scholarly journals Identification of Structures for Ion Channel Kinetic Models

2021 ◽  
Author(s):  
Kathryn E. Mangold ◽  
Wei Wang ◽  
Eric K. Johnson ◽  
Druv Bhagavan ◽  
Jonathan D. Moreno ◽  
...  
Keyword(s):  
Markov Model ◽  
Ion Channel ◽  
Markov Models ◽  
Left Ventricular ◽  
Channel Dynamics ◽  
Voltage Gated ◽  
Minimum Number ◽  
Voltage Gated Ion Channels ◽  
Channel Currents ◽  
Channel Kinetic

AbstractMarkov models of ion channel dynamics have evolved as experimental advances have improved our understanding of channel function. Past studies have examined various topologies for Markov models of channel dynamics. We present a systematic method for identification of all possible Markov model topologies using experimental data for two types of native voltage-gated ion channel currents: mouse atrial sodium and human left ventricular fast transient outward potassium currents. In addition to optional biophysically inspired restrictions on the number of connections from a state and elimination of long-range connections, this study further suggests successful models have more than minimum number of connections for set number of states. When working with topologies with more than the minimum number of connections, the topologies with three and four connections to the open state tend to serve well as Markov models of ion channel dynamics.Significance StatementHere, we present a computational routine to thoroughly search for Markov model topologies for simulating whole-cell currents given an experimental dataset. We test this method on two distinct types of voltage-gated ion channels that function in the generation of cardiac action potentials. Particularly successful models have more than one connection between an open state and the rest of the model, and large models may benefit from having even more connections between the open state and the rest of the other states.

scholarly journals Identification of structures for ion channel kinetic models

2021 ◽  
Vol 17 (8) ◽  
pp. e1008932
Author(s):  
Kathryn E. Mangold ◽  
Wei Wang ◽  
Eric K. Johnson ◽  
Druv Bhagavan ◽  
Jonathan D. Moreno ◽  
...  
Keyword(s):  
Experimental Data ◽  
Ion Channel ◽  
Channel Model ◽  
Markov Models ◽  
A Priori ◽  
Model Performance ◽  
Left Ventricular ◽  
Channel Dynamics ◽  
Channel Currents ◽  
Channel Kinetic

Markov models of ion channel dynamics have evolved as experimental advances have improved our understanding of channel function. Past studies have examined limited sets of various topologies for Markov models of channel dynamics. We present a systematic method for identification of all possible Markov model topologies using experimental data for two types of native voltage-gated ion channel currents: mouse atrial sodium currents and human left ventricular fast transient outward potassium currents. Successful models identified with this approach have certain characteristics in common, suggesting that aspects of the model topology are determined by the experimental data. Incorporating these channel models into cell and tissue simulations to assess model performance within protocols that were not used for training provided validation and further narrowing of the number of acceptable models. The success of this approach suggests a channel model creation pipeline may be feasible where the structure of the model is not specified a priori.

scholarly journals Approaches for unveiling the kinetic mechanisms of voltage gated ion channels in neurons

2019 ◽  
Author(s):  
◽  
Marco Antonio Navarro
Keyword(s):  
Experimental Data ◽  
Ion Channels ◽  
Ion Channel ◽  
Rate Constants ◽  
Markov Models ◽  
Neuronal Firing ◽  
Voltage Gated ◽  
Voltage Gated Ion Channels ◽  
Parameter Constraints ◽  
Gated Ion Channels

