discussed.     

Factors affecting selectivity in ion chromatography

Methods for separation of ions by ion-exchange, ion-pair, and zwitterion ion chromatography share at least one common thread--the induced formation of a cation-anion pair in the stationary phase. Selectivity can be defined as the relative ability of sample ions to form such a pair. Examples are given in anion-exchange chromatography to show the effect of variations in the geometry, bulkiness and polarity of the resin cation on selectivity. The type of resin matrix, the hydrophobic nature of the resin surface and the degree of solvation also affect chromatographic behavior. The selectivity series observed in ion chromatography seems to be best explained by the interplay of two components: electrostatic attraction (ES) and the enforced-pairing (EP) that is brought about by hydrophobic attraction and by water-enforced ion pairing. Selectivity in ion-pair chromatography (IPC) and in zwitterion ion chromatography (ZIC) is affected by both the mobile phase cation and anion. This leads to elution orders for anions that are different from conventional ion-exchange chromatography (IC) of anions where cations are excluded from the stationary phase and have little effect on a separation. The elution order of anions in ZIC is similar to that in IC except for small anions of 2-charge, which are retained more weakly in ZIC. A unique advantage of ZIC is that sample ions can be eluted as ion pairs with pure water as the eluent and a conductivity detector. The mechanism for separation of anions on a zwitterionic stationary phase has been a subject for considerable debate. The available facts point strongly to a partitioning mechanism or a mixed mechanism in which partitioning is dominant with a weaker ion-exchange component.     

Solvated ensemble averaging in the calculation of partial atomic charges

In the calculation of partial atomic charges, for use in molecular mechanics or dynamics simulations, it is common practice to select only a single conformation for the molecule of interest. For molecules that contain rotatable bonds, it is preferable to compute the charges from several relevant conformations. We present here results from a charge derivation protocol that determines the partial charges by averaging charges computed for conformations selected from explicitly solvated MD simulations, performed under periodic boundary conditions. This approach leads to partial charges that are weighted by a realistic population of conformations and that are suitable for condensed phase simulations. This protocol can, in principle, be applied to any class of molecule and to nonaqueous solvation. Carbohydrates contain numerous hydroxyl groups that exist in an ensemble of orientations in solution, and in this report we apply ensemble averaging to a series of methyl glycosides. We report the extent to which ensemble averaging leads to charge convergence among the various monosaccharides and among the constituent atoms within a given monosaccharide. Due to the large number of conformations (200) in our ensembles, we are able to compute statistically relevant standard deviations for the partial charges. An analysis of the standard deviations allows us to assess the extent to which equivalent atom types may, nevertheless, require unique partial charges. The configurations of the hydroxyl groups exert considerable influence on internal energies, and the limits of ensemble averaged charges are discussed in terms of these properties.     

镧对心肌细胞钾通道的作用研究

用全细胞膜片钳记录方式研究了La^3^+对大鼠心室肌细胞钾通道的作用机理。对酶解分离的大鼠心室肌细胞施一跃迁电压可引出一非钙依赖性电压去激活的外向钾电流。将10μmol/LLa^3^+加入细胞外液后，非钙依赖性电压去激活的外向钾电流明显减小，这提示在大鼠心室肌细胞钾通道上存在La^3^+结合位点。     

Control of the selectivity in partial oxidation of hydrocarbons

A simple kinetic model for the partial oxidation of hydrocarbons on two types of sites was used to study the factors influencing the selectivity to the desired product. It is possible to increase the selectivity significantly by regulating the ratio of the surface concentrations of partial and deep oxidation sites by a periodic temperature treatment.     

Synthetic ion channels in bilayer membranes

Natural ion channels are large protein complexes that regulate key functions of cells. Supramolecular chemists have been able to take hints from Nature to design and prepare completely synthetic ion channel systems that reproduce many of the fundamental functions of natural channels. This tutorial review introduces the field to non-specialists. It examines the design, synthesis, incorporation, and characterization of synthetic ion channels in bilayer membranes, and points to potential applications of synthetic ion channels.     

