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FoF1-ATP synthase is the enzyme that provides the 'chemical energy currency'adenosine triphosphate, ATP, for living cells. The formation of ATP isaccomplished by a stepwise internal rotation of subunits within the enzyme. Wemonitor subunit rotation by a single-molecule fluorescence resonance energytransfer (FRET) approach using two fluorophores specifically attached to theenzyme. To identify the stepsize of rotary movements by the motors of ATPsynthase we simulated the confocal single-molecule FRET data of freelydiffusing enzymes and developed a step finder algorithm based on 'Hidden MarkovModels' (HMM). The HMM is able to find the proximity factors, P, for athree-level system and for a five-level system, and to unravel the dwell timesof the simulated rotary movements. To identify the number of hidden states inthe system, a likelihood parameter is calculated for the series of one-state toeight-state HMMs applied to each set of simulated data. Thereby, the basicprerequisites for the experimental single-molecule FRET data are defined thatallow for discrimination between a 120 degree stepping mode or a 36 degreesubstep rotation mode for the proton-driven Fo motor of ATP synthase.Comment: 12 pages, 5 figure

Detecting substeps in the rotary motors of F o F 1 -ATP synthase by Hidden Markov Models