Nonconducting State Research Articles

PEG blocking of single pores arising on phase transitions in unmodified lipid bilayers

Changes in ionic permeability of bilayer lipid membranes (BLM) from dipalmitoyl phosphatidylcholine at temperature of phase transition in 1 M LiCl solution in the presence of polyethyleneglycols (PEG) of various molecular masses are studied. The transition of ionic membrane channels from conducting to blocked nonconducting state using polymers makes it possible to calibrate lipid pores. It is shown that low-molecular weight glycerol and PEG with molecular weights of 300 and 600 decrease the amplitude of current fluctuations through the membrane, the decrease being proportional to the size of the polymer molecule incorporated. The addition of PEG with molecular masses of 1450, 2000, and 3350 decrease the current fluctuations to the basal noise level. The result is considered as a complete blockade of ion channel conductivity. In the presence of rather large polymers, such as PEG with molecular masses of 6000 and 20000, which are hardly incorporated in the pore, single current fluctuations occur again; however, their amplitudes are somewhat smaller than in the absence of PEG. It is assumed that a complete blockade of the conductivity of lipid ionic channels by PEG with molecular masses of 1450, 2000, and 3350 is due to dehydration of the pore gap and the conversion of the hydrophilic pore to a hydrophobic one.

Intrinsic Free Energy of the Conformational Transition of the KcsA Signature Peptide from Conducting to Nonconducting State

We explore a conformational transition of the TATTVGYG signature peptide of the KcsA ion selectivity filter and its GYG to AYA mutant from the conducting α-strand state into the nonconducting pII-like state using a novel technique for multidimensional optimization of transition path ensembles and free energy calculations. We find that the wild type peptide, unlike the mutant, intrinsically favors the conducting state due to G77 backbone propensities and additional hydrophobic interaction between the V76 and Y78 side chains in water. The molecular mechanical free energy profiles in explicit water are in very good agreement with the corresponding adiabatic energies from the Generalized Born Molecular Volume (GBMV) implicit solvent model. However comparisons of the energies to higher level B3LYP/6-31G(d) Density Functional Theory calculations with Polarizable Continuum Model (PCM) suggest that the nonconducting state might be more favorable than predicted by molecular mechanics simulations. By extrapolating the single peptide results to the tetrameric channel, we propose a novel hypothesis for the ion selectivity mechanism.

Conducting Polymer Memory Devices Based on Dynamic Doping

Molecular electronic junctions consisting of a 20 nm thick layer of polypyrrole (PPy) and 10 nm of TiO2 between conducting layers of carbon and gold were investigated as potential nonvolatile memory devices. By making the polymer layer much thinner than conventional polymer electronic devices, it is possible to dynamically oxidize and reduce the polypyrrole layer by an applied bias. When the electrode in contact with the PPy is biased positive, oxidation of the PPy occurs to yield a conducting polaron state. The junctions exhibit a large increase in conductance in response to the positive bias, which is reversed by a subsequent negatively biased pulse. Switching between the conducting and nonconducting state can occur for pulses at least as short as 10 micros, and the conducting state persists after a positive bias pulse for at least 1 week. The read/write/read/erase cycle may be repeated for at least 1700 cycles, although with an error rate of approximately 3% due mainly to an incomplete "erase" step. The speed and retention of the PPy/TiO2 junctions are far superior to those of the analogous fluorene/TiO2 devices lacking the polymer, and the conductance changes are absent if SiO2 is substituted for TiO2. The observations are consistent with "dynamic doping" of the solid-state polymer layer, with the possible involvement of adventitious mobile ions. Although the speed of the current polymer/TiO2 junctions is slower than commercial dynamic random access memory, their retention is approximately 5 orders of magnitude longer.

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.

A Genetic Screen for Dihydropyridine (DHP)-Resistant Worms Reveals New Residues Required for DHP-Blockage of Mammalian Calcium Channels

