Förster resonance energy transfer
Förster resonance energy transfer (FRET), fluorescence resonance energy transfer (FRET), resonance energy transfer (RET) or electronic energy transfer (EET) is a mechanism describing energy transfer between two light-sensitive molecules (chromophores). A donor chromophore, initially in its electronic excited state, may transfer energy to an acceptor chromophore through nonradiative dipole–dipole coupling. The efficiency of this energy transfer is inversely proportional to the sixth power of the distance between donor and acceptor, making FRET extremely sensitive to small changes in distance.
Measurements of FRET efficiency can be used to determine if two fluorophores are within a certain distance of each other. Such measurements are used as a research tool in fields including biology and chemistry.
FRET is analogous to near-field communication, in that the radius of interaction is much smaller than the wavelength of light emitted. In the near-field region, the excited chromophore emits a virtual photon that is instantly absorbed by a receiving chromophore. These virtual photons are undetectable, since their existence violates the conservation of energy and momentum, and hence FRET is known as a radiationless mechanism. Quantum electrodynamical calculations have been used to determine that radiationless (FRET) and radiative energy transfer are the short- and long-range asymptotes of a single unified mechanism.
Förster resonance energy transfer is named after the German scientist Theodor Förster. When both chromophores are fluorescent, the term "fluorescence resonance energy transfer" is often used instead, although the energy is not actually transferred by fluorescence. In order to avoid an erroneous interpretation of the phenomenon that is always a nonradiative transfer of energy (even when occurring between two fluorescent chromophores), the name "Förster resonance energy transfer" is preferred to "fluorescence resonance energy transfer"; however, the latter enjoys common usage in scientific literature. It should also be noted that FRET is not restricted to fluorescence. It can occur in connection with phosphorescence as well.
The FRET efficiency depends on many physical parameters that can be grouped as 1) the distance between the donor and the acceptor (typically in the range of 1–10 nm), 2) the spectral overlap of the donor emission spectrum and the acceptor absorption spectrum, and 3) the relative orientation of the donor emission dipole moment and the acceptor absorption dipole moment.
depends on the donor-to-acceptor separation distance with an inverse 6th-power law due to the dipole-dipole coupling mechanism:
with being the Förster distance of this pair of donor and acceptor, i.e. the distance at which the energy transfer efficiency is 50%. The Förster distance depends on the overlap integral of the donor emission spectrum with the acceptor absorption spectrum and their mutual molecular orientation as expressed by the following equation:
where is the fluorescence quantum yield of the donor in the absence of the acceptor, is the dipole orientation factor, is the refractive index of the medium, is Avogadro's number, and is the spectral overlap integral calculated as
where is the donor emission spectrum, is the donor emission spectrum normalized to an area of 1, and is the acceptor molar extinction coefficient normally obtained from an absorption spectrum. The orientation factor κ is given by
where denotes the normalized transition dipole moment of the respective fluorophore, and denotes the normalized inter-fluorophore displacement. = 2/3 is often assumed. This value is obtained when both dyes are freely rotating and can be considered to be isotropically oriented during the excited state lifetime. If either dye is fixed or not free to rotate, then = 2/3 will not be a valid assumption. In most cases, however, even modest reorientation of the dyes results in enough orientational averaging that = 2/3 does not result in a large error in the estimated energy transfer distance due to the sixth-power dependence of on . Even when is quite different from 2/3, the error can be associated with a shift in , and thus determinations of changes in relative distance for a particular system are still valid. Fluorescent proteins do not reorient on a timescale that is faster than their fluorescence lifetime. In this case 0 ≤ ≤ 4.
The FRET efficiency relates to the quantum yield and the fluorescence lifetime of the donor molecule as follows:
where and are the donor fluorescence lifetimes in the presence and absence of an acceptor respectively, or as
where and are the donor fluorescence intensities with and without an acceptor respectively.
