Diffusion and binding properties investigated by Fluorescence Correlation Spectroscopy (FCS)

Quantification of fluctuations from fluorescence correlation spectroscopy experiments in reaction-diffusion systems

Fluorescence correlation spectroscopy (FCS) is commonly used to estimate diffusion and reaction rates. In FCS the fluorescence coming from a small volume is recorded and the autocorrelation function (ACF) of the fluorescence fluctuations is computed. Scaling out the fluctuations due to the emission process, this ACF can be related to the ACF of the fluctuations in the number of observed fluorescent molecules. In this paper the ACF of the molecule number fluctuations is studied theoretically, with no approximations, for a reaction-diffusion system in which the fluorescence changes with binding and unbinding. Theoretical ACFs are usually derived assuming that fluctuations in the number of molecules of one species are instantaneously uncorrelated to those of the others and obey Poisson statistics. Under these assumptions, the ACF derived in this paper is characterized only by the diffusive timescale of the fluorescent species and its total weight is the inverse of the mean number of observed fluorescent molecules. The theory is then scrutinized in view of previous experimental results which, for a similar system, gave a different total weight and correct estimates of other diffusive timescales. The total weight mismatch is corrected by assuming that the variance of the number of fluorescent molecules depends on the variance of the particle numbers of the other species, as in the variance decomposition formula. Including the finite acquisition time in its computation, it is shown that the ACF depends on various timescales of the system and that its total weight coincides with the one obtained with the variance decomposition formula. This calculation implies that diffusion coefficients of nonobservable species can be estimated with FCS experiments performed in reaction-diffusion systems. Ways to proceed in future experiments are also discussed.

Evidence for Prenucleated Fibrilogenesis of Acid-Mediated Self-Assembling Oligopeptides via Molecular Simulation and Fluorescence Correlation Spectroscopy

An important step in controlling biomimetic amyloid systems is understanding the self-assembly reaction kinetics. We are interested in a family of such materials characterized by symmetric sequences of amino acids flanking a π-conjugated functional core. Many of these materials rapidly self-assemble into long fibers upon protonation in an acidic environment. Despite extensive investigation of these materials' properties, little is yet understood regarding their reaction kinetics. Based on previous studies, we have chosen DFAG-4T-GAFD as a representative system and conducted molecular dynamics simulations to show that although large-scale assembly is induced by lowering pH, some degree of assembly is thermodynamically favorable in high-pH nonprotonating environments. These results are consistent with findings for other systems such as DFAG-OPV-GAFD. The nonprotonated aggregation also appears to be concentration dependent, occurring at concentrations of 100 nM and above. Single molecule measurements using fluorescence correlation spectroscopy provide experimental support for these computational predictions. We find evidence of spontaneous aggregation in aqueous solutions of peptides with concentrations as low as 100 nM; however, 10 nM solutions appear to be largely homogeneous solutions of unassembled monomer. These results indicate that the simplest explanations for kinetics of acid-mediated assembly-protonation-induced nucleation by monomeric addition followed by subsequent stages of aggregation and elongation-are inappropriate in this system. In fact, the system only exists as pure monomer in very low concentrations, nucleation actually occurs in the absence of protonating elements at concentrations typically used for experiments, and pH triggered assembly proceeds from these preassembled aggregates. Accordingly, triggered assembly must be considered to operate outside the domain of nucleation-dependent models.

