%0 Journal Article %1 Vaiana2003a %A Vaiana, AC %A Neuweiler, H %A Schulz, A %A Wolfrum, J %A Sauer, M %A Smith, JC %C 1155 16TH ST, NW, WASHINGTON, DC 20036 USA %D 2003 %I AMER CHEMICAL SOC %J JOURNAL OF THE AMERICAN CHEMICAL SOCIETY %K hannes sauer %N 47 %P 14564-14572 %T Fluorescence quenching of dyes by tryptophan: Interactions at atomic detail from combination of experiment and computer simulation %U http://dx.doi.org/10.1021/ja036082j %V 125 %X Fluorescence spectroscopy and molecular dynamics (MD) simulation are combined to characterize the interaction of two organic fluorescent dyes, rhodamine 6G (R6G) and an oxazine derivative (MR121), with the amino acid tryptophan in aqueous solution. Steady-state and time-resolved fluorescence quenching experiments reveal the formation of essentially nonfluorescent ground-state dye/Trp complexes. The MD simulations are used to elucidate the molecular interaction geometries involved. The MD-derived probability distribution of the distance r between the centers of geometry of the dye and quencher ring systems, P(r), extends to higher distances for R6G than for MR121 due to population in the R6G/Trp system of fluorescent interaction geometries between Trp and the phenyl ring and ester group of the dye. The consequence of this is the experimental finding that under the conditions used in the simulations about 25\% of the R6G dye is fluorescent in comparison with 10\% of the MR121. Combining the above findings allows determination of the ``quenching distance'', r*, above which no quenching occurs. r* is found to be very similar (similar to5.5 Angstrom) for both dye/Trp systems, corresponding to close to van der Waals contact. Both experimental dynamic Stern-Volmer analysis and the MD trajectories demonstrate that the main determinant of the fluorescence intensity is static quenching. The approach presented is likely to be useful in the structural interpretation of data obtained from fluorescent conjugates commonly used for monitoring the binding and dynamics of biomolecular systems.

@article{Vaiana2003a, abstract = {Fluorescence spectroscopy and molecular dynamics (MD) simulation are combined to characterize the interaction of two organic fluorescent dyes, rhodamine 6G (R6G) and an oxazine derivative (MR121), with the amino acid tryptophan in aqueous solution. Steady-state and time-resolved fluorescence quenching experiments reveal the formation of essentially nonfluorescent ground-state dye/Trp complexes. The MD simulations are used to elucidate the molecular interaction geometries involved. The MD-derived probability distribution of the distance r between the centers of geometry of the dye and quencher ring systems, P(r), extends to higher distances for R6G than for MR121 due to population in the R6G/Trp system of fluorescent interaction geometries between Trp and the phenyl ring and ester group of the dye. The consequence of this is the experimental finding that under the conditions used in the simulations about 25\% of the R6G dye is fluorescent in comparison with 10\% of the MR121. Combining the above findings allows determination of the ``quenching distance{''}, r{*}, above which no quenching occurs. r{*} is found to be very similar (similar to5.5 Angstrom) for both dye/Trp systems, corresponding to close to van der Waals contact. Both experimental dynamic Stern-Volmer analysis and the MD trajectories demonstrate that the main determinant of the fluorescence intensity is static quenching. The approach presented is likely to be useful in the structural interpretation of data obtained from fluorescent conjugates commonly used for monitoring the binding and dynamics of biomolecular systems.