Advanced fluorescence correlation spectroscopy for studying biomolecular conformation

Dynamic Monitoring of Biomolecular Hydrodynamic Dimensions by Magnetization Motion on Quartz Crystal Microbalance

Hydrodynamic dimension (HD) is the primary indicator of the size of bioconjugated particles and biomolecules. It is an important parameter in the study of solid-liquid two-phase dynamics. HD dynamic monitoring is crucial for precise and customized medical research as it enables the investigation of the continuous changes in the physicochemical characteristics of biomolecules in response to external stimuli. However, current HD measurements based on Brownian motion, such as dynamic light scattering (DLS), are inadequate for meeting the polydisperse sample demands of dynamic monitoring. In this paper, we propose MMQCM method samples of various types and HD dynamic monitoring. An alternating magnetic field of frequency ωm excites biomolecule-magnetic bead particles (bioMBs) to generate magnetization motion, and the quartz crystal microbalance (QCM) senses this motion to provide HD dynamic monitoring. Specifically, the magnetization motion is modulated onto the thickness-shear oscillation of the QCM at the frequency ωq. By analysis of the frequency spectrum of the QCM output signal, the ratio of the magnitudes of the real and imaginary parts of the components at frequency ωq ± 2ωm is extracted to characterize the particle size. Using the MMQCM approach, we successfully evaluated the size of bioMBs with different biomolecule concentrations. The 30 min HD dynamic monitoring was implemented. An increase of ∼10 nm in size was observed upon biomolecular structural stretching. Subsequently, the size of bioMBs gradually reduced due to the continuous dissociation of biomolecules, with a total reduction of 20∼40 nm. This HD dynamic monitoring demonstrates that the release of biomolecules can be regulated by controlling the duration of magnetic stimulation, providing valuable insights and guidance for controlled drug release in personalized precision medicine.

Spectral characterization of the impact of modifiers and different prepare temperatures on snow lotus medicinal residue-biochar and dissolved organic matter

This study involved the production of 20 biochar samples derived from secondary medicinal residues of Snow Lotus Oral Liquid, processed within the temperature range of 200-600 °C. Additionally, four medicinal residues, including dissolved organic matter (DOM), from 24 samples obtained using the shaking method, served as the primary source material. The investigation focused on two key factors: the modifier and preparation temperature. These factors were examined to elucidate the spectral characteristics and chemical properties of the pharmaceutical residues, biochar, and DOM. To analyze the alterations in the spectral attributes of biochar and medicinal residues, we employed near-infrared spectroscopy (NIR) in conjunction with Fourier-infrared one-dimensional and two-dimensional correlation spectroscopy. These findings revealed that modifiers enhanced the aromaticity of biochar, and the influence of preparation temperature on biochar was diminished. This observation indicates the stability of the aromatic functional group structure. Comparative analysis indicated that Na2CO3 had a more pronounced structural effect on biochar, which is consistent with its adsorption properties. Furthermore, we utilized the fluorescence indices from UV-visible spectroscopy and excitation-emission-matrix spectra with the PARAFAC model to elucidate the characteristics of the fluorescence components in the DOM released from the samples. The results demonstrated that the DOM released from biochar primarily originated externally. Aromaticity reduction and increased decay will enhance the ability of the biochar to bind pollutants. Those results confirmed the link between the substantial increase in the adsorption performance of the high-temperature modified charcoal in the previous study and the structural changes in the biochar. We investigated the structural changes of biochar and derivative DOM in the presence of two perturbing factors, modifier and preparation temperature. Suitable modifiers were selected. Preparation for the study of adsorption properties of snow lotus medicinal residues.

Simple and Efficient Detection Scheme of Two-Color Fluorescence Correlation Spectroscopy for Protein Dynamics Investigation from Nanoseconds to Milliseconds

Nanosecond resolved fluorescence correlation spectroscopy (ns-FCS) based on two-color fluorescence detection is a powerful strategy for investigating the fast dynamics of biological macromolecules labeled with donor and acceptor fluorophores. The standard methods of ns-FCS use two single-photon avalanche diodes (SPADs) for the detection of single-color signals (four SPADs for two-color signals) to eliminate the afterpulse artifacts of SPAD at the expense of the efficiency of utilizing photon data in the calculation of correlograms. Herein, we demonstrated that hybrid photodetectors (HPDs) enable the recording of fluorescence photons in ns-FCS based on the minimal system using two HPDs for the detection of two-color signals. However, HPD exhibited afterpulses at a yield with respect to the rate of photodetection (<10-4) much lower than that of SPADs (∼10-2), which could still hamper correlation measurements. We demonstrated that the simple subtraction procedure could eliminate afterpulse artifacts. While the quantum efficiency of photodetection for HPDs is lower than that for high-performance SPADs, the developed system can be practically used for two-color ns-FCS in a time domain longer than a few nanoseconds. The fast chain dynamics of the B domain of protein A in the unfolded state was observed using the new method.

