Fluorescence lifetime distributions of parinaroyl phospholipids in choline plasmalogen and phosphatidylcholine bilayers containing different amounts of cholesterol

The fluorescence decay of alkenylparinaroyl- and palmitoylparinaroyl glycerophosphocholines in vesicles of the unlabeled alkenyloleoyl and palmitoyloleoyl analogs was determined by multifrequency phase and modulation fluorometry. The measured phase angles and demodulations could be equally well fitted to a biexponential decay, as well as unimodal or bimodal continuous lifetime distributions. The latter model was applied to study the influence of cholesterol on parinaroyl phospholipid fluorescence in vesicles. The long-living component of a bimodal lifetime distribution was sensitive toward the presence of the sterol. Upon increasing cholesterol concentrations, its lifetime center increased and its distribution widths decreased. Lifetime distribution widths in vesicles of alkenyloleoyl- or palmitoyloleoyl-glycerophosphocholine (choline plasmalogen and phosphatidylcholine, respectively) were reduced by the sterol to the same extent. We interprete the sterol-induced lifetime distribution narrowing as an effect due to an increase of membrane homogeneity in cholesterol-phospholipid membranes.     

Fluorescence polarization as an analytical tool to evaluate galectin-ligand interactions

Galectins are a family of beta-galactose binding lectins associated with functions such as immunological and malignant events. To study the binding affinity of galectins for natural and artificial saccharides and glycoconjugates we have developed an assay using fluorescence polarization. A collection of fluorescein-conjugated saccharides was synthesized and used as probes with galectins-1 and -3 and the two carbohydrate recognition domains of galectin-4. Direct binding of a fixed probe amount with different amounts of each galectin defined specificity and selectivity and permitted selection of the optimal probe for inhibition studies. Then fixed amounts of galectin and selected probe were used to screen the inhibitory potency of a library of nonfluorescent compounds. As the assay is in solution and does not require separation of free and bound probe, it is simple and rapid and can easily be applied to different unlabeled galectins. As all interaction components are known, K(d) values for galectin-inhibitor interaction can be directly calculated without approximation other than the assumption of a simple one-site competition.     

Fluorescence lifetime distributions in human superoxide dismutase. Effect of temperature and denaturation.

The internal dynamics of human superoxide dismutase has been studied using time-resolved fluorescence. The fluorescence decay has been analyzed using continuous distribution of lifetime values. The effect of temperature and conformational state on the lifetime distribution has been investigated. The emission of the single tryptophan residue depends on the nature and dynamics of the protein matrix. Conformational changes have been induced by increased concentration of guanidinium hydrochloride. We found that both temperature and conformation strongly effect the width of the lifetime distribution.     

Capillary affinophoresis as a versatile tool for the study of biomolecular interactions: a mini-review

Combination of capillary electrophoresis and bioaffinity interaction gave rise to powerful research tools for analyzing molecular recognition. They take advantages of the electrophoretic behavior of the complex formed between a target biomolecule and a specially designed mobile ligand molecule (affinophore or affinity probe), and enable detection of complex formation, determination of the equilibrium constants and stoichiometry, etc.     

A solid-state NMR study of phospholipid-cholesterol interactions: sphingomyelin-cholesterol binary systems

We used solid-state NMR techniques to probe the interactions of cholesterol (Chol) with bovine brain sphingomyelin (SM) and for comparison of the interactions of Chol with dipalmitoylphosphatidylcholine (DPPC), which has a similar gel-to-liquid crystalline transition temperature. (1)H-, (31)P-, and (13)C-MASNMR yielded high-resolution spectra from multilamellar dispersions of unlabeled brain SM and Chol for analysis of chemical shifts and linewidths. In addition, (2)H-NMR spectra of oriented lipid membranes with specific deuterium labels gave information about membrane ordering and mobility. Chol disrupted the gel-phase of pure SM and increased acyl chain ordering in the liquid crystalline phase. As inferred from (13)C chemical shifts, the boundaries between the ordered and disordered liquid crystalline phases (L and L) were similar for SM and DPPC. The solubility limit of Chol in SM was ~50 mol %, the same value as previously reported for DPPC membranes. We found no evidence for specific H-bonding between Chol and the amide group of SM. The order parameters of a probe molecule, d31-sn1-DPPC, in SM were slightly higher than in DPPC for all carbons except the terminal groups at 30 mol % but were not significantly different at 5 and 60 mol % Chol. These studies show a general similarity with some subtle differences in the way Chol interacts with DPPC and SM. In the environment of a typical biomembrane, the higher proportion of saturated fatty acyl chains in SM compared to other phospholipids may be the most significant factor influencing interactions with Chol.     