}, added-at = {2011-03-01T10:57:13.000+0100}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, affiliation = {Smith, JC (Reprint Author), Univ Heidelberg, IWR Computat Mol Biophys, Neuenheimer Feld 368, D-69120 Heidelberg, Germany. Univ Heidelberg, IWR Computat Mol Biophys, D-69120 Heidelberg, Germany. Univ Heidelberg, Inst Chem Phys, D-69120 Heidelberg, Germany.}, author = {Vaiana, AC and Neuweiler, H and Schulz, A and Wolfrum, J and Sauer, M and Smith, JC}, biburl = {https://www.bibsonomy.org/bibtex/276c100736cbed56e1447816e0d95d87c/reichert}, cited-references = {BISMUTO E, 2000, PROTEIN SCI, V9, P1730. BRENEMAN CM, 1990, J COMPUT CHEM, V11, P361. BROOKS BR, 1983, J COMPUT CHEM, V4, P187. BROOKS BR, 1995, J COMPUT CHEM, V16, P1522. CALLIS PR, 2003, CHEM PHYS LETT, V369, P409, DOI 10.1016/S0009-2614(02)02046-8. CHELLI R, 2002, J AM CHEM SOC, V124, P6133. CICHOS F, 1999, J PHYS CHEM A, V103, P2506. COURNIA Z, 2003, PURE APPL CHEM. ESSMANN U, 1995, J CHEM PHYS, V103, P8577. FOLOPPE N, 2000, J COMPUT CHEM, V21, P86. FRISCH MJ, 1995, GAUSSIAN 94 REVISION. HILL TL, 1956, STATISTICAL MECHANIC, P179. ICHIYE T, 1983, BIOCHEMISTRY-US, V22, P2884. JEAN JM, 2001, P NATL ACAD SCI USA, V98, P37. JONES G, 1995, BIOORG MED CHEM LETT, V5, P2385. JORGENSEN WL, 1983, J CHEM PHYS, V79, P926. KNEMEYER JP, 2000, ANAL CHEM, V72, P3717. LABOULAIS C, 2001, BIOPHYS J, V81, P473. LAPIDUS LJ, 2002, J PHYS CHEM B, V106, P11628, DOI 10.1021/jp020829v. LIM K, 1995, BIOCHEMISTRY-US, V34, P6962. LUDESCHER RD, 1987, BIOPHYS CHEM, V28, P59. MACKERELL AD, 1998, J PHYS CHEM B, V102, P3586. MACKERELL AD, 2000, J COMPUT CHEM, V21, P105. MUINO PL, 1992, P SOC PHOTO-OPT INS, V1640, P240. NEUWEILER H, 2002, ANGEW CHEM INT EDIT, V41, P4769. NEUWEILER H, 2003, J AM CHEM SOC, V125, P5324, DOI 10.1021/ja034040p. SAUER M, 1997, P SOC PHOTO-OPT INS, V2985, P61. VAIANA AC, 2003, J COMPUT CHEM, V24, P632, DOI 10.1002/jcc.10190. VANDENBERG PAW, 2002, J PHYS CHEM B, V106, P8858, DOI 10.1021/jp020356s. YEH IC, 2002, J AM CHEM SOC, V124, P6563. ZHONG DP, 2001, P NATL ACAD SCI USA, V98, P11867.}, doc-delivery-number = {745ZU}, groups = {public}, interhash = {d6d363e7ecb6d3a67819e7f3fe05e68d}, intrahash = {76c100736cbed56e1447816e0d95d87c}, issn = {0002-7863}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, journal-iso = {J. Am. Chem. Soc.}, keywords = {hannes sauer}, keywords-plus = {MOLECULAR-DYNAMICS SIMULATIONS; EMPIRICAL FORCE-FIELD; NUCLEIC-ACIDS; PROTEINS; STACKING; LIFETIME; PEPTIDES; SYSTEMS; PROBES; LEVEL}, language = {English}, month = {NOV 26}, number = 47, number-of-cited-references = {31}, pages = {14564-14572}, publisher = {AMER CHEMICAL SOC}, subject-category = {Chemistry, Multidisciplinary}, times-cited = {44}, timestamp = {2011-03-09T14:16:05.000+0100}, title = {Fluorescence quenching of dyes by tryptophan: Interactions at atomic detail from combination of experiment and computer simulation}, type = {Article}, unique-id = {ISI:000186722200073}, url = {http://dx.doi.org/10.1021/ja036082j}, username = {reichert}, volume = 125, year = 2003 }