Skip to main content
NCBI home page
Biophysical Journal logoLink to Biophysical Journal
. 2001 May;80(5):2093–2109. doi: 10.1016/S0006-3495(01)76183-8

Mechanisms of tryptophan fluorescence shifts in proteins.

J T Vivian 1, P R Callis 1
PMCID: PMC1301402  PMID: 11325713

Abstract

Tryptophan fluorescence wavelength is widely used as a tool to monitor changes in proteins and to make inferences regarding local structure and dynamics. We have predicted the fluorescence wavelengths of 19 tryptophans in 16 proteins, starting with crystal structures and using a hybrid quantum mechanical-classical molecular dynamics method with the assumption that only electrostatic interactions of the tryptophan ring electron density with the surrounding protein and solvent affect the transition energy. With only one adjustable parameter, the scaling of the quantum mechanical atomic charges as seen by the protein/solvent environment, the mean absolute deviation between predicted and observed fluorescence maximum wavelength is 6 nm. The modeling of electrostatic interactions, including hydration, in proteins is vital to understanding function and structure, and this study helps to assess the effectiveness of current electrostatic models.

Full Text

The Full Text of this article is available as a PDF (518.3 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Andrews L. J., Forster L. S. Protein difference spectra. Effect of solvent and charge on tryptophan. Biochemistry. 1972 May 9;11(10):1875–1879. doi: 10.1021/bi00760a023. [DOI] [PubMed] [Google Scholar]
  2. Axelsen P. H., Prendergast F. G. Molecular dynamics of tryptophan in ribonuclease-T1. II. Correlations with fluorescence. Biophys J. 1989 Jul;56(1):43–66. doi: 10.1016/S0006-3495(89)82651-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Beechem J. M., Brand L. Time-resolved fluorescence of proteins. Annu Rev Biochem. 1985;54:43–71. doi: 10.1146/annurev.bi.54.070185.000355. [DOI] [PubMed] [Google Scholar]
  4. Berman H. M., Westbrook J., Feng Z., Gilliland G., Bhat T. N., Weissig H., Shindyalov I. N., Bourne P. E. The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235–242. doi: 10.1093/nar/28.1.235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Burstein E. A., Permyakov E. A., Yashin V. A., Burkhanov S. A., Finazzi Agro A. The fine structure of luminescence spectra of azurin. Biochim Biophys Acta. 1977 Mar 28;491(1):155–159. doi: 10.1016/0005-2795(77)90051-4. [DOI] [PubMed] [Google Scholar]
  6. Burstein E. A., Vedenkina N. S., Ivkova M. N. Fluorescence and the location of tryptophan residues in protein molecules. Photochem Photobiol. 1973 Oct;18(4):263–279. doi: 10.1111/j.1751-1097.1973.tb06422.x. [DOI] [PubMed] [Google Scholar]
  7. Callis P. R. 1La and 1Lb transitions of tryptophan: applications of theory and experimental observations to fluorescence of proteins. Methods Enzymol. 1997;278:113–150. doi: 10.1016/s0076-6879(97)78009-1. [DOI] [PubMed] [Google Scholar]
  8. Chen Y., Barkley M. D. Toward understanding tryptophan fluorescence in proteins. Biochemistry. 1998 Jul 14;37(28):9976–9982. doi: 10.1021/bi980274n. [DOI] [PubMed] [Google Scholar]
  9. Eftink M. R. Fluorescence techniques for studying protein structure. Methods Biochem Anal. 1991;35:127–205. doi: 10.1002/9780470110560.ch3. [DOI] [PubMed] [Google Scholar]
  10. Egan D. A., Logan T. M., Liang H., Matayoshi E., Fesik S. W., Holzman T. F. Equilibrium denaturation of recombinant human FK binding protein in urea. Biochemistry. 1993 Mar 2;32(8):1920–1927. doi: 10.1021/bi00059a006. [DOI] [PubMed] [Google Scholar]
  11. Ervin J., Sabelko J., Gruebele M. Submicrosecond real-time fluorescence sampling: application to protein folding. J Photochem Photobiol B. 2000 Jan;54(1):1–15. doi: 10.1016/s1011-1344(00)00002-6. [DOI] [PubMed] [Google Scholar]
