Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions

Bollmann S, Löllmann M, Sauer M, Doose S (2011)
Physical Chemistry Chemical Physics 13(28): 12874-12882.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
Stacking interactions between organic fluorophores can cause formation of non-fluorescent H-dimers. Dimer formation and dissociation of two fluorophores site-specifically incorporated in a biomolecule result in fluorescence intermittency that can report on conformational dynamics. We characterize intramolecular dimerization of two oxazine fluorophores MR121 attached to an unstructured polypeptide. Formation of stable non-fluorescent complexes with nano- to microsecond lifetimes is a prerequisite for analysing the intermittent fluorescence emission by fluorescence correlation spectroscopy and extracting relaxation time constants on nano- to millisecond time scales. Destabilization of the generally very stable homodimers by chemical denaturation reduces the lifetime of H-dimers. We demonstrate that H-dimer formation of an oxazine fluorophore reports on end-to-end contact rates in unstructured glycine-serine polypeptides under denaturing conditions.
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Physical Chemistry Chemical Physics
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13
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28
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12874-12882
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Bollmann S, Löllmann M, Sauer M, Doose S. Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions. Physical Chemistry Chemical Physics. 2011;13(28):12874-12882.
Bollmann, S., Löllmann, M., Sauer, M., & Doose, S. (2011). Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions. Physical Chemistry Chemical Physics, 13(28), 12874-12882. doi:10.1039/c1cp21111k
Bollmann, S., Löllmann, M., Sauer, M., and Doose, S. (2011). Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions. Physical Chemistry Chemical Physics 13, 12874-12882.
Bollmann, S., et al., 2011. Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions. Physical Chemistry Chemical Physics, 13(28), p 12874-12882.
S. Bollmann, et al., “Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions”, Physical Chemistry Chemical Physics, vol. 13, 2011, pp. 12874-12882.
Bollmann, S., Löllmann, M., Sauer, M., Doose, S.: Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions. Physical Chemistry Chemical Physics. 13, 12874-12882 (2011).
Bollmann, Stefan, Löllmann, Marc, Sauer, Markus, and Doose, Soeren. “Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions”. Physical Chemistry Chemical Physics 13.28 (2011): 12874-12882.

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Daten bereitgestellt von Europe PubMed Central.

The Effect of Fluorophore Conjugation on Antibody Affinity and the Photophysical Properties of Dyes.
Szabó Á, Szendi-Szatmári T, Ujlaky-Nagy L, Rádi I, Vereb G, Szöllősi J, Nagy P., Biophys J 114(3), 2018
PMID: 29414714
Quantitative localization microscopy: effects of photophysics and labeling stoichiometry.
Nieuwenhuizen RP, Bates M, Szymborska A, Lidke KA, Rieger B, Stallinga S., PLoS One 10(5), 2015
PMID: 25992915
The N-terminal domains of spider silk proteins assemble ultrafast and protected from charge screening.
Schwarze S, Zwettler FU, Johnson CM, Neuweiler H., Nat Commun 4(), 2013
PMID: 24240554
Systematic evaluation of fluorescence correlation spectroscopy data analysis on the nanosecond time scale.
Steger K, Bollmann S, Noé F, Doose S., Phys Chem Chem Phys 15(25), 2013
PMID: 23685745

56 References

Daten bereitgestellt von Europe PubMed Central.

The protein folding problem.
Dill KA, Ozkan SB, Shell MS, Weikl TR., Annu Rev Biophys 37(), 2008
PMID: 18573083
Intrinsically unstructured proteins and their functions.
Dyson HJ, Wright PE., Nat. Rev. Mol. Cell Biol. 6(3), 2005
PMID: 15738986
Natively unfolded proteins.
Fink AL., Curr. Opin. Struct. Biol. 15(1), 2005
PMID: 15718131
Dynamic personalities of proteins.
Henzler-Wildman K, Kern D., Nature 450(7172), 2007
PMID: 18075575
Sending signals dynamically.
Smock RG, Gierasch LM., Science 324(5924), 2009
PMID: 19359576

Szabo, J. Chem. Phys. 72(), 1980
Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy.
Hoffmann A, Kane A, Nettels D, Hertzog DE, Baumgartel P, Lengefeld J, Reichardt G, Horsley DA, Seckler R, Bakajin O, Schuler B., Proc. Natl. Acad. Sci. U.S.A. 104(1), 2006
PMID: 17185422
Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins.
Nettels D, Muller-Spath S, Kuster F, Hofmann H, Haenni D, Ruegger S, Reymond L, Hoffmann A, Kubelka J, Heinz B, Gast K, Best RB, Schuler B., Proc. Natl. Acad. Sci. U.S.A. 106(49), 2009
PMID: 19933333
Collapse transition in proteins.
Ziv G, Thirumalai D, Haran G., Phys Chem Chem Phys 11(1), 2008
PMID: 19081910
The speed limit for protein folding measured by triplet-triplet energy transfer.
Bieri O, Wirz J, Hellrung B, Schutkowski M, Drewello M, Kiefhaber T., Proc. Natl. Acad. Sci. U.S.A. 96(17), 1999
PMID: 10449738
Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding.
Krieger F, Fierz B, Bieri O, Drewello M, Kiefhaber T., J. Mol. Biol. 332(1), 2003
PMID: 12946363
Measuring the rate of intramolecular contact formation in polypeptides.
Lapidus LJ, Eaton WA, Hofrichter J., Proc. Natl. Acad. Sci. U.S.A. 97(13), 2000
PMID: 10860987
Effects of denaturants on the dynamics of loop formation in polypeptides.
Buscaglia M, Lapidus LJ, Eaton WA, Hofrichter J., Biophys. J. 91(1), 2006
PMID: 16617069
Kinetics of end-to-end collision in short single-stranded nucleic acids.
Wang X, Nau WM., J. Am. Chem. Soc. 126(3), 2004
PMID: 14733555
Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation.
Vaiana AC, Neuweiler H, Schulz A, Wolfrum J, Sauer M, Smith JC., J. Am. Chem. Soc. 125(47), 2003
PMID: 14624606
A close look at fluorescence quenching of organic dyes by tryptophan.
Doose S, Neuweiler H, Sauer M., Chemphyschem 6(11), 2005
PMID: 16224752
Mechanisms of quenching of Alexa fluorophores by natural amino acids.
Chen H, Ahsan SS, Santiago-Berrios MB, Abruna HD, Webb WW., J. Am. Chem. Soc. 132(21), 2010
PMID: 20446733

