Interfacial interactions of glutamate, water and ions with carbon nanopore evaluated by molecular dynamics simulations

Molecular dynamics simulations were used to assess the transport of glutamate, water and ions (Na⁺ and Cl⁻) in a single wall carbon nanopore. The spatial profiles of Na⁺ and Cl⁻ ions are largely determined by the pore wall charges. Co-ions are repelled whereas the counter-ions are attracted by the pore charges, but this ‘rule’ breaks down when the water concentration is set to a level significantly below that in the physiological bulk solution. In such cases water is less able to counteract the ion-wall interactions (electrostatic or non-electrostatic), co-ions are layered near the counter-ions attracted by the wall charges and are thus layered as counter-ions. Glutamate is concentrated near the pore wall even at physiological water concentration, and irrespective of whether the pore wall is neutral or charged (positively or negatively), and its peak levels are up to 40 times above mean values. The glutamate is thus always layered as a counter-ion. Layering of water near the wall is independent of charges on the pore wall, but its peak levels near the wall are ‘only’ 6-8 times above the pore mean values. However, if the mean concentration of water is significantly below the level in the physiological bulk solution, its layering is enhanced, whereas its concentration in the pore center diminishes to very low levels. Reasons for such a ‘paradoxical’ behavior of molecules (glutamate and water) are that the non-electrostatic interactions are (except at very short distances) attractive, and electrostatic interactions (between the charged atoms of the glutamate or water and the pore wall) are also attractive overall. Repulsive interactions (between equally charged atoms) exist, and they order the molecules near the wall, whereas in the pore center the glutamate (and water) angles are largely randomly distributed, except in the presence of an external electric field. Diffusion of molecules and ions is complex. The translational diffusion is in general both inhomogeneous and anisotropic. Non-electrostatic interactions (ion-wall, glutamate-wall or water-wall) powerfully influence diffusion. In the neutral nanopore the effective axial diffusion constants of glutamate, water and Na⁺ and Cl⁻ ions are all < 10% of their values in the bulk, and the electrostatic interactions can reduce them further. Diffusion of molecules and ions is further reduced if the water concentration in the pore is low. Glutamate⁻ is slowed more than water, and ions are reduced the most especially co-ions. In conclusion the interfacial interactions influence the spatial distribution of glutamate, water and ions, and regulate powerfully, in a complex manner and over a very wide range their transport through nanosize pores.     

Ion behavior in the selectivity filter of HCN1 channels

Hyperpolarization-activated cyclic-nucleotide gated channels (HCNs) are responsible for the generation of pacemaker currents (I_f or I_h) in cardiac and neuronal cells. Despite the overall structural similarity to voltage-gated potassium (Kv) channels, HCNs show much lower selectivity for K⁺ over Na⁺ ions. This increased permeability to Na⁺ is critical to their role in membrane depolarization. HCNs can also select between Na⁺ and Li⁺ ions. Here, we investigate the unique ion selectivity properties of HCNs using molecular-dynamics simulations. Our simulations suggest that the HCN1 pore is flexible and dilated compared with Kv channels with only one stable ion binding site within the selectivity filter. We also observe that ion coordination and hydration differ within the HCN1 selectivity filter compared with those in Kv and cyclic-nucleotide gated channels. Additionally, the C358T mutation further stabilizes the symmetry of the binding site and provides a more fit space for ion coordination, particularly for Li⁺.     

