Anthocyanin,flavonol copigments,and pH responsible for larkspur flower color

The anthocyanin and flavonol glycosides in Larkspur flowers (cv. Dark Blue Supreme) are delphinidin 3-di(p-hydroxybenzoyl)glucosylglucoside, kaempferol 3-robinobioside-7-rhamnoside (robinin), kaempferol 3-rutinoside, kaempferol 7-rhamnoside, and kaempferol 3-(caffeylgalactosylxyloside)-7-rhamnoside. As young flowers age the pH of epidermal tissue increases from 5·5 to 6·6 and the color of many of the cells changes from moderate reddish-purple to light purplish-blue. Many of the older cells also contain blue crystals. Visible absorption spectra of moderate reddish-purple and light purplish-blue cells were simulated with a solution of the anthocyanin (10⁻² M) plus robinin (5 × 10⁻³ M) at pH 5·6 and 7·1, respectively. Changes in the absorption spectra of living tissue with heating or cooling and of concentrated solutions of the anthocyanin with dilution or moderate heat, indicate that in the natural state the pigment is present in an associated form.     

DNA-based biosensor for monitoring pH in vitro and in living cells

DNA is a promising material for the construction of a biosensor or bioindicator because its structure is sensitive to the binding of cofactors. In the current studies, we found that a combination of two DNA oligonucleotides, 5'-TCTTTCTCTTCT-3' and 5'-AGAAAGAGAAGA-3', exhibit a novel structural transition from a Watson-Crick antiparallel duplex to a parallel Hoogsteen duplex as the pH changes from pH 7.0 to 5.0. By labeling this DNA for fluorescence resonance energy transfer, we were able to develop a sensitive pH indicator that can detect changes between pH 7.0 and 5.0. Moreover, using DNA-based hairpin parallel-stranded duplex in conjunction with fluorescence microscopy, we were able to observe the pH changes in living cells during apoptosis as an easily detected change in color. These results indicate that the DNA-based pH indicator should be useful for detecting pH changes between pH 7.0 and 5.0 in living cells.     

Flow-cytometric determination of intracellular pH, esterase activity and cell volume in human leukemic cell lines following in vitro incubation with cytostatic drugs

A recently developed flow cytometric assay method using patient tumor cells allows the determination not only of their sensitivity to cytostatic drugs but also of biochemical and biophysical parameters after treatment, such as esterase concentration and intracellular pH of the living cells. DNA-content of the dead cells and cell volume of living and dead cells. The T-cell lines CEM, Molt4, Jurkat, the B-cell lines RPMI1788, Daudi, Raji and the promyelocytic line HL60 were incubated with: cytosine arabinoside (ara-C), L-asparaginase, daunorubicin, vincristine and prednisone for 48 h. Living cells then stained with esterase and pH-dye 1,4-diacetoxy-2,3-dicyanobenzene (ADB) and dead cells with DNA-dye propidium-iodide (PI). The esterase concentration, an index of metabolic activity, decreased in the T-cell lines under the influence of ara-C, daunorubicin and vincristine, whereas in the B-cell lines smaller changes in esterase concentration were observed (P less than 0.001). A decrease in intracellular pH was seen in the ara-C and daunorubicin-incubated cells Molt4, CEM and HL60, whereas in the B-cell lines no significant change in intracellular pH was found. In all lines except Jurkat the cell volume of the surviving cells increased under the influence of certain drugs (primarily ara-C and daunorubicin); B-cell lines showed a greater swelling than T-cell lines (P = 0.001).     

A new fluorescent pH probe for imaging lysosomes in living cells

A new rhodamine B-based pH fluorescent probe has been synthesized and characterized. The probe responds to acidic pH with short response time, high selectivity and sensitivity, and exhibits a more than 20-fold increase in fluorescence intensity within the pH range of 7.5–4.1 with the pK_a value of 5.72, which is valuable to study acidic organelles in living cells. Also, it has been successfully applied to HeLa cells, for its low cytotoxicity, brilliant photostability, good membrane permeability and no ‘alkalizing effect’ on lysosomes. The results demonstrate that this probe is a lysosome-specific probe, which can selectively stain lysosomes and monitor lysosomal pH changes in living cells.     

