Nanoscale organization in the cell membrane dynamically modulates the biophysics of voltage-gated sodium channels
Data files
May 13, 2026 version files 9.59 GB
-
raw_data.zip
9.59 GB
-
README.md
14.43 KB
Abstract
Precise regulation of ion channel biophysics is an essential life process that governs electrical signaling in excitable tissues. Many ion channels including voltage-gated Na+ channels (NaVs) exist in the membrane as clusters, which show distinct biophysical behavior not predicted by single-channel measurements. In both heterologous and native systems, we report that single-channel-based predictions significantly overestimated Na+ current (INa) amplitudes from multi-channel clusters. Computational modeling suggested that these observations could reflect interactions between adjacent channels, such as recently reported between NaVs, and identified specific biophysical consequences thereof. This updated model not only accurately predicted behaviors observed from NaV clusters and consequent cellular physiology, but also suggested the possibility that clustered NaVs may respond differently to use-dependent pharmacological agents. Experiments validated the latter prediction and further identified modulation of clustering as a novel approach to correcting macroscopic electrophysiological dysfunction resulting from NaV defects linked to life-threatening arrhythmias and seizures. Thus, our study not only motivates a fundamental revision of how ion channels behave when clustered but also highlights resulting biophysical effects as important considerations for pharmacology and a potential therapeutic target to address human disease.
Dataset DOI: 10.5061/dryad.0cfxpnwgh
Description of the data and file structure
The dataset contains data from single-channel, multi-channel and whole-cell patch-clamp and confocal and MINFLUX fluorescence microscopy experiments. The experiments were performed in heterologous expression systems (stably and transiently transfected Chinese Hamster Ovary (CHO) cells) and freshly isolated mouse ventricular cardiac myocytes.
Files and variables
File: raw_data.zip
Description: This zipped folder contains the "raw data" folder which contains the following datasets:
CHO BC2-NaV1.5 whole cell INa folder contains whole-cell patch-clamp recordings of sodium currents of NaV1.5 channels with or without BC2-tag (raw data files sub-folder) and their analysis (BC2 validation spreadsheet). BC2 validation spreadsheet contains analysis of peak sodium current densities and normalized peak sodium conductance (sheet: peak INa density and GGmax), steady-state inactivation of sodium currents (sheet: SSI, IImax), and late sodium currents (sheet: late INa, % of peak INa). Each sheet specifies experimental conditions (mNav1.5 – mouse NaV1.5 channel, or mNav1.5-BC2 – mouse NaV1.5 channel with inserted BC2-tag), file names, and results of measurements of corresponding parameters in each of the files.
Fluorescence microscopy folder contains all unprocessed and processed images obtained in confocal microscopy and MINFLUX measurements of NaV1.5 channel localizations in Fluorescence microscopy data sub-folder. These images are separated into 2 subfolders: CHO - Control, Taxol and Mouse – delKPQ containing images obtained from CHO cells in control conditions and after taxol treatment and cardiac myocytes from deltaKPQ mice, respectively. Abbreviations used in file names: Control_NaV15 - CHO cells expressing BC2 tagged NaV1.5 channel in control conditions, Taxol_NaV15 - CHO cells expressing BC2-tagged NaV1.5 channel and treated with taxol. D-KPQ_Ms_control: mouse cardiac myocytes from deltaKPQ mice in control condition, D-KPQ_Ms_SB2: SB2 treated mouse cardiac myocytes from deltaKPQ mice. MINFLUX spreadsheet contains results of MINFLUX measurements of cluster densities (# localization/nm2) in each condition specified above.
CHO WT-NaV1.5 whole cell INa VTD folder contains whole-cell patch-clamp recordings of sodium currents in control conditions and after treatment cells with veratridine (raw abf files sub-folder) and their analysis (CHO1.5 VTD spreadsheet). CHO1.5 VTD spreadsheet contains raw values of peak (peak INa) and tail (tail INa) sodium currents, ratios of tail to peak INa (tail INa % of peak INa) and cell capacitance values for each of the specified file names. The column “cond” indicate conditions of the corresponding peak and tail INa measurement (baseline: control condition, VTD 25 uM – after application of 25 uM of veratridine). Cell count is specified above each file name.
deltaKPQ myocytes action potentials folder contains whole-cell patch-clamp recordings of action potential in mouse cardiac myocytes from deltaKPQ mice (raw data files sub-folder) and their analysis (AP data files spreadsheet). In AP data files spreadsheet, the following parameters are specified: genotype of mouse, mouse #, mouse sex, DOB – mouse date of birth, DOE – date of experiment, condition (CTR – control condition, SB2 – cells treated with SB2), cell count for each mouse, files – file names associated with each of the cells, total time of recordings,s – total time of recording from each of the cells in seconds, # EAD – number of early after-depolarizations, #DAD – number of delayed after-depolarizations, freq EAD, Hz – frequency of EADs in Hertz, freq DAD, Hz – frequency of DADs in Hertz, APD90 mean, ms – mean action potential duration at 90% of repolarization in milliseconds.