Charge density identification in ion channels

Biological channels permeate ions through cell membranes. Ion channels carry a permanent charge that has a significant role in determining channel's permeation properties such as selectivity to certain ions, current amplitude, etc. In this paper we deal with the determination of the permanent charge from current-voltage curves. The ion channel current behavior is modelled by Poisson-Nernst-Planck (PNP) equations system. Previous works on the fixed charge density identification problem contain several ill-posed steps and linearization of the nonlinear PNP system. We suggest here several methods to make these algorithms more stable and accurate.     

Effect of temperature on retention and selectivity in ion chromatography of anions

The temperature dependence of retention of a wide range of inorganic anions is studied on two commercially available ion exchangers (Dionex AS11 and AS14 columns). Anion retention exhibited both exothermic and endothermic behavior, such that varying the temperature from ambient to 60°C produced selectivity changes. The anions displayed three groupings of temperature dependence: weakly retained singly charged anions (e.g., iodate, bromate, nitrite, bromide and nitrate); multiply charged anions (sulfate, oxalate, phosphate and thiosulfate); and strongly retained singly charged anions (iodide, thiocyanate and perchlorate). Temperature was ineffective at changing the selectivity of retention between anions of the same grouping. However, significant selectivity changes, including elution order reversal, could be achieved between anions from different groupings.     

Time-dependent ion selectivity in capacitive charging of porous electrodes

In a combined experimental and theoretical study, we show that capacitive charging of porous electrodes in multicomponent electrolytes may lead to the phenomenon of time-dependent ion selectivity of the electrical double layers (EDLs) in the electrodes. This effect is found in experiments on capacitive deionization of water containing NaCl/CaCl(2) mixtures, when the concentration of Na(+) ions in the water is five times the Ca(2+)-ion concentration. In this experiment, after applying a voltage difference between two porous carbon electrodes, first the majority monovalent Na(+) cations are preferentially adsorbed in the EDLs, and later, they are gradually replaced by the minority, divalent Ca(2+) cations. In a process where this ion adsorption step is followed by washing the electrode with freshwater under open-circuit conditions, and subsequent release of the ions while the cell is short-circuited, a product stream is obtained which is significantly enriched in divalent ions. Repeating this process three times by taking the product concentrations of one run as the feed concentrations for the next, a final increase in the Ca(2+)/Na(+)-ratio of a factor of 300 is achieved. The phenomenon of time-dependent ion selectivity of EDLs cannot be explained by linear response theory. Therefore, a nonlinear time-dependent analysis of capacitive charging is performed for both porous and flat electrodes. Both models attribute time-dependent ion selectivity to the interplay between the transport resistance for the ions in the aqueous solution outside the EDL, and the voltage-dependent ion adsorption capacity of the EDLs. Exact analytical expressions are presented for the excess ion adsorption in planar EDLs (Gouy-Chapman theory) for mixtures containing both monovalent and divalent cations.     

The effect of multi-component adsorption on selectivity in ion exchange displacement systems

This paper examines chemically selective displacement chromatography using affinity ranking plots, batch displacer screening experiments, column displacements, multi-component adsorption isotherms and spectroscopy. The affinity ranking plot indicated that the displacers, sucrose octasulfate (SOS) and tatrazine, should possess sufficient affinity to displace the proteins amyloglucosidase and apoferritin over a wide range of operating conditions. In addition, the plots indicated that the separation of these proteins by displacement chromatography would be extremely difficult. Further, the two proteins were shown to have very similar retention times under shallow linear gradient conditions. When batch displacement experiments were carried out, both tartrazine and SOS exhibited significant selectivity differences with respect to their ability to displace these two proteins, in contrast to the affinity ranking plot results. Column displacement experiments carried out with sucrose octasulfate agreed with the predictions of the affinity ranking plots, with both proteins being displaced but poorly resolved under several column displacement conditions. On the other hand, column displacement with tartrazine as the displacer resulted in the selective displacement and partial purification of apoferritin. Single- and multi-component isotherms of the proteins with or without the presence of displacers were determined and were used to help explain the selectivity reversals observed in the column and batch displacement experiments. In addition, fluorescence and CD spectra suggested that the displacers did not induce any structural changes to either of the proteins. The results in this paper indicate that multi-component adsorption behavior can be exploited for creating chemically selective displacement separations.