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Biophys. J. BioFAST: First Published October 6, 2006. doi:10.1529/biophysj.106.084715
© 2006 by the Biophysical Society.

A more recent version of this article appeared on January 1, 2007.
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BIOPHYSICAL THEORY AND MODELING

Possible Pathway for Ubiquinone Shuttling in Rhodospirillum rubrum Revealed by Molecular Dynamics Simulation

Andrew Aird 1, Jörg Wrachtrup 1, Klaus Schulten 2 and Carsten Tietz 1*

1 University of Stuttgart
2 University of Illinois 3143 Beckman Institute

* To whom correspondence should be addressed. E-mail: c.tietz{at}physik.uni-stuttgart.de.

Submitted on March 8, 2006
Revised on April 26, 2006
Accepted on 13 September 2006


  Abstract
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 Rhodobacter sphaeroides the ring shaped LH1 complex was found to be open whereas other species like Rhodospirillum 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. An upper limit for the mean first passage time for diffusion of ubiquinone through the LH1 ring based on a worst case scenario potential was calculated to {approx}8x10-3 s, which is still in agreement with known turnover rates of RC and RC-LH1 complexes in the range of {approx}1000 Hz.

Key Words: Free Energy Calculation, Light Harvesting Complex, Molecular Dynamics Simulation, Purple Bacteria, Steered Molecular Dynamics, Ubiquinone




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Copyright © 2006 by the Biophysical Society.