Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy

Advances in surface design and biomedical applications of magnetic nanoparticles

Despite significant efforts by scientists in the development of advanced nanotechnology materials for smart diagnosis devices and drug delivery systems, the success of clinical trials remains largely elusive. In order to address this biomedical challenge, magnetic nanoparticles (MNPs) have gained attention as a promising candidate due to their theranostic properties, which allow the simultaneous treatment and diagnosis of a disease. Moreover, MNPs have advantageous characteristics such as a larger surface area, high surface-to-volume ratio, enhanced mobility, mass transference and, more notably, easy manipulation under external magnetic fields. Besides, certain magnetic particle types based on the magnetite (Fe3O4) phase have already been FDA-approved, demonstrating biocompatible and low toxicity. Typically, surface modification and/or functional group conjugation are required to prevent oxidation and particle aggregation. A wide range of inorganic and organic molecules have been utilized to coat the surface of MNPs, including surfactants, antibodies, synthetic and natural polymers, silica, metals, and various other substances. Furthermore, various strategies have been developed for the synthesis and surface functionalization of MNPs to enhance their colloidal stability, biocompatibility, good response to an external magnetic field, etc. Both uncoated MNPs and those coated with inorganic and organic compounds exhibit versatility, making them suitable for a range of applications such as drug delivery systems (DDS), magnetic hyperthermia, fluorescent biological labels, biodetection and magnetic resonance imaging (MRI). Thus, this review provides an update of recently published MNPs works, providing a current discussion regarding their strategies of synthesis and surface modifications, biomedical applications, and perspectives.

Decoding Biomechanical Cues Based on DNA Sensors

Biological systems perceive and respond to mechanical forces, generating mechanical cues to regulate life processes. Analyzing biomechanical forces has profound significance for understanding biological functions. Therefore, a series of molecular mechanical techniques have been developed, mainly including single-molecule force spectroscopy, traction force microscopy, and molecular tension sensor systems, which provide indispensable tools for advancing the field of mechanobiology. DNA molecules with a programmable structure and well-defined mechanical characteristics have attached much attention to molecular tension sensors as sensing elements, and are designed for the study of biomechanical forces to present biomechanical information with high sensitivity and resolution. In this work, a comprehensive overview of molecular mechanical technology is presented, with a particular focus on molecular tension sensor systems, specifically those based on DNA. Finally, the future development and challenges of DNA-based molecular tension sensor systems are looked upon.

Up- and Down-Regulation of Enzyme Activity in Aggregates with Gold-Covered Magnetic Nanoparticles Triggered by Low-Frequency Magnetic Field

The modern global trend toward sustainable processes that meet the requirements of "green chemistry" provides new opportunities for the broad application of highly active, selective, and specific enzymatic reactions. However, the effective application of enzymes in industrial processes requires the development of systems for the remote regulation of their activity triggered by external physical stimuli, one of which is a low-frequency magnetic field (LFMF). Magnetic nanoparticles (MNPs) transform the energy of an LFMF into mechanical forces and deformations applied to enzyme molecules on the surfaces of MNPs. Here, we demonstrate the up- and down-regulation of two biotechnologically important enzymes, yeast alcohol dehydrogenase (YADH) and soybean formate dehydrogenase (FDH), in aggregates with gold-covered magnetic nanoparticles (GCMNPs) triggered by an LFMF. Two types of aggregates, "dimeric" (with the enzyme attached to several GCMNPs simultaneously), with YADH or FDH, and "monomeric" (the enzyme attached to only one GCMNP), with FDH, were synthesized. Depending on the aggregate type ("dimeric" or "monomeric"), LFMF treatment led to a decrease (down-regulation) or an increase (up-regulation) in enzyme activity. For "dimeric" aggregates, we observed 67 ± 9% and 47 ± 7% decreases in enzyme activity under LFMF exposure for YADH and FDH, respectively. Moreover, in the case of YADH, varying the enzyme or the cross-linking agent concentration led to different magnitudes of the LFMF effect, which was more significant at lower enzyme and higher cross-linking agent concentrations. Different responses to LFMF exposure depending on cofactor presence were also demonstrated. This effect might result from a varying cofactor binding efficiency to enzymes. For the "monomeric" aggregates with FDH, the LFMF treatment caused a significant increase in enzyme activity; the magnitude of this effect depended on the cofactor type: we observed up to 40% enzyme up-regulation in the case of NADP+, while almost no effect was observed in the case of NAD+.