Dihydropyridines (DHPs) are L-type calcium channel (Cav1) blockers prescribed to treat several diseases including hypertension. Cav1 channels normally exist in three states: a resting closed state, an open state that is triggered by membrane depolarization, followed by a non-conducting inactivated state that is triggered by the influx of calcium ions, and a rapid change in voltage. DHP binding is thought to alter the conformation of the channel, possibly by engaging a mechanism similar to voltage dependent inactivation, and locking a calcium ion in the pore, thereby blocking channel conductance. As a Cav1 channel crystal structure is lacking, the current model of DHP action has largely been achieved by investigating the role of candidate Cav1 residues in mediating DHP-sensitivity. To better understand DHP-block and identify additional Cav1 residues important for DHP-sensitivity, we screened 440,000 randomly mutated Caenorhabditis elegans genomes for worms resistant to DHP-induced growth defects. We identified 30 missense mutations in the worm Cav1 pore-forming (α1) subunit, including eleven in conserved residues known to be necessary for DHP-binding. The remaining polymorphisms are in eight conserved residues not previously associated with DHP-sensitivity. Intriguingly, all of the worm mutants that we analyzed phenotypically exhibited increased channel activity. We also created orthologous mutations in the rat α1C subunit and examined the DHP-block of current through the mutant channels in culture. Six of the seven mutant channels examined either decreased the DHP-sensitivity of the channel and/or exhibited significant residual current at DHP concentrations sufficient to block wild-type channels. Our results further support the idea that DHP-block is intimately associated with voltage dependent inactivation and underscores the utility of C. elegans as a screening tool to identify residues important for DHP interaction with mammalian Cav1 channels.

Pore Mutations of the Escherichia coli MscS Channel Affect Desensitization but Not Ionic Preference

Mechanosensitive channels rescue bacterial cells from a fate of lysis when they transfer from a high- to low-osmolarity environment. Of three Escherichia coli mechanosensitive proteins studied to date, only MscS-Ec demonstrates a small anionic preference and a desensitized, nonconducting state under sustained pressure. Little is known about the mechanisms generating these distinctive properties. Eliminating the sole positive charge in the MscS-Ec pore region (Arg88) did not alter anionic preference. Adding positive charges at either end of the pore did not augment anionic preference, and placing negative charges within the pore did not diminish it. Thus, pore charges do not control this characteristic. However, from this analysis we identified mutations in the hinge region of the MscS-Ec pore helix (at Gly113) that profoundly affected ability of the channel to desensitize. Substitution with nonpolar (Ala, Pro) or polar (Asp, Arg, Ser) residues inhibited transition to the desensitized state. Interestingly, Gly113 replaced with Met did not impede desensitization. Thus, although Gly is not specifically required at position 113, MscS desensitization is strongly influenced by the residue situated here. Mutations at residues further into the pore also regulated desensitization. Transition to this unique mechanosensitive channel state is discussed in terms of existing data.

Characterization of the Resting MscS: Modeling and Analysis of the Closed Bacterial Mechanosensitive Channel of Small Conductance

Channels from the MscS family are adaptive tension-activated osmolyte release valves that regulate turgor in prokaryotes and volume in plant chloroplasts. The crystal structure of Escherichia coli MscS has provided a starting point for detailed descriptions of its mechanism. However, solved in the absence of the lipid bilayer, this structure may deviate from a native conformation. In this study, we utilized molecular dynamics simulations and a new iterative extrapolated-motion protocol to pack the splayed peripheral TM1 and TM2 transmembrane helices along the central TM3 shaft. This modification restored the tension transmission route between the membrane and the channel gate. We also modeled the structure of the 26-amino acid N-terminal segments that were unresolved in the crystals. The resulting compact conformation, which we believe approximates the closed resting state of MscS, matches the hydrophobic thickness of the lipid bilayer with arginines 46, 54, and 74 facing the polar lipid headgroups. The pore-lining helices in this resting state feature alternative kinks near the conserved G121 instead of the G113 kinks observed in the crystal structure and the transmembrane barrel remains stable in extended molecular dynamics simulations. Further analysis of the dynamics of the pore constriction revealed several moderately asymmetric and largely dehydrated states. Biochemical and patch-clamp experiments with engineered double-cysteine mutants demonstrated cross-linking between predicted adjacent residue pairs, which formed either spontaneously or under moderate oxidation. The L72C-V99C bridge linking more peripheral TM2 to TM3 caused a shift of channel activation to higher pressures. TM3 to TM3 cross-links through the A84C-T93C, S95C-I97C, and A106C-G108C cysteine pairs were shown to lock MscS in a nonconductive state. Normal channel activity in these mutants could be recovered upon disulfide reduction with dithiothreitol. These results confirmed our modeling predictions of a closed MscS channel featuring a TM3 barrel that largely resembles the crystal conformation though with more tightly packed peripheral helices. From this closed-resting conformation, the TM3 helices must expand to allow for channel opening.

