Fluorescence resonance energy transfer between single fluorophores attached to a coiled-coil protein in aqueous solution

Kinetic frustration enables single-molecule computation

A fundamental challenge in physical systems is implementing computation at the microscopic scale where thermal fluctuations dominate. While biological systems achieve this through complex molecular networks, the physical principles enabling simpler systems to process temporal information remain unclear. Here we demonstrate how non-equilibrium dynamics can enable single molecules to perform sophisticated computation through thermal-kinetic frustration-a principle that creates a controlled discrepancy between thermodynamic stability and kinetic accessibility. By engineering this frustration in a linear polymer with N binary-state units, we create a physical realization of a deterministic finite automaton capable of accessing 2N configurations through non-equilibrium driving, far exceeding the N + 1 configurations available at equilibrium. Despite operating in a thermal environment, the molecule's dominant configuration evolves deterministically, enabling recognition of complex temporal patterns through mechanical control signals. Our framework establishes how stochastic microscopic dynamics can give rise to deterministic computation, providing new insights into non-equilibrium statistical mechanics and information processing in physical systems. The theoretical predictions can be tested using DNA nanotechnology, with potential applications in biosensing and adaptive materials.

Luminescence of carbon quantum dots and their application in biochemistry

Similar to fullerenes, carbon nanotubes and graphene, carbon dots (CDs) are causing a lot of research work in their own right. CDs are a type of surface-passivated quantum dot that contain carbon atoms. Their distinctive characteristics, such as luminescent emission that varies with size and wavelength, resistance to photobleaching, easy biological binding, lack of toxicity, and economical production without the need for intricate synthetic processes, have led to a noteworthy surge in attention within the research community. Different techniques can be utilized to create these CDs, spanning from basic candle burning to laser ablation. This review article delves into the principles of fluorescence technology, providing insights into how different synthesis methods of quantum dots impact their luminescent properties. Additionally, it highlights the latest applications of quantum dots in catalysis and biomedical fields, with special emphasis on the current status of luminescent properties in biology and chemistry. Towards the end, the article discusses the limitations of quantum dots in current practical applications, pointing out that CDs hold promising potential for future applications.

DNA-Liposome Hybrid Carriers for Triggered Cargo Release

The design of simple and versatile synthetic routes to accomplish triggered-release properties in carriers is of particular interest for drug delivery purposes. In this context, the programmability and adaptability of DNA nanoarchitectures in combination with liposomes have great potential to render biocompatible hybrid carriers for triggered cargo release. We present an approach to form a DNA mesh on large unilamellar liposomes incorporating a stimuli-responsive DNA building block. Upon incubation with a single-stranded DNA trigger sequence, a hairpin closes, and the DNA building block is allowed to self-contract. We demonstrate the actuation of this building block by single-molecule Förster resonance energy transfer (FRET), fluorescence recovery after photobleaching, and fluorescence quenching measurements. By triggering this process, we demonstrate the elevated release of the dye calcein from the DNA–liposome hybrid carriers. Interestingly, the incubation of the doxorubicin-laden active hybrid carrier with HEK293T cells suggests increased cytotoxicity relative to a control carrier without the triggered-release mechanism. In the future, the trigger could be provided by peritumoral nucleic acid sequences and lead to site-selective release of encapsulated chemotherapeutics.

An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch

The archetypical transcriptional crcB fluoride riboswitch from Bacillus cereus is an intricately structured non-coding RNA element enhancing gene expression in response to toxic levels of fluoride. Here, we used single molecule FRET to uncover three dynamically interconverting conformations appearing along the transcription process: two distinct undocked states and one pseudoknotted docked state. We find that the fluoride anion specifically snap-locks the magnesium-induced, dynamically docked state. The long-range, nesting, single base pair A40-U48 acts as the main linchpin, rather than the multiple base pairs comprising the pseudoknot. We observe that the proximally paused RNA polymerase further fine-tunes the free energy to promote riboswitch docking. Finally, we show that fluoride binding at short transcript lengths is an early step toward partitioning folding into the docked conformation. These results reveal how the anionic fluoride ion cooperates with the magnesium-associated RNA to govern regulation of downstream genes needed for fluoride detoxification of the cell.

Single molecule detection, thermal fluctuation and life

Single molecule detection has contributed to our understanding of the unique mechanisms of life. Unlike artificial man-made machines, biological molecular machines integrate thermal noises rather than avoid them. For example, single molecule detection has demonstrated that myosin motors undergo biased Brownian motion for stepwise movement and that single protein molecules spontaneously change their conformation, for switching to interactions with other proteins, in response to thermal fluctuation. Thus, molecular machines have flexibility and efficiency not seen in artificial machines.

Chromatin structure-dependent conformations of the H1 CTD

Linker histones are an integral component of chromatin but how these proteins promote assembly of chromatin fibers and higher order structures and regulate gene expression remains an open question. Using Förster resonance energy transfer (FRET) approaches we find that association of a linker histone with oligonucleosomal arrays induces condensation of the intrinsically disordered H1 CTD in a manner consistent with adoption of a defined fold or ensemble of folds in the bound state. However, H1 CTD structure when bound to nucleosomes in arrays is distinct from that induced upon H1 association with mononucleosomes or bare double stranded DNA. Moreover, the H1 CTD becomes more condensed upon condensation of extended nucleosome arrays to the contacting zig-zag form found in moderate salts, but does not detectably change during folding to fully compacted chromatin fibers. We provide evidence that linker DNA conformation is a key determinant of H1 CTD structure and that constraints imposed by neighboring nucleosomes cause linker DNAs to adopt distinct trajectories in oligonucleosomes compared to H1-bound mononucleosomes. Finally, inter-molecular FRET between H1s within fully condensed nucleosome arrays suggests a regular spatial arrangement for the H1 CTD within the 30 nm chromatin fiber.

