Biological and chemical applications of fluorescence correlation spectroscopy: a review

Light-controlled protein dynamics observed with neutron spin echo measurements

A photoresponsive surfactant has been used as a means to control protein structure and dynamics with light illumination. This cationic azobenzene surfactant, azoTAB, which undergoes a reversible photoisomerization upon exposure to the appropriate wavelength of light, adopts a relatively hydrophobic, trans structure under visible light illumination and a relatively hydrophilic cis structure under UV light illumination. Small-angle neutron scattering (SANS) and neutron spin echo (NSE) spectroscopy were used to measure the tertiary structure and internal dynamics of lysozyme in the presence of the photosurfactant, respectively. The SANS-based in vitro structures indicate that under visible light the photosurfactant induces partial unfolding that principally occurs away from the active site near the hinge region connecting the α and β domains. Upon UV exposure, however, the protein refolds to a nativelike structure. At the same time, enhanced internal dynamics of lysozyme were detected with the surfactant in the trans form through NSE measurements of the Q-dependent effective diffusion coefficient (D(eff)) of the protein. In contrast, the D(eff) values of lysozyme in the presence of cis azoTAB largely agree with the rigid-body calculation as well as those measured for pure lysozyme, suggesting that the native protein is dormant on the nanosecond time and nanometer length scales. Lysozyme internal motions were modeled by assuming a protein of two (α and β domains) or three (α and β domains and the hinge region) domains connects by either soft linkers or rigid, freely rotating bonds. Protein dynamics were also tracked with Fourier transform infrared spectroscopy through hydrogen-deuterium exchange kinetics, which further demonstrated enhanced protein flexibility induced by the trans form of the surfactant relative to the native protein. Ensemble-averaged intramolecular fluorescent resonance energy transfer measurements similarly demonstrated the enhanced dynamics of lysozyme with the trans form of the photosurfactant. Previous results have shown a significant increase in protein activity in the presence of azoTAB in the trans conformation. Combined, these results provide insight into a unique light-based method of controlling protein structure, dynamics, and function and strongly support the relevance of large domain motions for the activity of proteins.

Distinct conformations of DNA-stabilized fluorescent silver nanoclusters revealed by electrophoretic mobility and diffusivity measurements

Silver-DNA nanoclusters (Ag:DNAs) are novel fluorophores under active research and development as alternative biomolecular markers. Comprised of a few-atom Ag cluster that is stabilized in water by binding to a strand of DNA, they are also interesting for fundamental explorations into the properties of metal molecules. Here, we use in situ calibrated electrokinetic microfluidics and fluorescence correlation spectroscopy to determine the size, charge, and conformation of a select set of Ag:DNAs. Among them is a pair of spectrally distinct Ag:DNAs stabilized by the same DNA sequence, for which it is known that the silver cluster differs by two atoms. We find these two Ag:DNAs differ in size by ∼30%, even though their molecular weights differ by less than 3%. Thus a single DNA sequence can adopt very different conformations when binding slightly different Ag clusters. By comparing spectrally identical Ag:DNAs that differ in sequence, we show that the more compact conformation is insensitive to the native DNA secondary structure. These results demonstrate electrokinetic microfluidics as a practical tool for characterizing Ag:DNA.

Binding of organic dyes with human serum albumin: a single-molecule study

Kinetics of binding of dyes at different sites of human serum albumin (HSA) has been studied by single-molecule spectroscopy. The protein was immobilized on a glass surface. To probe different binding sites (hydrophobic and hydrophilic) two dyes, coumarin 153 (C153, neutral) and rhodamine 6G (R6G, cationic) were chosen. For both the dyes, a major (ca. 96-98%) and minor (ca. 3%) binding site were detected. Rate constants of association and dissociation were simultaneously determined from directly measuring fluctuations in fluorescence intensity (τ(off) and τ(on)) and from this the equilibrium (binding) constants were calculated. Fluorescence lifetimes at individual sites were obtained from burst-integrated lifetime analysis. Distributions of lifetime histograms for both the probes (C153 and R6G) exhibit two maxima, which indicates the presence of two binding domains in the protein. Unfolding of the protein has been studied by adding guanidinium hydrochloride (GdnHCl) to the solution. It is observed that addition of GdnHCl affects the dissociation and association kinetics and hence, binding equilibrium of the association of C153. However, the effect of binding of R6G is not affected much. It is proposed that GdnHCl affects the hydrophobic binding sites more than the hydrophilic site.