Fluorescence lifetime distributions of 1,6-diphenyl-1,3,5-hexatriene in phospholipid vesicles

The fluorescence emission properties of 1,6-diphenyl-1,3,5-hexatriene (DPH) in 1,2-dipalmitoyl-3-sn-phosphatidylcholine and 1,2-dimyristoyl-3-sn-phosphatidylcholine multilamellar vesicles have been measured by using multifrequency phase fluorometry. The fluorescence decay of DPH in the phospholipid vesicles has been analyzed by assuming either that the decay is made up of a discrete sum of exponential components or that the decay is made up of one or more continuous distributions of lifetime components. The fit of the decay curve using exponentials required at least two terms, and the reduced X2 was relatively large. The fit using a continuous distribution of lifetime values used two continuous components. Several symmetric distribution functions were used: uniform, Gaussian, and Lorentzian. The distribution function that best described the decay was the Lorentzian. The full width at half-maximum of the Lorentzian distribution was about 0.6 ns at temperatures below the phase transition temperature. At the phospholipid phase transition and at higher temperatures, the distribution became quite narrow, with a width of about 0.1 ns. It is proposed that the lifetime distribution is generated by a continuum of different environments of the DPH molecule characterized by different dielectric constants. Below the transition temperature in the gel phase, the dielectric constant gradient along the membrane normal determines the distribution of decay rates. Above the transition, in the liquid-crystalline phase, the translational and rotational mobility of the DPH molecule increases, and the DPH experiences an average environment during the excited-state lifetime. Consequently, the distribution becomes narrower.(ABSTRACT TRUNCATED AT 250 WORDS)     

Allele-specific suppression as a tool to study protein-protein interactions in bacteria

Suppression analysis is well suited to study the interactions of gene products. It offers the advantage of simplicity for any organism for which a convenient genetic system has been developed, which holds for a wide spectrum of bacteria and an ever-increasing number of unicellular as well as complex eukaryotes. No other method provides as much information about the functional relationships of biological macromolecules. The intrinsic value of suppression analysis is enhanced by advances in genomics and in biophysical techniques for investigating the properties of nucleic acids and proteins, such as X-ray crystallography, liquid and solid-state nuclear magnetic resonance, electron spin labeling, and isothermal calorimetry. These approaches confirm and complement whatever is revealed by genetics. Despite these sterling qualities, suppression analysis has its dangers, less in execution than in conceptualization of experiments and interpretation of data. A consistent nomenclature is essential for a uniform and widespread understanding of the results. Familiarity with the genetic background and idiosyncracies of the organism studied is critical in avoiding extraneous phenomena that can affect the outcome. Finally, it is imperative not to underestimate potentially bizarre and improbable consequences that can transpire when rigorous genetic selection is maintained for an appreciable length of time. The article begins with a somewhat pedagogical discussion of genetic terminology. It then moves on to the necessary precautions to observe while planning and conducting suppression analysis. The remainder of the article considers different manifestations of suppression: bypass suppression; gradients of suppression; suppression by relaxed specificity; allele-specific "suppression at a distance"; and true conformational suppression. The treatment is not exhaustive, but representative examples have been gleaned from the recent bacterial literature.     

