Protein Dynamics: Fluorescence Lifetime Distributions

  • Enrico Gratton
  • J. Ricardo Alcala
  • Franklyn G. Prendergast


It is now well established that proteins in their native conformation can exist in a large number of subconformations slightly different one from the other (Lakowicz & Weber, 1973; Austin et al., 1975; Careri et al., 1975, 1979; Karplus & McCammon, 1983). Subconformations originate from small structural fluctuations around the main conformation. The protein structure is very flexible and it allows rotations around the phi and psi angles of the polypeptide chain and around the C-alpha carbon on the side chain. The stabilization of one particular native structure depends on a large number of interactions which are affected by solvent, ions of the medium and chemico-physical parameters. Some parts of the protein structure are more stable than others due to a more favorable interaction between the amino acid residues and they form structural domains. Frequently, these domains are associated with secondary structural elements such as alpha helical segments or beta sheets. The connections or loops between domains are generally more flexible. Within a domain, a side chain exposed to the solvent can have large rotational freedom and fast motions can result with rates comparable to the rates of motion of the residue in the solvent. Alternatively, a side chain at the interface between two distinct domains can move only if the domains separate enough to allow the side chain to rotate. The resultant motion of this side chain is then modulated by the relatively slow motion of the two domains.


Fluorescence Lifetime Tryptophan Residue Fluorescence Decay Tryptophan Fluorescence Lifetime Distribution 
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  1. Alcala, J. R., Gratton, E., and Jameson, D. M., 1985, Multifrequency Phase Fluorometer Using the Harmonic Content of a Mode-Locked Laser, Anal. Instrum., 14:225.CrossRefGoogle Scholar
  2. Alcala, J. R., Gratton, E., and Prendergast, F. J., 1987a, Resolvability of Fluorescence Lifetime Distributions, Biophys. J., 51:587.PubMedCrossRefGoogle Scholar
  3. Alcala, J. R., Gratton, E., and Prendergast, F. J., 1987b, Fluorescence Lifetime Distributions in Proteins, Biophys. J., 51:597–604.PubMedCrossRefGoogle Scholar
  4. Alcala, J. R., Gratton, E., and Prendergast, F. J., 1987c, Interpretation of Fluorescence Decay in Proteins Using Continuous Lifetime Distributions, Biophys. J., 51:925.PubMedCrossRefGoogle Scholar
  5. Ansari, A., Berendzen, J., Bowne, S. F., Frauenfelder, H., Iben, I.E.T., Sauke, T. B., Shyamsunder, E., and Young, R. D., 1985, Protein States and Proteinquakes, Proc. Natl. Acad. Sci. USA, 82:5000.PubMedCrossRefGoogle Scholar
  6. Austin, R. H., Beeson, K. W., Eisenstein, L., Frauenfelder, H., and Gunsalus, I. C, 1975, Dynamics of Ligand Binding to Myoglobin, Biochemistry, 14:5355.PubMedCrossRefGoogle Scholar
  7. Beechem, J. M., and Brand, L., 1985, Time Resolved Fluorescence Decay in Proteins, Ann. Rev. Biochem., 54:43.PubMedCrossRefGoogle Scholar
  8. Careri, G., Fasella, P., and Gratton, E., 1975, Statistical Time Events in Enzymes: A Physical Assessment, CRC Crit. Rev. Biochem., 3:141.PubMedCrossRefGoogle Scholar
  9. Careri, G., Fasella, P., and Gratton, E., 1979), Enzyme Dynamics: The Statistical Physics Approach, Ann. Rev. Biophys. Bioeng., 8:69.CrossRefGoogle Scholar
  10. Caceri, M. S., and Cacheris, W. P., 1984, Fitting Curves to Data, The Simplex Algorithm is the Answer, Byte, May, 340.Google Scholar
  11. Chen, R. F., 1976, The Effect of Metal Cations on Intrinsic Protein Fluorescence, in: “Biochemical Fluorescence”, Vol. 2, R. F. Chen and H. Hedelhoch, eds., Marcel Dekker, NY.Google Scholar
  12. Creed, D., 1984a, The Photophysics and Photochemistry of the Near-UV Absorbing Amino Acids — I. Tryptophan and its Simple Derivatives, Photochem. Photobiol., 39:537.CrossRefGoogle Scholar