Influence of the length and grafting density of PNIPAM chains on the colloidal and optical properties of quantum dot/PNIPAM assemblies

Structural and optical characterization of water soluble, thermo-responsive quantum dot/poly(N-isopropyl acrylamide) (QD/PNIPAM) hybrid particles using fluorescence correlation spectroscopy (FCS) and time-correlated single photon counting (TCSPC) measurements performed at temperatures below and above the lower critical solution temperature (LCST) of PNIPAM is reported. By increasing the temperature above the LCST, the signature of the PNIPAM chain collapse covering the QDs is revealed by FCS measurements. Despite the significant structural change, the TCSPC measurements show that the fluorescence lifetimes remain of the same order of magnitude at T > LCST. Such QD/PNIPAM hybrid particles with water solubility and robust thermo-responsive behavior at physiologically relevant temperatures are potentially useful for (bio)molecular sensing and separation applications.

Dynamics of nucleosome invasion by DNA binding proteins

Nucleosomes sterically occlude their wrapped DNA from interacting with many large protein complexes. How proteins gain access to nucleosomal DNA target sites in vivo is not known. Outer stretches of nucleosomal DNA spontaneously unwrap and rewrap with high frequency, providing rapid and efficient access to regulatory DNA target sites located there; however, rates for access to the nucleosome interior have not been measured. Here we show that for a selected high-affinity nucleosome positioning sequence, the spontaneous DNA unwrapping rate decreases dramatically with distance inside the nucleosome. The rewrapping rate also decreases, but only slightly. Our results explain the previously known strong position dependence on the equilibrium accessibility of nucleosomal DNA, which is characteristic of both selected and natural sequences. Our results point to slow nucleosome conformational fluctuations as a potential source of cell-cell variability in gene activation dynamics, and they reveal the dominant kinetic path by which multiple DNA binding proteins cooperatively invade a nucleosome.

Investigating the distance limit of a metal nanoparticle based spectroscopic ruler

Conventional Förster resonance energy transfer (FRET) processes involving a pair of fluorophore and organic quencher are restricted to an upper distance limit of ~10 nm. The application of a metal nanoparticle as a quencher can overcome the distance barrier of the traditional FRET technique. However, no standard distance dependence of this resonance energy transfer (RET) process has been firmly established. We have investigated the nonradiative energy transfer process between an organic donor (fluorescein) and gold nanoparticle quencher connected by double stranded (ds) DNA. The quenching efficiency of the gold nanoparticle as a function of distance between the donor and acceptor was determined by time-resolved lifetime analyses of the donor. Our results showed a 1/d(4) distance dependence for the RET process for longer distances (>10 nm) and 1/d(6) distance dependence for shorter distances (<10 nm). Our results clearly indicate the applicability of metal nanoparticle based quenchers for studying systems that exceed the 10 nm FRET barrier.

Manning free counterion fraction for a rodlike polyion: aqueous solutions of short DNA fragments in presence of very low added salt

We quantified the Manning free (uncondensed) counterions fraction θ for dilute aqueous solutions of rodlike polyions: 150 bp DNA fragments, in the presence of a very low concentration of monovalent salt c(salt)<0.05 mM. Conductivity measurements of these solutions for DNA base pair concentration range 0.015≤c≤8 mM were complemented by fluorescence correlation spectroscopy (FCS) measurements of the DNA polyion diffusion coefficient D(p)(c). We observed a crossover in the normalized conductivity σ(c)/c that nearly halved across the c=0.05-1 mM range, while D(p)(c) remained rather constant, as we established by FCS. Analyzing these data we extracted θ(c)=0.30-0.45, and taking the Manning asymmetry field effect on polyelectrolyte conductivity into account we got θ(c)=0.40-0.60. We relate the θ(c) variation to gradual DNA denaturation occurring, in the very low salt environment, with the decrease in DNA concentration itself. The extremes of the experimental θ(c) range occur toward the highest, above 1 mM, and the lowest, below 0.05 mM, DNA concentrations and correspond to the theoretical θ values for dsDNA and ssDNA, respectively. Therefore, we confirmed Manning condensation and conductivity models to be valuable in description of dilute solutions of rodlike polyions.

Note: An easy way to enable total internal reflection-fluorescence correlation spectroscopy (TIR-FCS) by combining commercial devices for FCS and TIR microscopy

Total internal reflection-fluorescence correlation spectroscopy (TIR-FCS) is a powerful method for studying dynamic processes at liquid-solid interfaces that may have numerous applications in biology, physics, and material science. Despite of its power and versatility, however, the use of TIR-FCS is still rather limited. The main reason for this is the need of a complex, in-house constructed optical setup whose assembly and adjustment is a quite difficult task. Clearly, the availability of ready to use, commercial TIR-FCS setups will strongly boost the application of this important method in many research areas. In this note we show that although such setups are still not available in the market, a proper combination of commercial devices for confocal fluorescence correlation spectroscopy and for total internal reflection microscopy may enable TIR-FCS in a way that do not require any special optical alignments. Furthermore, we demonstrate the capabilities of the setup by measuring the diffusion coefficient of single dye molecule and quantum dots in the very proximity of a water-glass interface.

