Structural and functional consequences of an amide-to-ester substitution in the selectivity filter of a potassium channel

The selectivity filter of K(+) channels comprises four contiguous ion binding sites, S1 through S4. Structural and functional data indicate that the filter contains on average two K(+) ions at any given time and that these ions reside primarily in two configurations, namely to sites S1 and S3 or to sites S2 and S4. Maximum ion flux through the channel is expected to occur when the energy difference between these two binding configurations is zero. In this study, we have used protein semisynthesis to selectively perturb site 1 within the filter of the KcsA channel through use of an amide-to-ester substitution. The modification alters K(+) conduction properties. The structure of the selectivity filter is largely unperturbed by the modification, despite the loss of an ordered water molecule normally located just behind the filter. Introduction of the ester moiety was found to alter the distribution of K(+), Rb(+,) and Cs(+) within the filter, with the most dramatic change found for Rb(+). The redistribution of ions is associated with the appearance of a partially hydrated ion just external to the filter, at a position where no ion is observed in the wild-type channel. The appearance of this new ion-binding site creates a change in the distance between a pair of K(+) ions some fraction of the time, apparently leading to a reduction in the ion conduction rate. Importantly, this finding suggests that the selectivity filter of a potassium channel is optimized both in terms of absolute ion occupancy and in terms of the separation in distance between the conducting ions.     

Kinetic modeling of ion conduction in KcsA potassium channel

KcsA constitutes a potassium channel of known structure that shows both high conduction rates and selectivity among monovalent cations. A kinetic model for ion conduction through this channel that assumes rapid ion transport within the filter has recently been presented by Nelson. In a recent, brief communication, we used the model to provide preliminary explanations to the experimental current-voltage J-V and conductance-concentration g-S curves obtained for a series of monovalent ions (K(+),Tl(+), and Rb(+)). We did not assume rapid ion transport in the calculations, since ion transport within the selectivity filter could be rate limiting for ions other than native K(+). This previous work is now significantly extended to the following experimental problems. First, the outward rectification of the J-V curves in K(+) symmetrical solutions is analyzed using a generalized kinetic model. Second, the J-V and g-S curves for NH(4) (+) are obtained and compared with those of other ions (the NH(4) (+) J-V curve is qualitatively different from those of Rb(+) and Tl(+)). Third, the effects of Na(+) block on K(+) and Rb(+) currents through single KcsA channels are studied and the different blocking behavior is related to the values of the translocation rate constants characteristic of ion transport within the filter. Finally, the significantly decreased K(+) conductance caused by mutation of the wild-type channel is also explained in terms of this rate constant. In order to keep the number of model parameters to a minimum, we do not allow the electrical distance (an empirical parameter of kinetic models that controls the exponential voltage dependence of the dissociation rate) to vary with the ionic species. Without introducing the relatively high number of adjustable parameters of more comprehensive site-based models, we show that ion association to the filter is rate controlling at low concentrations, but ion dissociation from the filter and ion transport within the filter could limit conduction at high concentration. Although some experimental data from other authors were included to allow qualitative comparison with model calculations, the absolute values of the effective rate constants obtained are only tentative. However, the relative changes in these constants needed to explain qualitatively the experiments should be of significance.     

Incidence of partial charges on ion selectivity in potassium channels

Potassium channels are membrane proteins known to select potassium over sodium ions at a high diffusion rate. We conducted ab initio calculations on a filter model of KcsA of about 300 atoms at the Hartree-Fock level of theory. Partial charges were derived from the quantum mechanically determined electrostatic potential either with Merz-Kollman or Hinsen-Roux schemes. Large polarization and/or charge transfer occur on potassium ions located in the filter, while the charges on sodium ions remain closer to unity. As a result, a weaker binding is obtained for K(+) ions. Using a simplified version of a permeation model based on the concerted-motion mechanism for ion translocation within the single-file ion channel [P. H. Nelson, J. Chem. Phys. 117, 11396 (2002)], we discuss how differences in polarization effects in the adducts with K(+) and Na(+) can play a role as for ionic selectivity and conductance.     

