Interactions and Diffusion in Fine-Stranded β-lactoglobulin Gels Determined via FRAP and Binding

The effects of electrostatic interactions and obstruction by the microstructure on probe diffusion were determined in positively charged hydrogels. Probe diffusion in fine-stranded gels and solutions of β-lactoglobulin at pH 3.5 was determined using fluorescence recovery after photobleaching (FRAP) and binding, which is widely used in biophysics. The microstructures of the β-lactoglobulin gels were characterized using transmission electron microscopy. The effects of probe size and charge (negatively charged Na₂-fluorescein (376Da) and weakly anionic 70kDa FITC-dextran), probe concentration (50 to 200 ppm), and β-lactoglobulin concentration (9% to 12% w/w) on the diffusion properties and the electrostatic interaction between the negatively charged probes and the positively charged gels or solutions were evaluated. The results show that the diffusion of negatively charged Na₂-fluorescein is strongly influenced by electrostatic interactions in the positively charged β-lactoglobulin systems. A linear relationship between the pseudo-on binding rate constant and the β-lactoglobulin concentration for three different probe concentrations was found. This validates an important assumption of existing biophysical FRAP and binding models, namely that the pseudo-on binding rate constant equals the product of the molecular binding rate constant and the concentration of the free binding sites. Indicators were established to clarify whether FRAP data should be analyzed using a binding-diffusion model or an obstruction-diffusion model.     

Effect of cholesterol on lateral diffusion of fluorescent lipid probes in native hippocampal membranes

Cholesterol is an abundant lipid of mammalian membranes and plays a crucial role in membrane organization, dynamics, function and sorting. The role of cholesterol in membrane organization has been a subject of intense investigation that has largely been carried out in model membrane systems. An extension of these studies in natural membranes, more importantly in neuronal membranes, is important to establish a relationship between disease states and changes in membrane physical properties resulting from an alteration in lipid composition. We have monitored the lateral diffusion of lipid probes, DiIC(18)(3) and FAST DiI which are similar in their intrinsic fluorescence properties but differ in their structure, in native and cholesterol-depleted hippocampal membranes using the fluorescence recovery after photobleaching (FRAP) approach. Our results show that the mobility of these probes is in general higher in hippocampal membranes depleted of cholesterol. Interestingly, the increase in mobility of these probes does not linearly correlate with the extent of cholesterol depletion. These results assume significance in the light of recent reports on the requirement of cholesterol to support the function of the G-protein coupled serotonin(1A) receptor present endogenously in hippocampal membranes.     

Surface interaction forces of cellulose nanocrystals grafted with thermoresponsive polymer brushes

The colloidal stability and thermoresponsive behavior of poly(N-isopropylacrylamide) brushes grafted from cellulose nanocrystals (CNCs) of varying graft densities and molecular weights was investigated. Indication of the grafted polymer brushes was obtained after AFM imaging of CNCs adsorbed on silica. Also, aggregation of the nanoparticles carrying grafts of high degree of polymerization was observed. The responsiveness of grafted CNCs in aqueous dispersions and as an ultrathin film was evaluated by using light scattering, viscosimetry, and colloidal probe microscopy (CPM). Light transmittance measurements showed temperature-dependent aggregation originating from the different graft densities and molecular weights. The lower critical solution temperature (LCST) of grafted poly(NiPAAm) brushes was found to decrease with the ionic strength, as is the case for free poly(NiPAAm) in aqueous solution. Thermal responsive behavior of grafted CNCs in aqueous dispersions was observed by a sharp increase in dispersion viscosity as the temperature approached the LCST. CPM in liquid media for asymmetric systems consisting of ultrathin films of CNCs and a colloidal silica probe showed the distinctive effects of the grafted polymer brushes on interaction and adhesive forces. The origin of such forces was found to be mainly electrostatic and steric in the case of bare and grafted CNCs, respectively. A decrease in the onset of attractive and adhesion forces of grafted CNCs films were observed with the ionic strength of the aqueous solution. The decreased mobility of polymer brushes upon partial collapse and decreased availability of hydrogen bonding sites with higher electrolyte concentration were hypothesized as the main reasons for the less prominent polymer bridging between interacting surfaces.     

