Steps and bumps: precision extraction of discrete states of molecular machines

Max A. Little, Bradley C. Steel, Fan Bai, Yoshiyuki Sowa, Thomas Bilyard, David M. Mueller, Richard M. Berry, Nick S. Jones

    Research output: Contribution to journalArticlepeer-review


    We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techniques for estimating discrete state transitions buried in highly correlated molecular noise. We demonstrate the effectiveness of our approach on simulated and real examples of steplike rotation of the bacterial flagellar motor and the F1-ATPase enzyme. We show that our method can clearly identify molecular steps, periodicities and cascaded processes that are too weak for existing algorithms to detect, and can do so much faster than existing algorithms. Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided.
    Original languageEnglish
    Pages (from-to)477-485
    Number of pages9
    JournalBiophysical Journal
    Issue number2
    Publication statusPublished - 20 Jul 2011


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