Correlated Single-Molecule Magnetic Tweezers and Fluorescence Measurements of DNA-Enzyme Interactions

Combining force spectroscopy and fluorescence microscopy provides a substantial improvement to the single-molecule toolbox by allowing simultaneous manipulation and orthogonal characterizations of the conformations, interactions, and activity of biomolecular complexes. Here, we describe a combined magnetic tweezers and total internal reflection fluorescence microscopy setup to carry out correlated single-molecule fluorescence spectroscopy and force/twisting experiments. We apply the setup to reveal the DNA interactions of the CRISPR-Cas surveillance complex Cascade. Single-molecule fluorescence of a labeled Cascade allows to follow the DNA association and dissociation of the protein. Simultaneously, the magnetic tweezers probe the DNA unwinding during R-loop formation by the bound Cascade complexes. Furthermore, the setup supports observation of 1D diffusion of protein complexes on stretched DNA molecules. This technique can be applied to study a vast range of protein-DNA interactions.

Statistical Improvement of rGILCC 1 and rPOXA 1B Laccases Activity Assay Conditions Supported by Molecular Dynamics

Laccases (E.C. 1.10.3.2) are glycoproteins widely distributed in nature. Their structural conformation includes three copper sites in their catalytic center, which are responsible for facilitating substrate oxidation, leading to the generation of H2O instead of H2O2. The measurement of laccase activity (UL-1) results may vary depending on the type of laccase, buffer, redox mediators, and substrates employed. The aim was to select the best conditions for rGILCC 1 and rPOXA 1B laccases activity assay. After sequential statistical assays, the molecular dynamics proved to support this process, and we aimed to accumulate valuable insights into the potential application of these enzymes for the degradation of novel substrates with negative environmental implications. Citrate buffer treatment T2 (CB T2) (pH 3.0 ± 0.2; λ420nm, 2 mM ABTS) had the most favorable results, with 7.315 ± 0.131 UL-1 for rGILCC 1 and 5291.665 ± 45.83 UL-1 for rPOXA 1B. The use of citrate buffer increased the enzyme affinity for ABTS since lower Km values occurred for both enzymes (1.49 × 10-2 mM for rGILCC 1 and 3.72 × 10-2 mM for rPOXA 1B) compared to those obtained in acetate buffer (5.36 × 10-2 mM for rGILCC 1 and 1.72 mM for rPOXA 1B). The molecular dynamics of GILCC 1-ABTS and POXA 1B-ABTS showed stable behavior, with root mean square deviation (RMSD) values not exceeding 2.0 Å. Enzyme activities (rGILCC 1 and rPOXA 1B) and 3D model-ABTS interactions (GILCC 1-ABTS and POXA 1B-ABTS) were under the strong influence of pH, wavelength, ions, and ABTS concentration, supported by computational studies identifying the stabilizing residues and interactions. Integration of the experimental and computational approaches yielded a comprehensive understanding of enzyme-substrate interactions, offering potential applications in environmental substrate treatments.

Progression of Antiviral Agents Targeting Viral Polymerases

Viral DNA and RNA polymerases are two kinds of very important enzymes that synthesize the genetic materials of the virus itself, and they have become extremely favorable targets for the development of antiviral drugs because of their relatively conserved characteristics. There are many similarities in the structure and function of different viral polymerases, so inhibitors designed for a certain viral polymerase have acted as effective universal inhibitors on other types of viruses. The present review describes the development of classical antiviral drugs targeting polymerases, summarizes a variety of viral polymerase inhibitors from the perspective of chemically synthesized drugs and natural product drugs, describes novel approaches, and proposes promising development strategies for antiviral drugs.