Experimental confirmation of the Förster resonance energy transfer theoryEdit
The inverse sixth-power distance dependence of Förster resonance energy transfer was experimentally confirmed by Wilchek, Edelhoch and Brand using tryptophyl peptides. Stryer, Haugland and Yguerabide also experimentally demonstrated the theoretical dependence of Förster resonance energy transfer on the overlap integral by using a fused indolosteroid as a donor and a ketone as an acceptor. However, a lot of contradictions of special experiments with the theory was observed. The reason is that the theory has approximate character and gives overestimated distances of 50–100 ångströms.
Methods to measure FRET efficiencyEdit
In fluorescence microscopy, fluorescence confocal laser scanning microscopy, as well as in molecular biology, FRET is a useful tool to quantify molecular dynamics in biophysics and biochemistry, such as protein-protein interactions, protein–DNA interactions, and protein conformational changes. For monitoring the complex formation between two molecules, one of them is labeled with a donor and the other with an acceptor. The FRET efficiency is measured and used to identify interactions between the labeled complexes. There are several ways of measuring the FRET efficiency by monitoring changes in the fluorescence emitted by the donor or the acceptor.
One method of measuring FRET efficiency is to measure the variation in acceptor emission intensity. When the donor and acceptor are in proximity (1–10 nm) due to the interaction of the two molecules, the acceptor emission will increase because of the intermolecular FRET from the donor to the acceptor. For monitoring protein conformational changes, the target protein is labeled with a donor and an acceptor at two loci. When a twist or bend of the protein brings the change in the distance or relative orientation of the donor and acceptor, FRET change is observed. If a molecular interaction or a protein conformational change is dependent on ligand binding, this FRET technique is applicable to fluorescent indicators for the ligand detection.
FRET efficiencies can also be inferred from the photobleaching rates of the donor in the presence and absence of an acceptor. This method can be performed on most fluorescence microscopes; one simply shines the excitation light (of a frequency that will excite the donor but not the acceptor significantly) on specimens with and without the acceptor fluorophore and monitors the donor fluorescence (typically separated from acceptor fluorescence using a bandpass filter) over time. The timescale is that of photobleaching, which is seconds to minutes, with fluorescence in each curve being given by
where is the photobleaching decay time constant and depends on whether the acceptor is present or not. Since photobleaching consists in the permanent inactivation of excited fluorophores, resonance energy transfer from an excited donor to an acceptor fluorophore prevents the photobleaching of that donor fluorophore, and thus high FRET efficiency leads to a longer photobleaching decay time constant:
where and are the photobleaching decay time constants of the donor in the presence and in the absence of the acceptor respectively. (Notice that the fraction is the reciprocal of that used for lifetime measurements).
This technique was introduced by Jovin in 1989. Its use of an entire curve of points to extract the time constants can give it accuracy advantages over the other methods. Also, the fact that time measurements are over seconds rather than nanoseconds makes it easier than fluorescence lifetime measurements, and because photobleaching decay rates do not generally depend on donor concentration (unless acceptor saturation is an issue), the careful control of concentrations needed for intensity measurements is not needed. It is, however, important to keep the illumination the same for the with- and without-acceptor measurements, as photobleaching increases markedly with more intense incident light.
FRET efficiency can also be determined from the change in the fluorescence lifetime of the donor. The lifetime of the donor will decrease in the presence of the acceptor. Lifetime measurements of the FRET-donor are used in fluorescence-lifetime imaging microscopy (FLIM).
Fluorophores used for FRETEdit
One common pair fluorophores for biological use is a cyan fluorescent protein (CFP) – yellow fluorescent protein (YFP) pair. Both are color variants of green fluorescent protein (GFP). Labeling with organic fluorescent dyes requires purification, chemical modification, and intracellular injection of a host protein. GFP variants can be attached to a host protein by genetic engineering which can be more convenient. Additionally, a fusion of CFP and YFP ("tandem-dimer") linked by a protease cleavage sequence can be used as a cleavage assay.
A limitation of FRET performed with fluorophore donors is the requirement for external illumination to initiate the fluorescence transfer, which can lead to background noise in the results from direct excitation of the acceptor or to photobleaching. To avoid this drawback, bioluminescence resonance energy transfer (or BRET) has been developed. This technique uses a bioluminescent luciferase (typically the luciferase from Renilla reniformis) rather than CFP to produce an initial photon emission compatible with YFP.
BRET has also been implemented using a different luciferase enzyme, engineered from the deep-sea shrimp Oplophorus gracilirostris. This luciferase is smaller (19 kD) and brighter than the more commonly used luciferase from Renilla reniformis. Promega has developed this luciferase variant under the product name NanoLuc.
In general, "FRET" refers to situations where the donor and acceptor proteins (or "fluorophores") are of two different types. In many biological situations, however, researchers might need to examine the interactions between two, or more, proteins of the same type—or indeed the same protein with itself, for example if the protein folds or forms part of a polymer chain of proteins or for other questions of quantification in biological cells.
Obviously, spectral differences will not be the tool used to detect and measure FRET, as both the acceptor and donor protein emit light with the same wavelengths. Yet researchers can detect differences in the polarisation between the light which excites the fluorophores and the light which is emitted, in a technique called FRET anisotropy imaging; the level of quantified anisotropy (difference in polarisation between the excitation and emission beams) then becomes an indicative guide to how many FRET events have happened.
FRET has been used to measure distance and detect molecular interactions in a number of systems and has applications in biology and chemistry. FRET can be used to measure distances between domains in a single protein and therefore to provide information about protein conformation. FRET can also detect interaction between proteins. Applied in vivo, FRET has been used to detect the location and interactions of genes and cellular structures including integrins and membrane proteins. FRET can be used to obtain information about metabolic or signaling pathways. FRET is also used to study lipid rafts in cell membranes.
The applications of fluorescence resonance energy transfer (FRET) have expanded tremendously in the last 25 years, and the technique has become a staple technique in many biological and biophysical fields. FRET can be used as spectroscopic ruler in various areas such as structural elucidation of biological molecules and their interactions in vitro assays, in vivo monitoring in cellular research, nucleic acid analysis, signal transduction, light harvesting and metallic nanomaterial etc. Based on the mechanism of FRET a variety of novel chemical sensors and biosensors have been developed.
A different, but related, mechanism is Dexter electron transfer.
An alternative method to detecting protein–protein proximity is the bimolecular fluorescence complementation (BiFC), where two parts of a fluorescent protein are each fused to other proteins. When these two parts meet, they form a fluorophore on a timescale of minutes or hours.
- Cheng, Ping-Chin (2006). "The Contrast Formation in Optical Microscopy". In Pawley, James B. (ed.). Handbook Of Biological Confocal Microscopy (3rd ed.). New York, NY: Springer. pp. 162–206. doi:10.1007/978-0-387-45524-2_8. ISBN 978-0-387-25921-5.
- Helms, Volkhard (2008). "Fluorescence Resonance Energy Transfer". Principles of Computational Cell Biology. Weinheim: Wiley-VCH. p. 202. ISBN 978-3-527-31555-0.
- Harris, Daniel C. (2010). "Applications of Spectrophotometry". Quantitative Chemical Analysis (8th ed.). New York: W. H. Freeman and Co. pp. 419–44. ISBN 978-1-4292-1815-3.
- Zheng, Jie (2006). "Spectroscopy-Based Quantitative Fluorescence Resonance Energy Transfer Analysis". In Stockand, James D.; Shapiro, Mark S. (eds.). Ion Channels: Methods and Protocols. Methods in Molecular Biology, Volume 337. 337. Totowa, NJ: Humana Press. pp. 65–77. doi:10.1385/1-59745-095-2:65. ISBN 978-1-59745-095-9. PMID 16929939.
- Andrews, David L. (1989). "A unified theory of radiative and radiationless molecular energy transfer". Chemical Physics. 135 (2): 195–201. Bibcode:1989CP....135..195A. doi:10.1016/0301-0104(89)87019-3.
- Andrews, David L; Bradshaw, David S (2004). "Virtual photons, dipole fields and energy transfer: A quantum electrodynamical approach". European Journal of Physics. 25 (6): 845–858. doi:10.1088/0143-0807/25/6/017.