FCS experiments to quantify Ca2+ diffusion and its interaction with buffers

Ca²⁺ signals are ubiquitous. One of the key factors for their versatility is the variety of spatio-temporal distributions that the cytosolic Ca²⁺ can display. In most cell types Ca²⁺ signals not only depend on Ca²⁺ entry from the extracellular medium but also on Ca²⁺ release from internal stores, a process which is in turn regulated by cytosolic Ca²⁺ itself. The rate at which Ca²⁺ is transported, the fraction that is trapped by intracellular buffers, and with what kinetics are thus key features that affect the time and spatial range of action of Ca²⁺ signals. The quantification of Ca²⁺ diffusion in intact cells is quite challenging because the transport rates that can be inferred using optical techniques are intricately related to the interaction of Ca²⁺ with the dye that is used for its observation and with the cellular buffers. In this paper, we introduce an approach that uses Fluorescence Correlation Spectroscopy (FCS) experiments performed at different conditions that in principle allows the quantification of Ca²⁺ diffusion and of its reaction rates with unobservable (non-fluorescent) Ca²⁺ buffers. To this end, we develop the necessary theory to interpret the experimental results and then apply it to FCS experiments performed in a set of solutions containing Ca²⁺, a single wavelength Ca²⁺ dye, and a non-fluorescent Ca²⁺ buffer. We show that a judicious choice of the experimental conditions and an adequate interpretation of the fitting parameters can be combined to extract information on the free diffusion coefficient of Ca²⁺ and of some of the properties of the unobservable buffer. We think that this approach can be applied to other situations, particularly to experiments performed in intact cells.

Fluorescence correlation spectroscopy study of the complexation of DNA hybrids, IgG antibody, and a chimeric protein of IgG-binding ZZ domains fused with a carbohydrate binding module

Fluorescence correlation spectroscopy (FCS) was used to characterize the molecular interactions between the four components of a DNA recognition system.

Micelles from self-assembled double-hydrophilic PHEMA-glycopolymer-diblock copolymers as multivalent scaffolds for lectin binding

We introduce a novel double-hydrophilic hydroxyethylmethacrylate (HEMA) based diblock glycopolymer which self-assembles into homogeneous spherical micellar structures in water.

How long should a system be observed to obtain reliable concentration estimates from the measurement of fluctuations?

The interior of cells is a highly fluctuating environment. Fluctuations set limits to the accuracy with which endogenous processes can occur. The physical principles that rule these limits also affect the experimental quantification of biophysical parameters in situ. The characterization of fluctuations, on the other hand, provides a way to quantify biophysical parameters. But as with any random process, enough data has to be collected to achieve a reliable quantitative description. In this article we study the accuracy with which intracellular concentrations can be estimated using fluorescence correlation spectroscopy. We show that, when the observed molecules interact with immobile species or experience other restrictions to their movement, the hypotheses commonly used to estimate concentrations are no longer valid. The interactions with immobile sites reduce the fluorescence variance by a finite amount. The time that is necessary to obtain an accurate concentration estimate, on the other hand, is hundreds of times larger than the slowest correlation time and is much larger when the sites move slowly than when they are immobile. Our analysis is applicable to other related techniques and it also sheds light on the way in which effector concentrations are read by target molecules in cells.

FRET based quantification and screening technology platform for the interactions of leukocyte function-associated antigen-1 (LFA-1) with intercellular adhesion molecule-1 (ICAM-1)

The interaction between leukocyte function-associated antigen-1(LFA-1) and intercellular adhesion molecule-1 (ICAM-1) plays a pivotal role in cellular adhesion including the extravasation and inflammatory response of leukocytes, and also in the formation of immunological synapse. However, irregular expressions of LFA-1 or ICAM-1 or both may lead to autoimmune diseases, metastasis cancer, etc. Thus, the LFA-1/ICAM-1 interaction may serve as a potential therapeutic target for the treatment of these diseases. Here, we developed one simple 'in solution' steady state fluorescence resonance energy transfer (FRET) technique to obtain the dissociation constant (Kd) of the interaction between LFA-1 and ICAM-1. Moreover, we developed the assay into a screening platform to identify peptides and small molecules that inhibit the LFA-1/ICAM-1 interaction. For the FRET pair, we used Alexa Fluor 488-LFA-1 conjugate as donor and Alexa Fluor 555-human recombinant ICAM-1 (D1-D2-Fc) as acceptor. From our quantitative FRET analysis, the Kd between LFA-1 and D1-D2-Fc was determined to be 17.93±1.34 nM. Both the Kd determination and screening assay were performed in a 96-well plate platform, providing the opportunity to develop it into a high-throughput assay. This is the first reported work which applies FRET based technique to determine Kd as well as classifying inhibitors of the LFA-1/ICAM-1 interaction.