Modulation of α-Chymotrypsin Conjugated to Magnetic Nanoparticles by the Non-Heating Low-Frequency Magnetic Field: Molecular Dynamics, Reaction Kinetics, and Spectroscopy Analysis

Enzymes conjugated to magnetic nanoparticles (MNPs) undergo changes in the catalytic activity of the non-heating low-frequency magnetic field (LFMF). We apply in silico simulations by molecular dynamics (MD) and in vitro spectroscopic analysis of the enzyme kinetics and secondary structure to study α-chymotrypsin (CT) conjugated to gold-coated iron oxide MNPs. The latter are functionalized by either carboxylic or amino group moieties to vary the points of enzyme attachment. The MD simulation suggests that application of the stretching force to the CT globule by its amino or carboxylic groups causes shrinkage of the substrate-binding site but little if any changes in the catalytic triad. Consistent with this, in CT conjugated to MNPs by either amino or carboxylic groups, LFMF alters the Michaelis-Menten constant but not the apparent catalytic constant k _cat (= V _max/[E]_o). Irrespective of the point of conjugation to MNPs, the CT secondary structure was affected with nearly complete loss of α-helices and increase in the random structures in LFMF, as shown by attenuated total reflection Fourier transformed infrared spectroscopy. Both the catalytic activity and the protein structure of MNP-CT conjugates restored 3 h after the field exposure. We believe that such remotely actuated systems can find applications in advanced manufacturing, nanomedicine, and other areas.

Stimuli-Responsive Regulation of Biocatalysis through Metallic Nanoparticle Interaction

The remote control of biocatalytic processes in an extracellular medium is an exciting idea to deliver innovative solutions in the biocatalysis field. With this purpose, metallic nanoparticles (NPs) are great candidates, as their inherent thermal, electric, magnetic, and plasmonic properties can readily be manipulated upon external stimuli. Exploring the unique NP properties beyond an anchoring platform for enzymes brings up the opportunity to extend the efficiency of biocatalysts and modulate their activity through triggered events. In this review, we discuss a set of external stimuli, such as light, electricity, magnetism, and temperature, as tools for the regulation of nanobiocatalysis, including the challenges and perspectives regarding their use. In addition, we elaborate on the use of combined stimuli that create a more refined framework in terms of a multiresponsive system. Finally, we envision this review might instigate researchers in this field of study with a set of promising opportunities in the near future.

Understanding the Optimal Cooperativity of Human Glucokinase: Kinetic Resonance in Nonequilibrium Conformational Fluctuations

The cooperativity of a monomeric enzyme arises from dynamic correlation instead of spatial correlation and is a consequence of nonequilibrium conformation fluctuations. We investigate the conformation-modulated kinetics of human glucokinase, a monomeric enzyme with important physiological functions, using a five-state kinetic model. We derive the non-Michealis-Menten (MM) correction term of the activity (i.e., turnover rate), predict its relationship to cooperativity, and reveal the violation of conformational detailed balance. Most importantly, we reproduce and explain the observed resonance effect in human glucokinase (i.e., maximal cooperativity when the conformational fluctuation rate is comparable to the catalytic rate). With the realistic parameters, our theoretical results are in quantitative agreement with the reported measurement by Miller and co-workers. The analysis can be extended to a general chemical network beyond the five-state model, suggesting the generality of kinetic cooperativity and resonance.

Study of the Enzyme Activity Change due to Inkjet Printing for Biosensor Fabrication

Enzymes, the most commonly used biosensing element, have a great influence on the performance of biosensors. Recently, drop-on-demand (DOD) printing technique has been widely employed for the fabrication of biosensors due to its merits of noncontact, less waste, and rapid deposition. However, enzyme printing studies were rarely conducted on the effect of printing parameters from the aspect of the pressure wave propagation mechanism. This study investigated the effects of pressure wave propagation on enzyme activity from the aspects of wave superposition, wave amplitude, resulting mechanical stress, and protein conformation change using pyruvate oxidase as the model enzyme. We found that the mechanical stress increased the activity of pyruvate oxidase during the inkjet printing process. A shear rate of 3 × 10⁵ s^-1 enhanced the activity by 14.10%. The enhancement mechanism was investigated, and the mechanical activation or mild proteolysis was found to change the conformation of pyruvate oxidase and improve its activity. This study is fundamental to understand the effect of both printing mechanism and induced mechanical stress on the properties of biomolecules and plays an important role in modulating the activity of other enzyme-based inks, which is crucial for the development of biosensors.

