Oxygen distribution and migration within Mbdes Fe and Hbdes Fe. Multifrequency phase and modulation fluorometry study.

Quenching of the intensity and lifetime of porphyrin fluorescence from Mbdes Fe and Hbdes Fe (iron-free myoglobin and hemoglobin) by oxygen was investigated using a multifrequency cross-correlation phase fluorometer. The single exponential decay characteristic of porphyrin emission of Mbdes Fe and Hbdes Fe became doubly exponential upon application of oxygen pressure. The results were interpreted in terms of a general model of dynamic quenching of fluorescence in globular proteins. The model accounted for the rate k+ of acquisition of quencher by the protein, the exit rate k- of quencher from the protein, and the migration rate chi of quencher in the protein interior. The values of k+, k-, and chi were different for Mbdes Fe and Hbdes Fe. The addition of 40% sucrose, which increased the bulk viscosity sixfold, modified these rates. These results are discussed and compared with previous quenching studies on proteins. The significance of these results and the model for the interpretation of protein quenching studies is emphasized.     

Diffusion of small molecules through the structure of myoglobin. Environmental effects

The effect of the ambient solvent viscosity on the mobility of small molecules within myoglobin was studied by substituting Zn-protoporphyrin (ZnPP) for the native Fe-protoporphyrin and using it as an optical probe in the protein (ZnPPMb). The quenching of the ZnPPMb triplet state by oxygen, by anthraquinonesulfonate, and by methyl viologen was followed by exciting it with a laser flash and measuring its decay rate as a function of quencher concentration. The quenching rate constants were taken to measure the diffusion rate of the quencher within the protein. At room temperature, these constants were determined in aqueous and in 37% and 55% (by weight) glycerol-water solutions by measuring the ZnPPMb-delayed fluorescence at 606 nm. It was found that although the quenching rate constants varied the activation energies in the protein were very similar for the different quenchers. In aqueous solution, Ea = 6.0-7.4 kcal/mol; in 37% glycerol, Ea = 6.8-7.5 kcal/mol; and in 55% glycerol, Ea = 8.5-9.2 kcal/mol. The quenching rate of ZnPPMb by oxygen was also measured between 190K and 293K in 80% glycerol, and its triplet decay in the absence of oxygen was determined down to 120K in 88% glycerol. In all experiments, the quenching rates in the protein were compared to those of Zn-hematoporphyrin in the same solvent. The results are discussed in terms of Northrup and McCammon's gated reaction theory.(ABSTRACT TRUNCATED AT 250 WORDS)     

Compartmental analysis in photophysics: kinetics and identifiability of models for quenching of fluorescent probes in micelles

The parameters describing the kinetics of excited-state processes can possibly be recovered by analysis of the fluorescence decay surface measured as a function of the experimental variables. The identifiability analysis of a photophysical model assuming errorless time-resolved fluorescence data can verify whether the model parameters can be determined. In this work, we have used the methods of similarity transformation and Taylor series to investigate the identifiability of two models utilized to describe the time-resolved fluorescence quenching of stationary probes in micelles. The first model assumes that exchange of the quencher between micelles is much slower than the fluorescence decay of the unquenched probe (the 'immobile' quencher model). The second model assumes that quenchers exchange between the aqueous and micellar phases (the 'mobile' quencher model). For the 'immobile' quencher model, the rate constants for deactivation (k(0)) and quenching (k(q)) of the excited probe are uniquely identified together with the average number of quencher molecules per micelle. For the 'mobile' quencher model, the rate constants k(0) and k(q) are uniquely identified, as are the rate constants for entry (k(+)) and exit (k(-)) of one quencher molecule into and from a micelle, and the micellar aggregation number. The concomitant rate equations describing the time-resolved fluorescence are solved using z-transforms.     

Acrylamide and oxygen fluorescence quenching studies with liver alcohol dehydrogenase using steady-state and phase fluorometry

The fluorescence lifetime of liver alcohol dehydrogenase (LADH) has been determined by phase fluorometry at various emission wavelengths and as a function of the concentration of the quencher acrylamide. Acrylamide selectively quenches the fluorescence of the surface tryptophanyl residue Trp-15, thus allowing the fluorescence lifetime of this residue and the buried residue Trp-314 to be evaluated. Values of tau15 = 6.9 ns and tau314 = 3.6 ns are obtained, in qualitative agreement with lifetimes of these residues determined from fluorescence decay studies [Ross, J.B.A., Schmidt, C.J., & Brand, L. (1981) Biochemistry 20, 4369-4377]. The quenching of the fluorescence of LADH by oxygen has also been studied. Quenching by oxygen results in a blue shift in the fluorescence of the protein and a downward-curving Stern-Volmer plot. These data, along with oxygen quenching studies in the presence of 1 M acrylamide, are consistent with a model in which oxygen quenches the fluorescence of Trp-314 and -15 with quenching constants of 3.5 and 25 M-1, respectively. Thus, as in studies with other quenchers, Trp-314 is found to be less accessible to the quencher oxygen than is Trp-15. A lifetime Stern-Volmer plot has also been obtained for the oxygen quenching of LADH. Such a plot deviates somewhat from the intensity Stern-Volmer plot as predicted by simulations of the quenching of two-component systems.     

Acrylamide quenching of Yt-base fluorescence in aqueous solution

Acrylamide was found to be an effective quencher of Yt-base (Y-4,9-dihydro-4,6-dimethyl-9-oxo-1H-imidazo-1,2a-purine) in water. In the absence of collisional quenching the decay of Yt-base in water is predominantly a single exponential. The intensity decays become increasingly heterogeneous when quenched by acrylamide. The frequency-domain data were analyzed using the radiation model, which provides estimates of molecular parameters characteristic of the system. The mutual diffusion coefficient at 20 degrees C was found to be 0.5 x 10(5) cm2/s, the Yt-base acrylamide interaction radius was 8 A, and the rate constant for quenching was 100 cm/s. These values indicate that quenching is diffusion-limited, i.e., the encounter complex is deactivated at least 2-fold faster than the rate of diffusive encounters.     

Triplet-state kinetics of Zn-porphyrin cytochrome c in micellar media. Measurement of intermicellar exchange rates

The interactions of protein molecules with surfactant assemblies in aqueous and hydrocarbon media have been studied via the triplet-state kinetics of Zn-porphyrin cytochrome c in solutions containing an anionic [sodium bis(2-ethylhexyl)sulfosuccinate, AOT] or a cationic (cetyltrimethylammonium bromide, CTAB) surfactant. In aqueous solution, the observed triplet state decay is single exponential with a lifetime of 8 ms. In aqueous solutions of AOT and in AOT-reversed micellar solutions, biexponential triplet state decays were observed, indicating that interactions between the surfactant and the protein occur, resulting in a change in protein conformation near the porphyrin ring. In CTAB-reversed micellar solutions, quenching of the Zn-porphyrin cytochrome c triplet state by ferricyanide and methyl viologen was studied. Because the quenching is exchange-limited under the conditions used, the exchange rate constants for the water pools can be obtained from these experiments. The observed exchange rate constants are in the range (1-5) x 10(7) M-1 S-1, depending on the water content of the reversed micelles and on the type of quencher used. These values are three orders of magnitude lower than the calculated collision rate of the reversed micelles.     

Determination of the aggregation number of detergent micelles using steady-state fluorescence quenching.

The development of a simple, reliable method for determination of detergent micelle aggregation number that relies solely on measurement of steady-state fluorescence quenching is presented. The degree of steady-state fluorescence quenching of a micelle-solubilized fluorophore (pyrene) by a quencher that partitions greatly into the micelles (coumarin 153) is dependent on the micelle concentration, which can therefore be determined. The aggregation number is calculated as the micelle concentration/detergent monomer concentration (the total detergent concentration above the critical micelle concentration). For the determination to be accurate, the partition coefficient of the quencher into the micelle phase is determined and used to calculate the micellar concentration of quencher. Also, the quenching of pyrene by a coumarin 153 molecule within the same micelle must be complete, and this was confirmed by time-resolved fluorescence measurements. Aggregation numbers were determined for one cationic and several nonionic detergents and were found to be consistent with literature values. The approach presented is an improvement on a previous luminescence quenching technique (Turro, N.J., and A. Yekta. 1978. J. Am. Chem. Soc. 100:5951-5952) and can be used on cationic, anionic, and nonionic detergents with micelles ranging greatly in size and under varying conditions, such as detergent concentration, ionic strength, or temperature.     