MMP-2/9-Specific Activatable Lifetime Imaging Agent

Optical (molecular) imaging can benefit from a combination of the high signal-to-background ratio of activatable fluorescence imaging with the high specificity of luminescence lifetime imaging. To allow for this combination, both imaging techniques were integrated in a single imaging agent, a so-called activatable lifetime imaging agent. Important in the design of this imaging agent is the use of two luminophores that are tethered by a specific peptide with a hairpin-motive that ensured close proximity of the two while also having a specific amino acid sequence available for enzymatic cleavage by tumor-related MMP-2/9. Ir(ppy)3 and Cy5 were used because in close proximity the emission intensities of both luminophores were quenched and the influence of Cy5 shortens the Ir(ppy)3 luminescence lifetime from 98 ns to 30 ns. Upon cleavage in vitro, both effects are undone, yielding an increase in Ir(ppy)3 and Cy5 luminescence and a restoration of Ir(ppy)3 luminescence lifetime to 94 ns. As a reference for the luminescence activation, a similar imaging agent with the more common Cy3-Cy5 fluorophore pair was used. Our findings underline that the combination of enzymatic signal activation with lifetime imaging is possible and that it provides a promising method in the design of future disease specific imaging agents.

Direct quantification of circulating miRNAs in different stages of nasopharyngeal cancerous serum samples in single molecule level with total internal reflection fluorescence microscopy

MicroRNAs (miRNAs) are small noncoding RNAs that regulate human gene expression at the post-transcriptional level. Growing evidence indicates that the expression profile of miRNAs is highly correlated with the occurrence of human diseases including cancers. Playing important roles in complex gene regulation processes, the aberrant expression pattern of various miRNAs is implicated in different types and even stages of cancer. Besides localizing in cells, many of these miRNAs are found circulating around the body in a wide variety of fluids such as urine, serum and saliva. Surprisingly, these extracellular circulating miRNAs are highly stable and resistant to degradation, and therefore, are considered as promising biomarkers for early cancer diagnostic via noninvasive extraction from body fluids. Unfortunately, the abundance of these small RNAs is ultralow in the body fluids, making it challenging to quantify them in complex sample matrixes. Establishing a sensitive, specific yet simple assay for an accurate quantification of circulating miRNAs is therefore desirable. Our group previously reported a sensitive and specific detection assay of miRNAs in single molecule level with the aid of total internal reflection fluorescence microscopy. In this work, we advanced the assay to differentiate the expression of a nasopharyngeal carcinoma (NPC) up-regulator hsa-mir-205 (mir-205) in serum collected from patients of different stages of NPC. To overcome the background matrix interference in serum, a locked nucleic acid-modified molecular beacon (LNA/MB) was applied as the detection probe to hybridize, capture and detect target mir-205 in serum matrix with enhanced sensitivity and specificity. A detection limit of 500 fM was achieved. The as-developed method was capable of differentiating NPC stages by the level of mir-205 quantified in serum with only 10 μL of serum and the whole assay can be completed in 1 h. The experimental results agreed well with those previously reported whereas the quantity of miR-205 determined by our assay was found comparable to that of quantitative reverse transcription polymerase chain reaction (qRT-PCR), supporting that this assay can be served as a promising noninvasive detection tool for early NPC diagnosis, monitoring and staging.

Synergistic interactions between Alzheimer's Aβ40 and Aβ42 on the surface of primary neurons revealed by single molecule microscopy

Two amyloid-β peptides (Aβ40 and Aβ42) feature prominently in the extracellular brain deposits associated with Alzheimer’s disease. While Aβ40 is the prevalent form in the cerebrospinal fluid, the fraction of Aβ42 increases in the amyloid deposits over the course of disease development. The low in vivo concentration (pM-nM) and metastable nature of Aβ oligomers have made identification of their size, composition, cellular binding sites and mechanism of action challenging and elusive. Furthermore, recent studies have suggested that synergistic effects between Aβ40 and Aβ42 alter both the formation and stability of various peptide oligomers as well as their cytotoxicity. These studies often utilized Aβ oligomers that were prepared in solution and at μM peptide concentrations. The current work was performed using physiological Aβ concentrations and single-molecule microscopy to follow peptide binding and association on primary cultured neurons. When the cells were exposed to a 1:1 mixture of nM Aβ40:Aβ42, significantly larger membrane-bound oligomers developed compared to those formed from either peptide alone. Fluorescence resonance energy transfer experiments at the single molecule level reveal that these larger oligomers contained both Aβ40 and Aβ42, but that the growth of these oligomers was predominantly by addition of Aβ42. Both pure peptides form very few oligomers larger than dimers, but either membrane bound Aβ40/42 complex, or Aβ40, bind Aβ42 to form increasingly larger oligomers. These findings may explain how Aβ42-dominant oligomers, suspected of being more cytotoxic, develop on the neuronal membrane under physiological conditions.

Single molecule FRET observation of kinesin-1's head-tail interaction on microtubule

Kinesin-1 (conventional kinesin) is a molecular motor that transports various cargo such as endoplasmic reticulum and mitochondria in cells. Its two head domains walk along microtubule by hydrolyzing ATP, while the tail domains at the end of the long stalk bind to the cargo. When a kinesin is not carrying cargo, its motility and ATPase activity is inhibited by direct interactions between the tail and head. However, the mechanism of this tail regulation is not well understood. Here, we apply single molecule fluorescence resonance energy transfer (smFRET) to observe this interaction in stalk-truncated kinesin. We found that kinesin with two tails forms a folding conformation and dissociates from microtubules, whereas kinesin with one tail remains bound to the micro-tubule and is immobile even in the presence of ATP. We further investigated the head-tail interaction as well as head-head coordination on the microtubule at various nucleotide conditions. From these results, we propose a two-step inhibition model for kinesin motility.

Etiology of Alzheimer's disease: kinetic, thermodynamic and fluorimetric analyses of interactions of pseudo Aβ-peptides with neuronal nitric oxide synthase

Aggregated β-amyloid deposit is a hallmark in the neuropathology of Alzheimer's disease but their mechanism of formation still remains unresolved. Previously we reported that a normal pentapeptide Aβ(17-21) and glycine zipper peptide Aβ(29-33) strongly inhibited nitric oxide synthase and rapidly initiated fibrillogenesis. Critical amino acids within these fragments were not identified. We now report on the interaction of four pseudo-peptides with nNOS - two peptides with a reversed amino acid sequence [Aβ(17-21r); Aβ(29-33r)] and two peptides with Phe19, Phe20 and Ile31, Ile32 substituted with polar glutamic acid [Aβ(17-21p); Aβ(29-33p)]. It was shown that while the inhibitor constants (Ki) increased 2-3 fold for each of the pseudo-peptides when compared with the normal peptides the dissociation constant Kd increased between 20 and 50 fold. Stern-Volmer fluorescence quenching constants (K(SV)) for Aβ(17-21p) and Aβ(29-33p) were 7.2×10(-3) and 6.1×10(-3) μM(-1) respectively at 298 K some 2-3 fold lower than the corresponding Aβ(17-21r); Aβ(29-33r). With temperature increase there was an increase in K(SV) and Kd, suggesting a dynamic quenching mechanism. Thermodynamic parameters, ΔH, ΔS and ΔG were all positive indicating endothermic, non-spontaneous, hydrophobic-hydrophobic associations of the pseudo-peptides with the enzyme. By FRET analysis the efficiency of fluorescence transfer between enzyme tryptophans and the pseudo-peptides was 90% (compared to 97% for the natural substrate). The distance the tryptophans moved after interaction with Aβ(17-21r) and Aβ(17-21p) was 10% greater, while for Aβ(29-33r) and Aβ(29-33p) it was 20-25% greater, than with the normal peptides; the fluorescence intensity was 20-75% higher. This increase in distance, fluorescent intensity and transfer efficiency illustrate an increase in interaction energy for the pseudo-peptides with nNOS lending support for the strategic position of the Phe19, Phe20, Ile31 and Ile32 in the original peptides not only for inhibition of the nNOS but for initiation of fibrillogenesis.

Interaction of glycine zipper fragments of Aβ-peptides with neuronal nitric oxide synthase: kinetic, thermodynamic and spectrofluorimetric analysis

Five peptide fragments [Aβ(17-21); Aβ(25-29); Aβ(29-33); Aβ(33-37); Aβ(25-37)] of the toxic Aβ(1-40(42)) amyloid peptide were shown to bind with neuronal nitric oxide synthase by means of hydrophobic-hydrophobic forces. The enzyme has a single site for the amyloid peptide binding, which resulted in a quenching of the intrinsic fluorescence of the enzyme. Binding constants determined from Stern-Volmer analysis were between 9×10(-3) and 1.8×10(-2) μM(-1). As temperature increased these binding constants increased reflecting that the interaction of the amyloid peptides with nNOS was endothermic and the quenching was dynamic. Kinetic analysis revealed a non-competitive interaction of the amyloid peptides to the enzyme with inhibitor constants of 5.1 μM for Aβ(17-21) to about 8-12 μM for the other peptides. According to the van't Hoff relationship the thermodynamic parameters, ΔH, ΔS and ΔG for the interaction of the amyloid peptides were all positive and between 41.28 and 77.86 kJ mol(-1)K(-1), 104.92 and 220.82 J mol(-1)K(-1) and 9.92 and 13.13 kJ mol(-1)K(-1), respectively. This suggested that the transition state, created by the amyloid peptide-nNOS complex and generated during the initial stages of Aβ aggregation had to, initially, overcome an activation barrier. Since the ΔG values decreased as temperature increased it not only implied a non-spontaneous interaction but that hydrophobic forces were operative during the binding. By FRET analysis the distance between the donor enzyme and the acceptor amyloid peptide was between 2.7 and 2.8 nm. As the temperature increased from 298 K through 313 K (and higher) the fraction of these tryptophan residues that became exposed increased, to approach a value of 1. There was strong support for the initial interaction being through the glycine zipper regions of Aβ(25-37).

Squeezing at entrance of proton transport pathway in proton-translocating pyrophosphatase upon substrate binding

Homodimeric proton-translocating pyrophosphatase (H(+)-PPase; EC 3.6.1.1) is indispensable for many organisms in maintaining organellar pH homeostasis. This unique proton pump couples the hydrolysis of PPi to proton translocation across the membrane. H(+)-PPase consists of 14-16 relatively hydrophobic transmembrane domains presumably for proton translocation and hydrophilic loops primarily embedding a catalytic site. Several highly conserved polar residues located at or near the entrance of the transport pathway in H(+)-PPase are essential for proton pumping activity. In this investigation single molecule FRET was employed to dissect the action at the pathway entrance in homodimeric Clostridium tetani H(+)-PPase upon ligand binding. The presence of the substrate analog, imidodiphosphate mediated two sites at the pathway entrance moving toward each other. Moreover, single molecule FRET analyses after the mutation at the first proton-carrying residue (Arg-169) demonstrated that conformational changes at the entrance are conceivably essential for the initial step of H(+)-PPase proton translocation. A working model is accordingly proposed to illustrate the squeeze at the entrance of the transport pathway in H(+)-PPase upon substrate binding.

The coiled coil motif in polymer drug delivery systems

The coiled coil is a superhelical structural protein motif that has been thoroughly investigated in recent years. Because of the relatively well-understood principles that determine the properties of coiled coil peptides and proteins, macromolecular systems containing the coiled coil motif have been suggested for various applications. This short review focuses on hybrid polymer coiled coil systems designed for drug delivery purposes. After a short introduction, the most important features of the coiled coils (stability, association number, oligomerization selectivity and orientation of helices) are described, and the factors influencing these characteristics are discussed. Several examples of the most interesting biomedical applications of the polymer-coiled coil systems (according to the authors' opinion) are presented.

EXPLORING THE FOLDING FREE ENERGY LANDSCAPE OF SMALL RNA MOLECULES BY SINGLE-PAIR FÖRSTER RESONANCE ENERGY TRANSFER

Proteins and RNA are biological macromolecules built from linear polymers. The process by which they fold into compact, well-defined, three-dimensional architectures to perform their functional tasks is still not well understood. It can be visualized by Brownian motion of an ensemble of molecules through a rugged energy landscape in search of an energy minimum corresponding to the native state. To explore the conformational energy landscape of small RNAs, single pair Förster resonance energy transfer (spFRET) experiments on solutions as well as on surface-immobilized samples have provided new insights. In this review, we focus on our recent work on two FRET-labeled small RNAs, the Diels-Alderase (DAse) ribozyme and the human mitochondrial tRNA Lys . For both RNAs, three different conformational states can be distinguished, and the associated mean FRET efficiencies provide clues about their structural properties. The systematic variation of their free energies with the concentration of Mg 2+ counterions was analyzed quantitatively by using a thermodynamic model that separates conformational changes from Mg 2+ binding. Furthermore, time-resolved spFRET studies on immobilized DAse reveal slow interconversions between intermediate and folded states on the time scale of ~ 100 ms. The quantitative data obtained from spFRET experiments may likely assist in the further development of theories and models addressing the folding dynamics and (counterion-dependent) energetics of RNA molecules.

