Ion Channel Gating Kinetics Research Articles

Model-free idealization: Adaptive integrated approach for idealization of ion-channel currents

Single-channel electrophysiological recordings provide insights into transmembrane ion permeation and channel gating mechanisms. The first step in the analysis of the recorded currents involves an "idealization" process, in which noisy raw data are classified into two discrete levels corresponding to the open and closed states of channels. This provides valuable information on the gating kinetics of ion channels. However, the idealization step is often challenging in cases of currents with poor signal-to-noise ratios and baseline drifts, especially when the gating model of the target channel is not identified. We report herein on a highly robust model-free idealization method for achieving this goal. The algorithm, called adaptive integrated approach for idealization of ion-channel currents (AI2), is composed of Kalman filter and Gaussian mixture model clustering and functions without user input. AI2 automatically determines the noise reduction setting based on the degree of separation between the open and closed levels. We validated the method on pseudo-channel-current datasets that contain either computed or experimentally recorded noise. We also investigated the relationship between the noise reduction parameter of the Kalman filter and the cutoff frequency of the low-pass filter. The AI2 algorithm was then tested on actual experimental data for biological channels including gramicidin A, a voltage-gated sodium channel, and other unidentified channels. We compared the idealization results with those obtained by the conventional methods, including the 50%-threshold-crossing method.

Heterogeneous stochastic bifurcations explain intrinsic oscillatory patterns in entorhinal cortical stellate cells

Stellate cells (SC) in the medial entorhinal cortex manifest intrinsic membrane potential oscillatory patterns. Although different theoretical frameworks have been proposed to explain these patterns, a robust unifying framework that jointly accounts for intrinsic heterogeneities and stochasticity is missing. Here, we first performed invitro patch-clamp electrophysiological recordings from rat SCs and found pronounced cell-to-cell variability in their characteristic physiological properties, including peri-threshold oscillatory patterns. We demonstrate that noise introduced into two independent populations (endowed with deterministic or stochastic ion-channel gating kinetics) of heterogeneous biophysical models yielded activity patterns that were qualitatively similar to electrophysiological peri-threshold oscillatory activity in SCs. We developed spectrogram-based quantitative metrics for the identification of valid oscillations and confirmed that these metrics reliably captured the variable-amplitude and arhythmic oscillatory patterns observed in electrophysiological recordings. Using these quantitative metrics, we validated activity patterns from both heterogeneous populations of SC models, with each model assessed with multiple trials of different levels of noise at distinct membrane depolarizations. Our analyses unveiled the manifestation of stochastic resonance (detection of the highest number of valid oscillatory traces at an optimal level of noise) in both heterogeneous populations of SC models. Finally, we show that a generalized network motif comprised of a slow negative feedback loop amplified by a fast positive feedback loop manifested stochastic bifurcations and stochastic resonance in the emergence of oscillations. Together, through a unique convergence of the degeneracy and stochastic resonance frameworks, our unifying framework centered on heterogeneous stochastic bifurcations argues for state-dependent emergence of SC oscillations.

AMPA receptor structure and auxiliary subunits

Fast excitatory synaptic transmission in the mammalian brain is largely mediated by AMPA-type ionotropic glutamate receptors (AMPARs), which are activated by the neurotransmitter glutamate. In synapses, the function of AMPARs is tuned by their auxiliary subunits, a diverse set of membrane proteins associated with the core pore-forming subunits of the AMPARs. Each auxiliary subunit provides distinct functional modulation of AMPARs, ranging from regulation of trafficking to shaping ion channel gating kinetics. Understanding the molecular mechanism of the function of these complexes is key to decoding synaptic modulation and their global roles in cognitive activities, such as learning and memory. Here, we review the structural and molecular complexity of AMPAR-auxiliary subunit complexes, as well as their functional diversity in different brain regions. We suggest that the recent structural information provides new insights into the molecular mechanisms underlying synaptic functions of AMPAR-auxiliary subunit complexes.

