Acrylamide quenching of Trp phosphorescence in liver alcohol dehydrogenase: Evidence of gated quencher penetration

Biochemistry

Volumn 48, Issue 31, 2009, Pages 7482-7491

  Strambini, Giovanni B ^a   Gonnelli, Margherita ^a  

^a CNR Consiglio Nazionale delle Ricerche   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ACRYLAMIDES; BIOLOGICAL FUNCTIONS; CONCENTRATION RANGES; DIFFUSION MECHANISMS; DIMER INTERFACE; DIPHOSPHATES; FRICTIONAL DRAG; LIFETIME MEASUREMENTS; LIVER ALCOHOL DEHYDROGENASE; LOW FREQUENCY; MODEL PROTEINS; NONLINEAR DEPENDENCE; PROTEIN COMPLEXES; PROTEIN MOTION; QUENCHER CONCENTRATION; QUENCHING MECHANISMS; QUENCHING RATE; SATURATION EFFECTS; SIDE CHAINS; SLOW MOTION; STERN-VOLMER PLOT;

AMIDES; ENZYMES; GLYCEROL; LIGHT EMISSION; LIVER; PHOSPHORESCENCE;

QUENCHING;

ACRYLAMIDE; LACTATE DEHYDROGENASE; NICOTINAMIDE ADENINE DINUCLEOTIDE;

ARTICLE; CONCENTRATION RESPONSE; CONTROLLED STUDY; MOLECULAR DYNAMICS; PHOSPHORESCENCE; PHOTOCHEMICAL QUENCHING; PRIORITY JOURNAL; PROTEIN BINDING;

ACRYLAMIDE; ALCOHOL DEHYDROGENASE; ANIMALS; CRYSTALLOGRAPHY, X-RAY; DIFFUSION; DOSE-RESPONSE RELATIONSHIP, DRUG; HORSES; LIVER; LUMINESCENT MEASUREMENTS; MODELS, CHEMICAL; SOLUTIONS; TEMPERATURE; TRYPTOPHAN;

EID: 68249115779     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi9009659     Document Type: Article

References (34)