Post-formulation peptide drug loading of nanostructures for metered control of NF-κB signaling

The NF-κB signaling pathway is an attractive therapeutic target for cancer and chronic inflammatory diseases. In this study, we report the first strategy to achieve NF-κB inhibition with a peptide inhibitor loaded into perfluorocarbon nanoparticles with the use of a simple post-formulation mixing approach that utilizes an amphipathic cationic fusion peptide linker strategy for cargo insertion. A stable peptide-nanoparticle complex is formed (dissociation constant ∼ 0.14 μM) and metered inhibition of both NF-κB signaling and downstream gene expression (ICAM-1) is demonstrated in leukemia/lymphoma cells. This post-formulation cargo loading strategy enables the use of a generic synthetic or biologic lipidic nanostructure for drug conjugation that permits flexible specification of types and doses of peptides and/or other materials as diagnostic or therapeutic agents for metered incorporation and cellular delivery.

Single-particle tracking of quantum dot-conjugated prion proteins inside yeast cells

Yeast is a model eukaryote with a variety of biological resources. Here we developed a method to track a quantum dot (QD)-conjugated protein in the budding yeast Saccharomyces cerevisiae. We chemically conjugated QDs with the yeast prion Sup35, incorporated them into yeast spheroplasts, and tracked the motions by conventional two-dimensional or three-dimensional tracking microscopy. The method paves the way toward the individual tracking of proteins of interest inside living yeast cells.

Probing the physical nature and composition of signalsomes

Background

Recent advances in our understanding of cell signaling have revealed assemblies of signaling components often viewed in fluorescence microscopy as very large, irregular "punctae". These punctae are often dynamic in nature, appearing to act as mobile scaffolds that function in integrating protein-protein interactions from large arrays of signaling components. The visualization of these punctae, termed "signalsomes" when applied to protein assemblies involved in cell signaling provokes the question, what is the physical nature of these structures made visible in live cells through the expression of fluorescently-tagged fusion molecules?

Results

Steric-exclusion chromatography on wide-bore matrices, fluorescence correlation spectroscopy, and advanced proteomics permits the analysis of several important physical properties of signalsomes. Wnt canonical signaling is essential to normal cell development and dysregulation can lead to cancers in humans. Punctae/signalsomes have been reported based upon the study of fluorescently-tagged mammalian Dishevelleds. Dishevelleds are phosphoprotein scaffolds that demonstrate dynamic character and mobility in cells stimulated with Wnt3a. Recent studies have successfully isolated Dvl3-based signalsomes from mouse totipotent embryonic teratocarcinoma F9 cells in culture and sized by application of steric exclusion chromatography (SEC), displaying large discrete M_r (0.5 and 2 MDa). Activation of the Wnt canonical β-catenin/LEF-Tcf-sensitive transcriptional response leads to an upfield shift of >5 MDa of the Dvl3-based signalsome. Fluorescence correlation spectroscopy (fcs) is a single molecule analysis performed in live cells that experimentally measures the diffusion coefficient and permits calculation of MW of the signalsome (0.2 and 30 MDa species in vivo), which also reveal an upfield shift in MW in response to Wnt3a. Proteomics provides for molecular dissection of the composition of the signalsome isolated from untreated and Wnt3a-treated cells.

Conclusion

Dvl3-based punctae/signalsomes made visible by fluorescent microscopy now can be interrogated by advanced physical means, defining such properties as signalsome M_r/MW, molecular composition, and intracellular locale.

Fluorescence fluctuation analysis of receptor kinase dimerization

Receptor kinases are essential for the cellular perception of signals. The classical model for activation of the receptor kinase involves dimerization, induced by the binding of the ligand. The mechanisms by which plant receptors transduce signals across the cell surface are largely unknown but plant receptors seem to dimerize as well. In this chapter, we describe two fluorescence fluctuation techniques, fluorescence cross-correlation spectroscopy and photon counting histogram analysis, to study the oligomerization state of receptor kinases in living plant cells in a quantitative manner.

A bipolar personality of yeast prion proteins

Prions are infectious, self-propagating protein conformations. [PSI+], [RNQ+] and [URE3] are well characterized prions in Saccharomyces cerevisiae and represent the aggregated states of the translation termination factor Sup35, a functionally unknown protein Rnq1, and a regulator of nitrogen metabolism Ure2, respectively. Overproduction of Sup35 induces the de novo appearance of the [PSI+] prion in [RNQ+] or [URE3] strain, but not in non-prion strain. However, [RNQ+] and [URE3] prions themselves, as well as overexpression of a mutant Rnq1 protein, Rnq1Δ100, and Lsm4, hamper the maintenance of [PSI+]. These findings point to a bipolar activity of [RNQ+], [URE3], Rnq1Δ100, and Lsm4, and probably other yeast prion proteins as well, for the fate of [PSI+] prion. Possible mechanisms underlying the apparent bipolar activity of yeast prions will be discussed.

