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Proceedings Paper

Detecting substeps in the rotary motors of FoF1-ATP synthase by Hidden Markov Models
Author(s): N. Zarrabi; M. G. Düser; R. Reuter; S. D. Dunn; J. Wrachtrup; M. Börsch
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Paper Abstract

FoF1-ATP synthase is the enzyme that provides the 'chemical energy currency' adenosine triphosphate, ATP, for living cells. The formation of ATP is accomplished by a stepwise internal rotation of subunits within the enzyme. We monitor subunit rotation by a single-molecule fluorescence resonance energy transfer (FRET) approach using two fluorophores specifically attached to the enzyme. To identify the stepsize of rotary movements by the motors of ATP synthase we simulated the confocal single-molecule FRET data of freely diffusing enzymes and developed a step finder algorithm based on 'Hidden Markov Models' (HMM). The HMM is able to find the proximity factors, P, for a three-level system and for a five-level system, and to unravel the dwell times of the simulated rotary movements. To identify the number of hidden states in the system, a likelihood parameter is calculated for the series of one-state to eight-state HMMs applied to each set of simulated data. Thereby, the basic prerequisites for the experimental single-molecule FRET data are defined that allow for discrimination between a 120o stepping mode or a 36o substep rotation mode for the proton-driven Fo motor of ATP synthase.

Paper Details

Date Published: 10 February 2007
PDF: 12 pages
Proc. SPIE 6444, Ultrasensitive and Single-Molecule Detection Technologies II, 64440E (10 February 2007); doi: 10.1117/12.701001
Show Author Affiliations
N. Zarrabi, Univ. of Stuttgart (Germany)
M. G. Düser, Univ. of Stuttgart (Germany)
R. Reuter, Univ. of Stuttgart (Germany)
S. D. Dunn, The Univ. of Western Ontario (Canada)
J. Wrachtrup, Univ. of Stuttgart (Germany)
M. Börsch, Univ. of Stuttgart (Germany)

Published in SPIE Proceedings Vol. 6444:
Ultrasensitive and Single-Molecule Detection Technologies II
Jorg Enderlein; Zygmunt K. Gryczynski, Editor(s)

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