DNA and nucleosomes direct distinct folding of a linker histone H1 C-terminal domain

We previously documented condensation of the H1 CTD consistent with adoption of a defined structure upon nucleosome binding using a bulk FRET assay, supporting proposals that the CTD behaves as an intrinsically disordered domain. In the present study, by determining the distances between two different pairs of sites in the C-terminal domain of full length H1 by FRET, we confirm that nucleosome binding directs folding of the disordered H1 C-terminal domain and provide additional distance constraints for the condensed state. In contrast to nucleosomes, FRET observed upon H1 binding to naked DNA fragments includes both intra- and inter-molecular resonance energy transfer. By eliminating inter-molecular transfer, we find that CTD condensation induced upon H1-binding naked DNA is distinct from that induced by nucleosomes. Moreover, analysis of fluorescence quenching indicates that H1 residues at either end of the CTD experience distinct environments when bound to nucleosomes, and suggest that the penultimate residue in the CTD (K195) is juxtaposed between the two linker DNA helices, proposed to form a stem structure in the H1-bound nucleosome.

Spectrofluorimetric analysis of the interaction of amyloid peptides with neuronal nitric oxide synthase: implications in Alzheimer's disease

BACKGROUND

The deposition of aggregated β-amyloid peptide senile plaques and the accumulation of arginine within the astrocytes in the brain of an Alzheimer's patient are classic observations in the neuropathology of the disease. It would be logical, in the aetiology and pathogenesis, to investigate arginine-metabolising enzymes and their intimate association with amyloid peptides.

METHODS

Neuronal nitric oxide synthase (nNOS) was isolated, purified and shown, through fluorescence quenching spectroscopy and fluorescence resonance energy transfer (FRET), to interact with structural fragments of Aβ(1-40) and be catalytic towards amyloid fibril formation.

RESULTS

Only one binding site on the enzyme was available for binding. Two amyloid peptide fragments of Aβ(1-40) (Aβ(17-28) and Aβ(25-35)) had Stern-Volmer values (K(SV)) of 0.111μM(-1) and 0.135μM(-1) indicating tight binding affinity to nNOS and easier accessibility to fluor molecules during binding. The polarity of this active site precludes binding of the predominantly hydrophobic amyloid peptide fragments contained within Aβ(17-28) and within two glycine zipper motifs [G-X-X-X-G-X-X-X-G] [Aβ(29-37)] and bind to the enzyme at a site remote to the active region.

CONCLUSIONS

The interaction and binding of Aβ(17-28) and Aβ(25-35) to nNOS causes the movement of two critical tryptophan residues of 0.77nm and 0.57nm respectively towards the surface of the enzyme.

GENERAL SIGNIFICANCE

The binding of Aβ-peptide fragments with nNOS has been studied by spectrofluorimetry. The information and data presented should contribute towards understanding the mechanism for deposition of aggregated Aβ-peptides and fibrillogenesis in senile plaques in an AD brain.

Determining serpin conformational distributions with single molecule fluorescence

Conformational plasticity is key to inhibitory serpin function, and this plasticity gives serpins relatively easy access to alternative, dysfunctional conformations. Thus, a given serpin population may contain both functional and dysfunctional proteins. Single molecule fluorescence (SMF), with its ability to interrogate one fluorescently labeled protein at a time, is a powerful method for elucidating conformational distributions and monitoring how these distributions change over time. SMF and related methods have been particularly valuable for characterizing serpin polymerization. Fluorescence correlation spectroscopy experiments have revealed a second lag phase during in vitro α(1)-antitrypsin polymerization associated with the formation of smaller oligomers that then condense to form longer polymers [Purkayastha, P., Klemke, J. W., Lavender, S., Oyola, R., Cooperman, B. S., and Gai, F. (2005). Alpha 1-antitrypsin polymerization: A fluorescence correlation spectroscopic study. Biochemistry44, 2642-2649.]. SMF studies of in vitro neuroserpin polymerization have confirmed that a monomeric intermediate is required for polymer formation while providing a test of proposed polymerization mechanisms [Chiou, A., Hägglöf, P., Orte, A., Chen, A. Y., Dunne, P. D., Belorgey, D., Karlsson-Li, S., Lomas, D., and Klenerman, D. (2009). Probing neuroserpin polymerization and interaction with amyloid-beta peptides using single molecule fluorescence. Biophys. J.97, 2306-2315.]. SMF has also been used to monitor protease-serpin interactions. Single pair Förster resonance energy transfer studies of covalent protease-serpin complexes suggest that the extent of protease structural disruption in the complex is protease dependent [Liu, L., Mushero, N., Hedstrom, L., and Gershenson, A. (2006). Conformational distributions of protease-serpin complexes: A partially translocated complex. Biochemistry45, 10865-10872.]. SMF techniques are still evolving and the combination of SMF with encapsulation methods has the potential to provide more detailed information on the conformational changes associated with serpin polymerization, protease-serpin complex formation, and serpin folding.

Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments

The breakthroughs in single molecule spectroscopy of the last decade and the recent advances in super resolution microscopy have boosted the popularity of cyanine dyes in biophysical research. These applications have motivated the investigation of the reactions and relaxation processes that cyanines undergo in their electronically excited states. Studies show that the triplet state is a key intermediate in the photochemical reactions that limit the photostability of cyanine dyes. The removal of oxygen greatly reduces photobleaching, but induces rapid intensity fluctuations (blinking). The existence of non-fluorescent states lasting from milliseconds to seconds was early identified as a limitation in single-molecule spectroscopy and a potential source of artifacts. Recent studies demonstrate that a combination of oxidizing and reducing agents is the most efficient way of guaranteeing that the ground state is recovered rapidly and efficiently. Thiol-containing reducing agents have been identified as the source of long-lived dark states in some cyanines that can be photochemically switched back to the emissive state. The mechanism of this process is the reversible addition of the thiol-containing compound to a double bond in the polymethine chain resulting in a non-fluorescent molecule. This process can be reverted by irradiation at shorter wavelengths. Another mechanism that leads to non-fluorescent states in cyanine dyes is cis–trans isomerization from the singlet-excited state. This process, which competes with fluorescence, involves the rotation of one-half of the molecule with respect to the other with an efficiency that depends strongly on steric effects. The efficiency of fluorescence of most cyanine dyes has been shown to depend dramatically on their molecular environment within the biomolecule. For example, the fluorescence quantum yield of Cy3 linked covalently to DNA depends on the type of linkage used for attachment, DNA sequence and secondary structure. Cyanines linked to the DNA termini have been shown to be mostly stacked at the end of the helix, while cyanines linked to the DNA internally are believed to partially bind to the minor or major grooves. These interactions not only affect the photophysical properties of the probes but also create a large uncertainty in their orientation.

