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Simulation and analysis of FRET

Fluorescence spectroscopy and FRET

Fluorescence spectroscopy is a powerful tool, which allows the study of the structure and dynamics of molecular systems. The diversity of physical parameters, which can be characterized by fluorescence, is astonishing: intra- and intermolecular distances, polarity, viscosity, structural ordering, molecular mobility, and electric potential (Valeur, 2001). One of the main advantages of the fluorescence method is its high sensitivity. For instance, modern techniques allow the tracking of a single fluorescent molecule (Keller et al., 1996).

This page is devoted to our work with one specific effect observed by spectroscopic studies: dipole-dipole radiationless resonance energy transfer (mainly known as Forster resonance energy transfer or fluorescence resonance energy transfer, FRET). See the article about FRET at Wikipedia. This effect is used by FRET spectroscopy (F?rster, 1965; Lakowicz, 1999; Stryer, 1978) in order to obtain distance and dynamic information about molecules and their parts. FRET spectroscopy has been successfully applied to several problems in biology as a means of estimating intra and intermolecular distances in macromolecular systems, especially proteins (Lakey et al., 1993; Stryer, 1978). The idea of FRET is labeling of the macromolecules with fluorescent labels of two kinds - a donor and an acceptor, and analysis of radiationless dipole-dipole energy transfer (Forster, 1948) between them. One of the advantages of such an approach is that several natural amino acid residues of a protein, such as Trp and Tyr, can be utilized as fluorescent labels (dos Remedios and Moens, 1995; Fleming et al., 1979).

  • dos Remedios, C.G.; Moens, P.D. (1995) Fluorescence resonance energy transfer spectroscopy is a reliable "ruler" for measuring structural changes in proteins. Dispelling the problem of the unknown orientation factor. J. Struct. Biol., 115(2), 175-185.
  • Fleming, P.J.; Koppel, D.E.; Lau, A.L.; Strittmatter, P. (1979) Intramembrane position of the fluorescent tryptophanyl residue in membrane-bound cytochrome b5. Biochemistry, 18(24), 5458-5464.
  • Forster, T. (1948) Intermolecular energy migration and fluorescence. Ann. Phys., 2, 55-75.
  • Keller, R.A.; Ambrose, W.P.; Goodwin, P.M.; Jett, J.H.; Martin, J.C.; Wu, M. (1996) Single-molecule fluorescence analysis in solution Appl. Spectrsc., 50(7), 12A-32A.
  • Lakey, J.H.; Duche, D.; Gonzalez-Manas, J.M.; Baty, D.; Pattus, F. (1993) Fluorescence energy transfer distance measurements. The hydrophobic helical hairpin of colicin A in the membrane bound state. J. Mol. Biol., 230(3), 1055-1067.
  • Lakowicz, J.R. (1999) Principles of fluorescence spectroscopy. Kluwer Academic/Plenum Publishers, New York.
  • Stryer, L. (1978) Fluorescence energy transfer as a spectroscopic ruler. Annu. Rev. Biochem., 47, 819-846.
  • Valeur, B. (2001) Molecular fluorescence: principles and applications. Wiley-VCH.


Simulation and analysis of FRET in the system of M13mcp inserted in a membrane


Time resolved simulation of FRET

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