Fluorescence quenching of the buried tryptophan residue of cod parvalbumin

Cod parvalbumin (isotype III) is a single tryptophan-containing protein. The fluorescence characteristics of this tryptophan residue (lambda em approximately 315 nm) suggest that it is buried from solvent and that it is located in an apolar core of the protein. Solute quenching studies of the tryptophan fluorescence of parvalbumin reveal dynamic quenching rate constants, kq, of 1.1 X 10(8) and 2.3 X 10(9) M-1 s-1 (at 25 degrees C) with acrylamide and oxygen, respectively, as quenchers. From temperature dependence studies, activation energies of 6.5 +/- 1.5 and 6.0 +/- 0.5 kcal/mol are found for acrylamide and oxygen quenching. The kq for acrylamide quenching is found to be relatively unchanged (+/- 10%) by an 8-fold increase in the bulk viscosity (glycerol/water mixture). These temperature and viscosity studies argue that the acrylamide quenching process involves a dynamic penetration of the quencher, facilitated by fluctuations in the protein's structure.     

Human β-Synuclein Rendered Fibrillogenic by Designed Mutations

Filamentous inclusions made of α-synuclein are found in nerve cells and glial cells in a number of human neurodegenerative diseases, including Parkinson disease, dementia with Lewy bodies, and multiple system atrophy. The assembly and spreading of these inclusions are likely to play an important role in the etiology of common dementias and movement disorders. Both α-synuclein and the homologous β-synuclein are abundantly expressed in the central nervous system; however, β-synuclein is not present in the pathological inclusions. Previously, we observed a poor correlation between filament formation and the presence of residues 73–83 of α-synuclein, which are absent in β-synuclein. Instead, filament formation correlated with the mean β-sheet propensity, charge, and hydrophilicity of the protein (global physicochemical properties) and β-strand contiguity calculated by a simple algorithm of sliding averages (local physicochemical property). In the present study, we rendered β-synuclein fibrillogenic via one set of point mutations engineered to enhance global properties and a second set engineered to enhance predominantly β-strand contiguity. Our findings show that the intrinsic physicochemical properties of synucleins influence their fibrillogenic propensity via two distinct but overlapping modalities. The implications for filament formation and the pathogenesis of neurodegenerative diseases are discussed.     

Oligonucleotide-based assays for integrase activity

Oligonucleotide assays have been invaluable for elucidation of the molecular mechanisms of retroviral integrases. A suite of rapid and sensitive fluorescence assays to measure the DNA binding, processing, and joining activities of integrase (IN) is described here. The assays are especially useful for characterizing the major activities of the enzyme, and for handling large numbers of samples efficiently. They can greatly facilitate further biochemical and structural analyses for HIV-1 and other IN proteins. The assays can also be adapted for moderate-high throughput testing of various inhibitory compounds.     

Overall assessment of Monodus subterraneus cultivation and EPA production in outdoor helical and bubble column reactors

The outdoor production of Monodus subterraneus wasstudied in bubble column and helical reactors, mainly analysing the influenceofdilution rate, air flow rate and solar irradiance on growth rate andbiochemicalcomposition. Photoinhibition and photo-oxidation phenomena were also analysed.The cultures were stressed at high solar irradiance and dissolved oxygenconcentrations. A clear relationship between stress of the cultures and thefluorescence from PSII measurements was observed, the Fv/Fm ratio being lowerinthe helical reactor than in the bubble column. Growth rate and biomassproductivity were both a function of the average irradiance and the Fv/Fmratio;maximum values of 0.040 h^–1 and 0.54 gL^–1 d^–1 were measured. The influenceofphotoinhibition and average irradiance was modelled, the model also fitting theexperimental data reported by another author. The chlorophyll contenthyperbolically decreased, whereas the carotenoid content decreased linearlywiththe average irradiance. The higher the dilution rate the higher the protein andcarbohydrate content of the biomass, and the lower the lipid content. Theeicosapentaenoic acid (EPA) content ranged from 2.3 to 3.2% d.wt, the higherthe dilution rate, the lower EPA content, although the higher the EPAproportion. Maximum EPA productivity was only 9 mg L^–1d^–1, due to the stress to which the cultures wereexposed.     

Maintenance of Acidic Lateral Intercellular Spaces by Endogenous Fixed Buffers in MDCK Cell Epithelium

The lateral intercellular spaces (LIS) of MDCK cell epithelia grown on permeable supports are about 0.4 pH units acidic to the bathing solutions, presumably because of buffering by the fixed negative charges on the surface of the lateral cell membranes. To test the hypothesis that fixed buffers are responsible for the acidity, a theoretical and experimental approach was developed for the determination of the concentration and pK of the fixed buffer constituted by the glycocalyx. The pH of the solution in the LIS was measured by ratiometric fluorescence microscopy while the buffer concentration or composition of the bathing solutions was altered. In addition, the divalent cation Sr²⁺ was added to the perfusion solutions to displace protons from the fixed buffer sites for the determination of the fixed buffer properties. We conclude that the LIS contain 3.7 mm of pK 6.2 fixed buffer and that this buffer is responsible for the acidic microenvironment in the LIS. Received: 9 April 1998/Revised: 28 July 1998     