DNA assembly and re-assembly activated by cationic comb-type copolymer

Guanine-rich oligonucleotides, such as TG(4)T and TG(5)T, assemble into a tetramolecular quadruplexes with layers of G-quartets stabilized by coordination to monovalent cations. Association rates of the quadruplexes are extremely slow, likely owing to electrostatic repulsion among the four strands. We have shown that comb-type copolymers with a polycation backbone and abundant hydrophilic graft chains form water-soluble polyelectrolyte complexes with DNA and promote DNA hybridization. Here, we report the effect of cationic comb-type copolymers on the kinetics of tetramolecular quadruplex formation. The copolymer significantly increased the association rate of tetramolecular quadruplexes without altering kinetic effects of metal cations in quadruplex formation. Dissociation rates of the quadruplexes were also accelerated by the copolymer suggesting that the copolymer has chaperone-like activity that reduces the energy barriers associated with dissociation and re-assembly of base pairs. This hypothesis was further supported by the observation that the copolymer activated the strand exchange reaction between the quadruplex and a constituting single-stranded.

Seeing the forest for the trees: fluorescence studies of single enzymes in the context of ensemble experiments

Enzymes are remarkable molecular machines that make many difficult biochemical reactions possible under mild biological conditions with incredible precision and efficiency. Our understanding of the working principles of enzymes, however, has not reached the level where one can readily deduce the mechanism and the catalytic rates from an enzyme's structure. Resolving the dynamics that relate the three-dimensional structure of an enzyme to its function has been identified as a key issue. While still challenging to implement, single-molecule techniques have emerged as one of the most useful methods for studying enzymes. We review enzymes studied using single-molecule fluorescent methods but placing them in the context of results from other complementary experimental work done on bulk samples. This review primarily covers three enzyme systems--flavoenzymes, dehydrofolate reductase, and adenylate kinase--with additional enzymes mentioned where appropriate. When the single-molecule experiments are discussed together with other methods aiming at the same scientific question, the weakness, strength, and unique contributions become clear.

Biophysical characterization of copolymer-protected gene vectors

A copolymer-protected gene vector (COPROG) is a three-component gene delivery system consisting of a preformed DNA and branched polyethylenimine (bPEI) complex subsequently modified by the addition of a copolymer (P6YE5C) incorporating both poly(ethylene glycol) (PEG) and anionic peptides. Using fluorescence correlation spectroscopy (FCS) and atomic force microscopy (AFM), we characterized and compared the self-assembly of bPEI/DNA particles and COPROG complexes. In low salt buffer, both bPEI/DNA and COPROG formulations form stable nanoparticles with hydrodynamic radii between 60-120 nm. COPROG particles, as compared to bPEI/DNA, show greatly improved particle stability to both physiological salt as well as low pH conditions. Binding stoichiometry of the three-component COPROG system was investigated by dual-color fluorescence cross-correlation spectroscopy (FCCS). It was found that a significant fraction of P6YE5C copolymer aggregates with excess bPEI forming bPEI/P6YE5C "ghost complexes" with no DNA inside. The ratio of ghost particles to COPROG complexes is about 4:1. In addition, we find a large fraction of excess P6YE5C copolymer, which remains unbound in solution. We observe a 2-4-fold enhanced reporter gene expression with COPROG formulations at various equivalents as compared to bPEI-DNA alone. We believe that both complex stabilization as well as the capture of excess bPEI into ghost particles induced by the copolymer is responsible for the improvement in gene expression.

Role of cytoskeleton in controlling the disorder strength of cellular nanoscale architecture

Cytoskeleton is ubiquitous throughout the cell and is involved in important cellular processes such as cellular transport, signal transduction, gene transcription, cell-division, etc. Partial wave spectroscopic microscopy is a novel optical technique that measures the statistical properties of cell nanoscale organization in terms of the disorder strength. It has been found previously that the increase in the disorder strength of cell nanoarchitecture is one of the earliest events in carcinogenesis. In this study, we investigate the cellular components responsible for the differential disorder strength between two morphologically (and hence microscopically) similar but genetically altered human colon cancer cell lines, HT29 cells and Csk shRNA-transfected HT29 cells that exhibit different degrees of neoplastic aggressiveness. To understand the role of cytoskeleton in nanoarchitectural alterations, we performed selective drug treatment on the specific cytoskeletal components of these cell types and studied the effects of cytoskeletal organization on disorder strength differences. We report that altering the cell nanoarchitecture by disrupting cytoskeletal organization leads to the attenuation of the disorder strength differences between microscopically indistinguishable HT29 and CSK constructs. We therefore demonstrate that cytoskeleton plays a role in the control of cellular nanoscale disorder.