Quantitative pH assessment of small-volume samples using a universal pH indicator

We developed a hue-based pH determination method to analyze digital images of samples in a 384-well plate after the addition of a universal pH indicator. The standard error of calibration for 69 pH standards was 0.078 pH units, and no sample gave an error greater than 0.23 units. We then used in-solution isoelectric focusing to determine the isoelectric point of Wnt3A protein in conditioned medium and after purification and applied the described method to assess the pH of these small-volume samples. End users may access our standard to assay the pH of their own samples with no additional calibration.     

A high-throughput colorimetric assay to measure the activity of glutamate decarboxylase

A pH-sensitive colorimetric assay has been established to quantitatively measure glutamate decarboxylase (GAD) activity in bacterial cell extracts using a microplate format. GAD catalyzes the irreversible α-decarboxylation of l-glutamate to γ-aminobutyrate. The assay is based on the color change of bromocresol green due to an increase in pH as protons are consumed during the enzyme-catalyzed reaction. Bromocresol green was chosen as the indicator because it has a similar pK_a to the acetate buffer used. The corresponding absorbance change at 620 nm was recorded with a microplate reader as the reaction proceeded. A difference in the enzyme preparation pH and optimal pH for GAD activity of 2.5 did not prevent this method from successfully allowing the determination of reaction kinetic parameters and the detection of improvements in enzymatic activity with a low coefficient of variance. Our assay is simple, rapid, requires minimal sample concentration and can be carried out in robotic high-throughput devices used as standard in directed evolution experiments. In addition, it is also applicable to other reactions that involve a change in pH.     

Stopped-flow studies of spectral changes in bilirubin-human serum albumin following an alkaline pH jump and following binding of bilirubin

A stopped-flow technique was used to study the spectral changes occurring in bilirubin-albumin following a pH jump as well as following binding of bilirubin at 25 degrees C. The changes were studied in two wavelength ranges, 280-310 nm (tyrosine residues) and 400-510 nm (bound bilirubin). The changes were analyzed according to a scheme of consecutive unimolecular reactions. Spectral monitoring of a pH jump from 11.3 to 11.8 reveals that the bilirubin-albumin complex changes its structure in several steps. The UV absorption spectra show that 3.8 tyrosine residues ionize in the first step, 2.5 in the second, none in the third, and 0.8 in the fourth and following steps. The visible absorption spectrum of bound bilirubin changes in the second, third, and fourth steps. The bilirubin spectra of the different bilirubin-albumin complexes occurring in the transition show a common isosbestic point at 445 nm, indicating a change of the dihedral angle between the two bilirubin chromophores in a three-step reaction. It is suggested that 1 tyrosine residue is located close to the bilirubin site and is externalized in the second step. Bilirubin binding to albumin was monitored at two pH values, 11.3 and 11.8. At pH 11.3 the complex changes its structure in a three-step relaxation sequence. A change of the dihedral angle between the bilirubin chromophores can explain the spectral changes observed in the second and third relaxations. Protonation of 0.7 tyrosine residues occurs in the third relaxation, suggesting internalization of a tyrosine residue as a late consequence of bilirubin binding. At pH 11.8 a two-step relaxation sequence follows bilirubin binding. No tyrosine protonation occurs. Bilirubin is probably bound more superficially at pH 11.8 than at pH 11.3.     

Ageladine A, a pyrrole-imidazole alkaloid from marine sponges, is a pH sensitive membrane permeable dye

The alkaloid ageladine A, a pyrrole-imidazole alkaloid isolated from marine Agelas sponges shows fluorescence in the blue-green range during excitation with UV light with the highest absorption at 370 nm. The fluorescence of this alkaloid is pH dependent. Highest fluorescence is observed at pH 4, lowest at pH 9 with the largest fluorescence changes between pH 6 and 7. Ageladine A is brominated, which facilitates membrane permeation and therefore allows for easy staining of living cells and even whole transparent animal staining. To calculate the exact pH in solutions, cells, and tissues, the actual concentration of the alkaloid has to be known. A ratiometric measurement at the commonly used excitation wavelengths at 340/380 nm allows pH measurements in living tissues with an attenuated influence of the ageladine A concentration on calculated values. The fluorescence changes report small intracellular pH changes induced by extracellular acidification and alkalization as well as intracellular alkalization induced by ammonium chloride.     