Dual-channel single-molecule fluorescence resonance energy transfer to establish distance parameters for RNA nanoparticles

The increasing interest in RNA nanotechnology and the demonstrated feasibility of using RNA nanoparticles as therapeutics have prompted the need for imaging systems with nanometer-scale resolution for RNA studies. Phi29 dimeric pRNAs can serve as building blocks in assembly into the hexameric ring of the nanomotors, as modules of RNA nanoparciles, and as vehicles for specific delivery of therapeutics to cancers or viral infected cells. The understanding of the 3D structure of this novel RNA dimeric particle is fundamentally and practically important. Although a 3D model of pRNA dimer has been proposed based on biochemical analysis, no distance measurements or X-ray diffraction data have been reported. Here we evaluated the application of our customized single-molecule dual-viewing system for distance measurement within pRNA dimers using single-molecule Fluorescence Resonance Energy Transfer (smFRET). Ten pRNA monomers labeled with single donor or acceptor fluorophores at various locations were constructed and eight dimers were assembled. smFRET signals were detected for six dimers. The tethered arm sizes of the fluorophores were estimated empirically from dual-labeled RNA/DNA standards. The distances between donor and acceptor were calculated and used as distance parameters to assess and refine the previously reported 3D model of the pRNA dimer. Distances between nucleotides in pRNA dimers were found to be different from those of the dimers bound to procapsid, suggesting a conformational change of the pRNA dimer upon binding to the procapsid.

Distance variations between active sites of H(+)-pyrophosphatase determined by fluorescence resonance energy transfer

Homodimeric H(+)-pyrophosphatase (H(+)-PPase; EC 3.6.1.1) is a unique enzyme playing a pivotal physiological role in pH homeostasis of organisms. This novel H(+)-PPase supplies energy at the expense of hydrolyzing metabolic byproduct, pyrophosphate (PP(i)), for H(+) translocation across membrane. The functional unit for the translocation is considered to be a homodimer. Its putative active site on each subunit consists of PP(i) binding motif, Acidic I and II motifs, and several essential residues. In this investigation structural mapping of these vital regions was primarily determined utilizing single molecule fluorescence resonance energy transfer. Distances between two C termini and also two N termini on homodimeric subunits of H(+)-PPase are 49.3 + or - 4.0 and 67.2 + or - 5.7 A, respectively. Furthermore, putative PP(i) binding motifs on individual subunits are found to be relatively far away from each other (70.8 + or - 4.8 A), whereas binding of potassium and substrate analogue led them to closer proximity. Moreover, substrate analogue but not potassium elicits significant distance variations between two Acidic I motifs and two His-622 residues on homodimeric subunits. Taken together, this study provides the first quantitative measurements of distances between various essential motifs, residues, and putative active sites on homodimeric subunits of H(+)-PPase. A working model is accordingly proposed elucidating the distance variations of dimeric H(+)-PPase upon substrate binding.

Construction of a laser combiner for dual fluorescent single molecule imaging of pRNA of phi29 DNA packaging motor

A customized laser combiner was designed and constructed for dual channel single molecule imaging. The feasibility of a combiner-incorporated imaging system was demonstrated in studies of single molecule FRET. Distance rulers made of dual-labeled dsDNA were used to evaluate the system by determining the distance between one FRET pair. The results showed that the system is sensitive enough to distinguish between distances differing by two base pair and the distances calculated from FRET efficiencies are close to those documented in the literature. The single molecule FRET with the dual-color imaging system was also applied to reconstructed phi29 motor pRNA monomers. Finally, techniques for dual laser alignment and tuning of laser power for dual-color excitation are discussed.

Analysis of complex single-molecule FRET time trajectories

Single-molecule methods have given researchers the ability to investigate the structural dynamics of biomolecules at unprecedented resolution and sensitivity. One of the preferred methods of studying single biomolecules is single-molecule fluorescence resonance energy transfer (smFRET). The popularity of smFRET stems from its ability to report on dynamic, either intra- or intermolecular interactions in real-time. For example, smFRET has been successfully used to characterize the role of dynamics in functional RNAs and their protein complexes, including ribozymes, the ribosome, and more recently the spliceosome. Being able to reliably extract quantitative kinetic and conformational parameters from smFRET experiments is crucial for the interpretation of their results. The need for efficient, unbiased analysis routines becomes more evident as the systems studied become more complex. In this chapter, we focus on the practical utility of statistical algorithms, particularly hidden Markov models, to aid in the objective quantification of complex smFRET trajectories with three or more discrete states, and to extract kinetic information from the trajectories. Additionally, we present a method for systematically eliminating transitions associated with uncorrelated fluorophore behavior that may occur due to dye anisotropy and quenching effects. We also highlight the importance of data condensation through the use of various transition density plots to fully understand the underlying conformational dynamics and kinetic behavior of the biological macromolecule of interest under varying conditions. Finally, the application of these techniques to studies of pre-mRNA conformational changes during eukaryotic splicing is discussed.

DNA-directed immobilisation of glycomimetics for glycoarrays application: comparison with covalent immobilisation, and development of an on-chip IC50 measurement assay

Glycoarrays are powerful tools for the understanding of protein/carbohydrate interactions and should find applications in the diagnosis of diseases involving these interactions. Immobilisation of the carbohydrate probe is a key issue in the elaboration of high performance devices. In the present study, we have compared the fluorescent signal intensity and determined the lower detection limit of glycoconjugates immobilised at two concentrations (0.5 and 25 microM) by DNA-directed immobilisation (DDI), to glycoconjugates covalently immobilised on the solid support (borosilicate glass slide). At 0.5 microM, DDI led to a stronger fluorescence signal (by a factor of 4.5) and to a lower detection limit (20 nM) than covalent immobilisation (higher than 200 nM). We also report the development of an IC(50) measurement assay of DDI immobilised glycoconjugates. We found that the relative affinity per galactose residue of RCA 120 for glycoconjugates bearing one or three galactose residues was different by a factor of 23 when measured under IC(50) conditions or by direct fluorescence reading.