deltaKPQ myocytes whole-cell INa folder contains whole-cell patch-clamp recordings of sodium currents in cardiac myocytes from deltaKPQ mice (data files sub-folder) and their analysis (deltaKPQ myocytes whole cell spreadsheet). In deltaKPQ myocytes whole cell spreadsheet, results of analysis are split into 3 sheets. Peak sheet contains analysis of peak sodium current densities. Late sheet contains analysis of late sodium current magnitudes. SSI sheet contains analysis of steady-state inactivation of sodium currents. Each sheet specifies mouse line, mouse number, mouse sex, mouse date of birth (DOB), date of experiment (date), mouse age in weeks on the day of experiment, experimental conditions (condition: control (ctr) or SB2 5 uM), file name, cell capacitance (pF), and results of measurements.
CHO-NaV1.6 cell-attached recordings - late and peak INa analysis folder contains cell-attached patch-clamp recordings of NaV1.6 sodium currents in single-channel (single channel recordings sub-folder) and multi-channel (multi channel recordings sub-folder) membrane patches. CHO-NaV1.6 cell-attached parameters spreadsheet contains results of analysis of late (in late INa, % of peak column) and peak ion channel activity (in average peak INa, pA column) in single-channel (single channel recordings - control condition merged row) and multi-channel (multi-channel recordings - control condition merged row) recordings from files specified in the file name column.
CHO deltaKPQ-NaV1.5 cell-attached recordings folder contains cell-attached patch-clamp recordings of deltaKPQ-NaV1.5 sodium currents in raw data files sub-folder. The recordings are sorted into two sub-folders: single-channel (dKPQ single-channels sub-folder) and multi-channel (dKPQ multi-channels sub-folder) recordings. CHO deltaKPQ-NaV1.5 cell-attached spreadsheed contains results of analysis of late (in late INa, % of peak column) and peak ion channel activity (in average peak INa, pA column) in single-channel (single channel recordings - merged row) and multi-channel (multi-channel recordings merged row) recordings from files specified in the file name column.
CHO-NaV1.5 cell-attached recordings - late and peak INa analysis folder contains cell-attached patch-clamp recordings of wild-type (WT) NaV1.5 sodium currents from CHO cells in raw data files sub-folder. The recordings are sorted into 4 sub-folders based on the experimental conditions: control single-channel recordings (CHO-NaV1.5 CTR single-channel recordings sub-folder), control multi-channel recordings (CHO-NaV1.5 CTR multi-channel recordings sub-folder), single-channel recordings in cells treated with taxol (TXL) (CHO-NaV1.5 + TXL single-channel recordings sub-folder), multi-channel recordings in cells treated with taxol (TXL) (CHO-NaV1.5 multi-channel + TXL recordings sub-folder). Results of analysis of these recordings are in CHO-NaV1.5 cell-attached parameters spreadsheet. In CHO-NaV1.5 cell-attached parameters spreadsheet, analyzed parameters are grouped into 3 sheets. Single-channel recordings sheet contains results of analysis of the following parameters: time constant (tau) of peak decay, ms, single-channel open probability (Po) time to peak, ms, single channel peak Po, late INa, % of peak, average peak INa, pA. These parameters are specified for each file indicated in the file name column. Results are grouped into two sub-sections: single channel recordings - control condition, and single channel recordings -TXL indicated by headers in merged lines. Mult-ch. peak and late sheet contains results of analysis of the following parameters: late INa, % of peak and average peak INa, pA. These parameters are specified for each of the files indicated in the file name column. Results are grouped into two sub-sections: multi channel recordings - control condition, and multi channel recordings - TXL indicated by headers in merged lines. Mult-ch. taus, DKL and VMR sheet contains results of analysis of the following parameters in multi-channel recordings: time constant (tau) of peak decay, ms, multi-channel Kullback-Leibler divergence (DKL) at peak and multi-ch variance-to-mean ratio (VMR) at peak current. These parameters are specified for each of the files indicated in the file name column. Results are grouped into two sub-sections: multi channel recordings - control condition, and multi channel recordings - TXL indicated by headers in merged lines.
CHO-NaV1.5 cell-attached recordings - lidocaine blockade folder contains cell-attached patch-clamp recordings of NaV1.5 sodium currents in CHO cells before and after treatment with 50 uM lidocaine in raw data files sub-folder and their analysis in CHO-NaV1.5 cell-attached lidocaine spreadsheet. Files in raw data files sub-folder are grouped into recordings from single-channel (lido single ch records sub-folder) and multi-channel patches (lido multi ch records sub-folder). CHO-NaV1.5 cell-attached lidocaine spreadsheet specifies file name and parameters measured in the corresponding files: average peak sodium current before lidocaine in picoAmpers (average peak I-ctr, pA) and average peak sodium current after lidocaine in picoAmpers (peak I-liod/peak I-ctr, pA), and ratio of average peak currents after lido to that before lido (peak I-liod/peak I-ctr). Results are split into 2 sections (merged rows): single-channel recordings and multi-channel recordings.