Sepal color variation of Hydrangea macrophylla and vacuolar pH measured with a proton-selective microelectrode

Sepal color of hydrangea varies with the environmental conditions. Although chemical and biological studies on this color variation have a long history, little correct knowledge has been generated about color development. All colored sepals contain the same anthocyanin, delphinidin 3-glucoside. Thus, there must be some other system for developing the wide variety of colors. In hydrangea sepals the cells of the epidermis are colorless and only the second layer of cells contain pigment. We prepared protoplasts without any color change during enzyme treatment of sepals and measured the vacuolar pH of each of the colored cells. We could correlate the color of a single hydrangea cell with its vacuolar pH using a combination of micro-spectrophotometry and a proton-selective microelectrode. Values for the vacuolar pH of blue (lambda vismax: 589 nm) and red cells (lambda vismax: 537 nm) were 4.1 and 3.3, respectively, the vacuolar pH of blue cells being significantly higher.     

Spectrophotometric determination of intracellular pH with cultured rat liver epithelial cells

A spectrophotometric method using 6-carboxyfluorescein (CF) was developed to determine intracellular pH in anchorage-dependent monolayers of control cells of rat hepatic origin. Until now, such studies have been carried out with ascites cells in suspension, which lack specific controls for comparative studies. The rat cell line is grown on plastic Leighton tube slides which fit directly into 3 cm spectrophotometer cuvettes. One sample, without CF, serves as a control for the light-scattering properties of the cell monolayers. Steady-state determinations show a decline in intracellular pH from 7.3 to 6.8 ten minutes after the addition of glucose and quercetin. Kinetic determinations show that with the addition of glucose to substrate-free cells the rate of acid formation is -0.02 pH units/min; the addition of quercetin results in a further acceleration of the kinetic rate to -0.10 pH units/min. In both types of analyses, the change in intracellular pH is standardized with nigericin and external buffers, based on the decrease in the maximum absorption of CF at 492 nm. The results demonstrate that even with anchorage-dependent monolayers of a control hepatocyte line which produces very little acid, this spectrophotometric method permits determinations sufficiently sensitive for analysis of intracellular pH.     

Analysis of the near-ultraviolet absorption and circular dichroic spectra of parsley plastocyanin for the effects of pH and copper center conformation changes

The absorption and circular dichroic (CD) spectra of parsley plastocyanin (PC) were measured in order to determine the effects of changes in primary amino acid sequence on both the copper center and protein components of the PC molecule. The near-ultraviolet (uv) absorption and CD spectra of parsley PC were found to be qualitatively similar to those of spinach, poplar, and lettuce PC, except for the near-uv CD spectrum of the reduced form at low pH (ca. pH 5.0). The CD spectrum of reduced parsley PC in the 250-265 nm wavelength region changes from positive to negative ellipticity upon reduction of pH, and is characterized by a pKa value of 5.7. This pKa value is the same as that for the protonation of the histidine 87 copper ligand, observed by NMR, and the change in conformation of the copper center. Similar processes are believed to occur in the other PC species at lower pH values. Thus, the pH-dependent perturbations of the near-uv CD spectra of reduced PC are interpreted as due to transitions in the reduced copper center. The increase in the near-uv absorption spectrum of reduced PC can be divided into pH-independent and pH-dependent portions. The pH-independent portion resembles the absorption spectrum of tetrahedral Cu(I) metallothionein, suggesting the presence of Cu(I)-Cys 84 and/or Cu(I)-Met 92 charge transfer transitions in the near-uv absorption spectra of reduced PC. The pH dependence of the absorption spectrum changes and the pH difference absorption spectrum indicate that tyrosine residues may contribute to at least a part of the pH-dependent portion of the absorption increase of reduced PC.     