Diazepam Prodrug Stabilizes Human Aminopeptidase B during Lyophilization

Human aminopeptidase B (APB) is a labile enzyme that is being investigated as a biocatalyst for intranasal delivery of prodrug/enzyme combinations. Therefore, the stability of APB is a major concern to ensure a viable drug product. Lyophilization is one technique commonly used to extend shelf life of enzymes. However, the lyophilization process itself can cause conformational changes and aggregation, leading to inactivation of enzymes. In this study, we demonstrate the use of the substrate avizafone (AVF), a prodrug for diazepam, as a stabilizer to minimize inactivation of APB during lyophilization. Permutations of APB samples combined with AVF, trehalose, and/or mannitol were snap-frozen and lyophilized, and subsequently reconstituted to measure the activity of APB. Of the formulation permutations, an APB + AVF + trehalose combination resulted in minimum degradation with 71% retention of activity. This was followed by APB + AVF and APB + trehalose with 60 and 56% retention of activity, respectively. In comparison, APB + mannitol and APB alone retained only 16 and 6.4% activity, respectively. Lyophilizates of the APB + AVF + trehalose formulation were subjected to a 6 month accelerated stability study, at the end of which negligible reduction in activity was observed. These results suggest that colyophilization of an enzyme with its substrate can impart stability on par with the commonly used lyoprotectant, trehalose, but the combination of substrate and trehalose provides a greater stabilizing effect than either additive alone.

Alleviated Inhibition of Single Enzyme in Confined and Crowded Environment

Most proteins perform functions in intracellular milieu. The crowding, compartmentalized cytosol environment affects the protein structure, folding, conformational stability, substrate diffusion, and substrate-enzyme binding. Moreover, enzymes are available at single or very low copy numbers in a cell, and thus the conformation fluctuations of a single enzyme in a crowding environment could also greatly influence its kinetics. However, the crowding effect is poorly understood in the kinetical aspect of enzymatic reactions. In the present study, individual horseradish peroxidase (HRP) is encapsulated in a liposome containing crowding reagents as mimics of viscous cytosol. The confined crowding environment possesses a profound influence on both the catalytic activity and the product inhibition of enzymes. By analyzing the correlation between product generation and product inhibition, we find that the allosteric noncompetitive inhibition of HRP is alleviated in the crowded and confined milieu. Small-angle X-ray scattering experiments provide straightforward proofs of structural changes of enzymes in crowding environments, which are responsible for the reduced enzyme activity and increased enzyme-substrate affinity. We expect that this work may deepen the understanding of correlations between enzymatic conformations and activity performance in real cellular environments.

Oscillating Piconewton Force Manipulation on Single-Molecule Enzymatic Conformational and Reaction Dynamics

Oscillation force has been demonstrated in theoretical studies as a critical role in unraveling the comprehensive enzymatic dynamics and addressing its regulation on enzyme activity. Utilizing the imposed external mechanical oscillation force by our newly developed magnetic tweezers coupled with a single-molecule photon-stamping imaging spectroscopic microscope, we experimentally studied a millisecond-scale oscillation force manipulation on single horseradish peroxidase enzymatic conformational and reaction dynamics. We have studied the enzymatic reaction dynamics and found that the enzyme activity changes under the real-time oscillatory force manipulation. Moreover, the oscillation force shows the capability of manipulating the enzyme active-site conformational state as well as the nascent-formed product's interaction with the active site of the enzyme, which impacts on the product release pathways. Specifically, we have identified that there are two product releasing pathways, the solvation-mediated diffusion releasing pathway and the spilling-out releasing pathway. We have observed that the spilling-out pathway can be significantly perturbed by the oscillatory force manipulation. Our correlated interpretation of enzymatic conformational and reaction dynamics provides a new insight into the comprehensive understanding of the complex conformational dynamics evolved in an enzymatic reaction. Technically, we have also demonstrated a novel approach capable of unfolding an enzyme under an enzymatic reaction condition in real time and, furthermore, by using an oscillatory mechanical weak piconewton force to manipulate enzyme conformations, and the enzyme thermal fluctuation is fully maintained. The real-time in situ fluorescence probe at the enzymatic active site reports the active-site conformational dynamics through each enzymatic reaction turnovers.