Supra-physiological membrane potential induced conformational changes in K+ channel conducting system of skeletal muscle fibers

The effects of a supra-physiological membrane potential shock on the conducting system of the delayed rectifier K(+) channels in the skeletal muscle fibers of frogs were studied. An improved double Vaseline gap voltage clamp technique was used to deliver stimulation pulses and to measure changes in the channel currents. Our results showed that a single 4 ms, -400 mV pulsed shock can cause a reduction in the K(+) channel conductance and a negative-shift of the channel open-threshold. Following the Boltzmann theory of channel voltage-dependence, we analyzed the shock-induced changes in the channel open-probability by employing both two-state and multi-state models. The results indicate a reduction in the number of channel gating particles after the electric shock, which imply possible conformational changes at domains that gate the channels proteins. This study provides further evidence supporting our hypothesis that high intensity electric fields can cause conformational changes in membrane proteins, most likely in the channel gating system. These structural changes in membrane proteins, and therefore their dysfunctions, may be involved in the mechanisms underlying electrical injury.     

(De)constructing the ryanodine receptor: modeling ion permeation and selectivity of the calcium release channel

Biological ion channels are proteins that passively conduct ions across membranes that are otherwise impermeable to ions. Here, we present a model of ion permeation and selectivity through a single, open ryanodine receptor (RyR) ion channel. Combining recent mutation data with electrodiffusion of finite-sized ions, the model reproduces the current/voltage curves of cardiac RyR (RyR2) in KCl, LiCl, NaCl, RbCl, CsCl, CaCl(2), MgCl(2), and their mixtures over large concentrations and applied voltage ranges. It also reproduces the reduced K(+) conductances and Ca(2+) selectivity of two skeletal muscle RyR (RyR1) mutants (D4899N and E4900Q). The model suggests that the selectivity filter of RyR contains the negatively charged residue D4899 that dominates the permeation and selectivity properties and gives RyR a DDDD locus similar to the EEEE locus of the L-type calcium channel. In contrast to previously applied barrier models, the current model describes RyR as a multi-ion channel with approximately three monovalent cations in the selectivity filter at all times. Reasons for the contradicting occupancy predictions are discussed. In addition, the model predicted an anomalous mole fraction effect for Na(+)/Cs(+) mixtures, which was later verified by experiment. Combining these results, the binding selectivity of RyR appears to be driven by the same charge/space competition mechanism of other highly charged channels.     

Density functional theory investigations on the chemical basis of the selectivity filter in the K+ channel protein

The chemical-physical basis of loading and release of K(+) and Na(+) ions in and out of the selectivity filter of the K(+) channel has been investigated using the B3LYP method of density functional theory. We have shown that the difference between binding free energies of K(+) and Na(+) to the cavity end of the filter is smaller than the difference between the K(+) and Na(+) solvation free energies. Thus, the loading of K(+) ions into the cavity end of the selectivity filter from the solution phase is suggested to be selective prior to the subsequent conduction process. It is shown that the extracellular end of the filter is only optimal for K(+) ions, because K(+) ions prefer the coordination environment of eight carbonyl oxygens. Na(+) ions do not fit into the extracellular end of the filter, since they prefer the coordination environment of six carbonyl oxygens. Overall, the results suggest that the rigid C(4) symmetric selectivity filter is specifically designed for conduction of K(+) ions.     

