Single‐Molecule Methods to Study Membrane Receptor Oligomerization

Membrane receptors control fundamental cellular processes. Binding of a specific ligand to a receptor initiates communication through the membrane and activation of signaling cascades. This activation process often leads to a spatial rearrangement of receptors in the membrane at the molecular level. Single‐molecule techniques contributed significantly to the understanding of receptor organization and rearrangement in membranes. Here, we review four prominent single‐molecule techniques that have been applied to membrane receptors, namely, stepwise photobleaching, Förster resonance energy transfer, sub‐diffraction localization microscopy and co‐tracking. We discuss the requirements, benefits and limitations of each technique, discuss target labeling, present a selection of applications and results and compare the different methodologies.     

Forced Folding of a Disordered Protein Accesses an Alternative Folding Landscape

Intrinsically disordered proteins (IDPs) are involved in diverse cellular functions. Many IDPs can interact with multiple binding partners, resulting in their folding into alternative ligand‐specific functional structures. For such multi‐structural IDPs, a key question is whether these multiple structures are fully encoded in the protein sequence, as is the case in many globular proteins. To answer this question, here we employed a combination of single‐molecule and ensemble techniques to compare ligand‐induced and osmolyte‐forced folding of α‐synuclein. Our results reveal context‐dependent modulation of the protein′s folding landscape, suggesting that the codes for the protein′s native folds are partially encoded in its primary sequence, and are completed only upon interaction with binding partners. Our findings suggest a critical role for cellular interactions in expanding the repertoire of folds and functions available to disordered proteins.     

Dynamics of Fluorescent Dyes Attached to G‐Quadruplex DNA and their Effect on FRET Experiments

FRET spectroscopy is a promising approach for investigating the dynamics of G‐quadruplex DNA folds and improving the targeting of G‐quadruplexes by potential anticancer compounds. To better interpret such experiments, classical and replica‐exchange molecular dynamics simulations and fluorescence‐lifetime measurements are used to understand the behavior of a range of Cy3‐based dyes attached to the 3′ end of G‐quadruplex DNA. The simulations revealed that the dyes interact extensively with the G‐quadruplex. Identification of preferred dye positions relative to the G‐quadruplex in the simulations allows the impact of dye–DNA interactions on FRET results to be determined. All the dyes show significant deviations from the common approximation of being freely rotating and not interacting with the host, but one of the Cy3 dye analogues is slightly closer to this case.     

Rational Design of Ratiometric Fe3+ Fluorescent Probes Based on FRET Mechanism

As the most abundant transition metal element in mammals, iron(Fe) plays a vital role in life activities. It is of great significance to study the variation of Fe³⁺ level in living organisms. In virtue of the advantages of high sensitivity, good selectivity and low damage to living systems, the fluorescence detection of Fe³⁺ has attracted much attention. Compared with the intensity-based fluorescent probe, the ratiometric fluorescent probe has less interference of environmental and can realize quantitative detection. In this study, four ratiometric Fe³⁺ fluorescent probes, R1, R2, R3 and R4_, were designed and synthesized using fluorescence resonance energy transfer(FRET) mechanism to achieve quantitative detection of Fe³⁺. In the FRET systems, 1,8-naphthalimide fluorophore derivatives were adopted as donors while rhodamine B derivatives were selected as receptors. The connection sites of the donor and acceptor in R3 and R4 are different from those in R1 and R2. All the four probes showed good response and selectivity to Fe³⁺. The energy transfer efficiencies of R3 and R4 were obviously higher than those of R1 and R2. This work provided a promising strategy for the development of fluorescent ratiometic Fe³⁺sensors.     

Enhanced energy transfer from diolefinic laser dyes to meso-tetrakis (4-sulfonatophenyl) porphyrin immobilized on silver nanoparticles: DFT,TD-DFT and spectroscopic studies

