dorsal/arxiv
View SchemaDetecting substeps in the rotary motors of FoF1-ATP synthase by Hidden Markov Models
| Authors | N. Zarrabi, M. G. Dueser, R. Reuter, S. D. Dunn, J. Wrachtrup, M. Boersch |
|---|---|
| Categories | |
| ArXiv ID | physics/0701214 |
| URL | https://arxiv.org/abs/physics/0701214 |
| DOI | 10.1117/12.701001 |
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 120 degree stepping mode or a 36 degree substep rotation mode for the proton-driven Fo motor of ATP synthase.
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"abstract": "FoF1-ATP synthase is the enzyme that provides the \u0027chemical energy currency\u0027\nadenosine triphosphate, ATP, for living cells. The formation of ATP is\naccomplished by a stepwise internal rotation of subunits within the enzyme. We\nmonitor subunit rotation by a single-molecule fluorescence resonance energy\ntransfer (FRET) approach using two fluorophores specifically attached to the\nenzyme. To identify the stepsize of rotary movements by the motors of ATP\nsynthase we simulated the confocal single-molecule FRET data of freely\ndiffusing enzymes and developed a step finder algorithm based on \u0027Hidden Markov\nModels\u0027 (HMM). The HMM is able to find the proximity factors, P, for a\nthree-level system and for a five-level system, and to unravel the dwell times\nof the simulated rotary movements. To identify the number of hidden states in\nthe system, a likelihood parameter is calculated for the series of one-state to\neight-state HMMs applied to each set of simulated data. Thereby, the basic\nprerequisites for the experimental single-molecule FRET data are defined that\nallow for discrimination between a 120 degree stepping mode or a 36 degree\nsubstep rotation mode for the proton-driven Fo motor of ATP synthase.",
"arxiv_id": "physics/0701214",
"authors": [
"N. Zarrabi",
"M. G. Dueser",
"R. Reuter",
"S. D. Dunn",
"J. Wrachtrup",
"M. Boersch"
],
"categories": [
"physics.bio-ph",
"physics.data-an"
],
"doi": "10.1117/12.701001",
"title": "Detecting substeps in the rotary motors of FoF1-ATP synthase by Hidden Markov Models",
"url": "https://arxiv.org/abs/physics/0701214"
},
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