Non-Equilibrium Dynamics Contribute to Ion Selectivity in the KcsA Channel

The ability of biological ion channels to conduct selected ions across cell membranes is critical for the survival of both animal and bacterial cells. Numerous investigations of ion selectivity have been conducted over more than 50 years, yet the mechanisms whereby the channels select certain ions and reject others are not well understood. Here we report a new application of Jarzynski’s Equality to investigate the mechanism of ion selectivity using non-equilibrium molecular dynamics simulations of Na⁺ and K⁺ ions moving through the KcsA channel. The simulations show that the selectivity filter of KcsA adapts and responds to the presence of the ions with structural rearrangements that are different for Na⁺ and K⁺. These structural rearrangements facilitate entry of K⁺ ions into the selectivity filter and permeation through the channel, and rejection of Na⁺ ions. A mechanistic model of ion selectivity by this channel based on the results of the simulations relates the structural rearrangement of the selectivity filter to the differential dehydration of ions and multiple-ion occupancy and describes a mechanism to efficiently select and conduct K⁺. Estimates of the K⁺/Na⁺ selectivity ratio and steady state ion conductance for KcsA from the simulations are in good quantitative agreement with experimental measurements. This model also accurately describes experimental observations of channel block by cytoplasmic Na⁺ ions, the “punch through” relief of channel block by cytoplasmic positive voltages, and is consistent with the knock-on mechanism of ion permeation.     

[14C]Carbon-dioxide fixation by isolated leaf epidermes with stomata closed or open

Following small hypo-osmotic shocks, ion concentrations (Na⁺, K⁺, Cl^-) in Platymonas subcordiformis decreased; this was due mainly to an increase of cell volume. With larger hypo-osmotic stresses, the decrease of ion concentration continued and, additionally, extrusion of mannitol was observed. The ion and mannitol concentrations were not regained after 240 min. In contrast, following hyperosmotic shocks, the ion concentrations increased transitorily during the first 20–40 min. The same was true for K⁺ following small hyperosmotic stresses and for Na⁺ and — partially — Cl^- with larger shocks. Large hyperosmotic stresses caused permanent accumulation of mannitol, which levelled off after 60–80 min. Thus the transient increase of ions bridged the concentration gap until mannitol was accumulated to a high enough concentration to account for the osmotic adaptation of Platymonas, together with a basal level of the ions K⁺, Na⁺, Cl^-.Abbreviations PS photosynthesis - Resp respiration     

Stage-Specific Changes in the Water,Na+, Cl- and K+ Contents of Organelles during Apoptosis,Demonstrated by a Targeted Cryo Correlative Analytical Approach

Many studies have demonstrated changes in the levels of several ions during apoptosis, but a few recent studies have reported conflicting results concerning the changes in water content in apoptotic cells. We used a correlative light and cryo-scanning transmission electron microscopy method to quantify water and ion/element contents simultaneously at a nanoscale resolution in the various compartments of cells, from the onset to the end of apoptosis. We used stably transfected HeLa cells producing H2B-GFP to identify the stages of apoptosis in cells and for a targeted elemental analysis within condensed chromatin, nucleoplasm, mitochondria and the cytosol. We found that the compartments of apoptotic cells contained, on average, 10% more water than control cells. During mitochondrial outer membrane permeabilization, we observed a strong increase in the Na⁺ and Cl^- contents of the mitochondria and a strong decrease in mitochondrial K⁺ content. During the first step in apoptotic volume decrease (AVD), Na⁺ and Cl^- levels decreased in all cell compartments, but remained higher than those in control cells. Conversely, during the second step of AVD, Na⁺ and Cl^- levels increased considerably in the nucleus and mitochondria. During these two steps of AVD, K⁺ content decreased steadily in all cell compartments. We also determined in vivo ion status during caspase-3 activity and chromatin condensation. Finally, we found that actinomycin D-tolerant cells had water and K⁺ contents similar to those of cells entering apoptosis but lower Na⁺ and Cl^- contents than both cells entering apoptosis and control cells.     