Ionic currents drive cellular function within all living cells to perform highly specific tasks. For excitable cells, such as muscle and neurons, voltage-gated ion channels have finely tuned kinetics that allow the transduction of Action potentials to other cells. Voltage-gated ion channels are molecular machines that open and close depending on electrical potential. Neuronal firing rates are largely determined by the overall availability of voltage-gated Na+ and K+ currents.This work describes new approaches for collecting and analyzing experimental data that can be used to streamline experiments. Ion channels are composed of multimeric complexes regulated by intracellular factors producing complex kinetics. The stochastic behavior of thousands of individual ion hannels coordinates to produce cellular activity. To describe their activity and test hypotheses about the channel, experimenters often fit Markov models to a set of experimental data. Markov models are defined by a set of states, whose transitions described by rate constants. To improve the modeling process, we have developed computational approaches to introduce kinetic constraints that reduces the parameter search space. This work describes the implementation and mathematical transformations required to describe linear and non-linear parameter constraints that govern rate constants. Not all ion channel behaviors can easily be described by rate constants. Therefore, we developed and implemented a penalty-based mechanism that can be used to guide the optimization engine to produce a model with a desired behavior, such as single-channel open probability and use dependent effects. To streamline data collection for experiments in brain slice preparations, we developed a 3D virtual software environment that incorporates data from micro-positioning motors and scientific cameras in real-time. This environment provides positional feedback to the investigator and allows for the creation of data maps including both images and electrical recordings. We have also produced semi-automatic targeting procedures that simplifies the overall experimental experience. Experimentally, this work also examines how the kinetic mechanism of voltage gated Na channels regulates the neuronal firing of brainstem respiratory neurons. These raphe neurons are intrinsic pacemakers that do not rely on synaptic connections to elicit activity. I explored how intracellular calcium regulates the kinetics of TTX-sensitive Na+ currents using whole-cell patch clamp electrophysiology. Established with intracellular Ca2+ buffers, high [Ca2+] levels greater than ~7 [micro]M did not change the voltage dependence of steady-state activation and inactivation, but slightly slowed inactivation time course. However, the recovery from inactivation and use dependence inactivation is slowed by high intracellular [Ca2+]. Overall, these approaches described in this work have improved data acquisition and data analysis to create better ion channel models and enhance the electrophysiology experience.

Modified Hodgkin-Huxley Equations Arising from Mesoscopic Voltage-Gated Processes

2012 ◽  
Vol 19 (02) ◽  
pp. 1250014 ◽  
Author(s):  
Mauricio Tejo A.
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Open System ◽  
Membrane Voltage ◽  
Propagation Of Chaos ◽  
Channel Dynamics ◽  
Voltage Gated ◽  
Huxley Equation ◽  
Voltage Gated Ion Channels ◽  
Gated Ion Channels

The voltage-gated ion channels system is an example of a classical open system. This work establishes conditions on open ion channel dynamics for which a modified Hodgkin-Huxley equation for the membrane voltage arises as propagation of chaos. This is the approach we propose in order to study the mesoscopic voltage-gated ion channel dynamics together with the macroscopic voltage equation.

scholarly journals Computing Optimal Properties of Drugs Using Mathematical Models of Single Channel Dynamics

2018 ◽  
Vol 6 (1) ◽  
pp. 41-64 ◽  
Author(s):  
Aslak Tveito ◽  
Mary M. Maleckar ◽  
Glenn T. Lines
Keyword(s):  
Differential Equations ◽  
Markov Model ◽  
Stochastic Models ◽  
Markov Models ◽  
Single Channel ◽  
Probability Density Functions ◽  
Density Functions ◽  
Mathematical Framework ◽  
Wild Type ◽  
Channel Dynamics

AbstractSingle channel dynamics can be modeled using stochastic differential equations, and the dynamics of the state of the channel (e.g. open, closed, inactivated) can be represented using Markov models. Such models can also be used to represent the effect of mutations as well as the effect of drugs used to alleviate deleterious effects of mutations. Based on the Markov model and the stochastic models of the single channel, it is possible to derive deterministic partial differential equations (PDEs) giving the probability density functions (PDFs) of the states of the Markov model. In this study, we have analyzed PDEs modeling wild type (WT) channels, mutant channels (MT) and mutant channels for which a drug has been applied (MTD). Our aim is to show that it is possible to optimize the parameters of a given drug such that the solution of theMTD model is very close to that of the WT: the mutation’s effect is, theoretically, reduced significantly.We will present the mathematical framework underpinning this methodology and apply it to several examples. In particular, we will show that it is possible to use the method to, theoretically, improve the properties of some well-known existing drugs.

