scholarly journals The Mechanism of Fast-Gate Opening in ClC-0

2007 ◽  
Vol 130 (4) ◽  
pp. 335-349 ◽  
Author(s):  
Anita M. Engh ◽  
José D. Faraldo-Gómez ◽  
Merritt Maduke
Keyword(s):  
Structural Changes ◽  
Single Channel ◽  
Companion Paper ◽  
State Model ◽  
Model Parameters ◽  
Chloride Binding ◽  
Gating Kinetics ◽  
Gate Opening ◽  
Starting Point ◽  
Voltage Dependent

ClC-0 is a chloride channel whose gating is sensitive to both voltage and chloride. Based on analysis of gating kinetics using single-channel recordings, a five-state model was proposed to describe the dependence of ClC-0 fast-gate opening on voltage and external chloride (Chen, T.-Y., and C. Miller. 1996. J. Gen. Physiol. 108:237–250). We aimed to use this five-state model as a starting point for understanding the structural changes that occur during gating. Using macroscopic patch recordings, we were able to reproduce the effects of voltage and chloride that were reported by Chen and Miller and to fit our opening rate constant data to the five-state model. Upon further analysis of both our data and those of Chen and Miller, we learned that in contrast to their conclusions, (a) the features in the data are not adequate to rule out a simpler four-state model, and (b) the chloride-binding step is voltage dependent. In order to be able to evaluate the effects of mutants on gating (described in the companion paper, see Engh et al. on p. 351 of this issue), we developed a method for determining the error on gating model parameters, and evaluated the sources of this error. To begin to mesh the kinetic model(s) with the known CLC structures, a model of ClC-0 was generated computationally based on the X-ray crystal structure of the prokaryotic homolog ClC-ec1. Analysis of pore electrostatics in this homology model suggests that at least two of the conclusions derived from the gating kinetics analysis are consistent with the known CLC structures: (1) chloride binding is necessary for channel opening, and (2) chloride binding to any of the three known chloride-binding sites must be voltage dependent.

scholarly journals The Role of a Conserved Lysine in Chloride- and Voltage-dependent ClC-0 Fast Gating

2007 ◽  
Vol 130 (4) ◽  
pp. 351-363 ◽  
Author(s):  
Anita M. Engh ◽  
José D. Faraldo-Gómez ◽  
Merritt Maduke
Keyword(s):  
Structural Changes ◽  
Computational Analysis ◽  
Voltage Dependence ◽  
Structural Information ◽  
Chloride Binding ◽  
Gate Opening ◽  
Voltage Dependent ◽  
Fast Gating ◽  
Homology Models

ClC-0 is a chloride channel whose gating is sensitive to voltage, chloride, and pH. In a previous publication, we showed that the K149C mutation causes a +70-mV shift in the voltage dependence of ClC-0 fast gating. In this paper we analyze the effects of a series of mutations at K149 on the voltage and chloride dependence of gating. By fitting our data to the previously proposed four-state model for ClC-0 fast gating, we show which steps in fast-gate opening are likely to be affected by these mutations. Computational analysis of mutant ClC-0 homology models show electrostatic contributions to chloride binding that may partially account for the effects of K149 on gating. The analysis of gating kinetics in combination with the available structural information suggests some of the structural changes likely to underpin fast-gate opening.

scholarly journals Voltage- and cold-dependent gating of single TRPM8 ion channels

2011 ◽  
Vol 137 (2) ◽  
pp. 173-195 ◽  
Author(s):  
José A. Fernández ◽  
Roman Skryma ◽  
Gabriel Bidaux ◽  
Karl L. Magleby ◽  
C. Norman Scholfield ◽  
...  
Keyword(s):  
Trp Channels ◽  
Single Channel ◽  
Membrane Depolarization ◽  
State Model ◽  
Hek293 Cells ◽  
General Mechanism ◽  
Channel Kinetics ◽  
Open Probability ◽  
Starting Point ◽  
Wide Range

