TCB Publications - Abstract

Andrew Aird, Jörg Wrachtrup, Klaus Schulten, and Carsten Tietz. Possible pathway for ubiquinone shuttling in R. rubrum revealed by molecular dynamics simulation. Biophysical Journal, 92:23-33, 2007. (PMC: 1697858)

AIRD2007 In the last decade, the structures of many components of the photosynthetic apparatus of purple bacteria as well as the mutual organization of these components within the purple membrane were resolved. One key question that emerged concerned the assembly of the core complex consisting of the reaction center and the light harvesting I complex. In some species like Rb. sphaeroides the ring shaped LH1 complex was found to be open whereas other species like R. rubrum have a closed ring surrounding the reaction center. This poses the question how the ubiquinone molecule which transports electrons and protons from the RC to the cytochrome bc1 complex overcomes the apparent barrier of the LH1 ring. In this study we investigated how in case of a closed LH1 ring the ubiquinone molecule diffuses through the LH1 ring. For this purpose the LH1 structure of R. rubrum was modeled and the potential of mean force along the diffusion pathway through the LH1 was determined by steered molecular dynamics simulations. The potential was reconstructed using the fluctuation theorem in combination with the stiff spring approximation. The mean first passage time for the ubiquinone through the ring based on the potential was calculated to 10$^{-3}$ s, which is in agreement with the known turnover rates of the reaction center of about 1000Hz.

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