Phase‐response curves of ion channel gating kinetics

Reduced models of single‐neuron dynamics are widely used to characterize neuronal properties such as stimulus encoding and a cell's contribution to network function. Low‐dimensional phase oscillator models based on phase‐response curves, in particular, permit to capture the essence of a neuron's input‐output dynamics at the level of spike times from high‐dimensional conductance‐based neuron models. In principle, these phase models allow for a direct translation of perturbations in the state variables (such as changes in specific ion channel conductances and kinetics) to shifts in the timing of spikes. Previous mathematical work, however, has predominantly focused on voltage and current perturbations and less on perturbations occurring in any of the involved kinetic equations of ionic channels. Here, we provide the means to mathematically relate properties in these variables to the phase‐dependent voltage dynamics. Specifically, we derive the vector of phase‐response curves near two different onset bifurcations: the physiologically prominent saddle node on invariant cycle bifurcation as well as the saddle‐node loop bifurcation. We demonstrate that, locally around the saddle node, the tangent space of the isochrons is spanned by the strongly stable manifold of the saddle node. This finding enables us to quantitatively relate perturbations in the gating kinetics of ion channels to the resulting changes in spike timing. These results lay the methodological foundation for future quantitative analyses of the impact of specific biophysical channel properties on spike timing, including, but not limited to, channel noise.

Acute temperature sensitivity in optic nerve axons explained by an electrogenic membrane potential.

Classical work in squid axon reports resting membrane potential is independent of temperature, but our findings suggest that this is not the case for axons in mammalian optic nerve. Refractory period duration changes over 10 times between 37°C and room temperature, and afterpotential polarity is also acutely temperature sensitive, inconsistent with changes in temperature impacting nerve function only through altered rates of ion channel gating kinetics. Our evidence suggests that the membrane potential is enhanced by warming, an effect reduced by exposure to ouabain. The temperature dependence can be explained if axonal Na(+)/K(+) ATPase continuously expels Na(+) ions that enter axons largely electroneutrally, thereby adding a substantial electrogenic component to the membrane potential. Block of the Na(+) transporter NKCC1 with bumetanide increases refractoriness, like depolarization, indicating that this is a probable route by which Na(+) enters, raising the expectation that the rate of electroneutral Na(+) influx increases with temperature and suggesting a temperature-dependent transmembrane Na(+) cycle that contributes to membrane potential.

Simulating Influence of Channel Kinetics and Temperature on Hodgkin-Huxley Threshold Dynamics

Information processing in the brain results from the spread and interaction of electrical and chemical signals among neurons. The Hodgkin-Huxley model, describes the spiking and refractory properties of real neurons and serves as a paradigm based on nonlinear conductance of ion channels. Activation of various ion channels establish the spiking behavior of a neuron which determines the communication and coding in nervous system. Firing rates, timing of spikes, and spiking threshold properties are major firing properties of neuronal sparking activities. The temperature influence on neuron spiking threshold regulates the neuronal activities as electrophysiological experiments on neural spiking actions are rarely conducted outside of room temperature in vitro or body temperature in vivo. Temperature changes affect the spiking dynamics of excitable neurons via maximum ion channel conductances and ion channel gating kinetics. The latter has a major impact on changing the shape and amplitude of action potential as well as the generation and propagation of spikes. The purpose of this research is to study, simulate and analyze how the temperature change influence spiking properties of a neuron, channel kinetics as well as activation and inactivation variables of the potassium and sodium channels which determine the dynamics of Hodgkin-Huxley model.

Ligand-Gated Ion Channel Gating Kinetics and the Opening/Closing Mechanism are Sensitive to Mutations Altering the Hydrophobicity of the Ion Conduction Pore