Single-Molecule Studies of Allosteric Inhibition of Individual Enzyme on a DNA Origami Reactor

Unraveling the conformational changes of enzymes together with inhibition kinetics during an enzymatic reaction has great potential in screening therapeutic candidates; however, it remains challenging due to the transient nature of each intermediate step. We report our study on the noncompetitive inhibition of horseradish peroxidase with single-turnover resolution using single-molecule fluorescence microscopy. By introducing DNA origami as an addressable nanoreactor, we observe the coexistence of nascent-formed fluorescent product on both catalytic and docking sites. We further propose a single-molecule kinetic model to reveal the interplay between product generation and noncompetitive inhibition and find three distinct inhibitor releasing pathways. Moreover, the kinetic isotope effect experiment indicates a strong correlation between catalytic and docking sites, suggesting an allosteric conformational change in noncompetitive inhibition. A memory effect is also observed. This work provides an in-depth understanding of the correlation between enzyme behavior and enzymatic conformational fluctuation, substrate conversion, and product releasing pathway and kinetics.

Shifting Retroviral Vector Integrations Away from Transcriptional Start Sites via DNA-Binding Protein Domain Insertion into Integrase

The unique ability of retroviruses to integrate genes into host genomes is of great value for long-term expression in gene therapy, but only when integrations occur at safe genomic sites. To reap the benefit of using retroviruses without severe detrimental effects, we developed several murine leukemia virus (MLV)-based gammaretroviral vectors with safer integration patterns by perturbing the structure of the integrase via insertion of DNA-binding zinc-finger domains (ZFDs) into an internal position of the enzyme. ZFD insertion significantly reduced the inherent, strong MLV integration preference for genomic regions near transcriptional start sites (TSSs), which are the most dangerous spots. The altered retroviral integration pattern was related to increased formation of residual primer-binding site sequences at the 3' end of proviruses. Several ZFD insertion mutants showed lower frequencies of integrations into the TSS genome regions when having the residual primer-binding site sequences in the proviruses. Our findings not only can extend the use of retroviruses in biomedical applications, but also provide a glimpse into the mechanisms underlying retroviral integration.

Improving the spectral resolution in fluorescence microscopy through shaped-excitation imaging

The visualization of distinct molecular species represents an important challenge of bio-imaging research. In past decades, the development of multicolor fluorescent (FL) labels has greatly improved our ability to track biological analytes, paving the way for important advances in understanding the cell dynamics. It remains challenging, however, to visualize a large number of different fluorephores simultaneously. Owing to a spectrally broad absorption of fluorescent dyes, only up to five color categories can be resolved at once. Here, we demonstrate a general strategy for distinguishing between multiple fluorescent targets in acquired microscopy images with improved accuracy. The present strategy is enabled through spectral shaping of the excitation light with an optical filter that uniquely attenuates the light absorption of each fluorophore in the investigated sample. The resulting emission changes, induced by such excitation modulation, are therefore target-specific and can be used for identifying various fluorescent species. The technique is demonstrated through an accurate identification of 8 different CdSe dyes with absorption maxima spanning the 520-620 spectral range. It is subsequently applied for accurate measurements of the pH balance in buffers emulating a metabolism of tumor cells.

