Theory of the energy transfer efficiency and fluorescence lifetime distribution in single-molecule FRET

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 20, 2012, Pages 7747-7752

  Gopich, Irina V ^a   Szabo, Attila ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

Connectivity of kinetic schemes; Diffusion; Quenching; Recoloring

Indexed keywords

ALGORITHM; ARTICLE; CONFORMATIONAL TRANSITION; DYNAMICS; ENERGY TRANSFER; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; HISTOGRAM; LASER; PHOTON; PRIORITY JOURNAL;

ALGORITHMS; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; MODELS, CHEMICAL; MOLECULAR CONFORMATION; PHOTONS;

EID: 84861216803     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1205120109     Document Type: Article

References (28)

1. Deniz AA, Mukhopadhyay S, Lemke EA (2008) Single-molecule biophysics: At the interface of biology, physics and chemistry. J R Soc Interface 5:15-45. (Pubitemid 350159184)
2. Schuler B, Eaton WA (2008) Protein folding studied by single-molecule FRET. Curr Opin Struct Biol 18:16-26.
3. Roy R, Hohng S, Ha T (2008) A practical guide to single-molecule FRET. Nat Methods 5:507-516. (Pubitemid 351761757)
4. Sisamakis E, Valeri A, Kalinin S, Rothwell PJ, Seidel CAM (2010) Accurate single-molecule FRET studies using multiparameter fluorescence detection. Methods Enzymol 475:455-514.
5. Gopich I, Szabo A (2005) Theory of photon statistics in single-molecule Förster resonance energy transfer. J Chem Phys 122:014707.
6. Gopich IV, Szabo A (2007) Single-molecule FRET with diffusion and conformational dynamics. J Phys Chem B 111:12925-12932. (Pubitemid 350136484)
7. Gopich IV, Szabo A (2012) Theory of single-molecule FRET efficiency histograms. Adv Chem Phys 146:245-298.
8. Eggeling C, et al. (2001) Data registration and selective single-molecule analysis using multi-parameter fluorescence detection. J Biotechnol 86:163-180. (Pubitemid 32217775)
9. Yang H, Xie XS (2002) Probing single-molecule dynamics photon by photon. J Chem Phys 117:10965-10979.
10. Kalinin S, Valeri A, Antonik M, Felekyan S, Seidel CAM (2010) Detection of structural dynamics by FRET: A photon distribution and fluorescence lifetime analysis of systems with multiple states. J Phys Chem B 114:7983-7995.
11. Laurence TA, Kong X, Jäger M, Weiss S (2005) Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins. Proc Natl Acad Sci USA 102:17348-17353. (Pubitemid 41740869)
12. Best RB, et al. (2007) Effect of flexibility and cis residues in single-molecule FRETstudies of polyproline. Proc Natl Acad Sci USA 104:18964-18969.
13. Hoffmann A, et al. (2007) Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy. Proc Natl Acad Sci USA 104:105-110. (Pubitemid 46067992)
14. Sorokina M, Koh HR, Patel SS, Ha T (2009) Fluorescent lifetime trajectories of a single fluorophore reveal reaction intermediates during transcription initiation. J Am Chem Soc 131:9630-9631.
15. Haas E, Katchalski-Katzir E, Steinberg IZ (1978) Brownian motion of the ends of oligopeptide chains in solution as estimated by energy transfer between the chain ends. Biopolymers 17:11-31. (Pubitemid 8275354)
16. Lakowicz JR (2006) Principles of Fluorescence Spectroscopy (Springer, New York) p 446.
17. Makarov DE, Plaxco KW (2009) Measuring distances within unfolded biopolymers using fluorescence resonance energy transfer: The effect of polymer chain dynamics on the observed fluorescence resonance energy transfer efficiency. J Chem Phys 131:085105.
18. Berezhkovskii AM, Szabo A, Weiss GH (1999) Theory of single-molecule fluorescence spectroscopy of two-state systems. J Chem Phys 110:9145-9150.
19. Gopich IV, Szabo A (2010) FRET efficiency distributions of multi-state single molecules. J Phys Chem B 114:15221-15226.
20. Gillespie DT (1992) Markov Processes: An Introduction for Physical Scientists (Academic, San Diego).
21. Gopich IV, Szabo A (2003) Single-macromolecule fluorescence resonance energy transfer and free-energy profiles. J Phys Chem B 107:5058-5063.
22. Huan B, Perroud TD, Zare RN (2004) Photon counting histogram: One-photon excitation. Chemphyschem 5:1523-1531.
23. Antonik M, Felekyan S, Gaiduk A, Seidel CAM (2006) Separating structural heterogeneities from stochastic variations in fluorescence resonance energy transfer distributions via photon distribution analysis. J Phys Chem B 110:6970-6978. (Pubitemid 43672169)
24. Nir E, et al. (2006) Shot-noise limited single-molecule FRET histograms: Comparison between theory and experiments. J Phys Chem B 110:22103-22124. (Pubitemid 44806929)
25. Gopich IV, Szabo A (2009) Decoding the pattern of photon colors in single-molecule FRET. J Phys Chem B 113:10965-10973.
26. Torella JP, Holden SJ, Santoso Y, Hohlbein J, Kapanidis AN (2011) Identifying molecular dynamics in single-molecule fret experiments with burst variance analysis. Biophys J 100:1568-1577.
27. Gopich IV, Szabo A (2008) Theory and Evaluation of Single-Molecule Signals, eds E Barkai, FLH Brown, M Orrit, and H Yang (World Scientific, Singapore), pp 181-244.
28. Chung HS, et al. (2011) Extracting rate coefficients from single-molecule photon trajectories and FRET efficiency histograms for a fast-folding protein. J Phys Chem A 115:3642-3656.