Transient receptor potential (TRP) channels play critical roles in cell signaling by coupling various environmental factors to changes in membrane potential that modulate calcium influx. TRP channels are typically activated in a polymodal manner, thus integrating multiple stimuli. Although much progress has been made, the underlying mechanisms of TRP channel activation are largely unknown. The TRPM8 cation channel has been extensively investigated as a major neuronal cold sensor but is also activated by voltage, calcium store depletion, and some lipids as well as by compounds that produce cooling sensations, such as menthol or icilin. Several models of TRPM8 activation have been proposed to explain the interaction between these diverse stimuli. However, a kinetic scheme is not yet available that can describe the detailed single-channel kinetics to gain further insight into the underlying gating mechanism. To work toward this goal, we investigated voltage-dependent single-channel gating in cell-attached patches at two different temperatures (20 and 30°C) using HEK293 cells stably expressing TRPM8. Both membrane depolarization and cooling increased channel open probability (Po) mainly by decreasing the duration of closed intervals, with a smaller increase in the duration of open intervals. Maximum likelihood analysis of dwell times at both temperatures indicated gating in a minimum of five closed and two open states, and global fitting over a wide range of voltages identified a seven-state model that described the voltage dependence of Po, the single-channel kinetics, and the response of whole-cell currents to voltage ramps and steps. The major action of depolarization and cooling was to accelerate forward transitions between the same two sets of adjacent closed states. The seven-state model provides a general mechanism to account for TRPM8 activation by membrane depolarization at two temperatures and can serve as a starting point for further investigations of multimodal TRP activation.

scholarly journals Different pathways for activation and deactivation in CaV1.2: a minimal gating model

2009 ◽  
Vol 134 (3) ◽  
pp. 231-241 ◽  
Author(s):  
Stanislav Beyl ◽  
Philipp Kügler ◽  
Michaela Kudrnac ◽  
Annette Hohaus ◽  
Steffen Hering ◽  
...  
Keyword(s):  
Rate Constants ◽  
Structural Changes ◽  
Voltage Dependence ◽  
Point Mutations ◽  
Model Parameters ◽  
Voltage Sensing ◽  
Gating Model ◽  
Voltage Dependent ◽  
Current Activation ◽  
Proline Substitution

Point mutations in pore-lining S6 segments of CaV1.2 shift the voltage dependence of activation into the hyperpolarizing direction and significantly decelerate current activation and deactivation. Here, we analyze theses changes in channel gating in terms of a circular four-state model accounting for an activation R–A–O and a deactivation O–D–R pathway. Transitions between resting-closed (R) and activated-closed (A) states (rate constants x(V) and y(V)) and open (O) and deactivated-open (D) states (u(V) and w(V)) describe voltage-dependent sensor movements. Voltage-independent pore openings and closures during activation (A–O) and deactivation (D–R) are described by rate constants α and β, and γ and δ, respectively. Rate constants were determined for 16-channel constructs assuming that pore mutations in IIS6 do not affect the activating transition of the voltage-sensing machinery (x(V) and y(V)). Estimated model parameters of 15 CaV1.2 constructs well describe the activation and deactivation processes. Voltage dependence of the “pore-releasing” sensor movement ((x(V)) was much weaker than the voltage dependence of “pore-locking” sensor movement (y(V)). Our data suggest that changes in membrane voltage are more efficient in closing than in opening CaV1.2. The model failed to reproduce current kinetics of mutation A780P that was, however, accurately fitted with individually adjusted x(V) and y(V). We speculate that structural changes induced by a proline substitution in this position may disturb the voltage-sensing domain.

scholarly journals Gating kinetics of Ca2+-activated K+ channels from rat muscle incorporated into planar lipid bilayers. Evidence for two voltage-dependent Ca2+ binding reactions.