1. Persson, E., and Halle, B. (2008) Nanosecond to microsecond protein dynamics probed by magnetic relaxation dispersion of buried water molecules. J. Am. Chem. Soc. 130, 1774-1787.
2. Eppler, R. K., Hudson, E. P., Chase, S. D., Dordick, J. S., Reimer, J. A., and Clark, D. S. (2008) Biocatalyst activity in nonaqueous environments correlates with centisecond-range protein motions. Proc. Natl. Acad. Sci. U.S.A. 105, 15672-15677.
3. Henzler-Wildman, K., and Kern, D. (2007) Dynamic personalities of proteins. Nature 450, 964-972.
4. Hammes-Schiffer, S., and Benkovic, S. J. (2006) Relating protein motion to catalysis. Annu. Rev. Biochem. 75, 519-541.
5. Kale, S., Ulas, G., Song, J., Brudvig, G. W., Furey, W., and Jordan, F. (2008) Efficient coupling of catalysis and dynamics in the E1 component of Escherichia coli pyruvate dehydrogenase multienzyme complex. Proc. Natl. Acad. Sci. U.S.A. 105, 1158-1163.
6. Bouvignies, G., Bernado, P., Meier, S., Cho, K., Grzesiek, S., Bruschweiler, R., and Blackledge, M. (2005) Identification of slow correlated motions in proteins using residual dipolar and hydrogenbond scalar couplings. Proc. Natl. Acad. Sci. U.S.A. 102, 13885-13890.
7. 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, 4171-4179.
8. Eftink, M. R. (1991) in Topics in Fluorescence Spectroscopy (Lakowicz, J. R., Ed.) p v, Plenum Press, New York.
9. Strambini, G. B. (1987) Quenching of alkaline phosphatase phosphorescence by O2 and NO. Evidence for inflexible regions of protein structure. Biophys. J. 52, 23-28.
10. Vanderkooi, J. M. (1991) in Topics in Fluorescence Spectroscopy (Lakowicz, J. R., Ed.) pp 113-132, Plenum Press, New York.
11. Cioni, P., and Strambini, G. B. (1998) Acrylamide quenching of protein phosphorescence as a monitor of structural fluctuations in the globular fold. J. Am. Chem. Soc. 120, 11749-11757.
12. Calhoun, D. B., Englander, S. W., Wright, W. W., and Vanderkooi, J. M. (1988) Quenching of room temperature protein phosphorescence by added small molecules. Biochemistry 27, 8466-8474.
13. Calhoun, D. B., Vanderkooi, J. M., and Englander, S. W. (1983) Penetration of small molecules into proteins studied by quenching of phosphorescence and fluorescence. Biochemistry 22, 1533-1539.
14. Cioni, P., Bramanti, E., and Strambini, G. B. (2005) Effects of sucrose on the internal dynamics of azurin. Biophys. J. 88, 4213-4222. (Pubitemid 40991132)
15. Cioni, P., and Strambini, G. B. (1999) Pressure/temperature effects on protein flexibilty from acrylamide quenching of protein phosphorescence. J. Mol. Biol. 291, 955-964.
16. Strambini, G. B., Kerwin, B. A., Mason, B. D., and Gonnelli, M. (2004) The triplet-state lifetime of indole derivatives in aqueous solution. Photochem. Photobiol. 80, 462-470.
17. Cioni, P., Gabellieri, E., Gonnelli, M., and Strambini, G. B. (1994) Heterogeneity of Protein Conformation in Solution from the Lifetime of Tryptophan Phosphorescence. Biophys. Chem. 52, 25-34.
18. Sillen, A., and Engelborghs, Y. (1998) The Correct Use of "Average" Fluorescence Parameters. Photochem. Photobiol. 65, 475-486.
19. Owen, C. S., and Vanderkooi, J. M. (1991) Diffusion-dependent and - independent collisional quenching of fluorescence and phosphorescence. Comments Mol. Cell. Biophys. 7, 235-257.
20. Vanderkooi, J. M., Englander, S. W., Papp, S., Wright, W. W., and Owen, C. S. (1990) Long-Range Electron Exchange Measured in Proteins by Quenching of Tryptophan Phosphorescence. Proc. Natl. Acad. Sci. U.S.A. 87, 5099-5103.
21. Szabo, A., Shoup, D., Northrup, S. H., and McCammon, J. A. (1982) Stochastically gated diffusion-influenced reactions. J. Chem. Phys. 77, 4484-4493.
22. Zhou, H.-X. (1998) Theory of the diffusion-influenced substrate binding rate to a buried and gated active site. J. Chem. Phys. 108, 8146-8154.
23. Somogyi, B., Norman, J. A., Punyiczki, M., and Rosenberg, A. (1992) Viscosity dependence of acrylamide quenching of ribonuclease T1 fluorescence. The gating mechanism. Biochim. Biophys. Acta 1119, 81-89.
24. Eklund, H., Samama, J. P., and Jones, T. A. (1984) Crystallographic investigations of nicotinamide adenine dinucleotide binding to horse liver alcohol dehydrogenase. Biochemistry 23, 5982-5986. (Pubitemid 15153472)
25. + and substituted benzyl alcohols. Biochemistry 33, 5230-5237.
26. Strambini, G. B., and Gonnelli, M. (1990) Tryptophan Luminescence from Liver Alcohol-Dehydrogenase in Its Complexes with Coenzyme: A Comparative Study of Protein Conformation in Solution. Biochemistry 29, 196-203.
27. Theorell, H., and Tatemoto, K. (1971) Thermal stability of horse liver alcohol dehydrogenase and its complexes. Arch. Biochem. Biophys. 143, 354-358.
28. Gekko, K., and Timasheff, S. N. (1981) Thermodynamic and kinetic examination of protein stabilization by glycerol. Biochemistry 20, 4677-4686.
29. Punyczki, M., Norman, J. A., and Rosenberg,A. (1993) Interaction of acrylamide with proteins in the concentration range used for fluorescence quenching studies. Biophys. Chem. 47, 9-19.
30. Kerwin, B. A., Chang, B. S., Gegg, C. V., Gonnelli, M., Li, T. S., and Strambini, G. B. (2002) Interactions between PEG and type I soluble tumor necrosis factor receptor: Modulation by pH and by PEGylation at the N terminus. Protein Sci. 11, 1825-1833. (Pubitemid 34663561)
31. Gavish, B. (1980) Position-dependent viscosity effect on rate coefficient. Phys. Rev. Lett. 44, 1160-1163.
32. Gavish, B., and Werber, M. M. (1979) Viscosity-dependent structural fluctuations in enzyme catalysis. Biochemistry 18, 1269-1275.
33. Marcus, R. A., and Sutin,N. (1985) Electron transfer in chemistry and biology. Biochim. Biophys. Acta 811, 265-322.
34. Whittaker, M. M., and Whittaker, J. W. (2008) Conformationally gated metal uptake by apomanganese superoxide dismutase. Biochemistry 47, 11625-11636.