Molecular dynamics of water and monovalent‐ions transportation mechanisms of pentameric sarcolipin

The Sarcolipin (SLN) is a transmembrane protein that can form a self‐assembled pentamer. In this work, the homology modeling and all‐atom molecular dynamic (MD) simulation was performed to study the model of SLN pentamer in POPC (1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphocholine) membrane. The potential of mean force (PMF) was calculated for transmembrane transportation of Na⁺, Cl^? and water molecule along the pore channel of penta‐SLN complex. The root mean square deviation (RMSD) of the SLN pentamer in POPC membrane showed that the stabilized SLN protein complex could exist in the membrane and that the Na⁺ and Cl^? could not permeate through the channel when the pore was under the vacuum state, but the water could permeate through from cytoplasm to lumen. Under the aqueous state, our simulation demonstrated that hydrated state of Na⁺ and Cl^? could pass through the channel. The PMF and radii of the pore showed that the channel had a gate at Leu²¹ that is a key hydrophobicity residue in the channel. Our simulations help to clarify and to understand better the SLN pentamer channel that had a hydrophobic gate and could switch Na⁺ and Cl^? ion permeability by hydrated and vacuum states. Proteins 2016; 84:73–81. © 2015 Wiley Periodicals, Inc.     

Hydration valve controlled non-selective conduction of Na and K in the NaK channel

The Na⁺ and K⁺ channels are essential to neural signaling, but our current knowledge at the atomic level is mainly limited to the conducting mechanism of K⁺. Unlike a K⁺ channel having four equivalent K⁺-binding sites in its selectivity filter, a NaK channel has a vestibule in the middle part of its selectivity filter, and can conduct both Na⁺ and K⁺ ions. However, the underlying mechanism for non-selective ion conduction in NaK remains elusive. Here we find four small grottos connecting with the vestibule of the NaK selectivity filter, which form a vestibule-grotto complex perpendicular to the filter pore with a few water molecules within it. It is shown that two or more of the water molecules coming to the vestibule to coordinate the cation are necessary for conducting both Na⁺ and K⁺ ions, while only one water molecule in the vestibule will obstruct ion permeation. Thus, the complex with the aid of interior water movement forms a dynamic hydration valve which is flexible in conveying different cations through the vestibule. Similar exquisite hydration valve mechanisms are expected to be utilized by other non-selective cation channels, and the results should shed new light on the importance of water in neural signaling.     

Quantitative ion localization within Suaeda maritima leaf mesophyll cells

Grown under saline conditions, Suaeda maritima accumulates Na⁺ and Cl^- into its leaves, where individual mesophyll cells behave differently in their compartmentation of these ions. Measurements of ion concentrations within selected subcellular compartments show that freeze-substitution with dry sectioning is a valuable preparative technique for analytical electron microscopy of highly vacuolate plant material. Using this approach, absolute estimates were made of Na⁺, K⁺ and Cl^- concentrations in the cytoplasm, cell walls, chloroplasts and vacuoles of leaf mesophyll cells.Abbreviation TAEM transmission analytical electron microscopy     

The Nature of the In Vivo Sodium and Chloride Uptake Mechanisms through the Epithelium of the Chilean Frog Calyptocephalella gayi (Dum. et Bibr., 1841) : Exchanges of hydrogen against sodium and of bicarbonate against chloride

The Chilean frog, Calyptocephallela gayi, placed in dilute NaCl solutions may pump Na⁺ and Cl^- at very different rates depending on the kind of bath solutions in which it was preadapted. Furthermore, Na⁺ and Cl^- may be absorbed from solutions in which the accompanying coion, such as sulfate and choline, respectively, is impermeant. In all these cases it is obligatory to postulate the existence of two ionic exchange mechanisms, Cl^- and Na⁺, being exchanged against endogenous anions and cations, respectively. It has been determined that Na⁺ is exchanged against endogenous H⁺ and that Cl^- is exchanged against HCO₃^-. In animals pumping Na⁺ and Cl^- from dilute NaCl solutions Na⁺ or Cl^- uptake may be selectively inhibited, while the flux of the accompanying ion remains unchanged. This is considered to be an additional proof that both Na⁺ and Cl^- fluxes are always independent. The role of the ionic exchange mechanisms in the direct regulation of the Na⁺ and Cl^- levels in the internal medium is discussed as well as their relationship in the regulation of the acid-base equilibrium; other physioecological considerations have been treated.     