Analytical ultracentrifugation as a tool for studying protein interactions

The last two decades have led to significant progress in the field of analytical ultracentrifugation driven by instrumental, theoretical, and computational methods. This review will highlight key developments in sedimentation equilibrium (SE) and sedimentation velocity (SV) analysis. For SE, this includes the analysis of tracer sedimentation equilibrium at high concentrations with strong thermodynamic non-ideality, and for ideally interacting systems, the development of strategies for the analysis of heterogeneous interactions towards global multi-signal and multi-speed SE analysis with implicit mass conservation. For SV, this includes the development and applications of numerical solutions of the Lamm equation, noise decomposition techniques enabling direct boundary fitting, diffusion deconvoluted sedimentation coefficient distributions, and multi-signal sedimentation coefficient distributions. Recently, effective particle theory has uncovered simple physical rules for the co-migration of rapidly exchanging systems of interacting components in SV. This has opened new possibilities for the robust interpretation of the boundary patterns of heterogeneous interacting systems. Together, these SE and SV techniques have led to new approaches to study macromolecular interactions across the entire spectrum of affinities, including both attractive and repulsive interactions, in both dilute and highly concentrated solutions, which can be applied to single-component solutions of self-associating proteins as well as the study of multi-protein complex formation in multi-component solutions.     

Microspectrofluorometry as a tool for investigation of non-calcium interactions of Indo-1.

Indo-1 is a fluorescent calcium probe used to measure intracellular free calcium concentrations. These measurements are often performed by comparing the fluorescence intensities of Indo-1-treated cells at two selected wavelengths corresponding to the maxima of the fluorescence spectra of the calcium-bound and calcium-free forms. In this study, we used an optical multichannel analyser to numerise the fluorescence emitted by a single cell. A computerised resolution of numerised spectra was used on intracellular Indo-1 fluorescence. Calculation of numerical and graphic estimators allows us to evaluate the fit of the resolution. Different sets of characteristic spectra were compared using this method. It appeared that no linear combination of the two known forms of Indo-1 and of the cell autofluorescence can fit with spectra of Indo-1-treated cells. In addition, a study of the physico-chemical properties of Indo-1 shows the existence of two other forms of the molecule: a protonated form (maximum emission at 455 nm) and a form in interaction with proteins (maximum emission at 438 nm). Taking into account the contribution of these two new forms leads to an improved spectral resolution of the fluorescence of Indo-1-treated living cells and, therefore, improves calcium measurements. Moreover, quantification of the amount of the protonated form of Indo-1 allows a measurement of intracellular pH at the same time as calcium determination.     

Treatment with lithium as a tool for the study of animal-vegetal interactions in sea urchin embryos

Summary The question about the nature of the effect of lithium on early sea urchin development is reexamined. Essential features of the morphogenetic changes of lithium treated embryos are followed with continuous comparisons with control embryos. The key to the lithium effect is the greater cytoplasmic susceptibility in the animal polar region as compared with the vegetal one. This is diagrammed in Fig. 23a-c on the basis of the double gradient concept. There is a decline of the animal gradient with increasing lithium concentration. As a consequence the level of differentiation of the terminal region becomes more and more vegetal, seean/veg-values in Fig. 23. The region suppressed by a prolonged exposure to lithium, e.g. 9–16 hours, cannot be restored. Nevertheless, there are data from previous research supporting the view that the primary effects of lithium are reversible within certain limits. However, when the normal balance is disturbed by decline of the animal gradient and particularly by suppression of its higher levels, there is a compensatory enhancement of the vegetal gradient system which stabilizes the suppression. As a consequence of the suppression of the higher animal levels, a certain accumulation of cells in an anterior direction has taken place in the blastula stage. The degree of accumulation reflects the degree of vegetalization. Later there is to varying extent a backflow of cells in the vegetal direction. It was shown how a great part of the blastula wall may have the aspect of an attachment zone (Fig. 7). The primary mesenchyme cells attach themselves only to a certain level of the ectoderm in which the relativean/veg-value is around 0.7 according to the conventions behind Fig. 23.Sections of Carnoy fixed embryos were exposed to trypsin. It proved that the external cytoplasm of blastodermic cells in lithium treated embryos was more strongly attacked than the internal one. The latter showed a strong resistance to tryptic action. On the other hand, in the control embryos the inner part of blastodermic cells was completely digested with exception of the vegetal region including the attachment zone. The trypsin resistant structure may be preformed and may be responsible for the higher rigidity of the cytoplasm in lithium treated embryos (section IIIf).It is proposed that in the period of lithium susceptibility, the colloidal state is most affected in the animal region, thereby creating a block to the diffusion of the animalizing substances which results in the shifts diagrammed in Fig. 23.     