RNA intramolecular dynamics by single-molecule FRET

Investigation of single RNA molecules using fluorescence resonance energy transfer (FRET) is a powerful approach to investigate dynamic and thermodynamic aspects of the folding process of a given RNA. Its application requires interdisciplinary work from the fields of chemistry, biochemistry, and physics. The present work gives detailed instructions on the synthesis of RNA molecules labeled with two fluorescent dyes interacting by FRET, as well as on their investigation by single-molecule fluorescence spectroscopy.

Computational Study of a Single Surface-Immobilized Two-Stranded Coiled-Coil Polypeptide

The equilibrium structure and dynamics of a two-stranded coiled-coil polypeptide are investigated via Langevin dynamics simulations. An off-lattice model of the polypeptide chain is employed, which gives rise to a well-defined helical dimer native state and two-state folding kinetics. The behavior of the freely diffusing and surface-immobilized polypeptide is studied under different surface and denaturation conditions. The effect of surface immobilization on the distributions of structural and dynamical properties is considered in detail. The relationship between the simulation results and recent single-molecule fluorescence resonance energy transfer experiments performed on the two-stranded coiled-coil from the yeast transcription factor GCN4 (Jia et al. Chem. Phys. 1999, 247, 69; Talaga et al. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 13021) is discussed.

Extracting the Time Scales of Conformational Dynamics from Single-Molecule Single-Photon Fluorescence Statistics

The quenching rate of a fluorophore attached to a macromolecule can be rather sensitive to its conformational state. The decay of the corresponding fluorescence lifetime autocorrelation function can therefore provide unique information on the time scales of conformational dynamics. The conventional way of measuring the fluorescence lifetime autocorrelation function involves evaluating it from the distribution of delay times between photoexcitation and photon emission. However, the time resolution of this procedure is limited by the time window required for collecting enough photons in order to establish this distribution with sufficient signal-to-noise ratio. Yang and Xie have recently proposed an approach for improving the time resolution, which is based on the argument that the autocorrelation function of the delay time between photoexcitation and photon emission is proportional to the autocorrelation function of the square of the fluorescence lifetime [Yang, H.; Xie, X. S. J. Chem. Phys. 2002, 117, 10965]. In this paper, we show that the delay-time autocorrelation function is equal to the autocorrelation function of the square of the fluorescence lifetime divided by the autocorrelation function of the fluorescence lifetime. We examine the conditions under which the delay-time autocorrelation function is approximately proportional to the autocorrelation function of the square of the fluorescence lifetime. We also investigate the correlation between the decay of the delay-time autocorrelation function and the time scales of conformational dynamics. The results are demonstrated via applications to a two-state model and an off-lattice model of a polypeptide.

Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis

Here, we report a single-molecule fluorescence resonance energy transfer (FRET) study of a Diels-Alderase (DAse) ribozyme, a 49-mer RNA with true catalytic properties. The DAse ribozyme was labeled with Cy3 and Cy5 as a FRET pair of dyes to observe intramolecular folding, which is a prerequisite for its recognition and turnover of two organic substrate molecules. FRET efficiency histograms and kinetic data were taken on a large number of surface-immobilized ribozyme molecules as a function of the Mg(2+) concentration in the buffer solution. From these data, three separate states of the DAse ribozyme can be distinguished, the unfolded (U), intermediate (I) and folded (F) states. A thermodynamic model was developed to quantitatively analyze the dependence of these states on the Mg(2+) concentration. The FRET data also provide information on structural properties. The I state shows a strongly cooperative compaction with increasing Mg(2+) concentration that arises from association with several Mg(2+) ions. This transition is followed by a second Mg(2+)-dependent cooperative transition to the F state. The observation of conformational heterogeneity and continuous fluctuations between the I and F states on the approximately 100 ms timescale offers insight into the folding dynamics of this ribozyme.

Probing orientations of single fluorescent labels on a peptide reversibly binding to the human delta-opioid receptor

We report the first in-depth study of single-molecule polarization behavior of a species that is undergoing reversible binding with its biological receptor. We examine the utility of the information in single-molecule polarization measurements for investigations of binding. The human delta-opioid receptor, which is a G protein-coupled receptor, was incorporated into a supported lipid bilayer. A Cy3 label was covalently attached by a hydrophilic linker to a peptide agonist, Deltorphin II (5,6 Ile-Ile). The fluorescence excitation was alternated between s- and p-polarization using a microscope having the capability of total internal reflectance fluorescence (TIRF) excitation. The polarization behavior reveals that nonspecific binding events for this system give emission that is mostly s-polarized, while binding to the receptor gives emission that has a strong component of p-polarization. The results show that a high signal-to-noise ratio is achievable with single-molecule polarization measurements. The experiment detected 37 binding events of short duration (<30 s) and 35 binding events of long duration (from 30 s to 500 s). The polarization studies indicate that the receptors in the bilayer do not freely rotationally diffuse in the plane of the bilayer when the peptide is bound. The system exhibits two types of polarization behavior. One type has the dye label with fixed orientation, which sometimes abruptly switches. The other type has the dye orientation continuously fluctuating over time, typically exhibiting occasional periods of fixed orientation. For a long binding event of fixed orientation, it is established through analysis of the variance that the orientation actually is fluctuating through a range of angles on the order of 6 degrees. It is shown that precise measurements of reorientation are achievable, with a detection limit of 1.3 degrees for a typical single-molecule signal.

Dynamic polymorphism of actin as activation mechanism for cell motility

Actin filament dynamics are crucial in cell motility. Actin filaments, and their bundles, networks, and gels assemble and disassemble spontaneously according to thermodynamic rules. These dynamically changing structures of actin are harnessed for some of its functions in cells. The actin systems respond to external signals, forces, or environments by biasing the fluctuation of actin assembly structures. In this study, dynamic conformation of actin molecules was studied by monitoring conformational dynamics of actin molecules at the single molecule level in real time. Actin conformation spontaneously fluctuates between multiple conformational states. Regarding myosin motility, the dynamic equilibrium of actin conformation was interpreted as between states that activates and inhibits the motility. The binding of myosin to actin filaments activates myosin motility by shifting the conformational fluctuation of actin towards the state that activates the motility. Thus, the activation mechanism based on thermal fluctuation is suggested at molecular level as well as at cellular level.