Interactions and Diffusion in Fine-Stranded β-lactoglobulin Gels Determined via FRAP and Binding

The effects of electrostatic interactions and obstruction by the microstructure on probe diffusion were determined in positively charged hydrogels. Probe diffusion in fine-stranded gels and solutions of β-lactoglobulin at pH 3.5 was determined using fluorescence recovery after photobleaching (FRAP) and binding, which is widely used in biophysics. The microstructures of the β-lactoglobulin gels were characterized using transmission electron microscopy. The effects of probe size and charge (negatively charged Na₂-fluorescein (376Da) and weakly anionic 70kDa FITC-dextran), probe concentration (50 to 200 ppm), and β-lactoglobulin concentration (9% to 12% w/w) on the diffusion properties and the electrostatic interaction between the negatively charged probes and the positively charged gels or solutions were evaluated. The results show that the diffusion of negatively charged Na₂-fluorescein is strongly influenced by electrostatic interactions in the positively charged β-lactoglobulin systems. A linear relationship between the pseudo-on binding rate constant and the β-lactoglobulin concentration for three different probe concentrations was found. This validates an important assumption of existing biophysical FRAP and binding models, namely that the pseudo-on binding rate constant equals the product of the molecular binding rate constant and the concentration of the free binding sites. Indicators were established to clarify whether FRAP data should be analyzed using a binding-diffusion model or an obstruction-diffusion model.     

An ultrastructural readout of fluorescence recovery after photobleaching using correlative light and electron microscopy

Fluorescence recovery after photobleaching (FRAP) provides an important quantitative readout of the mobility of fluorescently tagged structures in live tissue. Here we present a protocol for visualizing FRAP signal at the ultrastructural level, permitting the nature of recovered fluorescence signal to be studied at greater resolution than afforded by conventional light microscopy. Specifically we use FRAP, fixation, photoconversion and correlative light and electron microscopy (CLEM) to examine the ultrastructural organization of mobile FM1-43-labeled vesicles in synapses of cultured hippocampal neurons. At photobleached synapses, the FRAP signal can be visualized as photoconverted electron-dense vesicles. The combination of FRAP and CLEM provides a powerful tool for examining the specific localization of imported vesicles in relation to synaptic architecture. Moreover, with the increasing availability of photoconvertible fluorophores, this approach should be readily applicable to other systems where an ultrastructural characterization of FRAP signal is desirable. After cultures are prepared and ready to use, this protocol takes 2-3 days.     

LC3 fluorescent puncta in autophagosomes or in protein aggregates can be distinguished by FRAP analysis in living cells

LC3 is a marker protein that is involved in the formation of autophagosomes and autolysosomes, which are usually characterized and monitored by fluorescence microscopy using fluorescent protein-tagged LC3 probes (FP-LC3). FP-LC3 and even endogenous LC3 can also be incorporated into intracellular protein aggregates in an autophagy-independent manner. However, the dynamic process of LC3 associated with autophagosomes and autolysosomes or protein aggregates in living cells remains unclear. Here, we explored the dynamic properties of the two types of FP-LC3-containing puncta using fluorescence microscopy techniques, including fluorescence recovery after photobleaching (FRAP) and fluorescence resonance energy transfer (FRET). The FRAP data revealed that the fluorescent signals of FP-LC3 attached to phagophores or in mature autolysosomes showed either minimal or no recovery after photobleaching, indicating that the dissociation of LC3 from the autophagosome membranes may be very slow. In contrast, FP-LC3 in the protein aggregates exhibited nearly complete recovery (more than 80%) and rapid kinetics of association and dissociation (half-time < 1 sec), indicating a rapid exchange occurs between the aggregates and cytoplasmic pool, which is mainly due to the transient interaction of LC3 and SQSTM1/p62. Based on the distinct dynamic properties of FP-LC3 in the two types of punctate structures, we provide a convenient and useful FRAP approach to distinguish autophagosomes from LC3-involved protein aggregates in living cells. Using this approach, we find the FP-LC3 puncta that adjacently localized to the phagophore marker ATG16L1 were protein aggregate-associated LC3 puncta, which exhibited different kinetics compared with that of autophagic structures.     

