Testing the use of molecular dynamics to simulate fluorophore motions and FRET

Deplazes, Evelyne, Jayatilaka, Dylan and Corry, Ben (2011) Testing the use of molecular dynamics to simulate fluorophore motions and FRET. Physical Chemistry Chemical Physics, 13 23: 11045-11054. doi:10.1039/c1cp20447e

Author Deplazes, Evelyne
Jayatilaka, Dylan
Corry, Ben
Title Testing the use of molecular dynamics to simulate fluorophore motions and FRET
Journal name Physical Chemistry Chemical Physics   Check publisher's open access policy
ISSN 1463-9076
Publication date 2011-01-01
Sub-type Article (original research)
DOI 10.1039/c1cp20447e
Open Access Status Not Open Access
Volume 13
Issue 23
Start page 11045
End page 11054
Total pages 10
Place of publication Cambridge, United Kingdom
Publisher Royal Society of Chemistry
Collection year 2012
Language eng
Formatted abstract
Fluorescence resonance energy transfer (FRET) is commonly used to determine the proximity of fluorophores, but usually many assumptions are required to gain a quantitative relationship between the likelihood of energy transfer and fluorophore separation. Molecular Dynamics (MD) simulations provide one way of checking these assumptions, but before using simulations to study complex systems it is important to make sure that they can correctly model the motions of fluorophores and the likely FRET efficiency in a simple system. Here we simulate a well characterised situation of independent fluorophores in solution so that we can compare the predictions with expected values.  Our simulations reproduce the experimental fluorescence anisotropy of Alexafluor488 and predict that of AlexaFluor568. At the ensemble level we are able to reproduce the expected isotropic and dynamic motion of the fluorophores as well as the FRET efficiency of the system. At the level of single donor–acceptor pairs, however, very long simulations are required to adequately sample the translational motion of the fluorophores and more surprisingly also the rotational motion. Our studies demonstrate how MD simulations can be used in more complex systems to check if the dynamic orientation averaging regime applies, if the fluorophores have isotropic orientational motion, to calculate the likely values of the orientation factor k2 and to determine the FRET efficiency of the system in both dynamic and static orientational averaging regimes. We also show that it is possible in some situations to create system specific relationships between FRET efficiency and fluorophore separation that can be used to interpret experimental data and find any correlations between k2 and separation that may influence distance measurements.
Keyword Resonance energy-transfer
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Received 21st February 2011, Accepted 5th April 2011

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
School of Biomedical Sciences Publications
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Created: Fri, 16 Mar 2012, 11:36:28 EST by Susan Allen on behalf of School of Biomedical Sciences