The Cys-loop ligand-gated ion channel family includes the GABA-, glycine-, serotonin-, and nicotinergic acetylcholine receptors, which all play important roles in the nervous signal transduction pathway. They are critical targets for e.g. general anesthetics and alcohol, and all consist of five subunits organized around a central pore. Here, we investigate the prokaryotic Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) that is a homolog to the cys-loop superfamily. GLIC has the advantage of having several X-ray structures published, and we have previously used it for several different modeling studies. To better understand the relation between gating and the pore properties if ligand-gated channels in general, we have substituted several amino residues involved in the kinetics of open and closing of the channel, at different pH. We have characterized these substitutions using an in vitro electrophysiological functional assay (proton concentration response curves); expressing the substituted channels in Xenopus laevis oocytes for two-electrode voltage clamp experiments. We have also made single-channel recordings for investigating the kinetics (open, closing, and flickering behavior) of the substitutions, observed in silico. Our results indicate that the hydrophobicity of the pore is critical to determine both the balance and kinetics of the opening/closing process, and it is possible to alter the gating properties of the channel while still keeping it functional. This is an important step in the process of developing more effective anesthetics, with a better therapeutic window, but also to identify a possible molecular mechanism of how to reduce alcohol dependency.

Effects of electrical polarization on the opening rate constant of a voltage-gated ion channel

Ion channel gating kinetics can be described using Kramers' diffusion theory of reaction rates between several closed and open states, where transition rates between states depend exponentially on the membrane potential V. It has been suggested that transition rates have a more complex dependence on V at voltage extremes, but this has never been quantified. We measured the rate constant of the last closed to open transition in a voltage-gated ion channel and show that it does not depend exponentially on membrane potential at values of V greater than ≈150 mV. To explain this behavior, we estimate the effects of electrical polarization of the water contained in crevices within the channel protein, using an electrostatic model of the approximate three-dimensional geometry and the nonlinear effects of charges on the polarization of water.

Focusing in multiwell potentials: Applications to ion channels

We investigate nonequilibrium stationary distributions induced by stochastic dichotomous noise in double-well and multiwell models of ion channel gating kinetics. The channel kinetics is analyzed using both overdamped Langevin equations and master equations. With the Langevin equation approach we show a nontrivial focusing effect due to the external stochastic noise, namely, the concentration of the probability distribution in one of the two wells of a double-well system or in one or more of the wells of the multiwell model. In the multiwell system, focusing in the outer wells is shown to be achievable under physiological conditions, while focusing in the central wells has proved possible so far only at very low temperatures. We also discuss the strength of the focusing effect and obtain the conditions necessary for maximal focusing to appear. These conditions cannot be predicted by a simple master equation approach.

Wavelet-based protocols for ion channel electrophysiology

BackgroundFluctuation-induced phenomena caused by both random and deterministic stimuli have been previously studied in a variety of contexts. They are based on the interplay between the spectro-temporal patterns of the signal and the kinetics of the system it is applied to. The aim of this study was to develop a method for designing fluctuating inputs into nonlinear system which would elicit the most desired system output and to implement the method to studies of ion channels.ResultsWe describe an algorithm based on constructing the input as a superposition of wavelets and optimizing it according to a selected cost functional. The algorithm is applied to ion channel electrophysiology where the input is the fluctuating voltage delivered through a patch-clamp experimental apparatus and the output is the whole-cell ionic current. The algorithm is optimized to aid selection of Markov models of the gating kinetics of the voltage-gated Shaker K+ channel and tested by comparison of numerically obtained ionic currents predicted by different models with experimental data obtained from the Shaker K+ channels. Other applications and optimization criteria are also suggested.ConclusionThe method described in this paper can be useful in development and testing of models of ion channel gating kinetics, developing voltage inputs that optimize certain nonequilibrium phenomena in ion channels, such as the kinetic focusing, and potentially has applications to other fields.

Ion channel remodeling in gastrointestinal inflammation.

Gastrointestinal inflammation significantly affects the electrical excitability of smooth muscle cells. Considerable progress over the last few years have been made to establish the mechanisms by which ion channel function is altered in the setting of gastrointestinal inflammation. Details have begun to emerge on the molecular basis by which ion channel function may be regulated in smooth muscle following inflammation. These include changes in protein and gene expression of the smooth muscle isoform of L-type Ca(2+) channels and ATP-sensitive K(+) channels. Recent attention has also focused on post-translational modifications as a primary means of altering ion channel function in the absence of changes in protein/gene expression. Protein phosphorylation of serine/theronine or tyrosine residues, cysteine thiol modifications, and tyrosine nitration are potential mechanisms affected by oxidative/nitrosative stress that alter the gating kinetics of ion channels. Collectively, these findings suggest that inflammation results in electrical remodeling of smooth muscle cells in addition to structural remodeling. The purpose of this review is to synthesize our current understanding regarding molecular mechanisms that result in altered ion channel function during gastrointestinal inflammation and to address potential areas that can lead to targeted new therapies.