- Jones, Garth A; Bradshaw, David S (2019). "Resonance energy transfer: From fundamental theory to recent applications". Frontiers in Physics. 7: 100. doi:10.3389/fphy.2019.00100.
- Förster, Theodor (1948). "Zwischenmolekulare Energiewanderung und Fluoreszenz" [Intermolecular energy migration and fluorescence]. Annalen der Physik (in German). 437 (1–2): 55–75. Bibcode:1948AnP...437...55F. doi:10.1002/andp.19484370105.
- Valeur, Bernard; Berberan-Santos, Mario (2012). "Excitation Energy Transfer". Molecular Fluorescence: Principles and Applications, 2nd ed. Weinheim: Wiley-VCH. pp. 213–261. doi:10.1002/9783527650002.ch8. ISBN 9783527328376.
- FRET microscopy tutorial from Olympus Archived 2012-06-29 at Archive.today
- Glossary of Terms Used in Photochemistry (3rd ed.). IUPAC. 2007. p. 340.
- Moens, Pierre. "Fluorescence Resonance Energy Transfer spectroscopy". Retrieved July 14, 2012.
- Schaufele, Fred; Demarco, Ignacio; Day, Richard N. (2005). "FRET Imaging in the Wide-Field Microscope". In Periasamy, Ammasi; Day, Richard (eds.). Molecular Imaging: FRET Microscopy and Spectroscopy. Oxford: Oxford University Press. pp. 72–94. doi:10.1016/B978-019517720-6.50013-4. ISBN 978-0-19-517720-6.
- Hohng, Sungchul; Lee, Jinwoo; Lee, Sanghwa (2010-08-19). "Single-Molecule Three-Color FRET with Both Negligible Spectral Overlap and Long Observation Time". PLOS ONE. 5 (8): e12270. Bibcode:2010PLoSO...512270L. doi:10.1371/journal.pone.0012270. ISSN 1932-6203. PMC 2924373. PMID 20808851.
- Förster, Th. (1965). "Delocalized Excitation and Excitation Transfer". In Sinanoglu, Oktay (ed.). Modern Quantum Chemistry. Istanbul Lectures. Part III: Action of Light and Organic Crystals. 3. New York and London: Academic Press. pp. 93–137. Retrieved 2011-06-22.
- Clegg, Robert (2009). "Förster resonance energy transfer—FRET: what is it, why do it, and how it's done". In Gadella, Theodorus W. J. (ed.). FRET and FLIM Techniques. Laboratory Techniques in Biochemistry and Molecular Biology, Volume 33. Elsevier. pp. 1–57. doi:10.1016/S0075-7535(08)00001-6. ISBN 978-0-08-054958-3.
- Demchenko, Alexander P. (2008). "Fluorescence Detection Techniques". Introduction to Fluorescence Sensing. Dordrecht: Springer. pp. 65–118. doi:10.1007/978-1-4020-9003-5_3. ISBN 978-1-4020-9002-8.
- Majoul, Irina; Jia, Yiwei; Duden, Rainer (2006). "Practical Fluorescence Resonance Energy Transfer or Molecular Nanobioscopy of Living Cells". In Pawley, James B. (ed.). Handbook Of Biological Confocal Microscopy (3rd ed.). New York, NY: Springer. pp. 788–808. doi:10.1007/978-0-387-45524-2_45. ISBN 978-0-387-25921-5.
- ISRAEL JOURNAL OF CHEMISTRY Vol. 1. No. Sa. 1963.
- Edelhoch, H.; Brand, L.; Wilchek, M. (1967). "Fluorescence studies with tryptophyl peptides". Biochemistry. 6 (2): 547–559. doi:10.1021/bi00854a024. PMID 6047638.
- Lakowicz, Joseph R., ed. (1991). Principles. New York: Plenum Press. p. 172. ISBN 978-0-306-43875-2.
- Vekshin N. L. Energy Transfer in Macromolecules, SPIE, 1997; Vekshin N. L. Photonics of Biopolymers, Springer, 2002.
