MarkoLAB: A simulator to study ionic channel's stochastic behavior

MarkoLAB: A simulator to study ionic channel's stochastic behavior

Author da Silva, Robson Rodrigues Google Scholar
Goroso, Daniel Gustavo Autor UNIFESP Google Scholar
Bers, Donald M. Google Scholar
Puglisi, Jose Luis Google Scholar
Abstract A Summary: Mathematical models of the cardiac cell have started to include markovian representations of the ionic channels instead of the traditional Hodgkin & Huxley formulations. There are many reasons for this: Markov models are not restricted to the idea of independent gates defining the channel, they allow more complex description with specific transitions between open, closed or inactivated states, and more importantly those states can be closely related to the underlying channel structure and conformational changes. Methods: We used the LabVIEW (R) and MATLAB (R) programs to implement the simulator MarkoLAB that allow a dynamical 3D representation of the markovian model of the channel. The Monte Carlo simulation was used to implement the stochastic transitions among states. The user can specify the voltage protocol by setting the holding potential, the step-to voltage and the duration of the stimuli. Results: The most studied feature of a channel is the current flowing through it. This happens when the channel stays in the open state, but most of the time, as revealed by the low open probability values, the channel remains on the inactive or closed states. By focusing only when the channel enters or leaves the open state we are missing most of its activity. MarkoLAB proved to be quite useful to visualize the whole behavior of the channel and not only when the channel produces a current. Such dynamic representation provides more complete information about channel kinetics and will be a powerful tool to demonstrate the effect of gene mutations or drugs on the channel function. Conclusions: MarkoLAB provides an original way of visualizing the stochastic behavior of a channel. It clarifies concepts, such as recovery from inactivation, calcium-versus voltage-dependent inactivation, and tail currents. It is not restricted to ionic channels only but it can be extended to other transporters, such as exchangers and pumps. This program is intended as a didactical tool to illustrate the dynamical behavior of a channel. It has been implemented in two platforms MATLAB (R) and LabVIEW (R) to enhance the target users of this new didactical tool. The computational cost of implementing a stochastic simulation is within the range of a personal computer performance

making MarkoLAB suitable to be run during a lecture or presentation.
Keywords Ionic channels
Markov models
Experiments in silico
Language English
Sponsor Sao Paulo Research Foundation (FAPESP)
Mathematical Modeling and Simulation of Biological System
California North State University
Grant number FAPESP: 2013/20220-5
FAPESP: 2016/18422-7
Mathematical Modeling and Simulation of Biological System: 2016/2
California North State University: 02-02-01-1300-67535
Date 2017
Published in Computers In Biology And Medicine. Oxford, v. 87, p. 258-270, 2017.
ISSN 0010-4825 (Sherpa/Romeo, impact factor)
Publisher Pergamon-Elsevier Science Ltd
Extent 258-270
Access rights Closed access
Type Article
Web of Science ID WOS:000409151600026

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