Intracellular pH modulates quinary structure

NMR spectroscopy can provide information about proteins in living cells. pH is an important characteristic of the intracellular environment because it modulates key protein properties such as net charge and stability. Here, we show that pH modulates quinary interactions, the weak, ubiquitous interactions between proteins and other cellular macromolecules. We use the K10H variant of the B domain of protein G (GB1, 6.2 kDa) as a pH reporter in Escherichia coli cells. By controlling the intracellular pH, we show that quinary interactions influence the quality of in‐cell ¹⁵N–¹H HSQC NMR spectra. At low pH, the quality is degraded because the increase in attractive interactions between E. coli proteins and GB1 slows GB1 tumbling and broadens its crosspeaks. The results demonstrate the importance of quinary interactions for furthering our understanding of protein chemistry in living cells.     

The reduction of fungal laccase at high pH

1. 1. The nature and mechanism of the reduction of fungal laccase (p-diphenol: O₂ oxidoreductase, EC 1.10.3.2) obtained on an increase in pH have been studied by optical and electron paramagnetic resonance (EPR) spectroscopy and by measurements of O₂ concentration.

2. 2. The decreases in the optical absorption and the EPR signal of the “blue” Type 1 Cu²⁺ at high pH indicate that this ion is reduced. This is confirmed by oxidation with hexachloroiridate(IV) which restores the blue color. The “nonblue” Type 2 Cu²⁺ remains divalent over the pH range studied, as seen from the EPR spectra.

3. 3. Approximately one equivalent of hexachloroiridate(IV) is sufficient to restore the color of a pH-bleached protein which suggests that the reduction involves a single electron. A comparison between the optical spectra at pH 5 and 8 shows that the two-electron accepting unit, which at pH 5.5 is reduced concomitantly with the Type 1 Cu²⁺, remains oxidized in the protein brought to high pH. This unit can be reduced at pH 8.3 by octacyanotungstate(IV), as shown by the fact that this reductant in anaerobic titrations is found to add about two electrons (and no more) to a protein already having the Type 1 copper reduced. Thus, an increase in pH introduces a difference in the reduction behavior of the electron acceptors in fungal laccase.

4. 4. Oxygraph experiments show that there is no production of O₂ with an increase in pH, as would occur if water was oxidized by laccase. On the contrary, there is a continuous consumption of O₂ at both pH 5 and 8, indicating that the protein preparation contains a reducing substance which is responsible for the pH-dependent reduction.

Dual‐color‐emitting green fluorescent protein from the sea cactus Cavernularia obesa and its use as a pH indicator for fluorescence microscopy

We isolated and characterized a green fluorescent protein (GFP) from the sea cactus Cavernularia obesa. This GFP exists as a dimer and has absorption maxima at 388 and 498 nm. Excitation at 388 nm leads to blue fluorescence (456 nm maximum) at pH 5 and below, and green fluorescence (507 nm maximum) at pH 7 and above, and the GFP is remarkably stable at pH 4. Excitation at 498 nm leads to green fluorescence (507 nm maximum) from pH 5 to pH 9. We introduced five amino acid substitutions so that this GFP formed monomers rather than dimers and then used this monomeric form to visualize intracellular pH change during the phagocytosis of living cells by use of fluorescence microscopy. The intracellular pH change is visualized by use of a simple long‐pass emission filter with single‐wavelength excitation, which is technically easier to use than dual‐emission fluorescent proteins that require dual‐wavelength excitation. Copyright © 2013 John Wiley & Sons, Ltd.     

Phosphotyrosine as a substrate of acid and alkaline phosphatases

A new spectrophotometric method for following dephosphorylation of phosphotyrosine has been described. The absorption spectra of phosphotyrosine and tyrosine were plotted over the pH range from 3 to 9. The change in absorbance accompanying the conversion of phosphotyrosine to tyrosine was the greatest at 286 nm. The difference absorption coefficients were calculated for several pH values. Dephosphorylation of phosphotyrosine by acid phosphatases from human prostate gland, from wheat germ and potatoes obeys the Michaelis-Menten equation, whereas alkaline phosphatases calf intestine and E. coli are inhibited by excess of substrate.     