Improving the thermostability of Pseudoalteromonas Porphyrae κ-carrageenase by rational design and MD simulation

The industrial applications of the κ-carrageenases have been restricted by their poor thermostability. In this study, based on the folding free energy change (ΔΔG) and the flexibility analysis using molecular dynamics (MD) simulation for the alkaline κ-carrageenase KCgCD from Pseudoalteromonas porphyrae (WT), the mutant S190R was identified with improved thermostability. After incubation at 50 °C for 30 min, the residual activity of S190R was 63.7%, 25.7% higher than that of WT. The Tm values determined by differential scanning calorimetry were 66.2 °C and 64.4 °C for S190R and WT, respectively. The optimal temperature of S190R was 10 °C higher than that of WT. The κ-carrageenan hydrolysates produced by S190R showed higher xanthine oxidase inhibitory activity compared with the untreated κ-carrageenan. MD simulation analysis of S190R showed that the residues (V186-M194 and P196-G197) in F5 and the key residue R150 in F3 displayed the decreased flexibility, and residues of T169-N173 near the catalytic center displayed the increased flexibility. These changed flexibilities might be the reasons for the improved thermostability of mutant S190R. This study provides a useful rational design strategy of combination of ΔΔG calculation and MD simulation to improve the κ-carrageenase's thermostability for its better industrial applications.

Single-molecule tracking to determine the abundances and stoichiometries of freely-diffusing protein complexes in living cells: Past applications and future prospects

Most biological processes in living cells rely on interactions between proteins. Live-cell compatible approaches that can quantify to what extent a given protein participates in homo- and hetero-oligomeric complexes of different size and subunit composition are therefore critical to advance our understanding of how cellular physiology is governed by these molecular interactions. Biomolecular complex formation changes the diffusion coefficient of constituent proteins, and these changes can be measured using fluorescence microscopy-based approaches, such as single-molecule tracking, fluorescence correlation spectroscopy, and fluorescence recovery after photobleaching. In this review, we focus on the use of single-molecule tracking to identify, resolve, and quantify the presence of freely-diffusing proteins and protein complexes in living cells. We compare and contrast different data analysis methods that are currently employed in the field and discuss experimental designs that can aid the interpretation of the obtained results. Comparisons of diffusion rates for different proteins and protein complexes in intracellular aqueous environments reported in the recent literature reveal a clear and systematic deviation from the Stokes-Einstein diffusion theory. While a complete and quantitative theoretical explanation of why such deviations manifest is missing, the available data suggest the possibility of weighing freely-diffusing proteins and protein complexes in living cells by measuring their diffusion coefficients. Mapping individual diffusive states to protein complexes of defined molecular weight, subunit stoichiometry, and structure promises to provide key new insights into how protein-protein interactions regulate protein conformational, translational, and rotational dynamics, and ultimately protein function.

Single-molecule counting applied to the study of GPCR oligomerization

Single-molecule counting techniques enable a precise determination of the intracellular abundance and stoichiometry of proteins and macromolecular complexes. These details are often challenging to quantitatively assess yet are essential for our understanding of cellular function. Consider G-protein-coupled receptors-an expansive class of transmembrane signaling proteins that participate in many vital physiological functions making them a popular target for drug development. While early evidence for the role of oligomerization in receptor signaling came from ensemble biochemical and biophysical assays, innovations in single-molecule measurements are now driving a paradigm shift in our understanding of its relevance. Here, we review recent developments in single-molecule counting with a focus on photobleaching step counting and the emerging technique of quantitative single-molecule localization microscopy-with a particular emphasis on the potential for these techniques to advance our understanding of the role of oligomerization in G-protein-coupled receptor signaling.