Diffusion Measurements of Swimming Enzymes with Fluorescence Correlation Spectroscopy

Advancements in enzymatic biotransformation and bioactivities of rare ginsenosides: A review

Ginsenoside, the principal active constituent of ginseng, exhibits enhanced bioavailability and medicinal efficacy in rare ginsenosides compared to major ginsenosides. Current research is focused on efficiently and selectively removing sugar groups attached to the major ginsenoside sugar chains to convert them into rare ginsenosides that meet the demands of medical industry and functional foods. The methods for preparing rare ginsenosides encompass chemical, microbial, and enzymatic approaches. Among these, the enzyme conversion method is highly favored by researchers due to its exceptional specificity and robust efficiency. This review summarizes the biological activities of different rare ginsenosides, explores the various glycosidases used in the biotransformation of different major ginsenosides as substrates, and elucidates their respective corresponding biotransformation pathways. These findings will provide valuable references for the development, utilization, and industrial production of ginsenosides.

Activity-induced diffusion recovery in crowded colloidal suspensions

We show that the forces generated by active enzyme molecules are strong enough to influence the dynamics of their surroundings under artificial crowded environments. We measured the behavior of polymer microparticles in a quasi-two-dimensional system under aqueous environment, at various area fraction values of particles. In the presence of enzymatic activity, not only was the diffusion of the suspended particles enhanced at shorter time-scales, but the system also showed a transition from subdiffusive to diffusive dynamics at longer time-scale limits. Similar observations were also recorded with enzyme-functionalized microparticles. Brownian dynamics simulations have been performed to support the experimental observations.

Diffusion of Multiple Species Resolved by Fluorescence Lifetime Recovery after Photobleaching (FLRAP)

Fluorescence recovery after photobleaching (FRAP) is now an indispensable tool to analyze the diffusion of molecules in vivo and in vitro. However, a conventional fluorescence intensity-based approach has difficulty in analyzing the diffusion of multiple species simultaneously. Here, we report fluorescence lifetime recovery after photobleaching (FLRAP) that incorporates fluorescence lifetime information into FRAP. By using FLRAP, the fluorescence intensity-recovery curves of each species can be successfully extracted from the ensemble photon data by utilizing their species-specific fluorescence decay curves, which are verified by applying FLRAP to two heterogeneous systems. Thus, FLRAP can be a powerful tool to quantitatively elucidate the molecular diffusion of multiple species in complex systems such as in living cells.

Neural network informed photon filtering reduces fluorescence correlation spectroscopy artifacts

Fluorescence correlation spectroscopy (FCS) techniques are well-established tools to investigate molecular dynamics in confocal and super-resolution microscopy. In practice, users often need to handle a variety of sample- or hardware-related artifacts, an example being peak artifacts created by bright, slow-moving clusters. Approaches to address peak artifacts exist, but measurements suffering from severe artifacts are typically nonanalyzable. Here, we trained a one-dimensional U-Net to automatically identify peak artifacts in fluorescence time series and then analyzed the purified, nonartifactual fluctuations by time-series editing. We show that, in samples with peak artifacts, the transit time and particle number distributions can be restored in simulations and validated the approach in two independent biological experiments. We propose that it is adaptable for other FCS artifacts, such as detector dropout, membrane movement, or photobleaching. In conclusion, this simulation-based, automated, open-source pipeline makes measurements analyzable that previously had to be discarded and extends every FCS user's experimental toolbox.

Enzymatic micro/nanomotors in biomedicine: from single motors to swarms

Micro/nanomotors (MNMs) have evolved from single self-propelled entities to versatile systems capable of performing one or multiple biomedical tasks. When single MNMs self-assemble into coordinated swarms, either under external control or triggered by chemical reactions, they offer advantages that individual MNMs cannot achieve. These benefits include intelligent multitasking and adaptability to changes in the surrounding environment. Here, we provide our perspective on the evolution of MNMs, beginning with the development of enzymatic MNMs since the first theoretical model was proposed in 2005. These enzymatic MNMs hold immense promise in biomedicine due to their advantages in biocompatibility and fuel availability. Subsequently, we introduce the design and application of single motors in biomedicine, followed by the control of MNM swarms and their biomedical applications. In the end, we propose viable solutions for advancing the development of MNM swarms and anticipate valuable insights into the creation of more intelligent and controllable MNM swarms for biomedical applications.