The effect of the solvent viscosity on the migration of small molecules through the structure of myoglobin.

The migration rate of small molecules through the structure of proteins can be monitored by quenching the light emitted from an excited optical probe located within the protein. In the present study we examined the influence of the solvent viscosity on the migration rate of the quencher anthraquinone sulfonate through myoglobin towards an excited Zn protoporphyrin molecule at the binding site of the protein. The solvent viscosity was increased by adding dextrans of different molecular weight but forming isoviscous solutions. The results demonstrate that the migration rate in the protein decreases with increasing solvent viscosity. This suggests that the fluctuations on the protein structure, which make the above migration possible, are affected by the solvent macroviscosity.     

Impact of quenching failure of Cy dyes in differential gel electrophoresis

Background

Differential gel electrophoresis (DIGE) is a technology widely used for protein expression analysis. It is based on labelling with fluorescent Cy dyes. In comparative fluorescence gel electrophoresis experiments, however, unspecific labelling using N-hydroxy-succinimide-ester-based labelling protocols was recently detected. Cross-talk was observed due to failure of the quenching process. Here, the impact of this effect for DIGE experiments was investigated.

Methodology/Principal Findings

Experiments to test quenching efficiency were performed in replicate using Escherichia coli lysate. Parameters such as the amount of dye and quencher were varied. Labelling and quenching were reversed in one experiment. Differences in protein spot volumes due to limited quenching were determined. For some spots twice the volume was detected underscoring the importance of proper control of silencing of active dye.

Conclusions/Significance

It could be demonstrated that uncontrolled labelling increased protein spot volume, even doubling it in some cases. Moreover, proteins responded differently to the protocol. Such unpredictable and unspecific processes are not acceptable in protein regulation studies so that it is necessary to validate the correct amount of quencher for individual samples before the DIGE experiment is performed. Increase of the concentration of lysine, which is used as quencher, from 10 mM to 2500 mM, was sufficient to silence the dye. Alternatively, active dye molecules can be removed by filtration.     

Protein fluorescence quenching by small molecules: protein penetration versus solvent exposure

Experiments were done to test the thesis that acrylamide and similar small molecules can penetrate into proteins on a nanosecond time scale. The approach taken was to measure the pattern of fluorescence quenching exhibited by quenching molecules differing in molecular character (size, polarity, charge) when these are directed against protein tryptophans that cover the whole range of tryptophan accessibility. If quenching involves protein penetration and internal quencher migration, one expects that larger quenchers and more polar quenchers should display lesser quenching. In fact, no significant dependence on quencher character was found. For proteins that display measurable quenching, the disparate quenchers studied display very similar quenching rate constants when directed against any particular protein tryptophan. For several proteins having tryptophans known to be buried, no quenching occurs. These results are not consistent with the view that the kinds of small molecules studied can quite generally penetrate into and diffuse about within proteins at near-diffusion-limited rates. Rather the results suggest that when quenching is observed, the pathway involves encounters with tryptophans that are partially exposed at the protein surface. Available crystallographic results support this conclusion.     

Quenching of fluorescence in membrane protein by hypocrellin B

The hypocrellin B (HB) was used as a fluorescence quencher to study the basic physical characteris-tics of HB in membrane systems, including the diffusion speed of quencher from aqueous phase into membrane phase, the partition coefficient (P) of quencher between membrane and water, and the fluorescence quenching constant of protein (Ksv; Kq). The experimental results show that the quenching of fluorescence in membrane protein by HB can be determined by the principle of dynamic quenching. The experimental process of fluorescence quenching was ob-served in detail by using the ESR technique. The signal of HB" was found to arise from an electron transfer from ex-cited trytophan to HB.     