- "Fluorescence Resonance Energy Transfer Protocol". Wellcome Trust. Archived from the original on July 17, 2013. Retrieved 24 June 2012.
- Szöllősi, János; Alexander, Denis R. (2007). "The Application of Fluorescence Resonance Energy Transfer to the Investigation of Phosphatases". In Klumpp, Susanne; Krieglstein, Josef (eds.). Protein Phosphatases. Methods in Enzymology, Volume 366. Amsterdam: Elsevier. pp. 203–24. doi:10.1016/S0076-6879(03)66017-9. ISBN 978-0-12-182269-9.
- Periasamy, Ammasi (July 2001). "Fluorescence resonance energy transfer microscopy: a mini review". Journal of Biomedical Optics. 6 (3): 287–291. Bibcode:2001JBO.....6..287P. doi:10.1117/1.1383063. PMID 11516318.
- Nguyen, AW; Daugherty, PS (March 2005). "Evolutionary optimization of fluorescent proteins for intracellular FRET". Nature Biotechnology. 23 (3): 355–60. doi:10.1038/nbt1066. PMID 15696158.
- Bevan, Nicola; Rees, Stephen (2006). "Pharmaceutical Applications of GFP and RCFP". In Chalfie, Martin; Kain, Steven R. (eds.). Green Fluorescent Protein: Properties, Applications and Protocols. Methods of Biochemical Analysis, Volume 47 (2nd ed.). Hoboken, NJ: John Wiley & Sons. pp. 361–90. doi:10.1002/0471739499.ch16. ISBN 978-0-471-73682-0.
- Pfleger, Kevin D G; Eidne, Karin A (2006). "Illuminating insights into protein-protein interactions using bioluminescence resonance energy transfer (BRET)". Nature Methods. 3 (3): 165–174. doi:10.1038/nmeth841. PMID 16489332.
- Mo, Xiu-Lei; Luo, Yin; Ivanov, Andrei A.; Su, Rina; Havel, Jonathan J.; Li, Zenggang; Khuri, Fadlo R.; Du, Yuhong; Fu, Haian (2015-11-16). "Enabling systematic interrogation of protein-protein interactions in live cells with a versatile ultra-high-throughput biosensor platform". Journal of Molecular Cell Biology. 8 (3): 271–81. doi:10.1093/jmcb/mjv064. ISSN 1759-4685. PMC 4937889. PMID 26578655.
- Robers, Matthew B.; Dart, Melanie L.; Woodroofe, Carolyn C.; Zimprich, Chad A.; Kirkland, Thomas A.; Machleidt, Thomas; Kupcho, Kevin R.; Levin, Sergiy; Hartnett, James R. (2015-01-01). "Target engagement and drug residence time can be observed in living cells with BRET". Nature Communications. 6: 10091. Bibcode:2015NatCo...610091R. doi:10.1038/ncomms10091. ISSN 2041-1723. PMC 4686764. PMID 26631872.
- Stoddart, Leigh A.; Johnstone, Elizabeth K. M.; Wheal, Amanda J.; Goulding, Joëlle; Robers, Matthew B.; Machleidt, Thomas; Wood, Keith V.; Hill, Stephen J.; Pfleger, Kevin D. G. (2015-07-01). "Application of BRET to monitor ligand binding to GPCRs". Nature Methods. 12 (7): 661–663. doi:10.1038/nmeth.3398. ISSN 1548-7105. PMC 4488387. PMID 26030448.
- Machleidt, Thomas; Woodroofe, Carolyn C.; Schwinn, Marie K.; Méndez, Jacqui; Robers, Matthew B.; Zimmerman, Kris; Otto, Paul; Daniels, Danette L.; Kirkland, Thomas A. (2015-08-21). "NanoBRET--A Novel BRET Platform for the Analysis of Protein-Protein Interactions". ACS Chemical Biology. 10 (8): 1797–1804. doi:10.1021/acschembio.5b00143. ISSN 1554-8937. PMID 26006698.
- "NanoLuc product page".
