Berlin 2008 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 15: Single Molecules
BP 15.12: Vortrag
Mittwoch, 27. Februar 2008, 17:00–17:15, C 243
Data Analysis with Hidden Markov Models on a single Kdp-ATPase — •Nawid Zarrabi1, Michael Börsch1, Thomas Heitkamp2, and Jörg Greie2 — 13. Physikalisches Institut, Pfaffenwaldring 57, Universität Stuttgart, 70569 Stuttgart — 2Universität Osnabrück, Fachbereich Biologie/Chemie, Arbeitsgruppe Mikrobiologie, Barbarastraße 11, 49069 Osnabrück
The membrane-embedded KdpFABC complex belongs to the group of P-type ATPases which transports potassium across a lipid bilayer using ATP hydrolysis. This enzyme contains a central catalytic subunit which mediates ion transport and ATP-hydrolysis.
We measured the stepwise conformational changes of this protein using confocal single-molecule fluorescence resonance energy transfer (FRET) and analyzed this data with Hidden Markov Models (HMM).
To prove the capability of the HMM approach we generated single molecule data of freely diffusing enzymes in liposomes by a Monte-Carlo-simulation. Thereby we included the intensity fluctuations due to Brownian motion. The conformational states of the ATPases were described by a Markov process with predefined rates for the transitions of the reaction cycle.
The aim of the data analysis method was to investigate the reaction cycle of the KdpFABC-complex and, furthermore, to elucidate the effectiveness of different inhibitors of the ion transport mechanisms.