Selective fluorescence sensing and quantification of uric acid by naphthyridine-based receptor in biological sample

Naphthyridine-based fluorescent probe H1 was synthesized and characterized for the quantification and selective detection of Uric Acid (UA) in live cell. In presence of UA, H1 forms the specific host-guest complex mainly through intermolecular hydrogen bonding and aromatic stacking which produces “turn-off” fluorescence. The probe and UA is found to be 1:1 stoichiometry on the basis of absorption and fluorescence titrations. The probe H1 has been shown to detect UA up to 0.6 µM at pH 7.4. DFT-TDDFT calculations were performed in order to demonstrate the sensing mechanism and the electronic properties of the receptor-donor complex. The selectivity was evaluated in Vero cells in the presence of UA with other purine derivatives, structurally similar to UA. It was found to exhibit no cytotoxicity effect in tested concentration of H1 and good membrane permeability for the detection of UA in living cell system. The unknown concentration of UA in serum and urine can be measured easily using the fluorescence property of probe H1.     

Use of nonradiative decays of extrinsic fluorophores as structural and dynamical probes in protein environments: Fluorescence quenching

In this work a combined pulsed-laser, time-resolved photoacoustic calorimetry (PAC) and fluorescence study is presented on two widely used covalent protein probes, fluorescein-5-isothiocyanate (FITC) and 6-acryloyl-2-dimethylaminonaphtalene (acrylodan). Three proteins that contain a single free thiol, namely carbonic anhydrase, bovine serum albumin (BSA) and papain, have been selectively labelled with FITC and acrylodan, and their fluorescence emission was quenched with KI. Nonradiative decays of the excited states of FITC are used to complement the information usually obtained by monitoring the quenching of fluorescence emssion. Data analysis evidences the dependence of the nonradiative quenching constants on the exposure of the dye to the solvent, and shows the involvement of a triplet state of FITC in the non radiative deexcitation. The shielding of the binding sites from the solvent is demonstrated also by the fluorescence emission of acrylodan and by the Stern-Volmer analysis of fluorescence quenching by KI. From photoacoustic data, an estimate of the fluorescent quantum yield of bound FITC is obtained. This work demonstrates the complete equivalence of quenching data obtained by fluorescence and photoacoustics measurements and shows that this combined approach allows a better control of the photophysics of the dyes involved in the quenching process.     

The quenching of tryptophan fluorescence by protonated and unprotonated imidazole

The fluorescence life-time of N-acetyl-tryptophan-amide (NATA) was measured by multifrequency phase fluorometry, in the presence of increasing concentrations of imidazole. Two pH values were tested, pH 4.5 where imidazole is fully protonated and pH 9.0 where it is fully unprotonated. At both pH values, the inverse life-time increases in a non-linear way with the imidazole concentration, showing that imidazole is not a high efficiency collisional quencher. The data can be analysed in terms of the formation of a complex with a reduced fluorescence life-time. The rate constants for association (at 25°C) are around 5 (±0.2) × 10⁹ M^–1 s^–1 and are thus diffusion controlled. The association equilibrium constant is strongly pH dependent and is much higher than the expected value of 0.4 M^–1 for a collisional complex. The intrinsic fluorescence life-time of the complex is 1.56 (±0.02) ns at pH 9.0 and 1.82 (±0.03) ns at pH 4.5, as compared to 2.37 (±0.03) ns for free NATA at pH 9.0 and 2.83 (±0.05) at pH 4.5 (all atI = 0.34). This means that at both pH values the fluorescence life-time of NATA in the complex is reduced to 61 (±0.5)% of its value in the free state. Despite this, the protonated form of imidazole is a better quencher at low concentrations, owing to a longer residence-time of the complex. At high viscosity the association equilibration is too slow and the system is described by two life-times. The quenching effect ofHis-18 on the fluorescence of the proximalTrp-94 of barnase (Locwenthal et al. 1991, Willaert et al. 1991) is discussed in terms of these findings.     

Template assisted self-organized chemosensors

The self-organization of fluorescent dyes and receptors on a proper template to form an organized assembly is a new strategy for the realization of fluorescence chemosensors. In the assembly, the two subunits do not interact directly and the communication between the bound substrate and the dye is only determined by their spatial closeness ensured by the template. The method is simple and the main advantages are related to the minimization of the synthetic work, the ease of modification and optimization of the sensor, the possibility to tune its properties by the simple adjustment of the components ratio. Self-organizing methodologies can open new perspectives to fluorescence chemosensors, both by allowing a simplified preparation and by opening the way to new and more complex functions. This article deals with this new approach and discusses its evolution, applications, and limitations.     

On the rotational brownian motion of a bacterial idle motor. II. Theory of fluorescence correlation spectroscopy

The photon flux autocorrelation function of a fluorescent label attached to a bacterial motor shaft is calculated for the case in which the bacterial motor is considered to be actively but idly rotating. It is shown that even when the fluorescent label has a very short lifetime, fluorescence correlation spectroscopy should provide a useful tool for determining the rate of revolution of the bacterial motor under various solution conditions.