Impact of Total Ionizing Dose on the Analog Single Event Transient Sensitivity of a Linear Bipolar Integrated Circuit

Total ionizing dose (TID) strongly affects the single event transient (SET) sensitivity of a bipolar linear voltage comparator (LM139). The general rule that transistors in the non-conducting state are the most sensitive to SETs was verified, with some exceptions. The mechanisms responsible for those exceptions were identified and explained using circuit analysis. In the non typical behavior, a correlation of the degradation of the amplifier stages with the shape of the transient output signal was established. Following total dose exposure the SETs generally exhibit a reduction in amplitude due to the degradation of the slew rate. However, in some cases the transient signal is amplified because degradation of either the current source or of the current gain of some transistors forces the output transistor to the edge of conduction, so that it behaves like a voltage amplifier and amplifies the parasitic transient signal. Laser testing demonstrates that ASET sensitivity also is affected by TID degradation of transistors that are not directly hit by the laser.

WORM-Type Device with Rectifying Effect Based on a Conjugated Copolymer of Fluorene and Europium Complex

We report a nonvolatile, write-once-read-many-times (WORM) memory device based on a simple organic-inorganic heterojunction. The organic-based hybrid used is 9,9-dihexylfluorene and Eu-complexed benzoate, which contains both electron-donor (-dihexylfluorene) and electron-acceptor (europium complex) groups. Under current-voltage testing, the device is able to switch from one initial nonconducting state to a conducting state once a threshold voltage is reached. Diode rectifying characteristics, with a current ratio of four orders of magnitude, is also observed after the device is turned on, which is essential to address one memory cell in large passive matrix circuits.

Gating ASICs

Acid-sensing ion channels (ASICs) are members of a family of cation-selective ion channels that includes epithelial sodium channels and the degenerins, which shows a remarkable diversity of function and in the mechanisms of activation (see Canessa). Implicated in sensory perception, ASICs are sodium-selective and activated by extracellular protons independently of membrane potential. Jasti et al . combined crystallographic analysis with electrophysiology to explore the low-pH structure of ΔASIC1, a chicken ASIC deletion mutant (in a desensitized nonconducting state), and investigated the mechanism underlying its pH-dependent gating. Unexpectedly, they found that ΔASIC1 formed a homotrimer. Each subunit had two transmembrane helices and a large extracellular domain. Describing the overall domain structure of ΔASIC1 subunits as resembling an "upright forearm and clenched hand" (with the extracellular domain constituting the "hand"), the authors identified a group of acidic residues as proton-binding sites that constitute the pH sensor. They suggest that proton binding leads to movement of the disulfide-rich thumb region, which transmits a long-range conformational change to allow the channel to open. J. Jasti, H. Furukawa, E. B. Gonzales, E. Gouaux, Structure of acid-sensing ion channel 1 at 1.9 Å resolution and low pH. Nature 449 , 316-323 (2007). [PubMed] C. M. Canessa, Unexpected opening. Nature 449 , 293-294 (2007). [PubMed]

Origins of thep-type nature and cation deficiency inCu2Oand related materials

While most of crystalline wide gap oxides are both stoichiometric and insulating, a handful of them including ZnO and ${\mathrm{In}}_{2}{\mathrm{O}}_{3}$ are naturally anion-deficient and electron conductors. Even fewer of the oxides are naturally cation-deficient and hole conductors, the arch-type of which is ${\mathrm{Cu}}_{2}\mathrm{O}$. Based on first principles calculation of equilibrium nonstoichiometry and defect stability, we explain why the ${\mathrm{Cu}}^{(I)}({d}^{10})$ oxide-based materials are both $p$-type and naturally cation-deficient, and why cation vacancies lead to delocalized, conductive states, whereas in other oxides (e.g., ZnO and MgO), they lead to localized, nonconductive states.

Cardiac sodium channels: Dysregulation meets myocardial failure

See article by Hesse et al. [12] (pages 498–509) in this issue. Within the orchestra of cardiac ion channels, voltage–gated Na+ channels have a key function in the determination of the amplitude and slope of the action potential upstroke. Both are important in the control of impulse conduction velocity and maintenance of appropriate waves of excitation through the working myocardium. The main (α-) subunit of the cardiac sodium channel is encoded by the SCN5A (Nav1.5) gene, and the INa current mediated is responsible for the membrane depolarization. Fast inactivation of sodium channels appears within milliseconds, and the vast majority of sodium channels transit from the open state to a non-conductive state. Gating dysfunction or changes in the number of functional channels of cardiac sodium channels are linked to several cardiac arrhythmias [1–4]. Meanwhile, more than 170 different SCN5A mutations have been reported (currently, 77 for LQT-3, 90 for Brugada syndrome, 10 for conduction disease; see http://www.fsm.it/cardmoc/), and this has enabled evaluation of structure-function relationships of the sodium channel. Analysis of several of these mutations has consistently demonstrated that loss of function is the … * Tel.: +49 251 83 529 82; fax: +49 251 83 575 70. Eric.Schulze-Bahr{at}ukmuenster.de

Chemical modification of the electronic conducting states in polymer nanodevices

Organic materials offer new electronic functionality not available in inorganic devices. However, the integration of organic compounds within nanoscale electronic circuitry poses new challenges for materials physics and chemistry. Typically, the electronic states in organic materials are energetically misaligned with the Fermi level of metal contacts. Here, we study the voltage-induced change in conductivity in nanoscale devices comprising a monolayer of polyelectrolyte macromolecules. The devices are fabricated using integrated shadow masks. Reversible switching is observed between conducting (ON) and non-conducting (OFF) states in the devices. The open design of our devices easily permits chemical modification of the polyelectrolyte, which we show has a pronounced effect on the ON-OFF switching. We suggest that the switching voltage ionizes the polymers, creating a conducting channel of electronic levels aligned with the contact Fermi level.

Theory of microplasma fluctuations and noise in silicon diode in avalanche breakdown

A theory that explains physically the mechanism of microplasma switching from nonconducting to conducting state (turn-on process) and from conducting to nonconducting state (turn-off process) is presented. This theory describes the microplasma phenomenon in avalanche breakdown, and it provides relations between the microplasma properties (size, current density, and turn-on-off mechanism), noise properties (amplitude and wave form), and semiconductor properties (impurity concentration, lifetime constants, and diffusion coefficients). By use of this theory, the current-fluctuation [McIntyre, IEEE Trans. Electron Devices ED-13, 164 (1966)] and probability-dependent [Haitz, J. Appl. Phys. 35, 1370 (1964)] theories can be combined, and a very attractive characterization tool for investigation of semiconductor junctions in breakdown is developed.

Nonvolatile Memory Elements Based on the Intercalation of Organic Molecules Inside Carbon Nanotubes

We propose a novel class of nonvolatile memory elements based on the modification of the transport properties of a conducting carbon nanotube by the presence of an encapsulated molecule. The guest molecule has two stable orientational positions relative to the nanotube that correspond to conducting and nonconducting states. The mechanism, governed by a local gating effect of the molecule on the electronic properties of the nanotube host, is studied using density functional theory. The mechanisms of reversible reading and writing of information are illustrated with a F4TCNQ molecule encapsulated inside a metallic carbon nanotube. Our results suggest that this new type of nonvolatile memory element is robust, fatigue-free, and can operate at room temperature.

Structure prediction for the down state of a potassium channel voltage sensor

Voltage-gated potassium (Kv) channels, essential for regulating potassium uptake and cell volume in plants and electrical excitability in animals, switch between conducting and non-conducting states as a result of conformational changes in the four voltage-sensing domains (VSDs) that surround the channel pore. This process, known as gating, is initiated by a cluster of positively charged residues on the fourth transmembrane segment (S4) of each VSD, which drives the VSD into a 'down state' at negative voltages and an 'up state' at more positive voltages. The crystal structure of Kv1.2 probably corresponds to the up state, but the local environment of S4 in the down state and its motion in voltage gating remains unresolved. Here we employed several conditional lethal/second-site suppressor yeast screens to determine the transmembrane packing of the VSD in the down state. This screen relies on the ability of KAT1, a eukaryotic Kv channel, to conduct potassium when its VSDs are in the down state, thereby rescuing potassium-transport-deficient yeast. Starting with KAT1 channels bearing conditional lethal mutations, we identified second-site suppressor mutations throughout the VSD that recover yeast growth. We then constructed a down state model of the channel using six pairs of interacting residues as structural constraints and verified this model by engineering suppressor mutations on the basis of spatial considerations. A comparison of this down state model with the up state Kv1.2 structure suggests that the VSDs undergo large rearrangements during gating, whereas the S4 segment remains positioned between the central pore and the remainder of the VSD in both states.

Study of the negative resistance phenomenon in transition metal oxide films from a statistical mechanics point of view

The mechanism of the differential negative resistance behavior observable in transition metal oxides such as TiO2, NiO, and Nb2O5 is theoretically developed in terms of the order to disorder transition of local conducting pathways, so called filaments, by applying statistical mechanics. Joule heat is taken as a heat source giving rise to an increase of temperature in the filaments. The free energy of the filaments is evaluated by taking the site percolation model as well as the nonhomogeneity of an order parameter into account. It is concluded that the transition of a filament from the conducting state, which is dominated by the internal bonding energy term, to the nonconducting state is due to an increased contribution of the entropy term to the system’s total energy at a higher temperature. The calculation results also show that the rupture of a filament occurs in the middle of the filament when the filaments are in contact with thermally conducting metal electrodes, such as Pt.

Coherent transport in graphene nanoconstrictions

We study the effect of a structural nanoconstriction on the coherent transport properties of otherwise ideal zigzag-edged infinitely long graphene ribbons. The electronic structure is calculated with the standard one-orbital tight-binding model and the linear conductance is obtained using the Landauer formula. We find that, since the zero-bias current is carried in the bulk of the ribbon, this is very robust with respect to a variety of constriction geometries and edge defects. In contrast, the curve of zero-bias conductance versus gate voltage departs from the $(2n+1){e}^{2}∕h$ staircase of the ideal case as soon as a single atom is removed from the sample. We also find that wedge-shaped constrictions can present nonconducting states fully localized in the constriction close to the Fermi energy. The interest of these localized states in regards to the formation of quantum dots in graphene is discussed.

Ca2+-dependent Control of the Permeability Properties of the Mitochondrial Outer Membrane and Voltage-dependent Anion-selective Channel (VDAC)

Cell function depends on the distribution of cytosolic and mitochondrial factors across the outer mitochondrial membrane (OMM). Passage of metabolites through the OMM has been attributed to the voltage-dependent anion-selective channel (VDAC), which can form a large conductance and permanently open a channel in lipid bilayers. However, recent data indicate that the transport of metabolites through the OMM is controlled in the cells. Recognizing that the bilayer studies had been commonly conducted at supraphysiological [Ca2+] and [K+], we determined the effect of Ca2+ on VDAC activity. In liposomes, the purified VDAC displays Ca2+-dependent control of the molecular cut-off size and shows Ca2+-regulated Ca2+ permeability in the physiological [Ca2+] range. In bilayer experiments, at submicromolar [Ca2+], the purified VDAC or isolated OMM does not show sustained large conductance but rather exhibits gating between a nonconducting state and various subconductance states. Ca2+ addition causes a reversible increase in the conductance and may evoke channel opening to full conductance. Furthermore, single cell imaging data indicate that Ca2+ may facilitate the cation and ATP transport across the OMM. Thus, the VDAC gating is dependent on the physiological concentrations of cations, allowing the OMM to control the passage of ions and some small molecules. The OMM barrier is likely to decrease during the calcium signal.

Allosteric Interactions Required for High-Affinity Binding of Dihydropyridine Antagonists to CaV1.1 Channels Are Modulated by Calcium in the Pore

Dihydropyridines (DHPs) are an important class of drugs, used extensively in the treatment of angina pectoris, hypertension, and arrhythmia. The molecular mechanism by which DHPs modulate Ca(2+) channel function is not known in detail. We have found that DHP binding is allosterically coupled to Ca(2+) binding to the selectivity filter of the skeletal muscle Ca(2+) channel Ca(V)1.1, which initiates excitation-contraction coupling and conducts L-type Ca(2+) currents. Increasing Ca(2+) concentrations from approximately 10 nM to 1 mM causes the DHP receptor site to shift from a low-affinity state to a high-affinity state with an EC(50) for Ca(2+) of 300 nM. Substituting each of the four negatively charged glutamate residues that form the ion selectivity filter with neutral glutamine or positively charged lysine residues results in mutant channels whose DHP binding affinities are decreased up to 10-fold and are up to 150-fold less sensitive to Ca(2+) than wild-type channels. Analysis of mutations of amino acid residues adjacent to the selectivity filter led to identification of Phe-1013 and Tyr-1021, whose mutation causes substantial changes in DHP binding. Thermo-dynamic mutant cycle analysis of these mutants demonstrates that Phe-1013 and Tyr-1021 are energetically coupled when a single Ca(2+) ion is bound to the channel pore. We propose that DHP binding stabilizes a nonconducting state containing a single Ca(2+) ion in the pore through which Phe-1013 and Tyr-1021 are energetically coupled. The selectivity filter in this energetically coupled high-affinity state is blocked by bound Ca(2+), which is responsible for the high-affinity inhibition of Ca(2+) channels by DHP antagonists.