Adenine nucleotide translocase greatly increases the partition of trinitrophenyl-ATP into reduced Triton X-100 micelles.

The presence of adenine nucleotide translocase (ANT) was found to greatly enhance the partitioning of the ATP analog 2',3'-O-(2,4,6-trinitrophenyl)-adenosine 5'-triphosphate (TNP-ATP) into reduced Triton X-100 micelles. The protein's effect was studied through the quenching of fluorescence of purified ANT, irreversibly inhibited by carboxyatractyloside (CAT), solubilized in reduced Triton X-100 micelles. The dependence of quenching of the protein's time-resolved tryptophan fluorescence on TNP-ATP concentration was measured and found to follow a Stern-Volmer mechanism. However, the calculated quenching constant was too large to be accounted for by the aqueous TNP-ATP concentration. Experiments were therefore conducted to determine the partitioning of the quencher between the three phases present: aqueous, protein-free micelle, and protein micelle; a system also described by the equation of Omann, G. M., and M. Glaser (1985. Biophys. J. 47:623-627.). By measuring the dependence of the apparent quenching rate constant on the protein concentration and protein/micelle ratios, this equation was used to calculate both the quencher partition coefficient into protein-free micelles (Pm) and into protein-micelles (Ppm), as well as the bimolecular quenching rate constant (kpm) in protein micelles. From the quenching experiments, kpm = 5.0 x 10(8)M-1s-1,Pm = 290 and pyrene quenching experiment to be 325, and by a rapid filtration experiment to be 450. Clearly, the presence of the integral membrane protein ANT-CAT in reduced Triton X-100 micelles greatly increases the partition of TNP-ATP into the micelle. ANT alters the properties and thus, the structure of the detergent micelle, which has direct implications for the use of detergent micelles as a model system for membrane proteins and may indicate that analogous effects occur in the mitochondrial membrane.     

Chirality-dependent interactions between molecular propeller structures in solution. Chiral recognition and discrimination processes modulated by temperature and incremental changes in structural chirality

Time-resolved chiroptical luminescence (TR-CL) measurements are used to study chirality-dependent intermolecular interactions in dynamic excited-state quenching processes. The measurements are carried out on solution samples that contain a racemic mixture of chiral luminophore molecules (with enantiomeric structures denoted by LambdaL and DeltaL) and a small, optically resolved concentration of chiral quencher (CQ) molecules. The luminophores are excited with a pulse of linearly polarized laser radiation to produce an initially racemic excited-state population of LambdaL* and DeltaL* enantiomers, and TR-CL measurements are then used to monitor the differential decay kinetics of the LambdaL* and DeltaL* subpopulations. Observed differences between the LambdaL* and DeltaL* decay kinetics reflect differential rate processes and efficiencies for LambdaL*-CQ vs. DeltaL*-CQ quenching actions, and they are diagnostic of chiral discriminatory interactions between the luminophore and quencher molecules. Twelve different luminophore-quencher systems are examined, in both H(2)O and D(2)O solutions, and in each case the quenching kinetics are measured over the 273-308 K temperature range. In all of the systems examined here, quenching occurs via electronic energy-transfer processes in transient (LambdaL*-CQ) and (DeltaL*-CQ) encounter complexes, and the chiral discriminatory rate parameters reflect the relative stabilities and lifetimes of these complexes as well as their structures and internal (electronic and nuclear) dynamics. All of the luminophore and quencher molecules examined in this study have three-bladed propeller-like structures that are very similar in overall shape and size. However, they exhibit small differences in the structural details of their propeller blades, and it is found that these small differences in structure can produce both qualitative and very substantial quantitative differences in their chiral recognition and discrimination properties.     

Inverse effects of D-galactosamine and inorganic phosphate on glycogenolysis in isolated rat hepatocytes.