Effects of Inhibitors of Protein and Nucleic Acid Synthesis on the Development of Ion Uptake Mechanisms in Beetroot Slices (Beta vulgaris)

Mechanisms for the uptake of K⁺, Na⁺ and Cl^- develop sequentially in thin slices of beetroot tissue washed under aerobic conditions. Actinomycin D inhibited or prevented the development of K⁺, Na⁺ and Cl^- uptake mechanisms when added to freshly cut slices, but had no effect on net ion uptake when added after the development of the ion uptake mechanisms. The use of puromycin as a specific inhibitor of protein synthesis was unsatisfactory as it caused leakage of pigments and excessive loss of ions from the disks. Cycloheximide prevented the development of ion uptake mechanisms when added at the start of the experiment, but when added after the development of ion uptake mechanisms its inhibitory effect did not become apparent until after a certain time interval which varied from 3 hours for Cl^- to 25 hours for K⁺ uptake in the same experiment. p-Fluorophenylalanine caused an appreciable shortening of the time required for the development of Na⁺ and K⁺ uptake capabilities, while it completely prevented the development of a Cl^- uptake mechanism. p-Fluorophenylalanine-induced early uptake of Na⁺ and K⁺, however, was followed by periods of net leakage of these ions. It is suggested that the development of ion uptake mechanisms depends on the production of m-RNA, which appears to be relatively stable after its synthesis. The synthesis and decay characteristics of specific proteins required for the ion uptake mechanisms appear to differ for each ion species.     

Selectivity and permeation of alkali metal ions in K+-channels

Ion conduction in K⁺-channels is usually described in terms of concerted movements of K⁺ progressing in a single file through a narrow pore. Permeation is driven by an incoming ion knocking on those ions already inside the protein. A fine-tuned balance between high-affinity binding and electrostatic repulsive forces between permeant ions is needed to achieve efficient conduction. While K⁺-channels are known to be highly selective for K⁺ over Na⁺, some K⁺ channels conduct Na⁺ in the absence of K⁺. Other ions are known to permeate K⁺-channels with a more moderate preference and unusual conduction features. We describe an extensive computational study on ion conduction in K⁺-channels rendering free energy profiles for the translocation of three different alkali ions and some of their mixtures. The free energy maps for Rb⁺ translocation show at atomic level why experimental Rb⁺ conductance is slightly lower than that of K⁺. In contrast to K⁺ or Rb⁺, external Na⁺ block K⁺ currents, and the sites where Na⁺ transport is hindered are characterized. Translocation of K⁺/Na⁺ mixtures is energetically unfavorable owing to the absence of equally spaced ion-binding sites for Na⁺, excluding Na⁺ from a channel already loaded with K⁺.     

The Split Personality of Glutamate Transporters: A Chloride Channel and a Transporter

Transporters and ion channels are conventionally categorised into distinct classes of membrane proteins. However, some membrane proteins have a split personality and can function as both transporters and ion channels. The excitatory amino acid transporters (EAATs) in particular, function as both glutamate transporters and chloride (Cl^?) channels. The EAATs couple the transport of glutamate to the co-transport of three Na⁺ ions and one H⁺ ion into the cell, and the counter-transport of one K⁺ ion out of the cell. The EAAT Cl^? channel is activated by the binding of glutamate and Na⁺, but is thermodynamically uncoupled from glutamate transport and involves molecular determinants distinct from those responsible for glutamate transport. Several crystal structures of an EAAT archaeal homologue, Glt_Ph, at different stages of the transport cycle, alongside numerous functional studies and molecular dynamics simulations, have provided extensive insights into the mechanism of substrate transport via these transporters. However, the molecular determinants involved in Cl^? permeation, and the mechanism by which this channel is activated are not entirely understood. Here we will discuss what is currently known about the molecular determinants involved in EAAT-mediated Cl^? permeation and the mechanisms that underlie their split personality.     