Sonication as a tool for the study of adenylyl cyclase activity.

The technique of sonication was applied in studying adenylyl cyclase activity of cultured fibroblasts. Exposure of BHK 21 c/13 to brief periods of low power sonication gives cell preparations with greater basal, fluoride and hormone sensitive adenylyl cyclase activites than those of broken cell preparations of homogenized cells. The sonicated cells provide a convenient method to study adenylyl cyclase since they are added directly to the adenylyl cyclase reaction vessels without further processing. Maximal epinephrine stimulated activity in sonicated cells is nearly equivalent to that activated by sodium fluoride, but the apparent affinity of the enzyme system is similar to that of broken cell preparations. Furthermore, broken cell preparations of sonicated cells possess greater adenylyl cyclase activity than broken cell preparations of unsonicated cells. This procedure may provide a useful tool for the analysis of the hormonal regulation of adenylyl cyclase activity of isolated cells.     

Fluorescence lifetime distributions of DNA-4',6-diamidino-2-phenylindole complex

Time-resolved fluorescence of 4',6-diamidino-2-phenylindole (DAPI) complexes show that for a homogeneous polymer (polyd(AT) or polyd(A).polyd(T)) at high P/D (phosphate/dye) ratio, a single exponential component adequately describes the fluorescence decay. For the AT polymers at low P/D ratio or for native DNA, the decay cannot be described by a single-exponential term. A continuous distribution of lifetime values of Gaussian shape gives a good fit to the decay data. We propose that the lifetime distribution method for the analysis of the fluorescence decay of DNA-DAPI complexes provides a useful method of characterizing the microheterogeneity of site binding.     

Protein microarrays as a discovery tool for studying protein-protein interactions

Exploring the function of the genome and the encoded proteins has emerged as a new and exciting challenge in the postgenomic era. Novel technologies come into view that promise to be valuable for the investigation not only of single proteins, but of entire protein networks. Protein microarrays are the innovative assay platform for highly parallel in vitro studies of protein-protein interactions. Due to their flexibility and multiplexing capacity, protein microarrays benefit basic research, diagnosis and biomedicine. This review provides an overview on the basic principles of protein microarrays and their potential to multiplex protein-protein interaction studies.     

Yeast as a tool to study Bax/mitochondrial interactions in cell death

The budding yeast Saccharomyces cerevisiae has proven to be a powerful tool in investigations of the molecular aspects of the events involved in apoptosis, particularly the steps implicating mitochondria. Yeast does not have obvious homologs of the proteins involved in the regulation of apoptosis, and provides a simplified model system in which the function of these proteins can be unraveled. This review focuses on the interactions of two of the major pro-apoptotic Bcl-2 family members, Bax and Bid, with mitochondria. It is shown that yeast has allowed questioning of several crucial aspects of the function of these two proteins, namely the molecular mechanisms driving their insertion into the mitochondrial outer membrane and those leading to the permeabilization to cytochrome c. More recently, signaling pathways leading to Bax-induced cell death, as well as other forms of cell death, have been identified in yeast. Both 'apoptosis-like' and autophagy-related forms of cell degradation are involved, and mitochondria play a central role in these two signaling pathways.     

Fluorescence spectroscopy as a potential metabonomic tool for early detection of colorectal cancer

Fluorescence spectroscopy Excitation Emission Matrix (EEM) measurements were applied on human blood plasma samples from a case control study on colorectal cancer. Samples were collected before large bowel endoscopy and included patients with colorectal cancer or with adenomas, and from individuals with other non malignant findings or no findings (N = 308). The objective of the study was to explore the possibilities for applying fluorescence spectroscopy as a tool for detection of colorectal cancer. Parallel Factor Analysis (PARAFAC) was applied to decompose the fluorescence EEMs into estimates of the underlying fluorophores in the sample. Both the pooled score matrix from PARAFAC, holding the relative concentrations of the derived components, and the raw unfolded spectra were used as basis for discrimination models between cancer and the various controls. Both methods gave test set validated sensitivity and specificity values around 0.75 between cancer and controls, and poor discriminations between the various controls. The PARAFAC solution gave better options for analyzing the chemical mechanisms behind the discrimination, and revealed a blue shift in tryptophan emission in the cancer patients, a result that supports previous findings. The present findings show how fluorescence spectroscopy and chemometrics can help in cancer diagnostics, and with PARAFAC fluorescence spectroscopy can be a potential metabonomic tool.     