Trichloroethanol is an efficient quencher of indole fluorescence of model compounds and proteins [Eftink, M. R. and Ghiron, C. A. (1976) J. Phys. Chem. 80, 486--493]. At low quencher concentrations, the quenching follows the classical Stern-Volmer law. Bimolecular rate constants calculated from measured quenching constants and lifetimes are equal to 6 X 10(9) M-1s-1 and 1.2 X 10(9) M-1s-1 for N-acetyltrypotophanamide and wheat germ agglutinin, respectively. Upon ultraviolet irradiation in the presence of trichloroethanol, transformation of fluorescent tryptophan occurs, leading to a fluorescent photoproduct. This can be easily used as a method for the quantitative determination of fluorescent tryptophan residues in proteins. In good agreement with previous results, two fluorescent tryptophan residues per polypeptide chain are found in wheat germ agglutinin. Concomitantly with the photochemical reactions, the hemagglutinating protein activity and its affinity constant towards chitin oligomers are reduced. A probable location of tryptophan residues in the binding sites of wheat germ agglutinin is proposed.     

Fluorescence quenching of methyl-2-aminobenzoate in the presence of beta-cyclodextrin: A model for the dynamic quenching of chromophores in hydrophobic regions of biopolymers

The binding constant of methyl-2-aminobenzoate to beta-cyclodextrin was determined by fluorescence titration to be 92.1M^?1 at 25°C in pH 7 buffer. Beta-cyclodextrin dramatically protects methyl-2-aminobenzoate against quenching by iodate and protects, though much less efficiently, against the smaller quencher, iodide. The observed decrease in fluorescence lifetime of the methyl-2-aminobenzoate-beta-cyclodextrin complex on addition of quencher indicates that the quenching mechanism is collisional (dynamic). The dependence of quenching rate on solvent viscosity is less than expected from simple theoretical considerations. However, the extent of beta-cyclodextrin protection is essentially viscosity-independent. These model studies show the usefulness of iodate as a quencher and encourage further attempts at quantitative interpretation of quenching studies on chromophores attached to biopolymers.     

Organization and dynamics of pyrene and pyrene lipids in intact lipid bilayers. Photo-induced charge transfer processes.

The dynamics of fluorescence quenching and the organization of a series of pyrene derivatives anchored in various depths in bilayers of phosphatidylcholine small unilamellar vesicles was studied and compared with their behavior in homogeneous solvent systems. The studies include characterization of the environmental polarity of the pyrene fluorophore based on its vibronic peaks, as well as the interaction with three collisional quenchers: the two membrane-soluble quenchers, diethylaniline and bromobenzene, and the water soluble quencher potassium iodide. The system of diethylaniline-pyrene derivatives in the membrane of phosphatidylcholine vesicles was characterized in detail. The diethylaniline partition coefficient between the lipid bilayers and the buffer is approximately 5,800. Up to a diethylaniline/phospholipid mole ratio of 1:3 the perturbation to membrane structure is minimal so that all photophysical studies were performed below this mole ratio. The quenching reaction, in all cases, was shown to take place in the lipid bilayer interior and the relative quenching efficiencies of the various probe molecules was used to provide information on the distribution of both fluorescent probes and quencher molecules in the lipid bilayer. The quenching efficiency by diethylaniline in the lipid bilayer was found to be essentially independent on the length of the methylene chain of the pyrene moiety. These findings suggest that the quenching process, being a diffusion controlled reaction, is determined by the mobility of the diethylaniline quencher (with an effective diffusion coefficient D approximately 10(-7) cm2 s-1) which appears to be homogeneously distributed throughout the lipid bilayer. The pulsed laser photolysis products of the charge-transfer quenching reaction were examined. No exciplex (excited-complex) formation was observed and the yield of the separated radical ions was shown to be tenfold smaller than in homogenous polar solutions. The decay of the radical ions is considerably faster than the corresponding process in homogenous solutions. Relatively high intersystem crossing yields are observed. The results are explained on the basis of the intrinsic properties of a lipid bilayer, primarily, its rigid spatial organization. It is suggested that such properties favor ion-pair formation over exciplex generation. They also enhance primary geminate recombination of initially formed (solvent-shared) ion pairs. Triplet states are generated via secondary geminate recombination of ion pairs in the membrane interior. The results bear on the general mechanism of electron transfer processes in biomembranes.     