Wnt-dependent assembly of supermolecular Dishevelled-3-based complexes

Dishevelled-3 (Dvl3) is a multivalent scaffold protein that is essential to Wnt signaling during development. Although Dvl-based punctae have been visualized by fluorescence microscopy; the physical nature and dynamic character of the such complexes are enigmatic. We use steric-exclusion chromatography, affinity pull-downs, proteomics and fluorescence correlation microscopy to characterize supermolecular Dvl3-based complexes of totipotent mouse F9 cells. The molecular mass of the complexes ranges from that of homodimeric Dvl3 to well-defined peaks harboring supermolecular complexes of 0.4 to 2.0 MDa. Addition of Wnt3a stimulates the formation of Dvl3-based complexes of greater molecular mass within 30 minutes. The presence of DKK1 and knockdown of Dishevelled proteins block formation of the 2 MDa Dvl3-based complexes and also block Wnt3a stimulation of the canonical pathway. Fluorescent correlation microscopy identified supermolecular Dvl3-based complexes with a molecular mass >30 MDa in live cells; these complexes were provoked to form structures with even greater molecular mass by Wnt3a. We establish for the first time the physical and functional nature of very large, supermolecular Dvl3-based complexes.

An optical method to quantify the density of ligands for cell adhesion receptors in three-dimensional matrices

The three-dimensional matrix that surrounds cells is an important insoluble regulator of cell phenotypes. Examples of such insoluble surfaces are the extracellular matrix (ECM), ECM analogues and synthetic polymeric biomaterials. Cell-matrix interactions are mediated by cell adhesion receptors that bind to chemical entities (adhesion ligands) on the surface of the matrix. There are currently no established methods to obtain quantitative estimates of the density of adhesion ligands recognized by specific cell adhesion receptors. This article presents a new optical-based methodology for measuring ligands of adhesion receptors on three-dimensional matrices. The study also provides preliminary quantitative results for the density of adhesion ligands of integrins alpha(1)beta(1) and alpha(2)beta(1) on the surface of collagen-based scaffolds, similar to biomaterials that are used clinically to induce regeneration in injured skin and peripheral nerves. Preliminary estimates of the surface density of the ligands of these two major collagen-binding receptors are 5775 +/- 2064 ligands microm(-2) for ligands of alpha(1)beta(1) and 17 084 +/- 5353 ligands microm(-2) for ligands of alpha(2)beta(1). The proposed methodology can be used to quantify the surface chemistry of insoluble surfaces that possess biological activity, such as native tissue ECM and biomaterials, and therefore can be used in cell biology, biomaterials science and regenerative medical studies for quantitative description of a matrix and its effects on cells.

Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory

The problem of spontaneous folding of amino acid chains into highly organized, biologically functional three-dimensional protein structures continues to challenge the modern science. Understanding how proteins fold requires characterization of the underlying energy landscapes as well as the dynamics of the polypeptide chains in all stages of the folding process. In recent years, important advances toward these goals have been achieved owing to the rapidly growing interdisciplinary interest and significant progress in both experimental techniques and theoretical methods. Improvements in the experimental time resolution led to determination of the timescales of the important elementary events in folding, such as formation of secondary structure and tertiary contacts. Sensitive single molecule methods made possible probing the distributions of the unfolded and folded states and following the folding reaction of individual protein molecules. Discovery of proteins that fold in microseconds opened the possibility of atomic-level theoretical simulations of folding and their direct comparisons with experimental data, as well as of direct experimental observation of the barrier-less folding transition. The ultra-fast folding also brought new questions, concerning the intrinsic limits of the folding rates and experimental signatures of barrier-less "downhill" folding. These problems will require novel approaches for even more detailed experimental investigations of the folding dynamics as well as for the analysis of the folding kinetic data. For theoretical simulations of folding, a main challenge is how to extract the relevant information from overwhelmingly detailed atomistic trajectories. New theoretical methods have been devised to allow a systematic approach towards a quantitative analysis of the kinetic network of folding-unfolding transitions between various configuration states of a protein, revealing the transition states and the associated folding pathways at multiple levels, from atomistic to coarse-grained representations. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.

Hydrodynamic properties of human adhesion/growth-regulatory galectins studied by fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy is applied on homologous human lectins (i.e., adhesion/growth-regulatory galectins) to detect influence of ligand binding and presence of the linker peptide in tandem-repeat-type proteins on hydrodynamic properties. Among five tested proteins, lactose binding increased the diffusion constant only in the cases of homodimeric galectin-1 and the linkerless variant of tandem-repeat-type galectin-4. To our knowledge, the close structural similarity among galectins does not translate into identical response to ligand binding. Kinetic measurements show association and dissociation rate constants in the order of 1 to 10(3) M(-1) s(-1) and 10(-4) s(-1), respectively. Presence of the linker peptide in tandem-repeat-type protein leads to anomalous scaling with molecular mass. These results provide what we believe to be new insights into lectin responses to glycan binding, detectable so far only by small angle neutron scattering, and the structural relevance of the linker peptide. Methodologically, fluorescence correlation spectroscopy is shown to be a rather simple technical tool to characterize hydrodynamic properties of these proteins at a high level of sensitivity.