Soleus muscle H-reflex monitoring in endoscopic surgery under general anesthesia percutaneous interlaminar approach

The clinical value of soleus muscle H-reflex monitoring in general anesthesia percutaneous interlaminar approach was investigated. A total of 80 cases with unilateral L5-S1 disc herniation between January 2015 and October 2016 were randomly divided into control group (without soleus muscle H-reflex monitoring, n=40) and observation group (with soleus muscle H-reflex monitoring, n=40). Results showed that the operation time of the observation group was shorter than that of the control group (P<0.05), and the blood loss during the operation was less than that of the control group (P<0.05). The length of postoperative hospital stay was shorter than that of the control group (P<0.05). At 24 h after operation, the amplitude of H-reflex in diseased side soleus muscle was significantly lower than that in healthy side (P<0.05). The preoperative, postoperative and 24 h postoperatively, the latency of H-reflex in diseased side soleus muscle was shorter than that of healthy side (P<0.05). The latency and amplitude of H-reflex latency in soleus muscle were significantly lower (P<0.05), and the height of intervertebral space in observation group was significantly higher than that in control group (P<0.05). The total percentage of postsurgical sensory dysfunction, dyskinesia, post-root canal stenosis, disc herniation and cerebrospinal fluid leakage was lower than that of the control group (P<0.05). Japanese Orthopaedic Association score of the observation group was significantly higher at 1 month, and 1 year after operation lower than the control group (P<0.05). Taken together, soleus muscle H-reflex monitoring can effectively reduce the damage to the nerve roots under percutaneous endoscopic intervertebral endoscopic surgery under general anesthesia, improve the accuracy of surgery, reduce the complications, shorten the operation time and reduce the surgical bleeding, which is more beneficial to patients smooth recovery.

Force determination in lateral magnetic tweezers combined with TIRF microscopy

Combining single-molecule techniques with fluorescence microscopy has attracted much interest because it allows the correlation of mechanical measurements with directly visualized DNA : protein interactions. In particular, its combination with total internal reflection fluorescence microscopy (TIRF) is advantageous because of the high signal-to-noise ratio this technique achieves. This, however, requires stretching long DNA molecules across the surface of a flow cell to maximize polymer exposure to the excitation light. In this work, we develop a module to laterally stretch DNA molecules at a constant force, which can be easily implemented in regular or combined magnetic tweezers (MT)-TIRF setups. The pulling module is further characterized in standard flow cells of different thicknesses and glass capillaries, using two types of micrometer size superparamagnetic beads, long DNA molecules, and a home-built device to rotate capillaries with mrad precision. The force range achieved by the magnetic pulling module was between 0.1 and 30 pN. A formalism for estimating forces in flow-stretched tethered beads is also proposed, and the results compared with those of lateral MT, demonstrating that lateral MT achieve higher forces with lower dispersion. Finally, we show the compatibility with TIRF microscopy and the parallelization of measurements by characterizing DNA binding by the centromere-binding protein ParB from Bacillus subtilis. Simultaneous MT pulling and fluorescence imaging demonstrate the non-specific binding of BsParB on DNA under conditions restrictive to condensation.

Exploration of Multistate Conformational Dynamics upon Ligand Binding of a Monomeric Enzyme Involved in Pyrophosphoryl Transfer

HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) is a monomeric protein with 158 residues, which undergoes large-scale conformational changes between apo, open, and holo states responding to ligand binding for its function. It has been explored widely as an excellent target for potential antibacterial drug development. However, little is known about how conformational dynamics between the native states influences the substrate recognition and the functionality of enzymatic catalysis. Here, we report a coarse-grained triple-basin structure-based model upon ligand binding to describe such multiple-state system by the molecular dynamics simulation. With our model, we have made theoretical predictions that are in good agreement with the experimental measurements. Our results revealed the intrinsic conformational fluctuations between apo and open states without ligand binding. We found that HPPK can switch to the activated holo state upon the ordered binding of the two ligands (ATP and HP). We uncovered the underlying mechanism by which major induced fit and minor population shift pathways coexist upon ligand binding by quantitative flux analysis. Additionally, we pointed out the structural origin for the conformational changes and identified the key residues as well as contact interactions. We further explored the temperature effect on the conformational distributions and pathway weights. It gave strong support that higher temperatures promote population shift, while the induced fit pathway is always the predominant activation route of the HPPK system. These findings will provide significant insights of the mechanisms of the multistate conformational dynamics of HPPK upon ligand binding.