CHO WT-NaV1.5 and WT-NaV1.6 whole cell INa peak late folder contains whole-cell patch-clamp recordings of wild-type (WT) NaV1.5 and NaV1.6 channels in CHO cells in CHO WT-NaV1.5 whole cell INa peak-late row abf files and CHO WT-NaV1.6 whole cell INa peak-late row abf files sub-folders, respectively. Corresponding analysis spreadsheets (CHO NaV1.5 peak late correlation spreadsheet and CHO NaV1.6 peak late correlation spreadsheet) are organized as follows. Row 1: cell number, row 2: a name of an .abf file containing a raw recording, row 3: cell capacitance (pF), row 4: parameter identifiers (peak INa density, pA/pF and INa late, % of peak), row 4: average values of the corresponding parameters, each next row contains raw measurements of peak and late sodium current (INa) from each current sweeps.
CHO N1768D-NaV1.6 whole cell INa folder contains whole-cell patch-clamp recordings of mutant (N1768D) NaV1.6 channels in CHO cells in raw data files sub-folder. The corresponding analysis spreadsheet (CHO N1768D spreadsheets) is organized as follow, row 1: .abf file name, row 2: cell capacitance (pF), row 4: parameter identifiers (peak INa density, pA/pF and INa late, % of peak), row 4: average values of the corresponding parameters, each next row contain raw measurements of peak and late sodium current (INa) from each sweep.
CHO-NaV1.5 cell-attached recordings - recovery from inactivation folder contains cell-attached patch-clamp recordings of recovery from inactivation of NaV1.5 sodium currents in CHO cells in raw data files sub-folder and their analysis in CHO-NaV1.5 recovery from inactivation spreadsheet. Files in raw data files sub-folder are grouped into recordings from single-channel (single ch - recovery from inactivationsub-folder) and multi-channel patches (multi ch - recovery from inactivation sub-folder). CHO-NaV1.5 recovery from inactivation spreadsheet specifies file name and ratio peak 2 to peak 1 (P2/P1) for average peak sodium currents evoked by the two-pulse recovery from inactivation protocol. Results are split into 2 sections (merged rows): single-channel recordings and multi-channel recordings.
List of abbreviations:
CHO – Chinese hamster ovary cells
WT – wild-type variant of a protein
Ctr - control
NaV1.5 – Sodium channel protein type 5 subunit alpha (gene: Scn5a)
mNaV1.5 – mouse NaV1.5
deltaKPQ-NaV1.5 – deletion of 3 amino acids (1505 – 1507 KPQ) in the NaV1.5 channel
NaV1.6 - Sodium channel protein type 8 subunit (gene: Scn8a)
INa – sodium (Na+) current
INa-L – late INa
SSI – steady-state inactivation
G/Gmax – normalized to maximum conductance
I/Imax – normalized to maximum current
BC2 – peptide tag
MINFLUX – minimal fluorescence photon fluxes
TXL – taxol (generic name: paclitaxel), microtubule polymerization inhibitor
VTD – veratridine, voltage-gated sodium channels modifier
SB2 - SB216763, glycogen synthase 3 inhibitor
Lido – lidocaine, voltage-gated sodium channel inhibitor
DOB – date of birth
DOE – date of experiment
APD90 – action potential duration at 90% of repolarization
EAD – early after-depolarization in action potential
DAD - delayed after-depolarization in action potential
DKL – Kullback-Leibler divergence
VMR – variance-to-mean ratio
Code/software
Imspector software (v16.3.15645-m2205, open-source software available under MIT license: https://github.com/AbberiorInstruments/ImspectorDocs) is used for opening and analysis of fluorescence microscopy data stored in MRS files in Fluorescence microscopy\Fluorescence microscopy data). MRS files can also be viewed using the open source ImageJ/Fiji software.
All electrophysiology data (single ion channel, multi-channels and whole-cell patch-clamp recordings) are stored in ABF files which can be opened with ABFview software (open-source software available under MIT license: https://github.com/swharden/ABFview). ABF files can also be viewed in the free ABF Viewer here https://conductscience.com/tools/file-formats/abf-viewer.
LibreOffice open-source software (https://www.libreoffice.org/) can be used to open all spreadsheets.
Custom code used for analysis of cell-attached patch-clamp recordings and ion channel cluster density in MINFLUX experiments are deposited at GitHub: https://github.com/tarasov4/Analysis-and-modeling-of-voltage-gated-sodium-channels-clusters