Cellulose nanocrystals from celery stalk as quercetin scaffolds: A novel perspective of human holo-transferrin adsorption and digestion behaviours

In this study, cellulose nanocrystals (CNCs) were synthesized from celery stalks to be used as the platform for quercetin delivery. Additionally, CNCs and CNCs–quercetin were characterized using the results of scanning electron microscope (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, and zeta potential, while their interactions with human holo-transferrin (HTF) were also investigated. We examined their interaction under physiological conditions through the exertion of fluorescence, resonance light scattering, synchronized fluorescence spectroscopy, circular dichroism, three-dimensional fluorescence spectroscopy, and fluorescence resonance energy transfer techniques. The data from SEM and TEM exhibited the spherical shape of CNCs and CNCs–quercetin and also, a decrease was detected in the size of quercetin-loaded CNCs from 676 to 473 nm that indicated the intensified water solubility of quercetin. The success of cellulose acid hydrolysis was confirmed based on the XRD results. Apparently, the crystalline index of CNCs–quercetin was reduced by the interaction of CNCs with quercetin, which also resulted in the appearance of functional groups, as shown by FTIR. The interaction of CNCs–quercetin with HTF was also demonstrated by the induced quenching in the intensity of HTF fluorescence emission and Stern–Volmer data represent the occurrence of static quenching. Overall, the effectiveness of CNCs as quercetin vehicles suggests its potential suitability for dietary supplements and pharmaceutical products.     

Improving Parameter Inference from FRAP Data: an Analysis Motivated by Pattern Formation in the <Emphasis Type="BoldItalic">Drosophila</Emphasis> Wing Disc

Fluorescence recovery after photobleaching (FRAP) is used to obtain quantitative information about molecular diffusion and binding kinetics at both cell and tissue levels of organization. FRAP models have been proposed to estimate the diffusion coefficients and binding kinetic parameters of species for a variety of biological systems and experimental settings. However, it is not clear what the connection among the diverse parameter estimates from different models of the same system is, whether the assumptions made in the model are appropriate, and what the qualities of the estimates are. Here we propose a new approach to investigate the discrepancies between parameters estimated from different models. We use a theoretical model to simulate the dynamics of a FRAP experiment and generate the data that are used in various recovery models to estimate the corresponding parameters. By postulating a recovery model identical to the theoretical model, we first establish that the appropriate choice of observation time can significantly improve the quality of estimates, especially when the diffusion and binding kinetics are not well balanced, in a sense made precise later. Secondly, we find that changing the balance between diffusion and binding kinetics by changing the size of the bleaching region, which gives rise to different FRAP curves, provides a priori knowledge of diffusion and binding kinetics, which is important for model formulation. We also show that the use of the spatial information in FRAP provides better parameter estimation. By varying the recovery model from a fixed theoretical model, we show that a simplified recovery model can adequately describe the FRAP process in some circumstances and establish the relationship between parameters in the theoretical model and those in the recovery model. We then analyze an example in which the data are generated with a model of intermediate complexity and the parameters are estimated using models of greater or less complexity, and show how sensitivity analysis can be used to improve FRAP model formulation. Lastly, we show how sophisticated global sensitivity analysis can be used to detect over-fitting when using a model that is too complex.     

Electrophoretic mobility of high-molecular-weight, double-stranded DNA on agarose gels.

A new theoretical model for the migration of high-molecular-weight, double-stranded DNA on agarose gels is presented. This leads to the prediction that under certain conditions of electrophoresis, a linear relationship will exist between the molecular weight of a DNA molecule, raised to the (-2/3) power, and its electrophoretic mobility. Agarose gel electrophoresis of the fragments of bacteriophage lambda DNA produced by several restriction endonucleases confirms this relationship, and establishes some of the limits on its linearity. For this work, a polyacrylamide slab gel apparatus was modified for use with agarose gels. This apparatus has several advantages over others commercially available for agarose gel electrophoresis, including the abilities to run a larger number of samples at one time, to use lower-concentration gels, and to maintain better temperature stability across the width of the gel. The validation of the relationship developed here between molecular weight and electrophoretic mobility should make this a useful method for determining the molecular weights of DNA fragments.     

Convolution-based one and two component FRAP analysis: theory and application

The method of fluorescence redistribution after photobleaching (FRAP) is increasingly receiving interest in biological applications as it is nowadays used not only to determine mobility parameters per se, but to investigate dynamic changes in the concentration or distribution of diffusing molecules. Here, we develop a new simple convolution-based approach to analyze FRAP data using the whole image information. This method does not require information about the timing and localization of the bleaching event but uses the first image acquired directly after photobleaching to calculate the intensity distributions, instead. Changes in pools of molecules with different velocities, which are monitored by applying repetitive FRAP experiments within a single cell, can be analyzed by means of a global model by assuming two global diffusion coefficients with changing portions. We validate the approach by simulation and show that translocation of the YFP-fused PH-domain of phospholipase Cδ1 can be quantitatively monitored by FRAP analysis in a time-resolved manner. The new FRAP data analysis procedure may be applied to investigate signal transduction pathways using biosensors that change their mobility. An altered mobility in response to the activation of signaling cascades may result either from an altered size of the biosensor, e.g. due to multimerization processes or from translocation of the sensor to an environment with different viscosity. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Mobility-resolved 13C-NMR spectroscopy of primary plant cell walls