Artificial ion channel formed by cucurbit[n]uril derivatives with a carbonyl group fringed portal reminiscent of the selectivity filter of K+ channels

Novel artificial ion channels (1 and 2) based on CB[n] (n = 6 and 5, respectively) synthetic receptors with carbonyl-fringed portals (diameter 3.9 and 2.4 A, respectively) can transport proton and alkali metal ions across a lipid membrane with ion selectivity. Fluorometric experiments using large unilamellar vesicles showed that 1 mediates proton transport across the membranes, which can be blocked by a neurotransmitter, acetylcholine, reminiscent of the blocking of the K+ channels by polyamines. The alkali metal ion transport activity of 1 follows the order of Li+ > Cs+ approximately Rb+ > K+ > Na+, which is opposite to the binding affinity of CB[6] toward alkali metal ions. On the other hand, the transport activity of 2 follows the order of Li+ > Na+, which is also opposite to the binding affinity of 2 toward these metal ions, but virtually no transport was observed for K+, Rb+, and Cs+. It is presumably because the carbonyl-fringed portal size of 2 (diameter 2.4 A) is smaller than the diameters of these alkali metal ions. To determine the transport mechanism, voltage-clamp experiments on planar bilayer lipid membranes were carried out. The experiments showed that a single-channel current of 1 for Cs+ transport is approximately 5 pA, which corresponds to an ion flux of approximately 3 x 107 ions/s. These results are consistent with an ion channel mechanism. Not only the structural resemblance to the selectivity filter of K+ channels but also the remarkable ion selectivity makes this model system unique.     

ISFETs with sputtered sodium alumino-silicate glass membranes

Sodium ion sensitive field-effect transistors (ISFETs) based on reactively sputtered sodium aluminosilicate (NAS) glass membranes are investigated. Using an inverted cylindrical magnetron, NAS films with defined and reproducible composition are obtained. Radiation damage in the gate dielectric is largely eliminated by annealing at 450 degrees C. The Na(+) sensitivity, the selectivity with respect to H(+) and K(+) ions, the response time, the conditioning period, the long-term drift, and the lifetime are evaluated. The ISFETs exhibit a near-Nernstian Na(+) response down to 10(-4) mol/l in solutions of pH>/=7. The NAS films are physically very robust and have excellent chemical durability, e.g., a sensor with a 110 nm thick membrane lasts for about 8 months. The overall sensor properties compare well with those of a commercial Na(+) selective glass electrode.     

Is the mobility of the pore walls and water molecules in the selectivity filter of KcsA channel functionally important?

We performed in-depth analysis of the forces which act on the K(+) ions in the selectivity filter of the KcsA channel in order to estimate the relative importance of static and dynamic influence of the filter wall and water molecules on ion permeation and selectivity. The forces were computed using the trajectories of all-atom molecular dynamics simulations. It is shown that the dynamics of the selectivity filter contributes about 3% to the net force acting on the ions and can be neglected in the studies focused on the macroscopic properties of the channel, such as the current. Among the filter atoms, only the pore-forming carbonyl groups can be considered as dynamic in the studies of microscopic events of conduction, while the dynamic effects from all other atoms are negligible. We also show that the dynamics of the water molecules in the filter can not be neglected. The fluctuating forces from the water molecules can be as strong as net forces from the pore walls and can effectively drive the ions through the local energy barriers in the filter.     

Cesium-ion selective electrodes based on calix[4]arene dibenzocrown ethers

Four calix[4]arene dibenzocrown ether compounds have been prepared and evaluated as Cs(+)-selective ligands in solvent polymeric membrane electrodes. The ionophores include 25,27-bis(1-propyloxy)calix[4]arene dibenzocrown-6 1, 25,27-bis(1-alkyloxy)calix[4]arene dibenzocrown-7s 2 and 3, and 25,27-bis(1-propyloxy)calix[4]arene dibenzocrown-8 4. For an ion-selective electrode (ISE) based on 1, the linear response concentration range is 1x10(-1) to 1x10(-6) M of Cs(+). Potentiometric selectivities of ISEs based on 1-4 for Cs(+) over other alkali metal cations, alkaline earth metal cations, and NH(4)(+) have been assessed. For 1-ISE, a remarkably high Cs(+)/Na(+) selectivity was observed, the selectivity coefficient (K(Cs,Na)(Pot)) being ca. 10(-5). As the size of crown ether ring is enlarged from crown-6 (1) to crown-7 (2 and 3) to crown-8 (4), the Cs(+) selectivity over other alkali metal cations, such as Na(+) and K(+), is reduced successively. Effects of membrane composition and pH in the aqueous solution upon the electrode properties are also discussed.     