Cholesterol depletion mimics the effect of cytoskeletal destabilization on membrane dynamics of the serotonin1A receptor: A zFCS study

Single-point fluorescence correlation spectroscopy (FCS) of membrane-bound molecules suffers from a number of limitations leading to inaccurate estimation of diffusion parameters. To overcome such problems and with the overall goal of addressing membrane heterogeneities, we performed z-scan FCS (zFCS) of the serotonin(1A) receptor. We analyzed the results according to FCS diffusion laws that provide information on the organization of the diffusing species. Analysis of our results shows that the diffusion coefficients of the receptor and a fluorescently labeled phospholipid are similar when probed at length scales approximately 210 nm. We discuss the significance of the spatiotemporal evolution of dynamics of membrane-bound molecules in the overall context of membrane domains and heterogeneity. Importantly, our results show that the serotonin(1A) receptor exhibits confinement in cell membranes, possibly due to interaction with the actin cytoskeleton. Surprisingly, depletion of membrane cholesterol appears to reduce receptor confinement in a manner similar to that observed in the case of cytoskeletal destabilization, implying possible changes in the actin cytoskeleton induced upon cholesterol depletion. These results constitute the first report on G-protein-coupled receptor dynamics utilizing a combination of zFCS and the FCS diffusion laws, and present a convenient approach to explore cell membrane heterogeneity at the submicron level.

Identification of protein-protein and protein-ribosome interacting regions of the C-terminal tail of human mitochondrial inner membrane protein Oxa1L

The mammalian mitochondrial inner membrane protein Oxa1L is involved in the insertion of a number of mitochondrial translation products into the inner membrane. During this process, the C-terminal tail of Oxa1L (Oxa1L-CTT) binds mitochondrial ribosomes and is believed to coordinate the synthesis and membrane insertion of the nascent chains into the membrane. The C-terminal tail of Oxa1L does not contain any Cys residues. Four variants of this protein with a specifically placed Cys residue at position 4, 39, 67, or 94 of Oxa1L-CTT have been prepared. These Cys residues have been derivatized with a fluorescent probe, tetramethylrhodamine-5-maleimide, for biophysical studies. Oxa1L-CTT forms oligomers cooperatively with a binding constant in the submicromolar range. Fluorescence anisotropy and fluorescence lifetime measurements indicate that contacts near a long helix close to position 39 of Oxa1L-CTT occur during oligomer formation. Fluorescence correlation spectroscopy measurements demonstrate that all of the Oxa1L-CTT derivatives bind to mammalian mitochondrial ribosomes. Steady-state fluorescence quenching and fluorescence lifetime data indicate that there are extensive contacts between Oxa1L-CTT and the ribosome-encompassing regions around positions 39, 67, and 94. The results of this study suggest that Oxa1L-CTT undergoes conformational changes and induced oligomer formation when it binds to the ribosome.

Role of protein stabilizers on the conformation of the unfolded state of cytochrome c and its early folding kinetics: investigation at single molecular resolution

An insight into the conformation and dynamics of unfolded and early intermediate states of a protein is essential to understand the mechanism of its aggregation and to design potent inhibitor molecules. Fluorescence correlation spectroscopy has been used to study the effects of several model protein stabilizers on the conformation of the unfolded state and early folding dynamics of tetramethyl rhodamine-labeled cytochrome c from Saccharomyces cerevisiae at single molecular resolution. Special attention has been given to arginine, which is a widely used stabilizer for improving refolding yield of different proteins. The value of the hydrodynamic radius (r(H)) obtained by analyzing the intensity fluctuations of the diffusing molecules has been found to increase in a two-state manner as the protein is unfolded by urea. The results further show that the presence of arginine and other protein stabilizers favors a relatively structured conformation of the unfolded states (r(H) of 29 A) over an extended one (r(H) of 40 A), which forms in their absence. Also, the time constant of a kinetic component (tau(R)) of about 30 micros has been observed by analyzing the correlation functions, which represents formation of a collapsed state. This time constant varies with urea concentration representing an inverted Chevron plot that shows a roll-over and behavior in the absence of arginine. To the best of our knowledge, this is one of the first applications of fluorescence correlation spectroscopy to study direct folding kinetics of a protein.

Fluorescence correlation spectroscopy reveals strong fluorescence quenching of FITC adducts on PEGylated gold nanoparticles in water and the presence of fluorescent aggregates of desorbed thiolate ligands

Colloidal gold particles functionalised with oligoethylene-glycolated disulfide ligands and fluorescent moieties derived from fluorescein isothiocyanate (FITC) have been prepared and studied in aqueous suspension using fluorescence correlation spectroscopy (FCS). FCS probes the dynamics of the particles at the single object level, and reveals the desorption of fluorescent ligands which subsequently aggregate into larger (slower diffusing) objects. Cross-correlation spectroscopy of the FITC fluorescence and the Rayleigh-Mie scattering (RM-FCCS) of the gold cores shows that the only detectable fluorescent objects are free ligands and aggregates not associated with a gold particle. The fluorescence of bound fluorophores is quenched making their fluorescence too weak to be detected. FCS and RM-FCCS are useful tools for characterising functionalised noble metal particles in solution, under conditions similar to those used in optical bio-imaging. Desorption of thiolates from gold nanoparticles needs to be taken into account when working with these materials at low concentration.

Detecting intramolecular dynamics and multiple Förster resonance energy transfer states by fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) is a robust method for the detection of intramolecular dynamics in proteins but is also susceptible to interference from other dynamic processes such as triplet kinetics and photobleaching. We describe an approach for the detection of intramolecular dynamics in proteins labeled with a FRET dye pair based on global fitting to the two autocorrelation functions (green-green and red-red) and the two cross-correlation functions (green-red and red-green). We applied the method to detect intramolecular dynamics in the Ca(2+) signaling protein calmodulin. Dynamics were detected on the 100 mus time scale in Ca(2+)-activated calmodulin, whereas in apocalmodulin dynamics were not detected on this time scale. Control measurements on a polyproline FRET construct (Gly-Pro(15)-Cys) demonstrate the reliability of the method for isolating intramolecular dynamics from other dynamic processes on the microsecond time scale and confirm the absence of intramolecular dynamics of polyproline. We further show the sensitivity of the initial amplitudes of the FCS auto- and cross-correlation functions to the presence of multiple FRET states, static or dynamic. The FCS measurements also show that the diffusion of Ca(2+)-calmodulin is slower than that of apocalmodulin, indicating either a larger average hydrodynamic radius or shape effects resulting in a slower translational diffusion.

Tracer diffusion in silica inverse opals

We employed fluorescence correlation spectroscopy (FCS) to study the diffusion of small fluorescence tracers in liquid filled silica inverse opals. The inverse opals consisted of a nanoporous silica scaffold spanning a hexagonal crystal of spherical voids of 360 nm diameter connected by circular pores of 70 nm diameter. The diffusion of Alexa Fluor 488 in water and of perylene-3,4,9,10-tetracarboxylic diimide (PDI) in toluene was studied. Three diffusion modes could be distinguished: (1) Free diffusion limited by the geometric constraints given by the inverse opal, where, as compared to the free solution, this diffusion is slowed down by a factor of 3-4, (2) slow diffusion inside the nanoporous matrix of the silica scaffold, and (3) diffusion limited by adsorption. On the length scale of the focus of a confocal microscope of roughly 400 nm diffusion was non-Fickian in all cases.

Single-molecule spectroscopy and imaging of biomolecules in living cells

The number of reports per year on single-molecule imaging experiments has grown roughly exponentially since the first successful efforts to optically detect a single molecule were completed over two decades ago. Single-molecule spectroscopy has developed into a field that includes a wealth of experiments at room temperature and inside living cells. The fast growth of single-molecule biophysics has resulted from its benefits in probing heterogeneous populations, one molecule at a time, as well as from advances in microscopes and detectors. This Perspective summarizes the field of live-cell imaging of single biomolecules.

Fluorescence correlation spectroscopy in living cells: a practical approach

Fluorescence correlation spectroscopy (FCS) is a single-molecule fluorescence technique used to monitor molecular dynamics. It can be applied to living cells expressing fluorescently labeled proteins and lipids to determine the diffusion timescales and the total number of diffusing fluorescent molecules in the cell. A practical step-by-step approach to performing FCS with a commercial spectroscopy/microscopy system, the Zeiss Confocor 3, how to set up live-cell FCS experiments, acquire reliable data, and finally how to analyze the data acquired, are all described in this unit.

Probing the interactions between disulfide-based ligands and gold nanoparticles using a functionalised fluorescent perylene-monoimide dye

The binding of disulfides to gold nanoparticles was investigated using fluorescence spectroscopy and a perylene-monoimide dye coupled to a dissymmetric disulfide via a tetraethyleneglycolalkyl chain (PMImSS). Quantum chemical calculations using the polarizable continuum model (PCM) predict a strong quenching of perylene-monoimide fluorescence by gold nanoparticles as a result of efficient excitation energy transfer from the dye to the particle. Such quenching is indeed observed when unfunctionalised gold nanoparticles are added to a solution of PMImSS. The fluorimetric titration curves show behaviour indicative of the existence of an equilibrium between free and bound ligands (association constant 5 x 10(5) M(-1)), whereas the affinity of thiols and disulfide for gold surfaces is in general assumed to be much higher. Gold nanoparticles fully functionalised with PMImSS were synthesised and purified. Fluorescence correlation spectroscopy shows the appearance of free PMImSS ligands in dilute (approx. pM) suspensions of these PMImSS-functionalised nanoparticles over a period of several days.

Peripheral protein organization and its influence on lipid diffusion in biomimetic membranes

Protein organization on biomembranes and their dynamics are essential for cellular function. It is not clear, however, how protein binding may influence the assembly of underlying lipids or how the membrane structure leads to functional protein organization. Toward this goal, we investigated the effects of annexin a5 binding to biomimetic membranes using fluorescence imaging and correlation spectroscopy. Annexin a5 (anx a5), a peripheral intracellular protein that plays a membrane remodeling role in addition to other functions, binds specifically and tightly to anionic (e.g., phosphatidylserine)-containing membranes in the presence of calcium ion. Our fluorescence microscopy reveals that annexin likely forms assemblies, along with a more dispersed population, upon binding to anionic biomembranes in the presence of calcium ion, which is reflected in its two-component Brownian motion. To investigate the effects of annexin binding on the underlying lipids, we used specific acyl chain labeled phospholipid analogues, NBD-phosphatidylcholine (NBD-PC) and NBD-phosphatidylserine (NBD-PS). We find that both NBD-labeled lipids cluster under anx a5 assemblies, as compared with when they are found under the dispersed annexin population, and NBD-PS exhibits two-component lateral diffusion under the annexin assemblies. In contrast, NBD-PC diffusion is slower by an order of magnitude under the annexin assemblies in contrast to its diffusion when not localized under anx a5 assemblies. Our results indicate that, upon binding to membranes, the peripheral protein annexin organizes the underlying lipids into domains, which may have functional implications in vivo.

Photoacoustic correlation spectroscopy and its application to low-speed flow measurement

A photoacoustic correlation technique, inspired by its optical counterpart-the fluorescence correlation spectroscopy (FCS)-was tested for the first time, to our knowledge, to demonstrate the feasibility of low-speed flow measurement based on photoacoustic signal detection. A pulsed laser was used to probe the flow of light-absorbing beads. A photoacoustic correlation system of 0.8 s temporal resolution was built and flow speeds ranging from 249 to 14.9 microm/s with corresponding flow times from 4.42 to 74.1 s were measured. The experiment serves as a proof of concept for photoacoustic correlation spectroscopy, which may have many potential applications similar to the FCS.

Realistic modeling of the illumination point spread function in confocal scanning optical microscopy

In this paper we present a rigorous and general theoretical model for the illumination point spread function of a confocal microscope that correctly reproduces the optical setup. The model uses vectorial theory and assumes that monochromatic light with a Gaussian intensity distribution (such as from a laser or a single-mode fiber) is focused by a microscope objective with high numerical aperture and passes through stratified media on its way to the sample. This covers the important practical case of illumination through up to three layers, which is the situation most commonly encountered in biological microscopy (immersion oil, glass coverslip, aqueous sample medium). It also accounts for objectives that are corrected for a certain coverslip thickness and refractive index but operated under non-design conditions. Furthermore, illumination with linearly, circularly, or elliptically polarized light is covered by introducing a Babinet-Soleil compensator into the beam path. The model leads to a set of analytical equations that are readily evaluated. Two-dimensional intensity distributions for particular cases of interest are presented and discussed.

Recent developments in fluorescence correlation spectroscopy for diffusion measurements in planar lipid membranes

Fluorescence correlation spectroscopy (FCS) is a single molecule technique used mainly for determination of mobility and local concentration of molecules. This review describes the specific problems of FCS in planar systems and reviews the state of the art experimental approaches such as 2-focus, Z-scan or scanning FCS, which overcome most of the artefacts and limitations of standard FCS. We focus on diffusion measurements of lipids and proteins in planar lipid membranes and review the contributions of FCS to elucidating membrane dynamics and the factors influencing it, such as membrane composition, ionic strength, presence of membrane proteins or frictional coupling with solid support.

Fluorescence spectroscopy in thermodynamic and kinetic analysis of pH-dependent membrane protein insertion

Experimental determination of the free energy stabilizing the structure of membrane proteins in their native lipid environment is undermined by a lack of appropriate methods and suitable model systems. Here, we demonstrate how fluorescence correlation spectroscopy can be used to characterize thermodynamics of pH-triggered bilayer insertion of nonconstitutive membrane proteins (e.g., bacterial toxins, colicins). The experimental design is guided by the appropriate thermodynamic scheme which considers two independent processes: pH-dependent formation of a membrane-competent form and its insertion into the lipid bilayer. Measurements of a model protein annexin B12 under conditions of lipid saturation demonstrate that protonation leading to the formation of the membrane-competent state occurs near membrane interface. Lipid titration experiments demonstrate that the free energy of transfer to the intermediate interfacial state is especially favorable, while the free energy of final insertion is modulated by interplay of hydrophobic and electrostatic interactions on the bilayer interface. The general principles of kinetic measurements along the insertion pathway containing interfacial intermediate are discussed and practical examples emphasizing appropriate fitting and normalization procedures are presented.