  12. Gehlen J. N., Marchi M., Chandler D. Dynamics affecting the primary charge transfer in photosynthesis. Science. 1994 Jan 28;263(5146):499–502. doi: 10.1126/science.263.5146.499. [DOI] [PubMed] [Google Scholar]
  13. Hayes D. M., Kollman P. A. Electrostatic potentials of proteins. 2. Role of electrostatics in a possible catalytic mechanism for carboxypeptidase A. J Am Chem Soc. 1976 Nov 24;98(24):7811–7814. doi: 10.1021/ja00440a057. [DOI] [PubMed] [Google Scholar]
  14. Honig B., Nicholls A. Classical electrostatics in biology and chemistry. Science. 1995 May 26;268(5214):1144–1149. doi: 10.1126/science.7761829. [DOI] [PubMed] [Google Scholar]
  15. Ilich P., Prendergast F. G. Electronic states of the indole-acrylamide molecular pair. Photochem Photobiol. 1991 Apr;53(4):445–453. doi: 10.1111/j.1751-1097.1991.tb03655.x. [DOI] [PubMed] [Google Scholar]
  16. Langsetmo K., Fuchs J. A., Woodward C. The conserved, buried aspartic acid in oxidized Escherichia coli thioredoxin has a pKa of 7.5. Its titration produces a related shift in global stability. Biochemistry. 1991 Jul 30;30(30):7603–7609. doi: 10.1021/bi00244a032. [DOI] [PubMed] [Google Scholar]
  17. Lockhart D. J., Kim P. S. Electrostatic screening of charge and dipole interactions with the helix backbone. Science. 1993 Apr 9;260(5105):198–202. doi: 10.1126/science.8469972. [DOI] [PubMed] [Google Scholar]
  18. Lockhart D. J., Kim P. S. Internal stark effect measurement of the electric field at the amino terminus of an alpha helix. Science. 1992 Aug 14;257(5072):947–951. doi: 10.1126/science.1502559. [DOI] [PubMed] [Google Scholar]
  19. Pierce D. W., Boxer S. G. Stark effect spectroscopy of tryptophan. Biophys J. 1995 Apr;68(4):1583–1591. doi: 10.1016/S0006-3495(95)80331-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sham Y. Y., Muegge I., Warshel A. The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins. Biophys J. 1998 Apr;74(4):1744–1753. doi: 10.1016/S0006-3495(98)77885-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Sitkoff D., Lockhart D. J., Sharp K. A., Honig B. Calculation of electrostatic effects at the amino terminus of an alpha helix. Biophys J. 1994 Dec;67(6):2251–2260. doi: 10.1016/S0006-3495(94)80709-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Strickland E. H., Horwitz J., Billups C. Near-ultraviolet absorption bands of tryptophan. Studies using indole and 3-methylindole as models. Biochemistry. 1970 Dec 8;9(25):4914–4921. doi: 10.1021/bi00827a013. [DOI] [PubMed] [Google Scholar]
  23. Szabo A. G., Stepanik T. M., Wayner D. M., Young N. M. Conformational heterogeneity of the copper binding site in azurin. A time-resolved fluorescence study. Biophys J. 1983 Mar;41(3):233–244. doi: 10.1016/S0006-3495(83)84433-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Takigawa T., Ashida T., Sasada Y., Kakudo M. The crystal structures of L-tryptophan hydrochloride and hydrobromide. Bull Chem Soc Jpn. 1966 Nov;39(11):2369–2378. doi: 10.1246/bcsj.39.2369. [DOI] [PubMed] [Google Scholar]
  25. Varadarajan R., Lambright D. G., Boxer S. G. Electrostatic interactions in wild-type and mutant recombinant human myoglobins. Biochemistry. 1989 May 2;28(9):3771–3781. doi: 10.1021/bi00435a022. [DOI] [PubMed] [Google Scholar]
  26. WEBER G. Fluorescence-polarization spectrum and electronic-energy transfer in tyrosine, tryptophan and related compounds. Biochem J. 1960 May;75:335–345. doi: 10.1042/bj0750335. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Warshel A., Aqvist J. Electrostatic energy and macromolecular function. Annu Rev Biophys Biophys Chem. 1991;20:267–298. doi: 10.1146/annurev.bb.20.060191.001411. [DOI] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES