Distance distributions of short polypeptides recovered by fluorescence resonance energy transfer in the 10 A domain

Fluorescence resonance energy transfer (FRET) between tryptophan (Trp) as donor and 2,3-diazabicyclo[2.2.2]oct-2-ene (Dbo) as acceptor was studied by steady-state and time-resolved fluorescence spectroscopy. The unique feature of this FRET pair is its exceptionally short F?rster radius (10 A), which allows one to recover distance distributions in very short structureless peptides. The technique was applied to Trp-(GlySer)n-Dbo-NH2 peptides with n = 0-10, for which the average probe/quencher distance ranged between 8.7 and 13.7 A experimentally (in propylene glycol, analysis according to wormlike chain model) and 8.6-10.2 A theoretically (for n = 0-6, GROMOS96 molecular dynamics simulations). The larger FRET efficiency in steady-state compared to time-resolved fluorescence experiments was attributed to a static quenching component, suggesting that a small but significant part (ca. 10%) of the conformations are already in van der Waals contact when excitation occurs.     

Design and synthesis of fluorogenic substrates that target protein phosphatases

We have successfully designed and synthesized new fluorogenic probes that specifically target different classes of protein phosphatases. The fluorescence profiles of the probes have been studied using 12 different phosphatases, and results showed that, besides alkaline and tyrosine phosphatases, our probes were able to detect serine/threonine as well as acid phosphatases.     

A 10-A spectroscopic ruler applied to short polyprolines

Fluorescence resonance energy transfer (FRET) from the amino acid tryptophan (Trp) as donor and a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine (Dbo) as acceptor in peptides of the general structure Trp-(Pro)n-Dbo-NH2 (n = 1-6) was investigated by steady-state and time-resolved fluorescence, CD, and NMR spectroscopy as well as by molecular dynamics (MD) simulations (GROMOS96 force field). The Trp/Dbo FRET pair is characterized by a very short F?rster radius (R0 ca. 9 A), which allowed distance determinations in such short peptides. Water and propylene glycol were investigated as solvents. The peptides were designed to show an early nucleation of the poly(Pro)II (PPII) secondary helix structure for n > or = 2, which was confirmed by their CD spectra. The shortest peptide (n = 1) adopts preferentially the trans conformation about the Trp-Pro bond, as confirmed by NMR spectra. The FRET efficiencies ranged 2-72% and were found to depend sensitively on the peptide length, i.e., the number of intervening proline residues. The analysis of the FRET data at different levels of theory (assuming either a fixed distance or distance distributions according to a wormlike chain or Gaussian model) afforded donor-acceptor distances between ca. 8 A (n = 1) and ca. 16 A (n = 6) in water, which were found to be similar or slightly higher in propylene glycol. The distances afforded by the Trp/Dbo FRET pair were found to be reasonable in comparison to literature data, expectations from the PPII helix structure, and the results from MD simulations. The persistence lengths for the longer peptides were found to lie at 30-70 A in water and 220 +/- 40 A in propylene glycol, suggesting a more rigid PPII helical structure in propylene glycol. A detailed comparison with literature data on FRET in polyprolines demonstrates that the donor-acceptor distances extracted by FRET are correlated with the F?rster radii of the employed FRET pairs. This demonstrates the limitations of using FRET as a spectroscopic ruler for short polyprolines, which is presumably due to the breakdown of the point dipole approximation in F?rster theory, when the size of the chromophores becomes comparable or larger than the distances under investigation.     

Synthesis of 3,5-difluorotyrosine-containing peptides: application in substrate profiling of protein tyrosine phosphatases

Fully protected 3,5-difluorotyrosine (F2Y), Fmoc-F2Y(tBu)-OH, is efficiently prepared by a chemoenzymatic process and incorporated into individual peptides and combinatorial peptide libraries. The F2Y-containing peptides display kinetic properties toward protein tyrosine phosphatases (PTPs) similar to their corresponding tyrosine-containing counterparts but are resistant to tyrosinase action. These properties make F2Y a useful tyrosine surrogate during peptide library screening for optimal PTP substrates.     

Development of fluorescence-based selective assays for serine/threonine and tyrosine phosphatases

A number of aromatic substrates were evaluated for their ability to detect tyrosine phosphatase and serine/threonine phosphatase activity. Results demonstrated that the fluorinated coumarin DiFMUP is the most sensitive substrate for detecting LAR and PP-2A activity. Using this substrate, selective high-throughput screening assays for serine/threonine and tyrosine phosphatases were developed. Specific inhibitor cocktails were added to each assay to limit the activity of other phosphatases. LAR, CD-45, and PTP-1B all rapidly hydrolyze DiFMUP in the tyrosine phosphatase assay. The activity of non-tyrosine phosphatases is less than 6% of the LAR activity. PP-1 and PP-2A are highly active in the serine/threonine phosphatase assay. Inhibition of LAR and PP-2A in these assays is demonstrated using known inhibitors. Both of these assays are sensitive, robust, kinetic assays that can be used to quantify enzyme activity.     

Induction of pH sensitivity on the fluorescence lifetime of quantum dots by NIR fluorescent dyes

Modulation of the fluorescence lifetime (FLT) of CdTeSe/ZnS quantum dots (QDs) by near-IR (NIR) organic chromophores represents a new strategy for generating reproducible pH-sensing nanomaterials. The hybrid construct transfers the pH sensitivity of photolabile NIR cyanine dyes to highly emissive and long-lifetime pH-insensitive QDs, thereby inducing a reproducible FLT change from 29 ns at pH >7 to 12 ns at pH <5. This approach provides an unparalleled large dynamic FLT range for pH sensing at NIR wavelengths.     

Self-reporting fluorescent substrates of protein tyrosine kinases

A new mechanistic principle by which protein tyrosine kinase substrates fluorescently report the introduction of a phosphate moiety has been developed. NMR was used to establish that tyrosine phosphorylation induces the disruption of pi-pi stacking interactions of the tyrosine moiety with a proximal fluorophore on the peptide substrate. We have demonstrated that (1) the peptide substrates described in this study are useful for a wide variety of different tyrosine kinases, (2) physiological concentrations of ATP can be employed (unlike the standard radioactive ATP kinase assays), thus providing a more realistic assessment of inhibitor potency, and (3) protein kinase self-activation can be observed in real-time.     

FLASH PHOTOLYSIS OF RIBONUCLEASE A

Abstract— Flash photolysis spectra show that ultraviolet irradiation of RNase (Λ > 250 nm) at pH 11.5 generates the hydrated electron and a long-lived transient with absorption maxima at 390 nm and 410 nm, attributed to the phenoxyl type radical from tyrosyl residues. Comparison of the initial yields with flash photolysis spectra obtained from aqueous tyrosine and mixtures of the chromophoric amino acids indicates that 3–4 tyrosyl residues are photoionized in the primary act. This process is almost completely quenched at pH 1–9, even though the p -alanylphenoxyl radical is obtained with tyrosine over this pH range and the accompanying electron is observed at pH 7. The negative result is not altered by denaturation of RNase with 8 M urea or heating to 70°C, suggesting that a primary chain interaction is responsible for the suppression of tyrosyl residue photolysis. This mechanism is supported by flash photolysis spectra of small peptides, showing that the initial radical yield from tyrosylglycylglycine is strongly quenched compared to tyrosine when the phenolic group is protonated. Comparion of this work with published results on fluorescence and inactivation quantum yields indicates that photochemical electron ejection from RNase in alkaline solutions takes place in the dissociable residues and does not contribute to loss of enzymic activity.     

A FLUORESCENCE STUDY OF TRYPTOPHAN-HISTIDINE INTERACTIONS IN THE PEPTIDE ANANTIN AND IN SOLUTION

Abstract—Anantin is a heptadecapeptide in which the C-terminal peptide chain pierces the covalently cyclized peptide ring formed by an amide link between the α-NH₂ end group and the β-carboxyl group of Asp(8). It contains a tryptophan and a histidine at positions 5 and 12 , respectively. Des-Phe(17)-anantin lacks the C-terminal phenylalanine. Fluorescence emission intensity as a function of pH follows the ionization of a single residue. The pK_a amounts to 7.23 ± 0.03 for anantin and is attributed to His(12). At pH 9 the quantum yield is 0.12 ± 0.01 for anantin, whereas at pH 4.5 the quantum yield decreases more than two-fold (0.05 2 0.01). Practically identical parameters are observed for des-Phe(17)-anantin. This pH dependency reveals intramolecular quenching of the excited indole ring of Trp(5) by the imidazole of His(12), which results in a marked decrease of the tryptophan fluorescence at low pH. In a multifrequency phase fluorometric study the fluorescence lifetimes for both peptides at pH 4.5 and pH 9 are determined. At both, pH fluorescence decay is well described by a sum of two exponentials. For anantin at pH 4.5 the lifetimes are 0.72 ± 0.07 ns and 1.67 ± 0.07 ns. At pH 9 the lifetimes are 1.11 ±0.12 ns and 2.55 ± 0.03 ns. In methanol we find two lifetimes for anantin: 0.68 ± 0.01 ns and 2.57 ± 0.01 ns. The lifetimes are found to be slightly dependent upon emission wavelength. For des-Phe(17)-anantin practically the same values are observed. The quenching of tryptophan fluorescence by histidine is further studied in solution using N-acetyl-tryptophanamide in the presence of increasing concentrations of imidazole in the protonated (pH 4.5) and unprotonated (pH 9) state and in methanol. At both pH values and in methanol, a linear increase in both the inverse of the steady-state fluorescence F_o/F and the inverse of the lifetime 1/τ with increasing imidazole concentration indicates that a collisional mechanism is at the root of the observed quenching. The quenching efficiency values, γ, are calculated and amount to about 0.32 at pH 4. 5 , 0.02 at pH 9 and 0.002 in methanol, showing that protonated imidazole is a better quencher than the unprotonated form, and that the nature of the solvent is involved even in the quenching by unprotonated imidazole. Tryptophan-histidine interactions in solution and in the peptide are compared.     

pH-dependent spectral behavior of substituted quinolones: potential fluorophore for metallofluorescent indicators

The 7-methoxy and 7-hydroxy derivatives of 2,3-dimethyl-4-quinolone have been characterized with respect to absorbance, steady-state fluorescence excitation and emission, and acid-base behavior in perchloric acid (H(0) -5.68-pH 2.0) and aqueous buffers (pH 2.2-14.2); susceptibility to alkaline hydrolysis has been examined absorptiometrically. 7-Hydroxy-2,3-dimethyl-4-quinolone is resistant to attack by hydroxide ion. Aqueous solutions of it exhibit moderate to high fluorescence emission, which is dependent on solution acidity. It is recommended for incorporation into metallofluorescent indicators of the Calcein Blue type.     

Structural basis of fluorescence fluctuation dynamics of green fluorescent proteins in acidic environments

Green fluorescent proteins (GFPs) have become powerful markers for numerous biological studies due to their robust fluorescence properties, site-specific labeling, pH sensitivity, and mutations for multiple-site labeling. Fluorescence correlation spectroscopy (FCS) studies have indicated that fluorescence blinking of anionic GFP mutants takes place on a time scale of 45-300 ms, depending on pH, and have been attributed to external proton transfer. Here we present experimental evidence indicating that conformational change in the protein &beta-barrel is a determining step for the external protonation of GFP-S65T (at low pH) using time-resolved fluorescence and polarization anisotropy measurements. While the average anionic fluorescence lifetime of GFP-S65T is reduced by approximately 18% over a pH range of 3.6-10.0, the fluorescence polarization anisotropy decays mostly as a single exponential with a rotational time of phi = 17 +/- 1 ns, which indicates an intact beta-barrel with a hydrodynamic volume of 78 +/- 5 nm3. In contrast, the total fluorescence (525 +/- 50 nm) of the excited neutral state of S65T reveals a strong correlation between the fluorescence lifetime, structural conformation, and pH. The average fluorescence lifetime of the excited neutral state of S65T as a function of pH yields pKa approximately 5.9 in agreement with literature values using steady-state techniques. In contrast to the intact beta-barrel at high pH, the anisotropy of neutral S65T (at pH 相似文献   

Time-resolution of the antheraxanthin- and delta pH-dependent chlorophyll a fluorescence components associated with photosystem II energy dissipation in Mantoniella squamata

The electronic excited-state behavior of photosystem II (PSII) in Mantoniella squamata, as influenced by the xanthophyll cycle and the transthylakoid pH gradient (delta pH), was examined in vivo. Mantoniella is distinguished from other photosynthetic organisms by two main features namely (1) a unique light-harvesting complex that serves both photosystems I (PSI) and II (PSII); and (2) a violaxanthin (V) cycle that undergoes only one de-epoxidation step in excess light to accumulate the monoepoxide antheraxanthin (A) as opposed to the epoxide-free zeaxanthin (Z). The cells were treated first with high light to induce the delta pH and A accumulation, followed by herbicide-induced closure of PSII traps and a chilling treatment, to sustain and stabilize the delta pH and nigericin-sensitive fluorescence level in the dark. De-epoxidation was controlled with subsaturating concentrations of dithiothreitol (DTT) and was 5-10 times more sensitive to DTT than higher plant thylakoids. The PSII energy dissipation involved two steps: (1) the pH activation of the xanthophyll binding site that was associated with a narrowing and slight attenuation of the main 2 ns (ns = 10(-9) s) fluorescence lifetime distribution; and (2) the concentration-dependent binding of A to the activated binding site yielding a second distribution centered around 0.9 ns. Consistent with the model of Gilmore et al. (1998) (Biochemistry 37, 13,582-13,593), the fractional intensity of the 0.9 ns component depended almost entirely on the A concentration and correlated linearly with the decrease of the steady-state chlorophyll alpha fluorescence intensity.     

Phosphorylation‐Responsive Membrane Transport of Peptides

Phosphorylation and dephosphorylation of peptides by kinases and phosphatases is essential for signal transduction in biological systems, and many diseases involve abnormal activities of these enzymes. Herein, we introduce amphiphilic calixarenes as key components for supramolecular, phosphorylation‐responsive membrane transport systems. Dye‐efflux experiments with liposomes demonstrated that calixarenes are highly active counterion activators for established cell‐penetrating peptides, with EC₅₀ values in the low nanomolar range. We have now found that they can even activate membrane transport of short peptide substrates for kinases involved in signal transduction, whereas the respective phosphorylated products are much less efficiently transported. This allows regulation of membrane transport activity by protein kinase A (PKA) and protein kinase C (PKC), as well as monitoring of their activity in a label‐free kinase assay.     

Competitive fluorescence polarization assays for the detection of phosphoinositide kinase and phosphatase activity

We describe the development and implementation of competitive fluorescence polarization (FP) based assays for determining activity of phosphoinositide 3-kinase (PI 3-K) and the type-II SH2-domain-containing inositol 5-phosphatase (SHIP2). These assays are based on the interaction of specific phosphoinositide binding proteins with fluorophore-labeled phosphoinositide and inositol phosphate tracers. Enzyme reaction products are detected by their ability to compete with the fluorescent tracers for protein binding, leading to an increase in the amount of free tracer and a decrease in polarization (mP) values. A variety of fluorophore-labeled tracers were evaluated, and assay sensitivity and specificity for products of PI 3-K and SHIP2 activity was determined. Assay performance was evaluated using recombinant PI 3-Kalpha and SHIP2 with diC(8)-PI(4,5)P(2) and diC(8)-PI(3,4,5)P(3) as respective substrates. IC(50) values for previously characterized PI 3-K inhibitors were within expected ranges. These assays are homogeneous, sensitive, and rapid, and suitable for HTS applications, and will facilitate screening for novel inhibitors of phosphoinositide kinases and phosphatases in drug development.     

Photometric and fluorimetric assay of alkaline phosphatase with new coumarin-derived substrates

Summary Two new coumarin-derived synthetic substrates for use in the direct and continuous kinetic assay of alkaline phosphatase are presented. They have been studied with respect to optimum pH (9.5) and rate of enzymatic hydrolysis (1.5–1.8 nmol/min at pH 9.5) by alkaline phosphatase from calf intestine. Detection limits were 0.0005 units/ml for the photometric assay, and 0.00001 units/ml for the fluorimetric one. The relatively longwave shifted absorption and emission maxima of the new substrates in addition to the large Stoke's shifts allow the determination of enzyme activities in a spectral range distinctly outside the intrinsic fluorescence of biological matter such as serum.     

Simultaneous determination of metals in two-component mixtures with 5-sulfo-8-quinolinol by using phase-resolved fluorimetry

Determinations of metals in two-component mixtures are described in which 5-sulfo-8-quinolinol is used to produce fluorescent chelates of the metals. The metal chelates have broad, overlapping fluorescence spectra but the fluorescence lifetimes (τ) of the chelates are sufficiently different to permit phase-resolved fluorimetric determinations in which the fluorescence contributions of the two chelates can be resolved. Average determination errors ranged from ?4.1% to 2.1% for each metal chelate in mixtures of zinc and cadmium (Δτ = 1.0 ns), gallium and indium (Δτ = 1.7 ns) and aluminum and gallium (Δτ = 5.3 ns). Limits of detection and determination for each individual metal chelate were found to be three times and five times greater, respectively, for the phase-resolved measurements relative to steady-state measurements under the same experimental conditions. Effects of pH on the fluorescence lifetimes and intesities of the metal chelates were studied.     

The primary photophysics of the Avena sativa phototropin 1 LOV2 domain observed with time-resolved emission spectroscopy

The phototropins are blue-light receptors that base their light-dependent action on the reversible formation of a covalent bond between a flavin mononucleotide (FMN) cofactor and a conserved cysteine in light, oxygen or voltage (LOV) domains. The primary reactions of the Avena sativa phototropin 1 LOV2 domain were investigated by means of time-resolved and low-temperature fluorescence spectroscopy. Synchroscan streak camera experiments revealed a fluorescence lifetime of 2.2 ns in LOV2. A weak long-lived component with emission intensity from 600 to 650 nm was assigned to phosphorescence from the reactive FMN triplet state. This observation allowed determination of the LOV2 triplet state energy level at physiological temperature at 16600 cm(-1). FMN dissolved in aqueous solution showed pH-dependent fluorescence lifetimes of 2.7 ns at pH 2 and 3.9-4.1 ns at pH 3-8. Here, too, a weak phosphorescence band was observed. The fluorescence quantum yield of LOV2 increased from 0.13 to 0.41 upon cooling the sample from 293 to 77 K. A pronounced phosphorescence emission around 600 nm was observed in the LOV2 domain between 77 and 120 K in the steady-state emission.     

Bisimidazoacridones: Effect of Molecular Environment on Conformation and Photophysical Properties

Bisimidazoacridones (BIA) are highly selective antineoplastic and antiviral agents. Ultraviolet-visible spectroscopy and steady-state and time-resolved fluorescence spectroscopy studies were carried out to probe the behavior of BIA in aqueous and nonaqueous (organic solvents, colloid micelles) solutions. Three ranges of fluorescence lifetimes were revealed: approximately 0.2-0.5 ns (presumably reflecting the chromophore-chromophore interaction), approximately 1-5 ns (interpreted as linker-perturbed chromophore decay) and approximately 6-12 ns (nonperturbed chromophore decay). The pre-exponential and steady-state contributions of these components to the decay signal as well as the data on steady-state fluorescence intensities, wavelength maxima and bandwidths showed that the BIA conformations in solution were sensitive to the environment and influenced strongly by their propensity to minimize hydrophobic interactions. In water, the molecules tend to adopt condensed conformations that bring the two imidazoacridone moieties into close proximity (resulting in intramolecular fluorescence energy transfer), while in nonaqueous systems the conformations become more relaxed. The transfer from a polar to more lipophilic environment of macromolecules is suggested to be the main driving force for binding of BIA to biomacromolecules, such as nucleic acids.     

Fluorescence decay of α-chymotrypsin studied by the picosecond-resolved single photon-counting technique

The fluorescence decay of the multi-tryptophan-containing enzyme α-chymotrypsin in Tris buffer (pH 7.8) at room temperature was studied using a frequency-doubled, synchronously-pumped picosecond rhodamine-6G laser excitation source with time-correlated single photon-counting detection. The fluorescence decay parameters were computed with a non-linear least-squares iterative reconvolution program. The goodness-of-fit was tested with well-known graphical methods such as residuals plots and the autocorrealtion function. Numerical tests (reduced chi-square, ordinary runs test and the Durbin—Watson statistic) were included to improve the reliability of the residuals analysis. Normal distribution of the weighted residuals was checked with the normal probability plot, and with computation of the mean and standard deviation of the weighted residuals. α-Chymotrypsin exhibited triple-exponential fluorescence decay kinetics with decay times of 615 ± 76 ps, 1.7 ± 0.2 ns, and 4.3 ± 0.3 ns. The fractional fluorescence contributions depended on the emission wavelength. The fluorescence spectra of the components contributing to the total fluorescence were calculated from the steady-state fluorescence spectrum and fluorescence decays at different emission wavelengths, and from convoluted time-resolved emission spectra and a fluorescence decay measurement.     

Enzymatic assay of marine bacterial phosphatases by capillary electrophoresis with laser-induced fluorescence detection

Microbial ectoenzyme activities in aquatic environments are important determinants of polymer hydrolysis and indicators of the state of microbial carbon, nitrogen, and phosphorus nutrition. Marine ectoenzymes are found on the cell surface or in the periplasmic space of gram-negative heterotrophic bacteria. Phosphatases, which remove phosphate groups from substrates, are one example of an ectoenzyme. Enzyme assays based on-capillary electrophoresis (CE) take advantage of CE's high-efficiency separation, extremely low sample volume requirements, and its ability to electrophoretically mix and separate zones of enzymes, substrates, and products all in one experimental run. CE has better resolving power and, when utilized with laser-induced fluorescence (LIF) detection, it is more sensitive than chromatography. CE-LIF is a promising tool for determining different phosphatases within a single microbial strain as well as the functional diversity between strains. In this study, four bacterial strains were studied (Shewanella sp., TW7, BB2AT2, and Vibrio alginolyticus) with each yielding at least one phosphatase that was kinetically characterized. K(m) values were calculated and found to be in the range of 0.0725-3.35 microM, whereas V(max) values ranged from 1.02 x 10(-3) to 1.05 x 10(-2) microM/min. The large range of values demonstrates differences among the phosphatases, suggesting different roles for each phosphatase not only between the species but also within a single bacterial species. This can have the important implications for organic matter processing in the sea.