Fluorescence depolarization dynamics of ionic strength sensors using time-resolved anisotropy

Translational diffusion, molecular brightness, and energy transfer analysis of mEGFP-linker-mScarlet-I crowding biosensor using fluorescence correlation spectroscopy

Recently, we have investigated the sensitivity of an mEGFP-linker-mScarlet-I construct (GE2.3) in response to macromolecular crowding using ensemble time-resolved two-photon (2P) fluorescence measurements [Mersch et al., Phys. Chem. Chem. Phys. 2024, 26(5), 3927-3940] as a point of reference for developing a single-molecule approach for Förster resonance energy transfer (FRET). Here, we investigate the fluorescence fluctuations, FRET, molecular brightness, and translational diffusion of GE2.3 as a model system using fluorescence correlation spectroscopy (FCS), at the single molecule level, as a function of the excitation and detection wavelengths of the donor (mEGFP) and the acceptor (mScarlet-I). We hypothesize that the molecular brightness (number of fluorescence photons per molecule) of the donor of GE2.3, in the presence and absence of the acceptor, would be distinct due to FRET at the single-molecule level. To test this hypothesis, we used wavelength-dependent FCS to quantify the molecular brightness of intact and enzymatically cleaved GE2.3 as a function of Ficoll-70 (a crowding agent, 0-300 g L-1) at room temperature. Our results indicate that the molecular brightness of intact GE2.3 in a buffer is smaller than that of the cleaved counterpart under 488-nm excitation of the donor, which is attributed to FRET. In contrast, the molecular brightness of both cleaved and intact GE2.3 seems to be the same under the 561-nm excitation of the acceptor due to the absence of FRET. Our results also show that the FRET efficiency of GE2.3 increases as the concentration of Ficoll increases up to 200 g L-1, which agrees with our previous time-resolved 2P-fluorescence measurements. Fluctuation autocorrelation analysis shows that the translational diffusion of intact and cleaved GE2.3 sensors deviates from the Stokes-Einstein model in Ficoll crowded solutions. Additionally, we highlight the multiscale translational and rotational diffusion coefficients of GE2.3 in terms of the average distance between neighboring Ficoll molecules, over the same concentration range, to elucidate the spatio-temporal scaling aspect of FRET and protein-protein interactions. These single-molecule studies would be beneficial for future studies in living cells, where very low GE2.3 expression levels will be required as compared with ensemble, time-resolved 2P-fluorescence measurements.

Advancing Native Mass Spectrometry Toward Cellular Biology

Protein structure, including various post-translational modifications and higher-order structures, regulates diverse biological functions. Native mass spectrometry (native MS) is a powerful analytical technique used to determine the masses of biomolecules, such as proteins and their complexes, while preserving their native folding in solution. This method provides structural information on the composition of monomers or complexes and the stoichiometry of subunits within each complex, significantly contributing to protein structural analysis. Native MS has evolved to incorporate top-down approaches, enabling the characterization of proteoforms and non-covalent interactions between metabolites or proteins and specific targets. This perspective highlights the advancements in native MS for intracellular proteins and protein complexes, and discusses future research directions toward cellular biology.

Surfactant-induced alterations in optoelectronic properties of perylene diimide dyes: modulating sensing responses in the aqueous environment

The compartmentalization effect of microheterogeneous systems, like surfactant aggregates, showcases altered optoelectronic properties of a perylene diimide-based chromogenic dye (PDI-Ala) compared to bulk water. The relatively hydrophobic microenvironment, poor hydration, and exceptionally large local concentration of dye molecules in the confined environment affect their interaction with target analytes. This realization intrigued us to investigate if micellization can modify the sensing properties (selectivity, sensitivity, response kinetics, output signal, etc.) of the encapsulated dye molecules in the aqueous medium. Response comparisons of PDI-Ala to the ionic analyte (Fe3+) and biomolecule (heparin) in aqueous and surfactant-bound states highlighted significant variations. Fe3+ interaction exhibited a "turn-off" fluorescence response in a water medium, while surfactant-bound conditions triggered "turn-on" fluorescence, enhancing selectivity at the micelle-water interface. Conversely, the native probe showed no interaction with heparin in water but displayed a turn-on fluorescence response in cetyltrimethylammonium bromide (CTAB) micelles, indicating the transformation of a silent molecule into a turn-on fluorescence sensor. This study underscores the influence of micellar environments on dye molecules, altering the sensing responses and selectivity toward analytes, crucial for applications in understanding cellular pathways and toxicity mechanisms.