From free to effective diffusion coefficients in fluorescence correlation spectroscopy experiments

Diffusion is one of the main transport processes that occur inside cells determining the spatial and time distribution of relevant action molecules. In most cases these molecules not only diffuse but also interact with others as they get transported. When these interactions occur faster than diffusion the resulting transport can be characterized by "effective diffusion coefficients" that depend on both the reaction rates and the "free" diffusion coefficients. Fluorescence correlation spectroscopy (FCS) gives information on effective rather than free diffusion coefficients under this condition. In the present paper we investigate what coefficients can be drawn from FCS experiments for a wide range of values of the ratio of reaction to diffusion time scales, using different fitting functions. We find that the effective coefficients can be inferred with relatively small errors even when the condition of fast reactions does not exactly hold. Since the diffusion time scale depends on the size of the observation volume and the reaction time scale depends on concentrations, we also discuss how by changing either one or the other property one can switch between the two limits and extract more information on the system under study.

Measurement of diffusion in articular cartilage using fluorescence correlation spectroscopy

BACKGROUND

Fluorescence correlation spectroscopy (FCS) provides information about translational diffusion of fluorescent molecules in tiny detection volumes at the single-molecule level. In normal states, cartilage tissue lacks vascularity, so chondrocyte metabolism depends on diffusion for molecular exchanges. The abundant extracellular matrix (ECM) of cartilage is maintained by a limited number of chondrocytes. ECM plays an important role in the regulation of chondrocyte functions. In this study, FCS was used to measure diffusion behaviors of albumin, the major protein of the intra-articular space, using normal and degenerated cartilage. Preliminary investigation of fluorescence dyes including Alexa 488, Rhodamine 6G and Rhodamine 123 was conducted to evaluate their properties in cartilage.

RESULTS

The results indicate that the diffusion behaviors of fluorescently labeled albumin can be observed using FCS in both normal and chemically degenerated cartilage.

CONCLUSIONS

This work demonstrates the capability of FCS for direct measurement of diffusion in cartilaginous ECM. When the diffusion characteristics of fluorescent probes in ECM are clarified using FCS evaluation, FCS will be applicable as a method for early diagnosis of osteoarthritis, which is accompanied by increased abnormalities of ECM and also as tool for evaluating bio-engineered artificial cartilage for autologous chondrocyte implantation.

Optical techniques provide information on various effective diffusion coefficients in the presence of traps

In many cell-signaling pathways information is transmitted via the diffusion of messenger molecules. In most cases, messengers react with other substances and diffuse at the same time. Effective diffusion coefficients may be introduced to characterize the net transport rate that results from the combined effect of these two processes. It was shown in [B. Pando, Proc. Natl. Acad. Sci. U.S.A. 103, 5338 (2006)] that even in the simplest scenario in which one bimolecular reaction is involved, two different effective coefficients are relevant. One gives the rate at which small perturbations spread out with time while the other relates the mean square displacement of a single particle to the time elapsed. They coincide in the absence of reactions but may be very different in other cases. Optical techniques provide a relatively noninvasive means by which transport rates can be estimated. In the above mentioned paper it was discussed why, under certain conditions, fluorescence recovery after photobleaching (FRAP), a technique commonly used to estimate diffusion rates in cells, provides information on one of the two effective coefficients. In the present paper we show that, under the same conditions, another commonly used optical technique, fluorescence correlation spectroscopy (FCS), gives information on the other one. This opens up the possibility of combining experiments to obtain information that goes beyond effective transport rates. In the present paper we discuss different ways to do so.