Porphyrin derivatives are known singlet oxygen sensitizers in photodynamic therapy (PDT). Energy transfer from a class of diolefinic laser dyes (DOLDs) as energy donors to the sodium salt of meso-tetrakis (4-sulfonatophenyl) porphyrin (TPPS) as the accepter of energy would extend the range of photon harvesting down to the UV-region. Energy transfer was substantially enhanced in the presence of metallic silver nanoparticles (AgNPs), as revealed by steady-state emission spectroscopy, lifetimes, and quantum mechanics. DOLDs under investigation are 2,5-distyrylpyrazine (DSP), 1,4-bis (β-pyridyl-2 vinyl) benzene (P2VB), and 1,4 bis (2-methylstyryl) benzene (MSB) as efficient donors of intense absorption in the UV-region. AgNPs enhance the rate of energy transfer from DOLDs to TPPS via bringing donor and acceptor into close- proximity with a concomitant increase in dipole–dipole interaction between excited state donor and ground-state acceptor. The DOLDs molecular structures were optimized using the DFT/CAM-B3LYP/6-311G++ (d, p) level of theory. The calculated electronic absorption spectra for the studied DOLDs in the gaseous phase and methanol solvent were studied using the time-dependent density functional theory (TD-DFT) at M06-2X/6-311G++ (2d,2p) level. The calculated absorption/emission spectra for DSP laser dye in methanol are obtained at the TD/ M06-2X/6-311G++(2d, 2p) method. Notably, all theoretical results of the molecular structures under study highly agreed with the practical optical results. Energy transfer rate constants (k_ET) amid energy donor/acceptor pairs were determined by Stern-Volmer constants (KSV) and donors' lifetime measurements. The KSV values indicate an enhanced Fluorescence Resonance Energy Transfer (FRET) efficiencies in the presence of negatively charged AgNPs. The critical transfer distances R_o were determined from the spectral overlap between the emission spectrum of donor and absorption spectrum of TTPS. These outcomes propose the application of designed metal-enhanced FRET for energy-transfer-based assays and photodynamic therapy (PDT) applications.     

Naphthalimide-rhodamine based fluorescent probe for ratiometric sensing of cellular pH

The pH values of lysosomes in cancer cells is slightly lower than that in normal cells, which can be used to distinguish cancer cells from normal cells. According to this, a naphthalimide-rhodamine based fluorescent probe(hereafter referred to as RBN) with a pK_a of 4.20 was designed and synthesized for ratiometric sensing of cellular pH via fluorescence resonance energy transfer(FRET), which can respond to different pH precisely through ratiometric fluorescence intensity(Ⅰ_(577)/Ⅰ_(540)). RBN can be employed to distinguish cancer cells from normal cells on the basis of different fluorescent response, in particular, RBN showed excellent water solubility and low cell toxicity, all these are quite significant for potential application in cancer diagnose and therapy.     

Phenanthroline-fluorescein molecular hybrid as a ratiometric and selective fluorescent chemosensor for Cu2+ via FRET strategy: synthesis,computational studies and in vitro applications

A FRET-based chemosensor L containing donor phenanthroline and acceptor fluorescein moiety was designed, synthesised and characterised for the ratiometric fluorescent detection of Cu²⁺ in organo-aqueous solution. Probe L showed high selectivity and excellent sensitivity towards Cu²⁺ ions by exhibiting both colorimetric and fluorometric changes due to opening of the spirolactum ring of fluorescein upon complexation with Cu²⁺. In presence of Cu²⁺ ions, probe L formed L-Cu²⁺ complex in 1:1 stoichiometric fashion which is established on the basis of Job’s plot and mass spectroscopy. We also performed DFT computational studies to know the binding nature and coordination feature of the complex. Furthermore, fluorescence imaging studies revealed that probe L was cell permeable and could be used to detect intracellular Cu²⁺ in living cells.     

Single-Molecule Photoactivation FRET: A General and Easy-To-Implement Approach To Break the Concentration Barrier

Single-molecule fluorescence resonance energy transfer (sm-FRET) has become a widely used tool to reveal dynamic processes and molecule mechanisms hidden under ensemble measurements. However, the upper limit of fluorescent species used in sm-FRET is still orders of magnitude lower than the association affinity of many biological processes under physiological conditions. Herein, we introduce single-molecule photoactivation FRET (sm-PAFRET), a general approach to break the concentration barrier by using photoactivatable fluorophores as donors. We demonstrate sm-PAFRET by capturing transient FRET states and revealing new reaction pathways during translation using μm fluorophore labeled species, which is 2–3 orders of magnitude higher than commonly used in sm-FRET measurements. sm-PAFRET serves as an easy-to-implement tool to lift the concentration barrier and discover new molecular dynamic processes and mechanisms under physiological concentrations.     

Dual Mechanism of an Intramolecular Charge Transfer (ICT)–FRET‐Based Fluorescent Probe for the Selective Detection of Hydrogen Peroxide

A dual‐mechanism intramolecular charge transfer (ICT)–FRET fluorescent probe for the selective detection of H₂O₂ in living cells has been designed and synthesized. This probe used a coumarin–naphthalimide hybrid as the FRET platform and a boronate moiety as the recognition group. Upon the addition of H₂O₂, the probe exhibited a redshifted (73 nm) fluorescence emission, and the ratio of fluorescence intensities at λ =558 and 485 nm (F ₅₅₈/F ₄₈₅) shifted notably (up to 100‐fold). Moreover, there was a good linearity (R ²=0.9911) between the ratio and concentration of H₂O₂ in the range of 0 to 60 μm , with a limit of detection of 0.28 μm (signal to noise ratio (S/N)=3). This probe could also detect enzymatically generated H₂O₂. Importantly, it could be used to visualize endogenous H₂O₂ produced by stimulation from epidermal growth factor.