Improved hidden Markov models for molecular motors, part 1: Basic theory

Fiona E. Müllner, Sheyum Syed, Paul R. Selvin, Fred J. Sigworth

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Hidden Markov models (HMMs) provide an excellent analysis of recordings with very poor signal/noise ratio made from systems such as ion channels which switch among a few states. This method has also recently been used for modeling the kinetic rate constants of molecular motors, where the observable variable - the position - steadily accumulates as a result of the motor's reaction cycle. We present a new HMM implementation for obtaining the chemical-kinetic model of a molecular motor's reaction cycle called the variable-stepsize HMM in which the quantized position variable is represented by a large number of states of the Markov model. Unlike previous methods, the model allows for arbitrary distributions of step sizes, and allows these distributions to be estimated. The result is a robust algorithm that requires little or no user input for characterizing the stepping kinetics of molecular motors as recorded by optical techniques.

Original languageEnglish (US)
Pages (from-to)3684-3695
Number of pages12
JournalBiophysical Journal
Volume99
Issue number11
DOIs
StatePublished - Dec 1 2010
Externally publishedYes

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Molecular Models
Chemical Models
Ion Channels

ASJC Scopus subject areas

  • Biophysics

Cite this

Improved hidden Markov models for molecular motors, part 1 : Basic theory. / Müllner, Fiona E.; Syed, Sheyum; Selvin, Paul R.; Sigworth, Fred J.

In: Biophysical Journal, Vol. 99, No. 11, 01.12.2010, p. 3684-3695.

Research output: Contribution to journalArticle

Müllner, Fiona E. ; Syed, Sheyum ; Selvin, Paul R. ; Sigworth, Fred J. / Improved hidden Markov models for molecular motors, part 1 : Basic theory. In: Biophysical Journal. 2010 ; Vol. 99, No. 11. pp. 3684-3695.
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