1983 ◽  
Vol 82 (4) ◽  
pp. 511-542 ◽  
Author(s):  
E Moczydlowski ◽  
R Latorre
Keyword(s):  
Linear Function ◽  
Lipid Bilayers ◽  
Single Channel ◽  
K Channel ◽  
Planar Bilayers ◽  
Gating Kinetics ◽  
Rat Muscle ◽  
Voltage Dependent ◽  
The Mean ◽  
Kinetics Of

The gating kinetics of a Ca2+-activated K+ channel from adult rat muscle plasma membrane are studied in artificial planar bilayers. Analysis of single-channel fluctuations distinguishes two Ca2+- and voltage-dependent processes: (a) short-lived channel closure (less than 1 ms) events appearing in a bursting pattern; (b) opening and closing events ranging from one to several hundred milliseconds in duration. The latter process is studied independently of the first and is denoted as the primary gating mode. At constant voltage, the mean open time of the primary gating mode is a linear function of the [Ca2+], whereas the mean closed time is a linear function of the reciprocal [Ca2+]. In the limits of zero and infinite [Ca2+], the mean open and the mean closed times are, respectively, independent of voltage. These results are predicted by a kinetic scheme consisting of the following reaction steps: (a) binding of Ca2+ to a closed state; (b) channel opening; (c) binding of a second Ca2+ ion. In this scheme, the two Ca2+ binding reactions are voltage dependent, whereas the open-closed transition is voltage independent. The kinetic constant derived for this scheme gives an accurate theoretical fit to the observed equilibrium open-state probability. The results provide evidence for a novel regulatory mechanism for the activity of an ion channel: modulation by voltage of the binding of an agonist molecule, in this case, Ca2+ ion.

scholarly journals Multi-Targeting Bioactive Compounds Extracted from Essential Oils as Kinase Inhibitors

Molecules ◽  
2020 ◽  
Vol 25 (9) ◽  
pp. 2174 ◽  
Author(s):  
Annalisa Maruca ◽  
Delia Lanzillotta ◽  
Roberta Rocca ◽  
Antonio Lupia ◽  
Giosuè Costa ◽  
...  
Keyword(s):  
Essential Oils ◽  
Binding Affinity ◽  
Structural Changes ◽  
Kinase Inhibitors ◽  
Synergistic Effects ◽  
Data Bank ◽  
Binding Modes ◽  
Starting Point ◽  
Target Action ◽  
Potential Resource

Essential oils (EOs) are popular in aromatherapy, a branch of alternative medicine that claims their curative effects. Moreover, several studies reported EOs as potential anti-cancer agents by inducing apoptosis in different cancer cell models. In this study, we have considered EOs as a potential resource of new kinase inhibitors with a polypharmacological profile. On the other hand, computational methods offer the possibility to predict the theoretical activity profile of ligands, discovering dangerous off-targets and/or synergistic effects due to the potential multi-target action. With this aim, we performed a Structure-Based Virtual Screening (SBVS) against X-ray models of several protein kinases selected from the Protein Data Bank (PDB) by using a chemoinformatics database of EOs. By evaluating theoretical binding affinity, 13 molecules were detected among EOs as new potential kinase inhibitors with a multi-target profile. The two compounds with higher percentages in the EOs were studied more in depth by means Induced Fit Docking (IFD) protocol, in order to better predict their binding modes taking into account also structural changes in the receptor. Finally, given its good binding affinity towards five different kinases, cinnamyl cinnamate was biologically tested on different cell lines with the aim to verify the antiproliferative activity. Thus, this work represents a starting point for the optimization of the most promising EOs structure as kinase inhibitors with multi-target features.

scholarly journals Determination of synchronous generator nonlinear model parameters based on power rejection tests using a gradient optimization algorithm

2017 ◽  
Vol 65 (4) ◽  
pp. 479-488 ◽  
Author(s):  
A. Boboń ◽  
A. Nocoń ◽  
S. Paszek ◽  
P. Pruski
Keyword(s):  
Parameter Estimation ◽  
Objective Function ◽  
Optimization Algorithm ◽  
Least Squares Method ◽  
Synchronous Generator ◽  
Operating Conditions ◽  
Model Parameters ◽  
State Variables ◽  
Starting Point ◽  
Gradient Optimization

