Literature DB >> 17557165

The power of two-dimensional dwell-time analysis for model discrimination, temporal resolution, multichannel analysis and level detection.

Tobias Huth1, Indra Schroeder, Ulf-Peter Hansen.   

Abstract

Two-dimensional (2D) dwell-time analysis of time series of single-channel patch-clamp current was improved by employing a Hinkley detector for jump detection, introducing a genetic fit algorithm, replacing maximum likelihood by a least square criterion, averaging over a field of 9 or 25 bins in the 2D plane and normalizing per measuring time, not per events. Using simulated time series for the generation of the "theoretical" 2D histograms from assumed Markov models enabled the incorporation of the measured filter response and noise. The effects of these improvements were tested with respect to the temporal resolution, accuracy of the determination of the rate constants of the Markov model, sensitivity to noise and requirement of open time and length of the time series. The 2D fit was better than the classical hidden Markov model (HMM) fit in all tested fields. The temporal resolution of the two most efficient algorithms, the 2D fit and the subsequent HMM/beta fit, enabled the determination of rate constants 10 times faster than the corner frequency of the low-pass filter. The 2D fit was much less sensitive to noise. The requirement of computing time is a problem of the 2D fit (100 times that of the HMM fit) but can now be handled by personal computers. The studies revealed a fringe benefit of 2D analysis: it can reveal the "true" single-channel current when the filter has reduced the apparent current level by averaging over undetected fast gating.

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Year:  2007        PMID: 17557165     DOI: 10.1007/s00232-006-0074-6

Source DB:  PubMed          Journal:  J Membr Biol        ISSN: 0022-2631            Impact factor:   1.843


  41 in total

1.  Applying hidden Markov models to the analysis of single ion channel activity.

Authors:  L Venkataramanan; F J Sigworth
Journal:  Biophys J       Date:  2002-04       Impact factor: 4.033

2.  Voltage sensor of Kv1.2: structural basis of electromechanical coupling.

Authors:  Stephen B Long; Ernest B Campbell; Roderick Mackinnon
Journal:  Science       Date:  2005-07-07       Impact factor: 47.728

3.  Yet another approach to the dwell-time omission problem of single-channel analysis.

Authors:  S C Crouzy; F J Sigworth
Journal:  Biophys J       Date:  1990-09       Impact factor: 4.033

4.  Estimating kinetic parameters for single channels with simulation. A general method that resolves the missed event problem and accounts for noise.

Authors:  K L Magleby; D S Weiss
Journal:  Biophys J       Date:  1990-12       Impact factor: 4.033

5.  Identifying kinetic gating mechanisms for ion channels by using two-dimensional distributions of simulated dwell times.

Authors:  K L Magleby; D S Weiss
Journal:  Proc Biol Sci       Date:  1990-09-22       Impact factor: 5.349

6.  A nonlinear filter algorithm for the detection of jumps in patch-clamp data.

Authors:  R Schultze; S Draber
Journal:  J Membr Biol       Date:  1993-02       Impact factor: 1.843

7.  Ion-channel gating mechanisms: model identification and parameter estimation from single channel recordings.

Authors:  F G Ball; M S Sansom
Journal:  Proc R Soc Lond B Biol Sci       Date:  1989-05-22

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Authors:  O B McManus; A L Blatz; K L Magleby
Journal:  Pflugers Arch       Date:  1987-11       Impact factor: 3.657

9.  Single channel currents at six microsecond resolution elicited by acetylcholine in mouse myoballs.

Authors:  F Parzefall; R Wilhelm; M Heckmann; J Dudel
Journal:  J Physiol       Date:  1998-10-01       Impact factor: 5.182

10.  Interaction between the pore and a fast gate of the cardiac sodium channel.

Authors:  C Townsend; R Horn
Journal:  J Gen Physiol       Date:  1999-02       Impact factor: 4.086

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  4 in total

Review 1.  How to resolve microsecond current fluctuations in single ion channels: the power of beta distributions.

Authors:  Indra Schroeder
Journal:  Channels (Austin)       Date:  2015       Impact factor: 2.581

2.  Using a five-state model for fitting amplitude histograms from MaxiK channels: beta-distributions reveal more than expected.

Authors:  Indra Schroeder; Ulf-Peter Hansen
Journal:  Eur Biophys J       Date:  2009-07-21       Impact factor: 1.733

3.  Four-mode gating model of fast inactivation of sodium channel Nav1.2a.

Authors:  Tobias Huth; Johann Schmidtmayer; Christian Alzheimer; Ulf-Peter Hansen
Journal:  Pflugers Arch       Date:  2008-04-19       Impact factor: 3.657

4.  Saturation and microsecond gating of current indicate depletion-induced instability of the MaxiK selectivity filter.

Authors:  Indra Schroeder; Ulf-Peter Hansen
Journal:  J Gen Physiol       Date:  2007-07       Impact factor: 4.086

  4 in total

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