title: Steps and bumps: precision extraction of discrete states of molecular machines.
abstract: 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.
authors.affiliation: Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Max A
authors.initials: MA
authors.lastname: Little
authors.forename: Bradley C
authors.initials: BC
authors.lastname: Steel
authors.forename: Fan
authors.initials: F
authors.lastname: Bai
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Sowa
authors.forename: Thomas
authors.initials: T
authors.lastname: Bilyard
authors.forename: David M
authors.initials: DM
authors.lastname: Mueller
authors.forename: Richard M
authors.initials: RM
authors.lastname: Berry
authors.forename: Nick S
authors.initials: NS
authors.lastname: Jones
mesh_terms: D000465:Algorithms; D055592:Biophysical Phenomena; D003198:Computer Simulation; D004926:Escherichia coli / Q000201:enzymology; D005407:Flagella / Q000378:metabolism; D020409:Molecular Motor Proteins / Q000378:metabolism*; D006180:Proton-Translocating ATPases / Q000378:metabolism; D013997:Time Factors
chemical_list: D020409:Molecular Motor Proteins; D006180:Proton-Translocating ATPases