Primary plant cell walls contain highly hydrated biopolymer networks, whose major chemistry is known but whose relationship to architectural and mechanical properties is poorly understood. Nuclear magnetic resonance spectroscopy has been used to characterize segmental mobilities via relaxation and anisotropy effects in order to add a dynamic element to emerging models for cell wall architecture. For hydrated onion cell wall material, single pulse excitation revealed galactan (pectin side chains), provided that dipolar decoupling was used, and some of the pectin backbone in the additional presence of magic angle spinning. Cross-polarization excitation revealed the remaining pectin backbones, which exhibited greater mobility (contact time dependence, dipolar dephasing) than the cellulose component, whose noncrystalline and crystalline fractions showed no mobility discrimination. ¹HT₂ behavior could be quantitatively interpreted in terms of high resolution observabilities. Mobility-resolved spectroscopy of cell walls from tomato fruit, pea stem, and tobacco leaf showed similar general effects. Nuclear magnetic resonance study of the sequential chemical extraction of onion cell wall material suggests that galactans fill many of the network pores, that extractability of pectins is not dependent on segmental mobility, and that some pectic backbone (and not side chain) is strongly associated with cellulose. Analysis of the state of cellulose in four hydrated cell walls suggests a noncrystalline content of 60–80% and comparable amounts of Iα and Iβ polymorphs in the crystalline fraction. Comparison with micrographs for onion cell walls shows that noncrystalline cellulose does not equate to chains on fibril surfaces, and chemical shifts show that fully solvated cellulose is not a significant component in cell walls. © 1996 John Wiley & Sons, Inc.     

Intracellular macromolecular mobility measured by fluorescence recovery after photobleaching with confocal laser scanning microscopes

Fluorescence recovery after photobleaching (FRAP) is a widely used tool for estimating mobility parameters of fluorescently tagged molecules in cells. Despite the widespread use of confocal laser scanning microscopes (CLSMs) to perform photobleaching experiments, quantitative data analysis has been limited by lack of appropriate practical models. Here, we present a new approximate FRAP model for use on any standard CLSM. The main novelty of the method is that it takes into account diffusion of highly mobile molecules during the bleach phase. In fact, we show that by the time the first postbleach image is acquired in a CLSM a significant fluorescence recovery of fast-moving molecules has already taken place. The model was tested by generating simulated FRAP recovery curves for a wide range of diffusion coefficients and immobile fractions. The method was further validated by an experimental determination of the diffusion coefficient of fluorescent dextrans and green fluorescent protein. The new FRAP method was used to compare the mobility rates of fluorescent dextrans of 20, 40, 70, and 500 kDa in aqueous solution and in the nucleus of living HeLa cells. Diffusion coefficients were lower in the nucleoplasm, particularly for higher molecular weight dextrans. This is most likely caused by a sterical hindrance effect imposed by nuclear components. Decreasing the temperature from 37 to 22 degrees C reduces the dextran diffusion rates by approximately 30% in aqueous solution but has little effect on mobility in the nucleoplasm. This suggests that spatial constraints to diffusion of dextrans inside the nucleus are insensitive to temperature.     

The effects of Ca2+ on lipid diffusion

The effects of Ca2+ on rotational and translational diffusion of lipids in multilamellar dimyristoylphosphatidylcholine (DMPC)-water systems were investigated by time-resolved phosphorescence anisotropy steady-state fluorescence polarization and fluorescence recovery after photobleaching (FRAP) experiments. Above the phase transition temperature (Tm), addition of Ca2+ caused a steady increase in the segmental motion of the phosphorescent probe, but resulted in slower diffusion of the fluorescent and lateral diffusion probes. The former result is attributed to changes in the structure of the lipid/water interface that affects the chromophore mobility on the phosphorescence time scale but does not reflect lipid motion. Below the phase transition temperature, slower diffusion of all probes were observed with increasing concentrations of Ca2+, with sudden large changes occurring at [Ca2+] approximately 500 mM. This behaviour is attributed to association of Ca2+ with the lipid phosphate groups and the exclusion of water molecules which results in tighter packing of lipids and smaller segmental motion, leading eventually to the immobilization of lipid molecules.     