Measuring and imaging diffusion with multiple scan speed image correlation spectroscopy

The intracellular mobility of biomolecules is determined by transport and diffusion as well as molecular interactions and is crucial for many processes in living cells. Methods of fluorescence microscopy like confocal laser scanning microscopy (CLSM) can be used to characterize the intracellular distribution of fluorescently labeled biomolecules. Fluorescence correlation spectroscopy (FCS) is used to describe diffusion, transport and photo-physical processes quantitatively. As an alternative to FCS, spatially resolved measurements of mobilities can be implemented using a CLSM by utilizing the spatio-temporal information inscribed into the image by the scan process, referred to as raster image correlation spectroscopy (RICS). Here we present and discuss an extended approach, multiple scan speed image correlation spectroscopy (msICS), which benefits from the advantages of RICS, i.e. the use of widely available instrumentation and the extraction of spatially resolved mobility information, without the need of a priori knowledge of diffusion properties. In addition, msICS covers a broad dynamic range, generates correlation data comparable to FCS measurements, and allows to derive two-dimensional maps of diffusion coefficients. We show the applicability of msICS to fluorophores in solution and to free EGFP in living cells.

Peptide nanoparticles serve as a powerful platform for the immunogenic display of poorly antigenic actin determinants

The role of actin in transcription and RNA processing is now widely accepted but the form of nuclear actin remains enigmatic. Monomeric, oligomeric or polymeric forms of actin seem to be involved in nuclear functions. Moreover, uncommon forms of actin such as the "lower dimer" have been observed in vitro. Antibodies have been pivotal in revealing the presence and distribution of different forms of actin in different cellular locations. Because of its high degree of conservation, actin is a poor immunogen and only few specific actin antibodies are available. To unravel the mystery of less common forms of actin, in particular those in the nucleus, we chose to tailor monoclonal antibodies to recognize distinct forms of actin. To increase the immune response, we used a new approach based on peptide nanoparticles, which are designed to mimic an icosahedral virus capsid and allow the repetitive, ordered display of a specific epitope on their surface. Actin sequences representing the highly conserved "hydrophobic loop," which is buried in the filamentous actin filament, were grafted onto the surface of nanoparticles by genetic engineering. After immunization with "loop nanoparticles," a number of monoclonal antibodies were established that bind to the hydrophobic loop both in vitro and in situ. Immunofluorescence studies on cells revealed that filamentous actin filaments were only labeled once the epitope had been exposed. Our studies indicate that self-assembling peptide nanoparticles represent a versatile platform that can easily be customized to present antigenic determinants in repetitive, ordered arrays and elicit an immune response against poor antigens.

Accurate measurements of protein interactions in cells via improved spatial image cross-correlation spectroscopy

The sensitive detection of protein interactions in living cells is an important first step toward understanding each of the multitude of cellular processes that are regulated by such interactions. Spatial image cross-correlation spectroscopy (ICCS) is one method used to measure protein-protein interactions from the analysis of two-channel fluorescence microscopy images. In spatial ICCS, cross-correlation of fluctuations in fluorescence intensity recorded as images from two independent wavelength detection channels in a fluorescence microscope is used to determine the average number of interacting particles in the imaged region. Even in situations where the particle number density is relatively high, ICCS provides an accurate measure of molecular interactions. However, it was shown previously that the method suffers from relatively high detection limits of interacting particles (approximately 20%) and can be perturbed by heterogeneous spatial distributions of the fluorescent particles within the images. Here, we demonstrate new approaches to circumvent some of the limitations of ICCS. Spatial scrambling of pixel blocks within fluorescence images was investigated as a way of extending the detection of spatial ICCS to measure lower interaction fractions as well as colocalization within cells. We also show that 'mean-intensity-padding' of regions of interest within fluorescence images is a feasible method of applying ICCS to arbitrarily selected areas of the cell with boundaries or edge morphologies that would be impossible to analyze with conventional ICCS. Using these newly developed strategies we were able to measure the fraction of actin that interacts with alpha-actinin in the leading edge of a migrating cell.