  13. Creed, D., 1984b, The Photophysics and Photochemistry of the Near-UV Absorbing Amino Acids — II. Tyrosine and its Simple Derivatives, Photochem. Photobiol., 39:563.CrossRefGoogle Scholar
  14. Fraunfelder, H., Petsko, G. A., and Tsernoglou, D., 1979, Temperature Dependent X-ray Temperature Diffraction as a Probe of Protein Structural Dynamics, Nature (London), 280:558.CrossRefGoogle Scholar
  15. Fraunfelder, H., Gratton, E., 1985, Protein Dynamics and Hydration, in: “Biomembranes, Protons and Water: Structure and Translocation”, Methods in Enzymology, 127:471.Google Scholar
  16. Gratton, E., and Limkeman, M., 1983, A Continuously Variable Frequency Cross-correlation Phase Fluorometer with Picosecond Resolution, Biophys. J., 44:315.PubMedCrossRefGoogle Scholar
  17. Gratton, E., Alcala, J. R., and Prendergast, F. G., 1986, Fluorescence Lifetime Distributions of Single Tryptophan Proteins: A Protein Dynamics Approach, in: “Progress and Challenges in Natural and Synthetic Polymer Research”, C. Kawabata and A. Bishop, eds., Ohmshu Press, Tokyo, Japan.Google Scholar
  18. Haydock, C, and Prendergast, F. G., 1986, A Model of Protein Fluorescence Incorporating Chromophore Interactions and Dynamics, Biophys. J., 49:62a.Google Scholar
  19. Ichiye, T., and Karplus, M., 1983, Fluorescence Depolarization of Tryptophan Residues in Proteins: A Molecular Dynamics Study, Biochemistry, 22:2884.PubMedCrossRefGoogle Scholar
  20. James, D. R., and Ware, W. R., 1985, A Fallacy in the Interpretation of Fluorescence Decay Parameters, Chem. Phys. Lett., 120:455.CrossRefGoogle Scholar
  21. James, D. R., Liu, Y. S., De Mayo, P., and Ware, E. R., 1985, Distribution of Fluorescence Lifetimes: Consequences for the Photophysics of Molecules Adsorbed on Surfaces, Chem. Phys. Lett., 120:460.CrossRefGoogle Scholar
  22. Karplus, M., and McCammon, J. A., 1983, Dynamics of Proteins, Elements and Function, Ann. Rev. Biochem., 53:263.CrossRefGoogle Scholar
  23. Lakowicz, J. R., and Weber, G., 1973, Quenching of Protein Fluorescence by Oxygen. Detection of Structural Fluctuations in Proteins on the Nanosecond Time Scale, Biochemistry, 12:4171.PubMedCrossRefGoogle Scholar
  24. Lakowicz, J. R., and Cherek, H., 1980, Dipolar Relaxation in Proteins on Nanosecond Timescale Observed by Wavelength-Resolved Phase Fluorometry of Tryptophan Fluorescence, J. Biol. Chem., 831.Google Scholar
  25. Lakowicz, J. R., Laczko, G., Cherek, H., Gratton, E., and Limkeman, M., 1984, Analysis of the Fluorescence Decay Kinetics from Variable-Frequency Phase Shift and Modulation Data, Biophys. J., 46:463.PubMedCrossRefGoogle Scholar
  26. Liebman, M., and Prendergast, F. G., 1985, Correlation of Protein Structure and Luminescence: Use of Molecular Electrostatic Potentials, Biochemistry, 24:3384.Google Scholar
  27. Longworth, J. W., 1971, Luminescence of Polypeptides and Proteins, in: “Excited States of Proteins and Nucleic Acids”, R. F. Steiner and I. Weinryb, eds., Plenum Press, NY.Google Scholar
  28. Lumry, R., and Hershberger, M., 1978, Status of Indole Photochemistry with Special Reference to Biological Applications, Photochem. Photobiol., 27:819.CrossRefGoogle Scholar
  29. Macgregor, R. B., and Weber, G., 1981, Fluorophores in Polar Media. Spectral Effects of the Langevin Distribution of Electrostatic Interactions, Ann. N. Y. Acad. Sci., 366:190.CrossRefGoogle Scholar
  30. Valeur, B., and Weber, G., 1977, Resolution of the Fluorescence Excitation Spectrum of Indole into the lLa and lLb, Excitation Bands, Photochem. Photobiol., 25:441.PubMedCrossRefGoogle Scholar
  31. Weber, G., 1981, Resolution of the Fluorescence Lifetime in a Heterogeneous System by Phase and Modulation Measurements, J. Phys. Chem., 85:949.CrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1989

Authors and Affiliations

  • Enrico Gratton
    • 1
  • J. Ricardo Alcala
    • 1
  • Franklyn G. Prendergast
    • 2
  1. 1.Department of PhysicsLaboratory for Fluorescence DynamicsUrbanaUSA
  2. 2.Department of BiochemistryMayo FoundationRochesterUSA

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