AbstractThe paper presents a method for determining electromagnetic parameters of different synchronous generator models based on dynamic waveforms measured at power rejection. Such a test can be performed safely under normal operating conditions of a generator working in a power plant. A generator model was investigated, expressed by reactances and time constants of steady, transient, and subtransient state in the d and q axes, as well as the circuit models (type (3,3) and (2,2)) expressed by resistances and inductances of stator, excitation, and equivalent rotor damping circuits windings. All these models approximately take into account the influence of magnetic core saturation. The least squares method was used for parameter estimation. There was minimized the objective function defined as the mean square error between the measured waveforms and the waveforms calculated based on the mathematical models. A method of determining the initial values of those state variables which also depend on the searched parameters is presented. To minimize the objective function, a gradient optimization algorithm finding local minima for a selected starting point was used. To get closer to the global minimum, calculations were repeated many times, taking into account the inequality constraints for the searched parameters. The paper presents the parameter estimation results and a comparison of the waveforms measured and calculated based on the final parameters for 200 MW and 50 MW turbogenerators.

scholarly journals Influence of Selected Model Parameters on the Electromagnetic Levitation Melting Efficiency

2021 ◽  
Vol 11 (9) ◽  
pp. 3827
Author(s):  
Blazej Nycz ◽  
Lukasz Malinski ◽  
Roman Przylucki
Keyword(s):  
Electromagnetic Levitation ◽  
Optimization Methods ◽  
Calculation Model ◽  
Model Parameters ◽  
Starting Point ◽  
Low Efficiency ◽  
The Relationship ◽  
Reactive Metals ◽  
Electromagnetic Levitation Melting ◽  
Metal Melting

The article presents the results of multivariate calculations for the levitation metal melting system. The research had two main goals. The first goal of the multivariate calculations was to find the relationship between the basic electrical and geometric parameters of the selected calculation model and the maximum electromagnetic buoyancy force and the maximum power dissipated in the charge. The second goal was to find quasi-optimal conditions for levitation. The choice of the model with the highest melting efficiency is very important because electromagnetic levitation is essentially a low-efficiency process. Despite the low efficiency of this method, it is worth dealing with it because is one of the few methods that allow melting and obtaining alloys of refractory reactive metals. The research was limited to the analysis of the electromagnetic field modeled three-dimensionally. From among of 245 variants considered in the article, the most promising one was selected characterized by the highest efficiency. This variant will be a starting point for further work with the use of optimization methods.

scholarly journals Sparse pursuit and dictionary learning for blind source separation in polyphonic music recordings

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Sören Schulze ◽  
Emily J. King
Keyword(s):  
Single Channel ◽  
Spectral Characteristics ◽  
Musical Instruments ◽  
Model Parameters ◽  
Blind Separation ◽  
Audio Signals ◽  
Frequency Spectra ◽  
Acoustic Instruments ◽  
Invariant Properties ◽  
Music Recordings

AbstractWe propose an algorithm for the blind separation of single-channel audio signals. It is based on a parametric model that describes the spectral properties of the sounds of musical instruments independently of pitch. We develop a novel sparse pursuit algorithm that can match the discrete frequency spectra from the recorded signal with the continuous spectra delivered by the model. We first use this algorithm to convert an STFT spectrogram from the recording into a novel form of log-frequency spectrogram whose resolution exceeds that of the mel spectrogram. We then make use of the pitch-invariant properties of that representation in order to identify the sounds of the instruments via the same sparse pursuit method. As the model parameters which characterize the musical instruments are not known beforehand, we train a dictionary that contains them, using a modified version of Adam. Applying the algorithm on various audio samples, we find that it is capable of producing high-quality separation results when the model assumptions are satisfied and the instruments are clearly distinguishable, but combinations of instruments with similar spectral characteristics pose a conceptual difficulty. While a key feature of the model is that it explicitly models inharmonicity, its presence can also still impede performance of the sparse pursuit algorithm. In general, due to its pitch-invariance, our method is especially suitable for dealing with spectra from acoustic instruments, requiring only a minimal number of hyperparameters to be preset. Additionally, we demonstrate that the dictionary that is constructed for one recording can be applied to a different recording with similar instruments without additional training.

scholarly journals Activation and Two Modes of Blockade by Strontium of Ca2+-activated K+ Channels in Goldfish Saccular Hair Cells