Kinetics of cellulose regeneration from cellulose--NaOH--water gels and comparison with cellulose--N-methylmorpholine-N-oxide--water solutions

The regeneration kinetics of cellulose from cellulose--NaOH--water gels immersed in a nonsolvent bath is studied in detail. Cellulose concentration, bath type, and temperature were varied, and diffusion coefficients were determined. The results were compared with data measured and taken from the literature on the regeneration kinetics of cellulose from cellulose--N-methylmorpholine-N-oxide (NMMO) monohydrate solutions. Different theories developed for the transport behavior of solutes in hydrogels or in porous media were tested on the systems studied. While the diffusion of NaOH from cellulose--NaOH--water gels into water has to be described with "porous media" approaches, the interpretation of NMMO diffusion is complicated because of the change of NMMO's state during regeneration (from solid crystalline to liquid) and the high concentration of NMMO in the sample. The activation energies were calculated from diffusion coefficient dependence on temperature for both systems and compared with the ones obtained from the rheological measurements. The activation energy of cellulose--NaOH--water systems does not depend on cellulose concentration or the way of measurement. This result shows that whatever the system is, pure NaOH--water solution, cellulose--NaOH--water solution, or cellulose--NaOH--water gel, it is NaOH hydrate with or without cellulose in solution, which is moving in the system. The swelling of cellulose in different nonsolvent liquids such as water or different alcohols during regeneration was investigated and interpreted using the Hildebrand parameter.     

Preparation by grafting onto, characterization, and properties of thermally responsive polymer-decorated cellulose nanocrystals

The grafting of thermosensitive amine-terminated statistical polymers onto the surface of cellulose nanocrystals (CNCs) was achieved by a peptidic coupling reaction, leading to unusual properties like colloidal stability at high ionic strength, surface activity, and thermoreversible aggregation. We have used a large variety of experimental techniques to investigate the properties of the polymer-decorated CNCs at different length-scales and as a function of the different reaction parameters. A high grafting density could be obtained when the reaction was performed in DMF rather than water. Infrared and solid-state NMR spectroscopy data unambiguously demonstrated the covalent character of the bonding between the CNCs and the macromolecules, whereas TEM images showed a preserved individualized character of the modified objects. Dynamic light scattering and zeta potential measurements were also consistent with individual nanocrystals decorated by a shell of polymer chains. Surface tension measurements revealed that CNCs became surface-active after the grafting of thermosensitive amines. Decorated CNCs were also stable against high electrolyte concentrations. A thermoreversible aggregation was also observed, which paves the way for the design of stimuli-responsive biobased nanocomposite materials.     

Evidence for restricted oligosaccharide mobility at the erythrocyte membrane surface: A fluorescence study

The glycophorins of whole, human erythrocytes were labeled at their sialic acid residues with one of three fluorescent probes. After preparation of the erythrocyte ghosts, the mobility of each fluorescent probe on the intact membrane was compared with its mobility on the isolated, labeled glycopeptides dissolved in aqueous buffer. A four- to ninefold decrease in the rotational relaxation time, as defined by the Perrin equation, accompanied the proteolytic removal of the labeled glycopeptides from the membrane. This suggests that the fluorescent probes, and by extrapolation, the sugars to which they are immediately attached, are restricted in their mobility at the membrane surface. A crude model of the carbohydrate layer of the erythrocyte surface was constructed by incorporating the labeled, tryptic glycopeptides into agarose gels of different agarose content. A decrease in the probe's mobility was observed as agarose content was raised. This indicates that the high oligosaccharide density at the erythrocyte membrane surface may contribute to the observed immobilization of the fluorescent probes in situ.     

A closed-form analytic expression for FRAP formula for the binding diffusion model

One of the most dominant methods cells use for a large class of cellular processes is reaction (or binding) diffusion kinetics, which are controlled by kinetic constants such as diffusion coefficients and on/off binding rate constants. Fluorescence recovery after photobleaching (FRAP) can be used to determine these kinetic constants in living cells. While an analytic expression for FRAP formulae for pure diffusion has been available for some time, an analytic FRAP formula for the binding diffusion model has not been reported yet. Here, we present an analytic FRAP formula for the binding diffusion model in an explicit form allowing for diffusion of the bound complex for either a uniform circle laser profile or a Gaussian laser profile.