Study on the interaction between nitroxide free radical and conjugated polyelectrolytes by fluorimetry

In this work, we studied the fluorescence quenching of the anionic conjugated polyelectrolyte PPE–SO₃ by the paramagnetic species 2,2,6,6‐tetramethylpiperidine‐N‐oxide free radical (TEMPO) in aqueous solution. At low quencher concentration the Stern–Volmer constant is 94 mol/L; as the quencher concentration increases the Stern–Volmer plots become superlinear. Ascorbic acid is used to reduce TEMPO to the corresponding hydroxylamine and the PPE–SO₃ fluorescence is fully recovered. Under a large excess of ascorbic acid over TEMPO, the rise of fluorescence followed pseudo‐first‐order kinetics. The second‐order rate constant calculated from this time course is 0.7 mol/L/s. Copyright © 2008 John Wiley & Sons, Ltd.     

Determination of the dioxygen quenching constant for protein and model indole triplets

The decay of the indole triplet of single tryptophan-containing proteins and model compounds can be readily determined at room temperature in solution by monitoring the triplet absorption or emission following an exciting laser pulse. The dioxygen triplet quenching constants, can be measured for all these molecules and compared to the analogous singlet values determined by fluorescence methods. The dioxygen triplet quenching constant (tkq) ranged from a high of 5.1.10(9) M-1.s-1 for the exposed indole of corticotropin to a low of 0.1.10(9) M-1.s-1 for the buried indole of asparaginase. The ratio of these values with their respective dioxygen singlet quenching constants (skq), tkq/skq, ranged from 0.3 to 0.6 for aqueous exposed polypeptide indoles. For globular proteins the tkq/skq value is observed to be 0.2 +/- 0.1. This lower value for protein indoles is not attributable to 'bulk' environmental or hydrogen bonding effects, since the magnitude of tkq/skq (= 0.5 +/- 0.1) for model indoles was independent of solvent dielectric constant, polarity, and proticity. Temperature-dependence studies were done to test whether tkq could be used to characterize the nature of the protein matrix. The activation energy (Ea) for tkq was found to be 11 +/- 2 kcal/mol for most proteins. This Ea was independent of whether the indole side-chain was solvent exposed or buried in the non-aqueous protein interior. Large Ea values were also obtained for model indoles, naphthalene and nalidixic acid, dissolved in water, whereas the same compounds dissolved in 95% ethanol exhibited much smaller Ea values. These data, in combination with the observation that the tkq of model indoles is insensitive to changes in solvent viscosity, indicate that dioxygen quenching at the triplet level can not be easily used to characterize the dynamics of proteins.     

A method for estimating lateral diffusion coefficients in membranes from steady-state fluorescence quenching studies.

The Stern-Volmer theory, in which the quantum yield ratio (Io/I) depends linearly on the quencher concentration, will typically be inapplicable to fluorescence quenching in membranes. Numerical analysis shows that diffusion-controlled quenching results in a nonlinear concentration dependence for diffusion coefficients less than or of the order of 10(-6) cm2 s-1 and probe fluorescence lifetimes in the region of 10-100 ns. Lateral diffusion coefficients in membranes are typically overestimated an order of magnitude or more by the Stern-Volmer theory. An alternative empirical method is presented, which represents nonlinear concentration curves by a single parameter linear approximation determined by a least-squares analysis. The fitting parameter, P, depends on the interaction distance, the membrane thickness, the maximum extent of quenching and, in the case of biexponential probe fluorescence decay, the fluorescence kinetic parameters. P is presented in tabular form for a useful range of these parameters. The method is used to estimate diffusion coefficients for plastoquinone and plastoquinol from pyrene fluorescence quenching in soya bean phosphatidylcholine liposomes. It is found that the diffusion coefficients are nearly equal and in the region of 1.3-3.5 X 10(-7) cm2 s-1 for interaction radii of 1.5-0.5 nm, respectively.