Molecular Dynamics Simulation Studies of the Limiting Conductances of CaCl2 using Extended Simple Point Charge and Revised Polarizable Models

We have carried out molecular dynamics (MD) simulations of the limiting conductances of CaCl₂ in ambient and supercritical states as a function of water density using extended simple point charge (SPC/E) and revised polarizable (RPOL) models for ions and water molecules. Both models predict the limiting conductances of CaCl₂ in supercritical water that are a linear dependence on water density. The effect of the electronic polarization on the limiting conductances is too small to cause a deduction in the lower water density of 0.6?～?0.7?g/cc in this study. The most significant effect of the electronic polarization is appeared in a decrease in the ion–water potential energy and, as a result, an increase in the limiting conductances for both ions. Different charge distributions of water molecules in the first hydration shell around the ions lead the opposite behavior of the induced dipole moment with water density for a positive and a negative ion in supercritical water; the induced dipole moment of Ca²⁺ decreases with increasing water density but for Cl^-, the opposite is observed. The same kind of opposite behavior due to the structure of water molecules around the ions is also found in hydrogen-bond correlations of water around the ions and of bulk water; hydrogen bonding around Ca²⁺ persists longer than in bulk water whereas the opposite is observed for Cl^-.     

Specific Binding of Chloride Ions to Lipid Vesicles and Implications at?Molecular Scale

Biological membranes composed of lipids and proteins are in contact with electrolytes like aqueous NaCl solutions. Based on molecular dynamics studies it is widely believed that Na⁺ ions specifically bind to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes, whereas Cl⁻ ions stay in solution. Here, we present a careful comparison of recent data from electrophoresis and isothermal titration calorimetry experiments as well as molecular dynamics simulations suggesting that in fact both ions show very similar affinities. The corresponding binding constants are 0.44(±0.05) M⁻¹ for Na⁺ and 0.40(±0.04) M⁻¹ for Cl⁻ ions. This is highlighted by our observation that a widely used simulation setup showing asymmetric affinities of Na⁺ and Cl⁻ for POPC bilayers overestimates the effect of NaCl on the electrophoretic mobility of a POPC membrane by an order of magnitude. Implications for previous simulation results on the effect of NaCl on polarization of interfacial water, transmembrane potentials, and mechanisms for ion transport through bilayers are discussed. Our findings suggest that a range of published simulations results on the interaction of NaCl with phosphocholine bilayers have to be reconsidered and revised and that force field refinements are necessary for reliable simulation studies of membranes at physiological conditions on a molecular level.     

Characterization of esophageal desalination in the seawater eel,Anguilla japonica

To characterize mechanisms of esophageal desalination, osmotic water permeability and ion fluxes were measured in the isolated esophagus of the seawater eel. The osmotic permeability coefficient in the seawater eel esophagus was 2·10^-4 cm·s^-1. This value was much lower than those in tight epithelial, although the eel esophagus is a leaky epithelium with a tissue resistance of 77 ohm·cm^-2. When the esophagus was bathed in normal Ringer solutions on both sides no net ion and water fluxes were observed. However, when mucosal NaCl concentration was increased by a factor of 3, Na⁺ und Cl^- ions were transferred from mucosa to serosa (desalination). If only Na⁺ or Cl^- concentration in the mucosal fluid was increased by a factor of 3, net Na⁺ and Cl^- fluxes were reduced to 30–40%, indicating that 60–70% of the net Na⁺ and Cl^- fluxes are coupled mutually. The coupled NaCl transport seems to be effective in desalting the luminal high NaCl. The remaining 30–40% of the total Na⁺ and Cl^- fluxes seems to be due to a simple diffusion, because these components are independent of each other and follow their electrochemical gradients, and also because these fluxes remain even after treatment with NaCN or ouabain. A half of the coupled NaCl transport could be explained by a Na⁺/H⁺–Cl^-/HCO ₃ ^- double exchanger on the apical membrane of the esophageal epithelium, because mucosal amiloride and 4.4-diisothiocyanatostilbene-2,2-disulphonic acid inhibited the net Na⁺ and Cl^- fluxes by approximately 30%. The other half of the coupled NaCl transport, which follows their electrochemical gradients, still remains to be explained.Abbreviations DIDS 4,4-diisothiocyanatostilbene-2,2-disulphonic acid - NMDG N-methyl-d-glucosamine - P _Cl Cl^- permeability coefficient - PD transepithelial potential difference - P _Na Na⁺ permeability coefficient - P _osm osinotic permeability coefficient - TALH thick ascending limb of Henle's loop     