Single-molecule observations of neck linker conformational changes in the kinesin motor protein

Kinesin-1 is a dimeric motor protein that moves cargo processively along microtubules. Kinesin motility has been proposed to be driven by the coordinated forward extension of the neck linker (a approximately 12-residue peptide) in one motor domain and the rearward positioning of the neck linker in the partner motor domain. To test this model, we have introduced fluorescent dyes selectively into one subunit of the kinesin dimer and performed 'half-molecule' fluorescence resonance energy transfer to measure conformational changes of the neck linker. We show that when kinesin binds with both heads to the microtubule, the neck linkers in the rear and forward heads extend forward and backward, respectively. During ATP-driven motility, the neck linkers switch between these conformational states. These results support the notion that neck linker movements accompany the 'hand-over-hand' motion of the two motor domains.

Conformational heterogeneity in RNA polymerase observed by single-pair FRET microscopy

Kinetic, structural, and single-molecule transcription measurements suggest that RNA polymerase can adopt many different conformations during elongation. We have measured the geometry of the DNA and RNA in ternary elongation complexes using single-pair fluorescence resonance energy transfer. Six different synthetic transcription elongation complexes were constructed from DNA containing an artificial transcription bubble, an RNA primer, and core RNA polymerase from Escherichia coli. Two different RNA primers were used, an 8-mer and a 5'-extended 11-mer. Fluorescent dye labels were attached at one of three positions on the DNA and at the RNA primer 5'-end. Structurally, the upstream DNA runs perpendicular to the proposed RNA exit channel. Upon nucleoside-triphosphate addition, DNA/RNA hybrid separation occurs readily in the 11-mer complexes but not in the 8-mer complexes. Clear evidence was obtained that RNA polymerase exists in multiple conformations among which it fluctuates.

Aryldithioethyloxycarbonyl (Ardec): A New Family of Amine Protecting Groups Removable under Mild Reducing Conditions and Their Applications to Peptide Synthesis

The development of phenyldithioethyloxycarbonyl (Phdec) and 2-pyridyldithioethyloxycarbonyl (Pydec) protecting groups, which are thiol-labile urethanes, is described. These new disulfide-based protecting groups were introduced onto the epsilon-amino group of L-lysine; the resulting amino acid derivatives were easily converted into N alpha-Fmoc building blocks suitable for both solid- and solution-phase peptide synthesis. Model dipeptide(Ardec)s were prepared by using classical peptide couplings followed by standard deprotection protocols. They were used to optimize the conditions for complete thiolytic removal of the Ardec groups both in aqueous and organic media. Phdec and Pydec were found to be cleaved within 15 to 30 min under mild reducing conditions: i) by treatment with dithiothreitol or beta-mercaptoethanol in Tris.HCl buffer (pH 8.5-9.0) for deprotection in water and ii) by treatment with beta-mercaptoethanol and 1,8-diazobicyclo[5.4.0]undec-7-ene (DBU) in N-methylpyrrolidinone for deprotection in an organic medium. Successful solid-phase synthesis of hexapeptides Ac-Lys-Asp-Glu-Val-Asp-Lys(Ardec)-NH2 has clearly demonstrated the full orthogonality of these new amino protecting groups with Fmoc and Boc protections. The utility of the Ardec orthogonal deprotection strategy for site-specific chemical modification of peptides bearing several amino groups was illustrated firstly by the preparation of a fluorogenic substrate for caspase-3 protease containing the cyanine dyes Cy 3.0 and Cy 5.0 as FRET donor/acceptor pair, and by solid-phase synthesis of an hexapeptide bearing a single biotin reporter group.

Detecting fluorescent protein expression and co-localisation on single secretory vesicles with linear spectral unmixing

Many questions in cell biology and biophysics involve the quantitation of co-localisation and the interaction of proteins tagged with different fluorophores. However, the incomplete separation of the different colour channels due to the presence of autofluorescence, along with cross-excitation and emission "bleed-through" of one colour channel into the other, all combine to render the interpretation of multi-band images ambiguous. Here we introduce a new live-cell epifluorescence spectral imaging and linear unmixing technique for classifying resolution-limited point objects containing multiple fluorophores. We demonstrate the performance of our technique by detecting, at the single-vesicle level, the co-expression of the vesicle-associated membrane protein, VAMP-2 (also called synaptobrevin-2), linked to either enhanced green fluorescent protein (EGFP) or citrine [a less pH-sensitive variant of enhanced yellow fluorescent protein (EYFP)], in mouse cortical astrocytes. In contrast, the co-expression of VAMP-2-citrine and the lysosomal transporter sialine fused to EGFP resulted in little overlap. Spectral imaging and linear unmixing permit us to fingerprint the expression of spectrally overlapping fluorescent proteins on single secretory organelles in the presence of a spectrally broad autofluorescence. Our technique provides a robust alternative to error-prone dual- or triple colour co-localisation studies.

Dynamic polymorphism of single actin molecules in the actin filament

Actin filament dynamics are critical in cell motility. The structure of actin filament changes spontaneously and can also be regulated by actin-binding proteins, allowing actin to readily function in response to external stimuli. The interaction with the motor protein myosin changes the dynamic nature of actin filaments. However, the molecular bases for the dynamic processes of actin filaments are not well understood. Here, we observed the dynamics of rabbit skeletal-muscle actin conformation by monitoring individual molecules in the actin filaments using single-molecule fluorescence resonance energy transfer (FRET) imaging with total internal reflection fluorescence microscopy (TIRFM). The time trajectories of FRET show that actin switches between low- and high-FRET efficiency states on a timescale of seconds. If actin filaments are chemically cross-linked, a state that inhibits myosin motility, the equilibrium shifts to the low-FRET conformation, whereas when the actin filament is interacting with myosin, the high-FRET conformation is favored. This dynamic equilibrium suggests that actin can switch between active and inactive conformations in response to external signals.

Quantitative electron microscopy and fluorescence spectroscopy of the membrane distribution of influenza hemagglutinin

Although lipid-dependent protein clustering in biomembranes mediates numerous functions, there is little consensus among membrane models on cluster organization or size. Here, we use influenza viral envelope protein hemagglutinin (HA(0)) to test the hypothesis that clustering results from proteins partitioning into preexisting, fluid-ordered "raft" domains, wherein they have a random distribution. Japan HA(0) expressed in fibroblasts was visualized by electron microscopy using immunogold labeling and probed by fluorescence resonance energy transfer (FRET). Labeled HA coincided with electron-dense, often noncircular membrane patches. Poisson and K-test (Ripley, B.D. 1977. J. R. Stat. Soc. Ser. B. 39:172-212) analyses reveal clustering on accessible length scales (20-900 nm). Membrane treatments with methyl-beta-cyclodextrin and glycosphingolipid synthesis inhibitors did not abolish clusters but did alter their pattern, especially at the shortest lengths, as was corroborated by changes in FRET efficiency. The magnitude and density dependence of the measured FRET efficiency also indicated a nonrandom distribution on molecular length scales (approximately 6-7 nm). This work rules out the tested hypothesis for HA over the accessible length scales, yet shows clearly how the spatial distribution of HA depends on lipid composition.