Thermal impact on spiking properties in Hodgkin-Huxley neuron with synaptic stimulus

The effect of environmental temperature on neuronal spiking behaviors is investigated by numerically simulating the temperature dependence of spiking threshold of the Hodgkin-Huxley neuron subject to synaptic stimulus. We find that the spiking threshold exhibits a global minimum in a "comfortable temperature" range where spike initiation needs weakest synaptic strength, indicating the occurrence of optimal use of synaptic transmission in neural system. We further explore the biophysical origin of this phenomenon in ion channel gating kinetics and also discuss its possible biological relevance in information processing in neural systems.

A Common SCN5A Variant Alters the Responsiveness of Human Sodium Channels to Class I Antiarrhythmic Agents

The potential pathophysiological role of common SCN5A polymorphisms in cardiac arrhythmias has been increasingly recognized. However, little is known about the impact of those polymorphisms on the pharmocological response of hNav1.5 to various antiarrhythmic agents. The known SCN5A polymorphism, S524Y, was studied in comparison with the wild type (WT) in [corrected] the SCN5A-Q1077del variant. The ion channel gating kinetics and pharmacology were evaluated using whole-cell patch-clamp methods in HEK-293 cells. Consistent with a previous report, the basal ion channel gating kinetics of S524Y were indistinguishable from the WT. Quinidine (20 microM) caused similar extent of tonic block reduction of sodium currents at -120 mV in WT and S524Y. Surprisingly, quinidine (20 microM) exerted a more use-dependent block by a 10 Hz pulse train in S524Y than in WT at 22 degrees C (Ki: WT, 51.3 microM; S524Y, 20.3 microM). S524Y significantly delayed recovery from the use-dependent block, compared with the WT (tau= 88.6 +/- 7.9 s vs 41.9 +/- 6.6 s, P < 0.005). Under more physiological conditions using a 2 Hz pulse train at 37 degrees C, S524Y similarly enhanced the use-dependent block by quinidine. In addition, S524Y enhanced the use-dependent block by flecainide (12.5 microM), but not by mexiletine (100 microM). A common SCN5A polymorphism, S524Y, can enhance a use-dependent block by class Ia and Ic antiarrhythmic agents. Our findings may have clinical implications in pharmacological management of cardiac arrhythmias since this common SCN5A polymorphism might be a contributing factor to the variable antiarrhythmic response.

An Interaction Involving an Arginine Residue in the Cytoplasmic Domain of the 5-HT3A Receptor Contributes to Receptor Desensitization Mechanism

A large cytoplasmic domain accounts for approximately one-third of the entire protein of one superfamily of ligand-gated membrane ion channels, which includes nicotinic acetylcholine (nACh), gamma-aminobutyric acid type A (GABA(A)), serotonin type 3 (5-HT3), and glycine receptors. Desensitization is one functional feature shared by these receptors. Because most molecular studies of receptor desensitization have focused on the agonist binding and channel pore domains, relatively little is known about the role of the large cytoplasmic domain (LCD) in this process. To address this issue, we sequentially deleted segments of the LCD of the 5-HT3A receptor and examined the function of the mutant receptors. Deletion of a small segment that contains three amino acid residues (425-427) significantly slowed the desensitization kinetics of the 5-HT3A receptor. Both deletion and point mutation of arginine 427 altered desensitization kinetics in a manner similar to that of the (425-427) deletion without significantly changing the apparent agonist affinity. The extent of receptor desensitization was positively correlated with the polarity of the amino acid residue at 427: the desensitization accelerates with increasing polarity. Whereas the R427L mutation produced the slowest desensitization, it did not significantly alter single channel conductance of 5-HT3A receptor. Thus, the arginine 427 residue in the LCD contributes to 5-HT3A receptor desensitization, possibly through forming an electrostatic interaction with its neighboring residues. Because the polarity of the amino acid residue at 427 is highly conserved, such a desensitization mechanism may occur in other members of the Cys-loop family of ligand-gated ion channels.

