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Obtaining transition rates from single-channel data without initial parameter seeding

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Obtaining transition rates from single-channel data without initial parameter seeding. / Voldsgaard Clausen, Michael.

In: Channels, Vol. 14, No. 1, 28.02.2020, p. 87-97.

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Voldsgaard Clausen, Michael. / Obtaining transition rates from single-channel data without initial parameter seeding. In: Channels. 2020 ; Vol. 14, No. 1. pp. 87-97.

Bibtex

@article{9c05dff93b5b4cb98d4be9a803925722,
title = "Obtaining transition rates from single-channel data without initial parameter seeding",
abstract = "Background and Purpose: Ion-channels are membrane proteins that can adopt several distinct structural conformations. Some of the conformations are open and allow the passage of ions through the membrane; others are closed and hinder ion flow. Patch-clamp recordings of single ion-channels show if a channel is open or closed, but does not immediately reveal the underlying mechanism, which typically includes several open and closed conformations.With kinetic analysis of single-channel data, sequences of observed open and closed times are fitted to proposed schemes to deduct the underlying kinetics of the ion-channel. Current programs to perform kinetic analysis uses initial parameter guessing. Here an alternative approach that uses a global fitting procedure and no initial parameter seeding is developed and tested.Methods: Different fitting algorithms that use variations and combinations of Simplex-optimization, Genetic Algorithm and Particle Swarm are tested against simulated data with brief events removed as in real resolution limited data.Results: A two-step fitting algorithm that uses Particle Swarm optimization to find initial parameters and then a modified Simplex approach to fine-adjust the initial parameters successfully find the correct rates used for data simulation.Conclusions: SCAIM (Single Channel Analysis in MATLAB) facilitate the deduction of kinetic schemes underlying single-channel data.",
author = "{Voldsgaard Clausen}, Michael",
year = "2020",
month = feb,
day = "28",
doi = "10.1080/19336950.2020.1732004",
language = "English",
volume = "14",
pages = "87--97",
journal = "Channels (Austin)",
issn = "1933-6950",
publisher = "Taylor & Francis Inc.",
number = "1",

}

RIS

TY - JOUR

T1 - Obtaining transition rates from single-channel data without initial parameter seeding

AU - Voldsgaard Clausen, Michael

PY - 2020/2/28

Y1 - 2020/2/28

N2 - Background and Purpose: Ion-channels are membrane proteins that can adopt several distinct structural conformations. Some of the conformations are open and allow the passage of ions through the membrane; others are closed and hinder ion flow. Patch-clamp recordings of single ion-channels show if a channel is open or closed, but does not immediately reveal the underlying mechanism, which typically includes several open and closed conformations.With kinetic analysis of single-channel data, sequences of observed open and closed times are fitted to proposed schemes to deduct the underlying kinetics of the ion-channel. Current programs to perform kinetic analysis uses initial parameter guessing. Here an alternative approach that uses a global fitting procedure and no initial parameter seeding is developed and tested.Methods: Different fitting algorithms that use variations and combinations of Simplex-optimization, Genetic Algorithm and Particle Swarm are tested against simulated data with brief events removed as in real resolution limited data.Results: A two-step fitting algorithm that uses Particle Swarm optimization to find initial parameters and then a modified Simplex approach to fine-adjust the initial parameters successfully find the correct rates used for data simulation.Conclusions: SCAIM (Single Channel Analysis in MATLAB) facilitate the deduction of kinetic schemes underlying single-channel data.

AB - Background and Purpose: Ion-channels are membrane proteins that can adopt several distinct structural conformations. Some of the conformations are open and allow the passage of ions through the membrane; others are closed and hinder ion flow. Patch-clamp recordings of single ion-channels show if a channel is open or closed, but does not immediately reveal the underlying mechanism, which typically includes several open and closed conformations.With kinetic analysis of single-channel data, sequences of observed open and closed times are fitted to proposed schemes to deduct the underlying kinetics of the ion-channel. Current programs to perform kinetic analysis uses initial parameter guessing. Here an alternative approach that uses a global fitting procedure and no initial parameter seeding is developed and tested.Methods: Different fitting algorithms that use variations and combinations of Simplex-optimization, Genetic Algorithm and Particle Swarm are tested against simulated data with brief events removed as in real resolution limited data.Results: A two-step fitting algorithm that uses Particle Swarm optimization to find initial parameters and then a modified Simplex approach to fine-adjust the initial parameters successfully find the correct rates used for data simulation.Conclusions: SCAIM (Single Channel Analysis in MATLAB) facilitate the deduction of kinetic schemes underlying single-channel data.

U2 - 10.1080/19336950.2020.1732004

DO - 10.1080/19336950.2020.1732004

M3 - Journal article

C2 - 32108549

VL - 14

SP - 87

EP - 97

JO - Channels (Austin)

JF - Channels (Austin)

SN - 1933-6950

IS - 1

ER -