Investigating the potassium interactions with the palytoxin induced channels in Na+/K+ pump

K(+) has been appointed as the main physiological inhibitor of the palytoxin (PTX) effect on the Na(+)/K(+) pump. This toxin acts opening monovalent cationic channels through the Na(+)/K(+) pump. We investigate, by means of computational modeling, the kinetic mechanisms related with K(+) interacting with the complex PTX-Na(+)/K(+) pump. First, a reaction model, with structure similar to Albers-Post model, describing the functional cycle of the pump, was proposed for describing K(+) interference on the complex PTX-Na(+)/K(+) pump in the presence of intracellular ATP. A mathematic model was derived from the reaction model and it was possible to solve numerically the associated differential equations and to simulate experimental maneuvers about the PTX induced currents in the presence of K(+) in the intra- and extracellular space as well as ATP in the intracellular. After the model adjusting to the experimental data, a Monte Carlo method for sensitivity analysis was used to analyze how each reaction parameter acts during each experimental maneuver involving PTX. For ATP and K(+) concentrations conditions, the simulations suggest that the enzyme substate with ATP bound to its high-affinity sites is the main substate for the PTX binding. The activation rate of the induced current is limited by the K(+) deocclusion from the PTX-Na(+)/K(+) pump complex. The K(+) occlusion in the PTX induced channels in the enzymes with ATP bound to its low-affinity sites is the main mechanism responsible for the reduction of the enzyme affinity to PTX.     

Xanthene dyes induce membrane permeabilization of bacteria and erythrocytes by photoinactivation

We analyzed the photoinactivation of the membrane functions of bacteria and erythrocytes induced by xanthene dyes. The dyes tested were rose bengal, phloxine B, erythrosine B and eosin B. These dyes induced the leakage of K(+) from Staphylococcus aureus cells within minutes of photoirradiation, in the order of rose bengal > phloxine B > erythrosine B > eosin B. The ability of dyes to inhibit respiration was weak, except for rose bengal, and the dyes dissipated the membrane potential in similar time traces with changes in K(+) permeability. The xanthene dyes also induced the leakage of K(+) from bovine erythrocytes upon photoirradiation in the same order as that observed with bacteria. Furthermore, we found that the ability to cause the leakage of K(+) from erythrocytes was associated with dye-induced morphological changes, forming a crenated form from the normal discoid. These results are discussed in connection with the ability of xanthene dyes to generate singlet oxygen and bind to bacterial cells, and further compared with the actions of cationic porphyrins, which induced photoinactivation of bacteria through respiratory inhibition.     

Studies on exchange equilibria of cations between cation-exchange membranes and electrolytic solutions

The variations of the selectivity coefficient K(A)(B) between Na(+)-H(+), Na(+)-K(+), and Na(+)-Cu(2+) systems and the separation factor alpha(A)(B) between Na(+)-Cu(2+) and K(+)-Cu(2+) systems in cation-exchange membranes as functions of loading and particle size of resin have been measured. The exchange affinities of all the membranes increase as H(+)相似文献   

Why voltage-gated Ca(2+) and bacterial Na(+) channels with the same EEEE motif in their selectivity filters confer opposite metal selectivity

Voltage-gated sodium (Na(v)) and calcium (Ca(v)) channels, which play essential biological roles, are characterized by their ability to discriminate the "native" ion from other competing cations. Surprisingly, Na(+)-selective bacterial Na(v) and high voltage-activated Ca(2+)-selective Ca(v) channels both exhibit selectivity filters (the narrowest part of the open pore) lined by four Glu residues that interact specifically with the permeating ions. This raises the intriguing question why selectivity filters with the same EEEE motif are Na(+)-selective in Na(v) channels but Ca(2+)-selective in Ca(v) channels. We show that the different degree of metal hydration inside the pore, which is related to the pore size and rigidity, can account for the opposite ion selectivity in Na(v) and Ca(v) channels with identical EEEE selectivity filters. The results are consistent with experimental estimates of the metal hydration structure in Na(v) and Ca(v) channels with the EEEE motif. They suggest that the protein matrix, which can enhance or attenuate ion-protein interactions relative to ion-solvent interactions by controlling the pore's solvent accessibility, size/rigidity, and charge state, is a key determinant of Ca(2+)vs. Na(+) selectivity in EEEE selectivity filters.     

Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel

Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.     

Model and simulation of Na+/K+ pump phosphorylation in the presence of palytoxin

The ATP hydrolysis reactions responsible for the Na(+)/K(+)-ATPase phosphorylation, according to recent experimental evidences, also occur for the PTX-Na(+)/K(+) pump complex. Moreover, it has been demonstrated that PTX interferes with the enzymes phosphorylation status. However, the reactions involved in the PTX-Na(+)/K(+) pump complex phosphorylation are not very well established yet. This work aims at proposing a reaction model for PTX-Na(+)/K(+) pump complex, with similar structure to the Albers-Post model, to contribute to elucidate the PTX effect over Na(+)/K(+)-ATPase phosphorylation and dephosphorylation. Computational simulations with the proposed model support several hypotheses and also suggest: (i) phosphorylation promotes an increase of the open probability of induced channels; (ii) PTX reduces the Na(+)/K(+) pump phosphorylation rate; (iii) PTX may cause conformational changes to substates where the Na(+)/K(+)-ATPase may not be phosphorylated; (iv) PTX can bind to substates of the two principal states E1 and E2, with highest affinity to phosphorylated enzymes and with ATP bound to its low-affinity sites. The proposed model also allows previewing the behavior of the PTX-pump complex substates for different levels of intracellular ATP concentrations.     

Design of a DNA electronic logic gate (INHIBIT gate) with an assaying application for Ag+ and cysteine

A DNA electronic logic gate (INHIBIT gate) with good selectivity and reversibility is developed based on using Ag(+) and Cys as inputs and current signal as output.     

SWNT-MWNT hybrid filter attains high viral removal and bacterial inactivation

We describe the concept and demonstrate the efficacy of a novel SWNT-MWNT hybrid filter for the removal and inactivation of microbial pathogens from water. The filter is composed of a thin SWNT layer (0.05 mg cm(-2)) on top of a thicker MWNT layer (0.27 mg cm(-2)) supported by a microporous support membrane. The SWNT-MWNT filter exhibits high log removal of several model viruses (MS2, PRD1, and T4 bacteriophages) by depth filtration, which predominantly takes place in the thicker and more uniform MWNT layer. The filter removes all bacteria by a sieving mechanism, with the top SWNT layer providing high levels of inactivation of model bacteria (Escherichia coli K12 and Staphylococcus epidermidis), as well as microbes from river water and treated wastewater effluent. The dual-layer SWNT-MWNT filter lays the framework for new possibilities in point-of-use water filtration.     

Mechanism for interplay between electron and ionic fluxes in KhFek[Fe(CN)6]l.mH2O compounds

This paper develops a framework for the interpretation of ionic insertion/deinsertion reactions in an aqueous environment taking place in transition-metal hexacyanoferrates of the general formula K(h)[Fe(2+) (CN)(6)](l).mH(2)O, also called Prussian Blue. Three different processes were fully separated in the electrochemistry of these films. It was clearly identified that one of these electrochemical processes involves the insertion/deinsertion of H(3)O(+) (hydrated protons) through the channels of the K(h)[Fe(2+) (CN)(6)](l).mH(2)O structure to reach the film electroneutrality during the electron transfer between Everitt's Salt and Prussian Blue. The other electrochemical processes involve K(+) or H(+) (proton) exchange through the water crystalline structure existing in the channels of the K(h)[Fe(2+)(CN)(6)](l).mH(2)O structure.