Manipulating motions of targeted single cells in solution by an integrated double-ring magnetic tweezers imaging microscope

Controlling and manipulating living cell motions in solution hold a high promise in developing new biotechnology and biological science. Here, we developed a magnetic tweezers device that employs a combination of two permanent magnets in up-down double-ring configuration axially fitting with a microscopic objective, allowing a picoNewton (pN) bidirectional force and motion control on the sample beyond a single upward pulling direction. The experimental force calibration and magnetic field simulation using finite element method magnetics demonstrate that the designed magnetic tweezers covers a linear-combined pN force with positive-negative polarization changes in a tenability of sub-pN scale, which can be utilized to further achieve motion manipulation by shifting the force balance. We demonstrate an application of the up-down double-ring magnetic tweezers for single cell manipulation, showing that the cells with internalized paramagnetic beads can be selectively picked up and guided in a controlled fine motion.

Tracking the Energy Flow on Nanoscale via Sample-Transmitted Excitation Photoluminescence Spectroscopy

Tracking the energy flow in nanoscale materials is an important yet challenging goal. Experimental methods for probing the intermolecular energy transfer (ET) are often burdened by the spectral crosstalk between donor and acceptor species, which complicates unraveling their individual contributions. This issue is particularly prominent in inorganic nanoparticles and biological macromolecules featuring broad absorbing profiles. Here, we demonstrate a general spectroscopic strategy for measuring the ET efficiency between nanostructured or molecular dyes exhibiting a significant donor-acceptor spectral overlap. The reported approach is enabled through spectral shaping of the broadband excitation light with solutions of donor molecules, which inhibits the excitation of respective donor species in the sample. The resulting changes in the acceptor emission induced by the spectral modulation of the excitation beam are then used to determine the quantum efficiency and the rate of ET processes between arbitrary fluorophores (molecules, nanoparticles, polymers) with high accuracy. The feasibility of the reported method was demonstrated using a control donor-acceptor system utilizing a protein-bridged Cy3-Cy5 dye pair and subsequently applied for studying the energy flow in a CdSe₅₆₀-CdSe₆₀₀ binary nanocrystal film.

Single-molecule fluorescence resonance energy transfer in molecular biology

Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful technique for studying the conformation dynamics and interactions of individual biomolecules. In this review, we describe the concept and principle of smFRET, illustrate general instrumentation and microscopy settings for experiments, and discuss the methods and algorithms for data analysis. Subsequently, we review applications of smFRET in protein conformational changes, ion channel open-close properties, receptor-ligand interactions, nucleic acid structure regulation, vesicle fusion, and force induced conformational dynamics. Finally, we discuss the main limitations of smFRET in molecular biology.

Probing conformational dynamics of an enzymatic active site by an in situ single fluorogenic probe under piconewton force manipulation

Unraveling the conformational details of an enzyme during the essential steps of a catalytic reaction (i.e., enzyme-substrate interaction, enzyme-substrate active complex formation, nascent product formation, and product release) is challenging due to the transient nature of intermediate conformational states, conformational fluctuations, and the associated complex dynamics. Here we report our study on the conformational dynamics of horseradish peroxidase using single-molecule multiparameter photon time-stamping spectroscopy with mechanical force manipulation, a newly developed single-molecule fluorescence imaging magnetic tweezers nanoscopic approach. A nascent-formed fluorogenic product molecule serves as a probe, perfectly fitting in the enzymatic reaction active site for probing the enzymatic conformational dynamics. Interestingly, the product releasing dynamics shows the complex conformational behavior with multiple product releasing pathways. However, under magnetic force manipulation, the complex nature of the multiple product releasing pathways disappears and more simplistic conformations of the active site are populated.