Open Questions of Chemically Powered Nano- and Micromotors

Chemically powered nano- and micromotors are microscopic devices that convert chemical energy into motion. Interest in these motors has grown over the past 20 years because they exhibit interesting collective behaviors and have found potential uses in biomedical and environmental applications. Understanding how these motors operate both individually and collectively and how environments affect their operation is of both fundamental and applied significance. However, there are still significant gaps in our knowledge. This Perspective highlights several open questions regarding the propulsion mechanisms of, interactions among, and impact of confinements on nano- and micromotors driven by self-generated chemical gradients. These questions are based on my own experience as an experimentalist. For each open question, I describe the problem and its significance, analyze the status-quo, identify the bottleneck problem, and propose potential solutions. An underlying theme for these questions is the interplay among reaction kinetics, physicochemical distributions, and fluid flows. Unraveling this interplay requires careful measurements as well as a close collaboration between experimentalists and theoreticians/numerical experts. The interdisciplinary nature of these challenges suggests that their solutions could bring new revelations and opportunities across disciplines such as colloidal sciences, material sciences, soft matter physics, robotics, and beyond.

Single-Molecule Tracking of Reagent Diffusion during Chemical Reactions

Recent experiments have shown that the diffusion of reagent molecules is inconsistent with what the Stokes-Einstein equation predicts during a chemical reaction. Here, we used single-molecule tracking to observe the diffusion of reactive reagent molecules during click and Diels-Alder (DA) reactions. We found that the diffusion coefficient of the reagents remained unchanged within the experimental uncertainty upon the DA reaction. Yet, diffusion of reagent molecules is faster than predicted during the click reaction when the reagent concentration and catalyst concentration exceed a threshold. A stepwise analysis suggested that the fast diffusion scenario is due to the reaction but not the involvement of the tracer with the reaction itself. The present results provide experimental evidence on the faster-than-expected reagent diffusion during a CuAAC reaction in specific conditions and propose new insights into understanding this unexpected behavior.

Response to Comment on "Following Molecular Mobility during Chemical Reactions: No Evidence for Active Propulsion" and "Molecular Diffusivity of Click Reaction Components: The Diffusion Enhancement Question"

In their Comment (DOI: 10.1021/jacs.2c02965) on two related publications by our group (J. Am. Chem. Soc.2022, 144, 1380–1388; DOI: 10.1021/jacs.1c11754) and another (J. Am. Chem. Soc.2021, 143, 20884–20890; DOI: 10.1021/jacs.1c09455), Huang and Granick refer to the diffusion NMR measurements of molecules during a copper-catalyzed azide–alkyne cycloaddition (CuAAC) “click” reaction. Here we respond to their comments and maintain that no measurable diffusion enhancement was observed during the reaction. We expand on the physical arguments presented in our original JACS Article regarding the appropriate reference state for the diffusion coefficient and present new data showing that the use of other reference states, as suggested by Huang and Granick, will still support our conclusion that the two reactants and one product of the CuAAC reaction do not exhibit boosted mobility during the reaction.