1998 ◽  
Vol 111 (2) ◽  
pp. 363-379 ◽  
Author(s):  
Izumi Sugihara
Keyword(s):  
Dissociation Constant ◽  
Time Constant ◽  
Hair Cells ◽  
Single Channel ◽  
Hill Coefficient ◽  
K Channels ◽  
Voltage Dependent ◽  
Time Courses ◽  
The Hill ◽  
Inside Out

Effects of internal Sr2+ on the activity of large-conductance Ca2+-activated K+ channels were studied in inside-out membrane patches from goldfish saccular hair cells. Sr2+ was approximately one-fourth as potent as Ca2+ in activating these channels. Although the Hill coefficient for Sr2+ was smaller than that for Ca2+, maximum open-state probability, voltage dependence, steady state gating kinetics, and time courses of activation and deactivation of the channel were very similar under the presence of equipotent concentrations of Ca2+ and Sr2+. This suggests that voltage-dependent activation is partially independent of the ligand. Internal Sr2+ at higher concentrations (>100 μM) produced fast and slow blockade both concentration and voltage dependently. The reduction in single-channel amplitude (fast blockade) could be fitted with a modified Woodhull equation that incorporated the Hill coefficient. The dissociation constant at 0 mV, the Hill coefficient, and zd (a product of the charge of the blocking ion and the fraction of the voltage difference at the binding site from the inside) in this equation were 58–209 mM, 0.69–0.75, 0.45–0.51, respectively (n = 4). Long shut events (slow blockade) produced by Sr2+ lasted ∼10–200 ms and could be fitted with single-exponential curves (time constant, τl−s) in shut-time histograms. Durations of burst events, periods intercalated by long shut events, could also be fitted with single exponentials (time constant, τb). A significant decrease in τb and no large changes in τl−s were observed with increased Sr2+ concentration and voltage. These findings on slow blockade could be approximated by a model in which single Sr2+ ions bind to a blocking site within the channel pore beyond the energy barrier from the inside, as proposed for Ba2+ blockade. The dissociation constant at 0 mV and zd in the Woodhull equation for this model were 36–150 mM and 1–1.8, respectively (n = 3).

scholarly journals Modeling Northern Hemisphere Summer Heat Extreme Changes and Their Uncertainties Using a Physics Ensemble of Climate Sensitivity Experiments

2006 ◽  
Vol 19 (17) ◽  
pp. 4418-4435 ◽  
Author(s):  
Robin T. Clark ◽  
Simon J. Brown ◽  
James M. Murphy
Keyword(s):  
Structural Changes ◽  
Heat Waves ◽  
Full Range ◽  
Daily Maximum ◽  
Model Parameters ◽  
Mean Values ◽  
Summer Heat ◽  
Modeling Uncertainties ◽  
Physics Ensemble ◽  
Projected Changes

Abstract Changes in extreme daily temperature events are examined using a perturbed physics ensemble of global model simulations under present-day and doubled CO2 climates where ensemble members differ in their representation of various physical processes. Modeling uncertainties are quantified by varying poorly constrained model parameters that control atmospheric processes and feedbacks and analyzing the ensemble spread of simulated changes. In general, uncertainty is up to 50% of projected changes in extreme heat events of the type that occur only once per year. Large changes are seen in distributions of daily maximum temperatures for June, July, and August with significant shifts to warmer conditions. Changes in extremely hot days are shown to be significantly larger than changes in mean values in some regions. The intensity, duration, and frequency of summer heat waves are expected to be substantially greater over all continents. The largest changes are found over Europe, North and South America, and East Asia. Reductions in soil moisture, number of wet days, and nocturnal cooling are identified as significant factors responsible for the changes. Although uncertainty associated with the magnitude of expected changes is large in places, it does not bring into question the sign or nature of the projected changes. Even with the most conservative simulations, hot extreme events are still expected to substantially increase in intensity, duration, and frequency. This ensemble, however, does not represent the full range of uncertainty associated with future projections; for example, the effects of multiple parameter perturbations are neglected, as are the effects of structural changes to the basic nature of the parameterization schemes in the model.

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