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Gating kinetics of potassium channel in rat dorsal root ganglion neurons analyzed with fractal model

The kinetics of ion channels have been widely modeled as a Markov process. In these models it is assumed that the channel protein has a small number of discrete conformational states and kinetic rate constants connecting these states are constant. To study the gating kinetics of voltage-dependent K + channel in rat dorsal root ganglion neurons, K + channel current were recorded using cell-attached patch-clamp technique. The K + channel characteristic of kinetics were found to be statistically self-similar at different time scales as predicted by the fractal model. The fractal dimension D for the closed times and for the open times depend on the pipette potential. For the open and closed times of kinetic setpoint, it was found dependent on the applied pipette potential, which indicated that the ion channel gating kinetics had nonlinear kinetic properties. Thus, the open and closed durations, which had the voltage dependence of the gating of this ion channel, were well described by the fractal model.

Poisson sampling-based inference for single ion channel data with time interval omission.

Patch-clamp recording allows investigations of the gating kinetics of single ion channels. Statistical analysis of kinetic data can enhance our understanding of channel gating at a molecular level. Experimental channel records suffer from time interval omission, i.e. failure to detect brief channel openings and closings. It is important to incorporate this phenomenon into statistical analyses of ion channel data. When time interval omission is ignored, the method of maximum likelihood can usually be used to estimate gating parameters from a single channel record. However, it is far more difficult to apply this method when time interval omission is incorporated. We present an alternative approach to parameter estimation based on Poisson sampling. A simulated homogeneous Poisson process is superimposed onto the channel record and inference is based on the numbers of points in successive open and closed sojourns, rather than on the sojourn times themselves. We describe the method for the two-state Markov model C<-->O, although it is applicable to more general models. Computer-simulated data are used to demonstrate the efficacy of the method. Modifications of the method are discussed briefly.

Single-channel data and missed events

Patch-clamp recording permits investigation of the gating kinetics of single ion channels. Careful statistical analysis of kinetic data can yield clues as to the molecular events underlying channel gating. However, it is important that such analysis should take full account of the limitations that arise from the finite time resolution of patch-clamp recording techniques. Single-ion-channel data are generally interpreted in terms of Markov process models of channel gating mechanisms. Experimental channel records suffer from time interval omission, i.e. failure to detect brief channel openings and closings. This leads to an identifiability problem when analysing single-channel data, i.e. different gating mechanisms provide equally convincing descriptions of the same experimental data. We consider a two-state Markov model of receptor-channel gating in which the channel opening rate is proportional to the agonist concentration, C in equilibrium with OA. By using computer-simulated data, the approximate likelihood of the data is maximized to yield parameter estimates for the model. At a single agonist concentration there is an identifiability problem in that two pairs of parameter estimates are obtained. The 'true' parameter estimates cannot be distinguished from the 'false' ones. By considering data corresponding to a range of agonist concentrations one may identify the 'true' parameter estimates as those that do not change as the agonist concentration is increased. Alternatively, one may identify the 'true' parameter estimates directly by maximizing a global likelihood, the latter being obtained by simultaneous consideration of data obtained at several different agonist concentrations.(ABSTRACT TRUNCATED AT 250 WORDS)

Comments on: The origin of fractal scaling mechanisms in ion channel gating kinetics

These comments concern the propriety of labelling two expressions, derived in the subject communication, as fractal scaling laws

Reply to comments on: The origin of fractal scaling mechanisms in ion channel gating kinetics

Discussing temporal scaling laws involving non-integer exponents, Nonnenmacher obviously followed in notation and interpretation the group of researchers working with Levy (stable) distribution functions