A Computational Study of the Correlations between Structure and Dynamics in Free and Surface-Immobilized Single Polymer Chains

The correlations between structure and dynamics in free and surface-immobilized polymers were investigated via Langevin dynamics simulations of a free-jointed homopolymer. A detailed analysis was performed for a polymer in free solution and a polymer attached to a surface. The cases of repulsive and attractive surfaces, as well as poor and good solvents, were considered. The analysis focuses on properties that are particularly relevant to single molecule measurements, namely: (1) the distribution of end-to-end distance, (2) the correlations between the conformational structure and the time scale of its motion, (3) the correlations, at equilibrium, between the end-to-end distance and its displacement, and (4) the correlation between the initial coil conformation and the collapse pathway into the globular state. The differences and similarities between this model and a previously considered model of a protein, with two-state folding kinetics and a well-defined native state, are also discussed.

Fluorescence labeling, purification, and immobilization of a double cysteine mutant calmodulin fusion protein for single-molecule experiments

We present a method of labeling and immobilizing a low-molecular-weight protein, calmodulin (CaM), by fusion to a larger protein, maltose binding protein (MBP), for single-molecule fluorescence experiments. Immobilization in an agarose gel matrix eliminates potential interactions of the protein and the fluorophore(s) with a glass surface and allows prolonged monitoring of protein dynamics. The small size of CaM hinders its immobilization in low-weight-percentage agarose gels; however, fusion of CaM to MBP via a flexible linker provides sufficient restriction of translational mobility in 1% agarose gels. Cysteine residues were engineered into MBP.CaM (MBP-T34C,T110C-CaM) and labeled with donor and acceptor fluorescent probes yielding a construct (MBP.CaM-DA) which can be used for single-molecule single-pair fluorescence resonance energy transfer (spFRET) experiments. Mass spectrometry was used to verify the mass of MBP.CaM-DA. Assays measuring the activity of CaM reveal minimal activity differences between wild-type CaM and MBP.CaM-DA. Single-molecule fluorescence images of the donor and acceptor dyes were fit to a two-dimensional Gaussian function to demonstrate colocalization of donor and acceptor dyes. FRET is demonstrated both in bulk fluorescence spectra and in fluorescence trajectories of single MBP.CaM-DA molecules. The extension of this method to other biomolecules is also proposed.

Single-molecule studies of synaptotagmin and complexin binding to the SNARE complex

The assembly of multiprotein complexes at the membrane interface governs many signaling processes in cells. However, very few methods exist for obtaining biophysical information about protein complex formation at the membrane. We used single molecule fluorescence resonance energy transfer to study complexin and synaptotagmin interactions with the SNARE complex in deposited lipid bilayers. Using total internal reflectance microscopy, individual binding events at the membrane could be resolved despite an excess of unbound protein in solution. Fluorescence resonance energy transfer (FRET)-efficiency derived distances for the complexin-SNARE interaction were consistent with the crystal structure of the complexin-SNARE complex. The unstructured N-terminal region of complexin showed broad distributions of FRET efficiencies to the SNARE complex, suggesting that information on conformational variability can be obtained from FRET efficiency distributions. The low-affinity interaction of synaptotagmin with the SNARE complex changed dramatically upon addition of Ca2+ with high FRET efficiency interactions appearing between the C2B domain and linker domains of synaptotagmin and the membrane proximal portion of the SNARE complex. These results demonstrate that single molecule FRET can be used as a "spectroscopic ruler" to simultaneously gain structural and kinetic information about transient multiprotein complexes at the membrane interface.

Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide

We report here an advanced approach for the characterization of the folding pattern of a de novo designed antiparallel coiled coil peptide by high-resolution methods. Incorporation of two fluorescence labels at the C- and N-terminus of the peptide chain as well as modification of two hydrophobic core positions by Phe/[15N,13C]Leu enable the study of the folding characteristics and of distinct amino acid side chain interactions by fluorescence resonance energy transfer (FRET) and NMR spectroscopy. Results of both experiments reveal the antiparallel alignment of the helices and thus prove the design concept. This finding is also supported by molecular dynamics simulations. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) in combination with NMR experiments was used for verification of the oligomerization equilibria of the coiled coil peptide.

Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence

To determine whether Forster resonance energy transfer (FRET) measurements can provide quantitative distance information in single-molecule fluorescence experiments on polypeptides, we measured FRET efficiency distributions for donor and acceptor dyes attached to the ends of freely diffusing polyproline molecules of various lengths. The observed mean FRET efficiencies agree with those determined from ensemble lifetime measurements but differ considerably from the values expected from Forster theory, with polyproline treated as a rigid rod. At donor-acceptor distances much less than the Forster radius R(0), the observed efficiencies are lower than predicted, whereas at distances comparable to and greater than R(0), they are much higher. Two possible contributions to the former are incomplete orientational averaging during the donor lifetime and, because of the large size of the dyes, breakdown of the point-dipole approximation assumed in Forster theory. End-to-end distance distributions and correlation times obtained from Langevin molecular dynamics simulations suggest that the differences for the longer polyproline peptides can be explained by chain bending, which considerably shortens the donor-acceptor distances.

Protein Structure and Dynamics from Single-Molecule Fluorescence Resonance Energy Transfer

The pros and cons of single-molecule vs ensemble-averaged fluorescence resonance energy transfer (FRET) experiments, performed on proteins, are explored with the help of Langevin dynamics simulations. An off-lattice model of the polypeptide chain is employed, which gives rise to a well-defined native state and two-state folding kinetics. A detailed analysis of the distribution of the donor-acceptor distance is presented at different points along the denaturation curve, along with its dependence on the averaging time window. We show that unique information on the correlation between structure and dynamics, which can only be obtained from single-molecule experiments, is contained in the correlation between the donor-acceptor distance and its displacement. The latter is shown to provide useful information on the free energy landscape of the protein, which is complementary to that obtained from the distribution of donor-acceptor distances.