Literature DB >> 15981713

A subsequent fit of time series and amplitude histogram of patch-clamp records reveals rate constants up to 1 per microsecond.

I Schröder1, P Harlfinger, T Huth, U P Hansen.   

Abstract

Fast gating in time series of patch-clamp current demands powerful tools to reveal the rate constants of the adequate Hidden Markov model. Here, two approaches are presented to improve the temporal resolution of the direct fit of the time series. First, the prediction algorithm is extended to include intermediate currents between the nominal levels as caused by the anti-aliasing filter. This approach can reveal rate constants that are about 4 times higher than the corner frequency of the anti-aliasing filter. However, this approach is restricted to time series with very low noise. Second, the direct fit of the time series is combined with a beta fit, i.e., a fit of the deviations of the amplitude histogram from the Gaussian distribution. Since the "theoretical" amplitude histograms for higher-order Bessel filters cannot be calculated by analytical tools, they are generated from simulated time series. In a first approach, a simultaneous fit of the time series and of the Beta fit is tested. This simultaneous fit, however, inherits the drawbacks of both approaches, not the benefits. More successful is a subsequent fit: The fit of the time series yields a set of rate constants. The subsequent Beta fit uses the slow rate constants of the fit of the time series as fixed parameters and the optimization algorithm is restricted to the fast ones. The efficiency of this approach is illustrated by means of time series obtained from simulation and from the dominant K+ channel in Chara. This shows that temporal resolution can reach the microsecond range.

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Year:  2005        PMID: 15981713     DOI: 10.1007/s00232-005-0734-y

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


  28 in total

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

Authors:  L Venkataramanan; F J Sigworth
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2.  A chi(2) test for model determination and sublevel detection in ion channel analysis.

Authors:  A Caliebe; U Rösler; U-P Hansen
Journal:  J Membr Biol       Date:  2002-01-13       Impact factor: 1.843

3.  Maximum likelihood estimation and identification directly from single-channel recordings.

Authors:  D R Fredkin; J A Rice
Journal:  Proc Biol Sci       Date:  1992-08-22       Impact factor: 5.349

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.  Analysis of multichannel patch clamp recordings by hidden Markov models.

Authors:  S Klein; J Timmer; J Honerkamp
Journal:  Biometrics       Date:  1997-09       Impact factor: 2.571

6.  Interpretation of current-voltage relationships for "active" ion transport systems: II. Nonsteady-state reaction kinetic analysis of class-I mechanisms with one slow time-constant.

Authors:  U P Hansen; J Tittor; D Gradmann
Journal:  J Membr Biol       Date:  1983-07       Impact factor: 1.843

7.  Statistical analysis of channel current from a membrane patch. II. A stochastic theory of a multi-channel system in the steady-state.

Authors:  S Kijima; H Kijima
Journal:  J Theor Biol       Date:  1987-10-21       Impact factor: 2.691

8.  On the stochastic properties of bursts of single ion channel openings and of clusters of bursts.

Authors:  D Colquhoun; A G Hawkes
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  1982-12-24       Impact factor: 6.237

9.  Hidden Markov model analysis of intermediate gating steps associated with the pore gate of shaker potassium channels.

Authors:  J Zheng; L Vankataramanan; F J Sigworth
Journal:  J Gen Physiol       Date:  2001-11       Impact factor: 4.086

10.  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

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  6 in total

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

Authors:  Tobias Huth; Indra Schroeder; Ulf-Peter Hansen
Journal:  J Membr Biol       Date:  2007-06-06       Impact factor: 1.843

Review 2.  High bandwidth approaches in nanopore and ion channel recordings - A tutorial review.

Authors:  Andreas J W Hartel; Siddharth Shekar; Peijie Ong; Indra Schroeder; Gerhard Thiel; Kenneth L Shepard
Journal:  Anal Chim Acta       Date:  2019-01-25       Impact factor: 6.558

3.  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.  Tl+-induced micros gating of current indicates instability of the MaxiK selectivity filter as caused by ion/pore interaction.

Authors:  Indra Schroeder; Ulf-Peter Hansen
Journal:  J Gen Physiol       Date:  2008-04       Impact factor: 4.086

5.  Strengths and limits of Beta distributions as a means of reconstructing the true single-channel current in patch clamp time series with fast gating.

Authors:  I Schroeder; U-P Hansen
Journal:  J Membr Biol       Date:  2006-08-14       Impact factor: 2.426

6.  Extended beta distributions open the access to fast gating in bilayer experiments-assigning the voltage-dependent gating to the selectivity filter.

Authors:  Oliver Rauh; Ulf-Peter Hansen; Sebastian Mach; Andreas J W Hartel; Kenneth L Shepard; Gerhard Thiel; Indra Schroeder
Journal:  FEBS Lett       Date:  2017-11-19       Impact factor: 4.124

  6 in total

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