Voltage-Gated Ion Channels and Hereditary Disease

1999 ◽  
Vol 79 (4) ◽  
pp. 1317-1372 ◽  
Author(s):  
Frank Lehmann-Horn ◽  
Karin Jurkat-Rott
Keyword(s):  
Ion Channels ◽  
Ion Channel ◽  
Recombinant Dna ◽  
Hereditary Disease ◽  
Hereditary Diseases ◽  
Technological Advancement ◽  
Myotonia Congenita ◽  
Voltage Gated ◽  
Voltage Gated Ion Channels ◽  
Gated Ion Channels

By the introduction of technological advancement in methods of structural analysis, electronics, and recombinant DNA techniques, research in physiology has become molecular. Additionally, focus of interest has been moving away from classical physiology to become increasingly centered on mechanisms of disease. A wonderful example for this development, as evident by this review, is the field of ion channel research which would not be nearly as advanced had it not been for human diseases to clarify. It is for this reason that structure-function relationships and ion channel electrophysiology cannot be separated from the genetic and clinical description of ion channelopathies. Unique among reviews of this topic is that all known human hereditary diseases of voltage-gated ion channels are described covering various fields of medicine such as neurology (nocturnal frontal lobe epilepsy, benign neonatal convulsions, episodic ataxia, hemiplegic migraine, deafness, stationary night blindness), nephrology (X-linked recessive nephrolithiasis, Bartter), myology (hypokalemic and hyperkalemic periodic paralysis, myotonia congenita, paramyotonia, malignant hyperthermia), cardiology (LQT syndrome), and interesting parallels in mechanisms of disease emphasized. Likewise, all types of voltage-gated ion channels for cations (sodium, calcium, and potassium channels) and anions (chloride channels) are described together with all knowledge about pharmacology, structure, expression, isoforms, and encoding genes.

scholarly journals Fluorescence Imaging of Electrically Stimulated Cells

2003 ◽  
Vol 8 (6) ◽  
pp. 660-667 ◽  
Author(s):  
Paul Burnett ◽  
Janet K. Robertson ◽  
Jeffrey M. Palmer ◽  
Richard R. Ryan ◽  
Adrienne E. Dubin ◽  
...  
Keyword(s):  
Membrane Potential ◽  
Ion Channels ◽  
Ion Channel ◽  
High Throughput ◽  
Pharmacological Intervention ◽  
Voltage Gradient ◽  
Channel Activity ◽  
Voltage Gated ◽  
Voltage Gated Ion Channels ◽  
Gated Ion Channels

Designing high-throughput screens for voltage-gated ion channels has been a tremendous challenge for the pharmaceutical industry because channel activity is dependent on the transmembrane voltage gradient, a stimulus unlike ligand binding to G-protein-coupled receptors or ligand-gated ion channels. To achieve an acceptable throughput, assays to screen for voltage-gated ion channel modulators that are employed today rely on pharmacological intervention to activate these channels. These interventions can introduce artifacts. Ideally, a high-throughput screen should not compromise physiological relevance. Hence, a more appropriate method would activate voltage-gated ion channels by altering plasma membrane potential directly, via electrical stimulation, while simultaneously recordingthe operation of the channel in populations of cells. The authors present preliminary results obtained from a device that is designed to supply precise and reproducible electrical stimuli to populations of cells. Changes in voltage-gated ion channel activity were monitored using a digital fluorescent microscope. The prototype electric field stimulation (EFS) device provided real-time analysis of cellular responsiveness to physiological and pharmacological stimuli. Voltage stimuli applied to SK-N-SH neuroblastoma cells cultured on the EFS device evoked membrane potential changes that were dependent on activation of voltage-gated sodium channels. Data obtained using digital fluorescence microscopy suggests suitability of this system for HTS.

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