Effects of heating at neutral and acid pH on the structure of beta-lactoglobulin A revealed by differential scanning calorimetry and circular dichroism spectroscopy

The structural change of beta-lactoglobulin A (betaLG A) on heating was measured at pH 3.0 and 7.5 with UV absorption difference spectra, differential scanning calorimetry (DSC), and circular dichroism (CD). At pH 3.0, betaLG A showed a reversible structural change by heating at 80 degrees C, while an irreversible change was observed and molecular aggregates of betaLG were formed by heating at 95 degrees C. DSC analysis of betaLG A gave endothermic peaks at 75 degrees C and 90 degrees C at pH 7.5, and 90 degrees C at pH 3.0. At pH 7.5, betaLG A modified with N-ethylmaleimide (NEM-betaLG A) gave two endothermic peaks: at 72 degrees C and 90 degrees C. CD spectra of betaLG A heated at various temperatures and pHs were measured and the spectra at pH 3.0 and 7.5 were not changed by heating to 95 degrees C and 80 degrees C, respectively. Unheated NEM-betaLG A gave a spectrum similar to that of heated betaLG A, suggesting that the secondary structure was changed by NEM treatment.     

Surface pH controls purple-to-blue transition of bacteriorhodopsin. A theoretical model of purple membrane surface.

We have developed a surface model of purple membrane and applied it in an analysis of the purple-to-blue color change of bacteriorhodopsin which is induced by acidification or deionization. The model is based on dissociation and double layer theory and the known membrane structure. We calculated surface pH, ion concentrations, charge density, and potential as a function of bulk pH and concentration of mono- and divalent cations. At low salt concentrations, the surface pH is significantly lower than the bulk pH and it becomes independent of bulk pH in the deionized membrane suspension. Using an experimental acid titration curve for neutral, lipid-depleted membrane, we converted surface pH into absorption values. The calculated bacteriohodopsin color changes for acidification of purple, and titrations of deionized blue membrane with cations or base agree well with experimental results. No chemical binding is required to reproduce the experimental curves. Surface charge and potential changes in acid, base and cation titrations are calculated and their relation to the color change is discussed. Consistent with structural data, 10 primary phosphate and two basic surface groups per bacteriorhodopsin are sufficient to obtain good agreement between all calculated and experimental curves. The results provide a theoretical basis for our earlier conclusion that the purple-to-blue transition must be attributed to surface phenomena and not to cation binding at specific sites in the protein.     

A simple method to determine urea concentration using intact Helicobacter pylori and BromoCresol Purple as a pH indicator

A modified method for urea quantification, by measuring the ammonia formed by urease, used the urease-positive Helicobacter pylori in place of purified urease with a pH indicator dye, BromoCresol Purple, to provide a color change. The color formed was stable for 20-min and could be read at 588-nm for urea quantification. Using this method, urea standard curves were linear up to 8.3-mM. As there was no need for centrifugation or precipitation, the assay was developed for use with 96-well microplates.     

31P NMR measurements of myocardial pH in vivo

A 31P NMR magnetization transfer method for measuring myocardial pH in vivo is demonstrated in the lamb, dog and cat. The method involves measuring the difference in chemical shift between the resonances of phosphocreatine and inorganic phosphate in magnetization transfer difference spectra in which the gamma-phosphate resonance of ATP has been saturated. The method has been verified by measuring the chemical shift difference between the resonances of 2-deoxyglucose 6-phosphate and phosphocreatine following infusion of the animals with 2-deoxyglucose. The measured pH values are significantly lower than those obtained in previous studies on the heart in vivo.     

Indication of intracellular physiological pH changes by L-cysteine-coated CdTe quantum dots with an acute alteration in emission color

A novel quantum dots (QDs) based biosensor was developed to monitor physiological pH changes in both fixed and living cells by means of pH-dependent emission color of the QDs. In our system, the nominally single-sized colloidal solution samples of the L-cysteine-capped CdTe QDs with intrinsically broadened size distributions were prepared by employing aqueous synthesis technique. The quench of fluorescence intensities of the QDs with a 16 nm red shift of the emission maximum and a color change from green to yellow was observed with a slight pH decrease (from 7.0 to 6.8) in the system. This pH-dependent emission could be attributed to the efficient exciton energy transfer from smaller QDs to larger ones, which was controlled by electrostatic-tuned aggregation/disaggregation (low/high pH values) processes of the QDs. In addition to high stability, the emission shift of the QDs was reversible for at least one cycle under optimal conditions. Our pH biosensor may find potential application for monitoring the intracellular pH changes in both physiological and pathological conditions.