- Gautier, I.; Tramier, M.; Durieux, C.; Coppey, J.; Pansu, R.B.; Nicolas, J.-C.; Kemnitz, K.; Coppey-Moisan, M. (2001). "Homo-FRET Microscopy in Living Cells to Measure Monomer-Dimer Transition of GFP-Tagged Proteins". Biophysical Journal. 80 (6): 3000–8. Bibcode:2001BpJ....80.3000G. doi:10.1016/S0006-3495(01)76265-0. PMC 1301483. PMID 11371472.
- Bader, Arjen N.; Hofman, Erik G.; Voortman, Jarno; Van Bergen En Henegouwen, Paul M.P.; Gerritsen, Hans C. (2009). "Homo-FRET Imaging Enables Quantification of Protein Cluster Sizes with Subcellular Resolution". Biophysical Journal. 97 (9): 2613–22. Bibcode:2009BpJ....97.2613B. doi:10.1016/j.bpj.2009.07.059. PMC 2770629. PMID 19883605.
- Gradinaru, Claudiu C.; Marushchak, Denys O.; Samim, Masood; Krull, Ulrich J. (2010). "Fluorescence anisotropy: From single molecules to live cells". The Analyst. 135 (3): 452–9. Bibcode:2010Ana...135..452G. doi:10.1039/b920242k. PMID 20174695.
- Lakowicz, Joseph R. (1999). Principles of fluorescence spectroscopy (2nd ed.). New York, NY: Kluwer Acad./Plenum Publ. pp. 374–443. ISBN 978-0-306-46093-7.
- Truong, Kevin; Ikura, Mitsuhiko (2001). "The use of FRET imaging microscopy to detect protein–protein interactions and protein conformational changes in vivo". Current Opinion in Structural Biology. 11 (5): 573–8. doi:10.1016/S0959-440X(00)00249-9. PMID 11785758.
- Pollok, B; Heim, R (1999). "Using GFP in FRET-based applications". Trends in Cell Biology. 9 (2): 57–60. doi:10.1016/S0962-8924(98)01434-2. PMID 10087619.
- Sekar, R. B.; Periasamy, A (2003). "Fluorescence resonance energy transfer (FRET) microscopy imaging of live cell protein localizations". The Journal of Cell Biology. 160 (5): 629–33. doi:10.1083/jcb.200210140. PMC 2173363. PMID 12615908.
- Ni, Qiang; Zhang, Jin (2010). "Dynamic Visualization of Cellular Signaling". In Endo, Isao; Nagamune, Teruyuki (eds.). Nano/Micro Biotechnology. Advances in Biochemical Engineering/Biotechnology, Volume 119. 119. Springer. pp. 79–97. Bibcode:2010nmb..book...79N. doi:10.1007/10_2008_48. ISBN 978-3-642-14946-7. PMID 19499207.
- Silvius, John R.; Nabi, Ivan Robert (2006). "Fluorescence-quenching and resonance energy transfer studies of lipid microdomains in model and biological membranes (Review)". Molecular Membrane Biology. 23 (1): 5–16. doi:10.1080/09687860500473002. PMID 16611577.
- Frommer, WB; Davidson, MW; Campbell, RE (October 2009). "Genetically encoded biosensors based on engineered fluorescent proteins". Chemical Society Reviews. 38 (10): 2833–41. doi:10.1039/b907749a. PMC 3000468. PMID 19771330.
- Sanchez‐Gaytan, Brenda L., et al. "Real‐Time Monitoring of Nanoparticle Formation by FRET Imaging." Angewandte Chemie 129.11 (2017): 2969-2972.
- Martin, Sarah F., et al. "Quantitative analysis of multi‐protein interactions using FRET: Application to the SUMO pathway." Protein Science 17.4 (2008): 777-784.
- Hu, Chang-Deng; Chinenov, Yurii; Kerppola, Tom K. (2002). "Visualization of Interactions among bZIP and Rel Family Proteins in Living Cells Using Bimolecular Fluorescence Complementation". Molecular Cell. 9 (4): 789–98. doi:10.1016/S1097-2765(02)00496-3. PMID 11983170.