Two-photon excited-state dynamics of mEGFP-linker-mScarlet-I crowding biosensor in controlled environments

Macromolecular crowding affects many cellular processes such as diffusion, biochemical reaction kinetics, protein-protein interactions, and protein folding. Mapping the heterogeneous, dynamic crowding in living cells or tissues requires genetically encoded, site-specific, crowding sensors that are compatible with quantitative, noninvasive fluorescence micro-spectroscopy. Here, we carried out time-resolved 2P-fluorescence measurements of a new mEGFP-linker-mScarlet-I macromolecular crowding construct (GE2.3) to characterize its environmental sensitivity in biomimetic crowded solutions (Ficoll-70, 0-300 g L-1) via Förster resonance energy transfer (FRET) analysis. The 2P-fluorescence lifetime of the donor (mEGFP) was measured under magic-angle polarization, in the presence (intact) and absence (enzymatically cleaved) of the acceptor (mScarlet-I), as a function of the Ficoll-70 concentration. The FRET efficiency was used to quantify the sensitivity of GE2.3 to macromolecular crowding and to determine the environmental dependence of the mEGFP-mScarlet-I distance. We also carried out time-resolved 2P-fluorescence depolarization anisotropy to examine both macromolecular crowding and linker flexibility effects on GE2.3 rotational dynamics within the context of the Stokes-Einstein model as compared with theoretical predictions based on its molecular weight. These time-resolved 2P-fluorescence depolarization measurements and conformational population analyses of GE2.3 were also used to estimate the free energy gain upon the structural collapse in crowded environment. Our results further the development of a rational engineering design for bioenvironmental sensors without the interference of cellular autofluorescence. Additionally, these results in well-defined environments will inform our future in vivo studies of genetically encoded GE2.3 towards the mapping of the crowded intracellular environment under different physiological conditions.

Ionic strength modulates excision of uracil by SMUG1 from nucleosome core particles

Ionic strength affects many cellular processes including the packaging of genetic material in eukaryotes. For example, chromatin fibers are compacted in high ionic strength environments as are the minimal unit of packaging in chromatin, nucleosome core particles (NCPs). Furthermore, ionic strength is known to modulate several aspects of NCP dynamics including transient unwrapping of DNA from the histone protein core, nucleosome gaping, and intra- and internucleosomal interactions of the N-terminal histone tails. Changes in NCP structure may also impact interactions of transcriptional, repair, and other cellular machinery with nucleosomal DNA. One repair process, base excision repair (BER), is impacted by NCP structure and may be further influenced by changes in ionic strength. Here we examine the effects of ionic strength on the initiation of BER using biochemical assays. Using a population of NCPs containing uracil (U) at dozens of geometric locations, excision of U by single-strand selective monofunctional uracil DNA glycosylase (SMUG1) is assessed at higher and lower ionic strengths. SMUG1 has increased excision activity in the lower ionic strength conditions. On duplex DNA, however, SMUG1 activity is largely unaffected by ionic strength except at short incubation times, suggesting that changes in SMUG1 activity are likely due to alterations in NCP structure and dynamics. These results allow us to further understand the cellular role of SMUG1 in a changing ionic environment and broadly contribute to the understanding of BER on chromatin and genomic stability.

Sensing of Fluidic Features Using Colloidal Microswarms

Sensing of key parameters in fluidic environments has attracted extensive attention because the physical features of body fluids could be used for point-of-care disease diagnosis. Although various sensing methods have been investigated, effective sensing strategies of microenvironments remains a major challenge. In this paper, we propose an approach that can realize sensing of fluidic viscosity and ionic strength using microswarms formed by simple colloidal nanoparticles. The influences of fluidic ionic strength and viscosity on two swarm behaviors are analyzed (i.e., the spreading of circular vortex-like swarms and the elongation of elliptical swarms). The data models for quantifying the fluidic viscosity and ionic strength are obtained from experiments, and the fluidic features can be sensed successfully using the swarm behaviors. Furthermore, we demonstrate that the microswarms have the capability of passing through tortuous and narrow microchannels for sensing. Continuous sensing of different fluidic environments using swarms is also realized. Finally, the sensing of viscosity and ionic strength of porcine whole blood is presented, which also validates the feasibility of the sensing strategy.

Molecular Brightness Approach for FRET Analysis of Donor-Linker-Acceptor Constructs at the Single Molecule Level: A Concept

In this report, we have developed a simple approach using single-detector fluorescence autocorrelation spectroscopy (FCS) to investigate the Förster resonance energy transfer (FRET) of genetically encoded, freely diffusing crTC2.1 (mTurquoise2.1-linker-mCitrine) at the single molecule level. We hypothesize that the molecular brightness of the freely diffusing donor (mTurquoise2.1) in the presence of the acceptor (mCitrine) is lower than that of the donor alone due to FRET. To test this hypothesis, the fluorescence fluctuation signal and number of molecules of freely diffusing construct were measured using FCS to calculate the molecular brightness of the donor, excited at 405 nm and detected at 475/50 nm, in the presence and absence of the acceptor. Our results indicate that the molecular brightness of cleaved crTC2.1 in a buffer is larger than that of the intact counterpart under 405-nm excitation. The energy transfer efficiency at the single molecule level is larger and more spread in values as compared with the ensemble-averaging time-resolved fluorescence measurements. In contrast, the molecular brightness of the intact crTC2.1, under 488 nm excitation of the acceptor (531/40 nm detection), is the same or slightly larger than that of the cleaved counterpart. These FCS-FRET measurements on freely diffusing donor-acceptor pairs are independent of the precise time constants associated with autocorrelation curves due to the presence of potential photophysical processes. Ultimately, when used in living cells, the proposed approach would only require a low expression level of these genetically encoded constructs, helping to limit potential interference with the cell machinery.