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Biophys. J. BioFAST: First Published September 30, 2005. doi:10.1529/biophysj.105.069351
© 2005 by the Biophysical Society.

A more recent version of this article appeared on December 1, 2005.
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BIOPHYSICAL THEORY AND MODELING

A flexible approach to the calculation of resonance energy transfer efficiency between multiple donors and acceptors in complex geometries

Ben Corry 1*, Dylan Jayatilaka 1 and Paul Rigby 1

1 University of Western Australia

* To whom correspondence should be addressed. E-mail: ben{at}theochem.uwa.edu.au.

Submitted on June 22, 2005
Revised on July 14, 2005
Accepted on 2 September 2005


  Abstract
Resonance energy transfer provides a practical way to measure distances in the range of 10 to 100 Å between sites in biological molecules. Although the relationship between the efficiency of energy transfer and the distance between sites is well described for a single pair of fluorophores, the situation is more difficult when more than two fluorophores are present. Using a Monte-Carlo calculation scheme we demonstrate how resonance energy transfer can be used to measure distances between fluorophores in complex geometries. We demonstrate the versatility of the approach by calculating the efficiency of energy transfer for individual fluorophores randomly distributed in 2 and 3 dimensions, for linked pairs of donors and acceptors and pentameric structures of 5 linked fluorophores. This approach can be used to relate the efficiency of energy transfer to the distances between fluorophores, R0, molecular concentrations, laser power and donor / acceptor ratios in ensembles of molecules or when many fluorophores are attached to a single molecule such as in multimeric proteins.

Key Words: FRET, Monte-Carlo, energy transfer, multimeric protein, spectroscopy, structural biology




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Copyright © 2005 by the Biophysical Society.