Effects of salinity on uptake and distribution of Na+, Cl- and K+ in two wheat cultivars

Plants of two wheat (Triticum aestivum L.) cultivars differing in salt tolerance were grown in sand with nutrient solutions. 35-d-old plants were subjected to 5 levels of salinity created by adding NaCl, CaCl₂ and Na₂SO₄. Growth reduction caused by salinity was accompanied by increased Na⁺ and Cl^- concentrations, Na⁺/K⁺ ratio, and decreased concentration of K⁺. The salt tolerant cv. Kharchia 65 showed better ionic regulation. Salinity up to 15.7 dS m^-1 induced increased uptake of Na⁺ and Cl^- but higher levels of salinity were not accompanied by further increase in uptake of these ions. Observed increases in Na⁺ and Cl^- concentrations at higher salinities seemed to be the consequence of reduction in growth. Uptake of K⁺ was decreased; more in salt sensitive cultivar. This was also accompanied by differences in its distribution.     

Na+ Inhibits the Epithelial Na+ Channel by Binding to a Site in an Extracellular Acidic Cleft

The epithelial Na⁺ channel (ENaC) has a key role in the regulation of extracellular fluid volume and blood pressure. ENaC belongs to a family of ion channels that sense the external environment. These channels have large extracellular regions that are thought to interact with environmental cues, such as Na⁺, Cl⁻, protons, proteases, and shear stress, which modulate gating behavior. We sought to determine the molecular mechanism by which ENaC senses high external Na⁺ concentrations, resulting in an inhibition of channel activity. Both our structural model of an ENaC α subunit and the resolved structure of an acid-sensing ion channel (ASIC1) have conserved acidic pockets in the periphery of the extracellular region of the channel. We hypothesized that these acidic pockets host inhibitory allosteric Na⁺ binding sites. Through site-directed mutagenesis targeting the acidic pocket, we modified the inhibitory response to external Na⁺. Mutations at selected sites altered the cation inhibitory preference to favor Li⁺ or K⁺ rather than Na⁺. Channel activity was reduced in response to restraining movement within this region by cross-linking structures across the acidic pocket. Our results suggest that residues within the acidic pocket form an allosteric effector binding site for Na⁺. Our study supports the hypothesis that an acidic cleft is a key ligand binding locus for ENaC and perhaps other members of the ENaC/degenerin family.     