Seidel, J. Phys. Chem. 100(), 1996
Inter- and intramolecular fluorescence quenching of organic dyes by tryptophan.
Marme N, Knemeyer JP, Sauer M, Wolfrum J., Bioconjug. Chem. 14(6), 2003
PMID: 14624626
Dynamics of unfolded polypeptide chains in crowded environment studied by fluorescence correlation spectroscopy.
Neuweiler H, Lollmann M, Doose S, Sauer M., J. Mol. Biol. 365(3), 2006
PMID: 17084857
The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy.
Kim J, Doose S, Neuweiler H, Sauer M., Nucleic Acids Res. 34(9), 2006
PMID: 16687657
Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains.
Daidone I, Neuweiler H, Doose S, Sauer M, Smith JC., PLoS Comput. Biol. 6(1), 2010
PMID: 20098498
Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments.
Noe F, Doose S, Daidone I, Lollmann M, Sauer M, Chodera JD, Smith JC., Proc. Natl. Acad. Sci. U.S.A. 108(12), 2011
PMID: 21368203

Jelly, Nature 138(), 1936

Scheibe, Angew. Chem. 50(), 1937

Kasha, Pure Appl. Chem. 11(), 1965

Rösch, Angew. Chem. 118(), 2006
Profluorescent protease substrates: intramolecular dimers described by the exciton model.
Packard BZ, Toptygin DD, Komoriya A, Brand L., Proc. Natl. Acad. Sci. U.S.A. 93(21), 1996
PMID: 8876189
Intramolecular dimers: a new strategy to fluorescence quenching in dual-labeled oligonucleotide probes.
Johansson MK, Fidder H, Dick D, Cook RM., J. Am. Chem. Soc. 124(24), 2002
PMID: 12059218

Johansson, Methods Mol. Biol. (Totowa, N. J.) (), 2006
Kinetics of folding of leucine zipper domains.
Wendt H, Berger C, Baici A, Thomas RM, Bosshard HR., Biochemistry 34(12), 1995
PMID: 7696274
Fluorescence quenching: A tool for single-molecule protein-folding study.
Zhuang X, Ha T, Kim HD, Centner T, Labeit S, Chu S., Proc. Natl. Acad. Sci. U.S.A. 97(26), 2000
PMID: 11121030
Global configuration of single titin molecules observed through chain-associated rhodamine dimers.
Grama L, Somogyi B, Kellermayer MS., Proc. Natl. Acad. Sci. U.S.A. 98(25), 2001
PMID: 11717390
The kinetics of conformational fluctuations in an unfolded protein measured by fluorescence methods.
Chattopadhyay K, Elson EL, Frieden C., Proc. Natl. Acad. Sci. U.S.A. 102(7), 2005
PMID: 15701687
Measuring unfolding of proteins in the presence of denaturant using fluorescence correlation spectroscopy.
Chattopadhyay K, Saffarian S, Elson EL, Frieden C., Biophys. J. 88(2), 2004
PMID: 15556973
Why kinesin is so processive.
Toprak E, Yildiz A, Hoffman MT, Rosenfeld SS, Selvin PR., Proc. Natl. Acad. Sci. U.S.A. 106(31), 2009
PMID: 19617538
H-type dimer formation of fluorophores: a mechanism for activatable, in vivo optical molecular imaging.
Ogawa M, Kosaka N, Choyke PL, Kobayashi H., ACS Chem. Biol. 4(7), 2009
PMID: 19480464
The preparation of guanidine hydrochloride.
Nozaki Y., Meth. Enzymol. 26(), 1972
PMID: 4680720
Viscosity and density of aqueous solutions of urea and guanidine hydrochloride.
Kawahara K, Tanford C., J. Biol. Chem. 241(13), 1966
PMID: 5912116

Perl, Biophys. J. 96(), 2002
Polymer properties of polythymine as revealed by translational diffusion.
Doose S, Barsch H, Sauer M., Biophys. J. 93(4), 2007
PMID: 17513377

Krichevsky, Rep. Prog. Phys. 65(), 2002

Marmé, Chem. Phys. Lett. 408(), 2005

Marmé, Anal. Bioanal. Chem. 288(), 2007

West, J. Phys. Chem. 69(), 1965

Brune, Proc. SPIE (), 2007

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