Fluorescence lifetime characterization of novel low-pH probes.

The structures and functions of the cellular acidic compartments are strongly dependent on the pH gradients across vesicular membranes. Measurement and imaging of the vesicular pH require fluorophores with appropriate pK(a) values. In this report, we characterized the pH-dependent lifetime responses of a family of acidotropic probes, LysoSensors, to evaluate their usefulness to low-pH lifetime imaging. LysoSensors are cell-permeable weak bases that selectively accumulate in acidic vesicles after being protonated. They have higher quantum yields at lower pH ranges to allow visualization of the lysosomes. For LysoSensors DND-167, DND-189, and DND-153, raising the buffer pH increased the quenching effects of their basic side chains and substantially reduced their steady-state fluorescence and lifetimes. The apparent pK(a) values determined from their lifetime responses were shifted to near neutral values because of the dominant intensity contribution from their protonated species. One unique property of LysoSensor DND-189 is its nonmonotonic lifetime responses of the maxima occurring between pH 4 and 5. LysoSensor DND-192 did not show significant lifetime changes over a wide pH range. LysoSensor DND-160, which was the only excitation and emission ratiometric probe, showed significant pH-dependent lifetime changes as well as its spectral shifts. Its apparent pK(a) values determined from the lifetime responses were comparable to the lysosomal pH because of its bright basic form. Because of the pH-dependent absorption spectra, the apparent pK(a) values could be manipulated between 3 and 5 by changing the excitation and/or emission wavelengths. These results indicate that LysoSensor DND-160 is a promising probe for lifetime imaging to determine lysosomal pH.     

Immobilized-metal-ion affinity chromatography as a tool for the qualitative study of pepsinogen phosphorylation.

Affinity chromatography on immobilized Fe(3+) ions--immobilized-metal-ion affinity chromatography (IMAC) method--was used for the determination of pepsin and pepsinogen phosphorylation. IMAC is a very powerful method for detailed studies of proteins. Dephosphorylation of the pepsinogens and pepsins has no effect on their proteolytic ability. For this reason, the determination of proteolytic activity was used for the detection of pepsinogen (pepsin) presence in the collected fractions as a very suitable and specific method. Pepsins and their zymogens probably have the same amounts of phosphate ions in their molecule. The exact definition of conditions is very important for the prepurification of the proteinases and for their analysis.     

Fluorescence and thermotropic studies of the interactions of PEI-cholesterol based PEI-chol lipopolymers with dipalmitoyl phosphatidylcholine membranes

Numerous PEI derived polymers have been explored for their use in gene delivery. Nine PEI-chol lipopolymers based on cholesterol grafting on three polyethyleneimines (PEI) of different molecular weights have been synthesized. Firstly their aggregation behavior has been studied using transmission electron microscopy and then their interactions with l-α-dipalmitoyl phosphatidylcholine (DPPC) membranes have been examined using fluorescence anisotropy and differential scanning calorimetry (DSC). These PEI-chol lipopolymers are found to quench the chain motion of the acyl chains of DPPC, when incorporated in membranes, depending upon the cholesterol grafting on PEI. These PEI-chol lipopolymers act as filler molecules in membranes. Electron microscopy shows the different aggregation behavior of these new PEI-chol lipopolymers depending upon the molecular weight of PEI and percentage of cholesterol grafting. Detailed analysis of the fluorescence anisotropy and DSC data indicate that the nature of perturbation induced by PEI-chol lipopolymers is dependent upon the molecular weight of the PEI used and the % of cholesterol grafting on PEI. In general, PEI-chol lipopolymers rigidify the liquid-crystalline phase of the membranes without any noticeable effect on the gel phase unlike natural cholesterol, which is known to fluidize the gel phase of the membranes.