Improved hidden Markov models for molecular motors, part 2: Extensions and application to experimental data

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

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Unbiased interpretation of noisy single molecular motor recordings remains a challenging task. To address this issue, we have developed robust algorithms based on hidden Markov models (HMMs) of motor proteins. The basic algorithm, called variable-stepsize HMM (VS-HMM), was introduced in the previous article. It improves on currently available Markovmodel based techniques by allowing for arbitrary distributions of step sizes, and shows excellent convergence properties for the characterization of staircase motor timecourses in the presence of large measurement noise. In this article, we extend the VS-HMM framework for better performance with experimental data. The extended algorithm, variable-stepsize integrating-detector HMM (VSI-HMM) better models the data-acquisition process, and accounts for random baseline drifts. Further, as an extension, maximum a posteriori estimation is provided. When used as a blind step detector, the VSI-HMM outperforms conventional step detectors. The fidelity of the VSI-HMM is tested with simulations and is applied to in vitro myosin V data where a small 10 nm population of steps is identified. It is also applied to an in vivo recording of melanosome motion, where strong evidence is found for repeated, bidirectional steps smaller than 8 nm in size, implying that multiple motors simultaneously carry the cargo.

Original languageEnglish (US)
Pages (from-to)3696-3703
Number of pages8
JournalBiophysical Journal
Volume99
Issue number11
DOIs
StatePublished - Dec 1 2010
Externally publishedYes

Fingerprint

Molecular Models
Myosin Type V
Melanosomes
Noise
Population
Proteins

ASJC Scopus subject areas

  • Biophysics

Cite this

Improved hidden Markov models for molecular motors, part 2 : Extensions and application to experimental data. / Syed, Sheyum; Müllner, Fiona E.; Selvin, Paul R.; Sigworth, Fred J.

In: Biophysical Journal, Vol. 99, No. 11, 01.12.2010, p. 3696-3703.

Research output: Contribution to journalArticle

Syed, Sheyum ; Müllner, Fiona E. ; Selvin, Paul R. ; Sigworth, Fred J. / Improved hidden Markov models for molecular motors, part 2 : Extensions and application to experimental data. In: Biophysical Journal. 2010 ; Vol. 99, No. 11. pp. 3696-3703.
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