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1. Model information:

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This is the readme for the model associated with the paper:

Neumaier F, Apldogan S, Hescheler J and Schneider T (2020) Zn²⁺-induced changes in Ca_v2.3 channel function: An electrophysiological and modeling study. J. Gen. Physiol. (https://doi.org/10.1085/jgp.202012585)

Model information:

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The state diagram for the Ca_v2.3 channel model in the absence of trace metal ions, which was developed based on channel structure, previous modeling studies and the ability to fit the data, is shown below (see also Fig. 15 in the accompanying paper). Horizontal transitions are voltage-dependent and correspond to movement of the four non-identical voltage-sensors and pore opening or closing respectively. Activation of two voltage-sensors (1 and 2) is obligatory for channel opening, giving rise to a total of 4 open states. Vertical transitions are voltage-independent and correspond to entry into and return from fast and slow inactivated states. The rates for voltage-dependent transitions were expressed in terms of the transition-state theory, and the parameters optimized by fitting the model to macroscopic currents recorded with various electrophysiological protocols (see below). The effects of Zn²⁺ were implemented by assuming that Zn²⁺ binding to a first site (K_Zn=0.003 mM) leads to electrostatic modification and mechanical slowing of one of the voltage-sensors while Zn²⁺-binding to a second, intra-pore site (K_Zn=0.1 mM) blocks the channel and modifies the opening and closing transitions (for details see the accompanying paper).

$Beschreibung: Beschreibung: Beschreibung: Beschreibung: Beschreibung: C:\Users\Felix\Dropbox\5. MANUSCRIPTS\Eigene\Zn Effects and Model Neu\Model (Site 1+2)\New folder\Final_Revised\Cav23\readme-Dateien\image001.jpg$

Experimental and modeling conditions:

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As a basis for model development, whole-cell patch-clamp recordings were performed in HEK-293 cells stably transfected with human Ca_v2.3+β₃ channel subunits. All recordings were performed at room temperature and with near-physiological extracellular solutions that contained 4 mM free Ca²⁺ for ionic currents or 4 mM free Mg²⁺ and 0.1 mM free La³⁺ for gating currents. The complete data set used for fitting included gating currents recorded at 15 different test potentials, long (400 ms) and short (25 ms) IV-currents recorded at 10 and 15 different test potentials respectively, IIV-currents recorded at 13 different test potentials and PPI-currents recorded at 14 different test potentials (for details on the voltage protocols see the accompanying paper and the simulations below). Parameter optimization and simulations were performed with an in silico one-compartmental model of a HEK293 cell with diameter and length 21.851 �m, which corresponds to a sphere with a surface area of 1500 �m². Default temperature, specific membrane capacitance and cytoplasmic resistivity were 22�C, 1 �F/cm² and 60 Ω*cm respectively. �

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2. Files:

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The following files are required to run one of the simulations:

'Cav23.mod', which contains the Markov-type kinetic model of Cav2.3 channels

'vclamp_pl.mod', which contains a voltage clamp model with five levels that has been adopted from a previous model by Balbi et al. (Accession: 230137)

'IV static.hoc', 'IV dynamic.hoc', 'IVlong static.hoc', 'IVlong dynamic.hoc', 'IIV.hoc' or 'PPI.hoc', which contain the code for the different simulations described in section 4

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3. Compiling the mechanism (.mod) files and starting a simulation:

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Under linux:

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Compile the mod files using the command 'nrnivmodl'.

Use one of the following commands to start the simulations:

nrngui IV static.hoc

nrngui IV dynamic.hoc

nrngui IVlong static.hoc

nrngui IVlong dynamic.hoc

nrngui IIV.hoc

nrngui PPI.hoc

Under Windows:

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Run 'mknrndll' to compile the mod files.

Double click on one of the hoc files to start the simulations.

Under MAC OS X:

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Drag the model folder onto the mknrndll icon to compile the mod files.

Drag one of the hoc files onto the nrngui icon to start the simulations.

More information on running NEURON models can be found at

https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.htm

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4. Simulation control:

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When one of the hoc files is started, several panels for simulation control will appear. The Clamp Control panel (middle) contains the start button for running simulations and several clamp parameters, which can be changed by the user to modify the default voltage protocol. The CaR Control panel (bottom) provides control over the number of channels per cm², the single channel permeability and the free Zn²⁺ concentration (in mM). The simulation speed can be adjusted by reducing or increasing the value of dt in the Run Control panel (top).

IV static.hoc:

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IV dynamic.hoc:

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With the default clamp parameters, a click on the start button runs a dynamic simulation with the same voltage protocol as above but a clamping increment of 1 mV and plots the peak current-voltage relationship.

IVlong static.hoc:

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IVlong dynamic.hoc:

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IIV.hoc:

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PPI.hoc:

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With the default clamp parameters, a click on the start button generates a family of current traces (bottom window) evoked with the same voltage protocol (top window) as that used in Fig. 15E and 16B of the paper and plots the normalized pre-pulse inactivation relationship. The simulation speed can be increased by deselecting the Display Button at the bottom of the Clamp Control panel, which switches off display of the current traces during the simulation.