Studies of the chloride transport in the gastric mucosa of the frog

The unidirectional fluxes of Cl^- and Na⁺ across the frog gastric mucosa in vitro were investigated with radioactive isotopes, and related to the secretory and electrical properties of the normal, and metabolically inhibited, mucosa. The flux of Cl^- from nutrient to secretory surface of the mucosa was observed to rise sharply with increasing acid secretion, while the corresponding flux of Na⁺ did not change appreciably. Lowering [NaCl] in the secretory solution caused a proportional drop in the fluxes from secretory to nutrient surface, of both Cl^- and Na⁺. Under the same conditions, the flux of Cl^- from nutrient to secretory surface fell by nearly the same amount as did the flux of Cl^- in the opposite direction, while the flux of Na⁺ from nutrient to secretory surface remained essentially unchanged. Electrical and hydrodynamic causes for this observation could be excluded. Metabolic inhibitors, including cyanide, azide, DNP, and anaerobiosis depressed Cl^- flux in both directions distinctly below the corresponding values observed with the normal, non-secreting mucosa. At the same time, a decrease in electrical potential difference and conductance was observed under inhibition. The flux of Na⁺ was little changed by metabolic inhibition. The relationship between fluxes and conductance of Cl^- during metabolic inhibition differs markedly from that observed under normal conditions, and is consistent with the view that during metabolic inhibition most of the Cl^- moving across the mucosa does so as a free ion. From the above data it is concluded that Cl^- is normally transported across the mucosa in combination with a carrier, the supply of which is impaired under metabolic inhibition. According to the behavior of the Na⁺ flux, the passive permeability of the mucosa appeared to be little affected by the metabolic inhibition applied, but seemed to rise considerably after death of the mucosa, probably due to structural damage.     

Mechanisms of Salinity Control in Sea Bass

Sea bass can regulate the concentration of Na⁺, K⁺, and Cl^-, among other ions, in their blood, skin, gills, and kidney. Therefore, the salinity of the water does not have a great influence on their metabolism, and sea bass can live in both sea and freshwater in accordance with the salt concentration. Most salinity control occurs in the gills, primarily through the control of chloride cells present there. The concentration of ions in the blood is controlled by the cotransporter Na⁺ / K⁺ / 2Cl^- (NKCC) in the chloride cell, and the subunits of Na⁺ / K⁺ ATPase (NKA) function to maintain homeostasis. The expression of NKA is regulated by subunits of the protein FXYD, allowing the sea bass to survive in compliance with the salinity. In this way, it is possible for sea bass to live in sea and freshwater by controlling the salinity of its body using functions of various channels, proteins, and genes present in the chloride cells of sea bass. In this study, we investigated recent studies of salt control mechanisms in sea bass and their application.     

Ion Selectivity of the KcsA Channel: A Perspective from Multi-Ion Free Energy Landscapes

Potassium (K⁺) channels are specialized membrane proteins that are able to facilitate and regulate the conduction of K⁺ through cell membranes. Comprising five specific cation binding sites (S₀-S₄) formed by the backbone carbonyl groups of conserved residues common to all K⁺ channels, the narrow selectivity filter allows fast conduction of K⁺ while being highly selective for K⁺ over Na⁺. To extend our knowledge of the microscopic mechanism underlying selectivity in K⁺ channels, we characterize the free energy landscapes governing the entry and translocation of a Na⁺ or a K⁺ from the extracellular side into the selectivity filter of KcsA. The entry process of an extracellular ion is examined in the presence of two additional K⁺ in the pore, and the three-ion potential of mean force is computed using extensive all-atom umbrella sampling molecular dynamics simulations. A comparison of the potentials of mean force yields a number of important results. First, the free energy minima corresponding to configurations with extracellular K⁺ or Na⁺ in binding site S₀ or S₁ are similar in depth, suggesting that the thermodynamic selectivity governed by the free energy minima for those two binding sites is insignificant. Second, the free energy barriers between stable multi-ion configurations are generally higher for Na⁺ than for K⁺, implying that the kinetics of ion conduction is slower when a Na⁺ enters the pore. Third, the region corresponding to binding site S₂ near the center of the narrow pore emerges as the most selective for K⁺ over Na⁺. In particular, while there is a stable minimum for K⁺ in site S₂, Na⁺ faces a steep free energy increase with no local free energy well in this region. Lastly, analysis shows that selectivity is not correlated with the overall coordination number of the ion entering the pore, but is predominantly affected by changes in the type of coordinating ligands (carbonyls versus water molecules). These results further highlight the importance of the central region near binding site S₂ in the selectivity filter of K⁺ channels.