Enzyme Purification Improves the Enzyme Loading, Self-Propulsion, and Endurance Performance of Micromotors

Enzyme-powered micro- and nanomotors make use of biocatalysis to self-propel in aqueous media and hold immense promise for active and targeted drug delivery. Most (if not all) of these micro- and nanomotors described to date are fabricated using a commercially available enzyme, despite claims that some commercial preparations may not have a sufficiently high degree of purity for downstream applications. In this study, the purity of a commercial urease, an enzyme frequently used to power the motion of micro- and nanomotors, was evaluated and found to be impure. After separating the hexameric urease from the protein impurities by size-exclusion chromatography, the hexameric urease was subsequently characterized and used to functionalize hollow silica microcapsules. Micromotors loaded with purified urease were found to be 2.5 times more motile than the same micromotors loaded with unpurified urease, reaching average speeds of 5.5 μm/s. After comparing a number of parameters, such as enzyme distribution, protein loading, and motor reusability, between micromotors functionalized with purified vs unpurified urease, it was concluded that protein purification was essential for optimal performance of the enzyme-powered micromotor.

Perspective: a stirring role for metabolism in cells

Based on recent findings indicating that metabolism might be governed by a limit on the rate at which cells can dissipate Gibbs energy, in this Perspective, we propose a new mechanism of how metabolic activity could globally regulate biomolecular processes in a cell. Specifically, we postulate that Gibbs energy released in metabolic reactions is used to perform work, allowing enzymes to self‐propel or to break free from supramolecular structures. This catalysis‐induced enzyme movement will result in increased intracellular motion, which in turn can compromise biomolecular functions. Once the increased intracellular motion has a detrimental effect on regulatory mechanisms, this will establish a feedback mechanism on metabolic activity, and result in the observed thermodynamic limit. While this proposed explanation for the identified upper rate limit on cellular Gibbs energy dissipation rate awaits experimental validation, it offers an intriguing perspective of how metabolic activity can globally affect biomolecular functions and will hopefully spark new research.

Displacement Statistics of Unhindered Single Molecules Show no Enhanced Diffusion in Enzymatic Reactions

Recent studies have sparked debate over whether catalytic reactions enhance the diffusion coefficients D of enzymes. Through high statistics of the transient (600 μs) displacements of unhindered single molecules freely diffusing in common buffers, we here quantify D for four enzymes under catalytic turnovers. We thus formulate how ∼ ±1% precisions may be achieved for D, and show no changes in diffusivity for catalase, urease, aldolase, and alkaline phosphatase under the application of wide concentration ranges of substrates. Our single-molecule approach thus overcomes potential limitations and artifacts underscored by recent studies to show no enhanced diffusion in enzymatic reactions.

Molecular Diffusivity of Click Reaction Components: The Diffusion Enhancement Question

Micrometer-sized objects are widely known to exhibit chemically driven motility in systems away from equilibrium. Experimental observation of reaction-induced motility or enhancement in diffusivity at the much shorter length scale of small molecules is, however, still a matter of debate. Here, we investigate the molecular diffusivity of reactants, catalyst, and product of a model reaction, the copper-catalyzed azide-alkyne cycloaddition click reaction, and develop new NMR diffusion approaches that allow the probing of reaction-induced diffusion enhancement in nanosized molecular systems with higher accuracy than the state of the art. Following two different approaches that enable the accounting of time-dependent concentration changes during NMR experiments, we closely monitored the diffusion coefficient of reaction components during the reaction. The reaction components showed distinct changes in the diffusivity: while the two reactants underwent a time-dependent decrease in their diffusivity, the diffusion coefficient of the product gradually increased and the catalyst showed only slight diffusion enhancement within the range expected for reaction-induced sample heating. The decrease in diffusion coefficient of the alkyne, one of the two reactants of click reaction, was not reproduced during its copper coordination when the second reactant, azide, was absent. Our results do not support the catalysis-induced diffusion enhancement of the components of the click reaction and, instead, point to the role of a relatively large intermediate species within the reaction cycle with diffusivity lower than that of both the reactants and product molecule.

Synchronization and Enhanced Catalysis of Mechanically Coupled Enzymes

We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is driven by stochastic steps along a biased chemical free energy landscape. We find conditions under which the enzymes can synchronize their catalytic steps, and discover that the coupling can lead to a significant enhancement in their overall catalytic rate. Both effects can be understood as arising from a global bifurcation in the underlying dynamical system at sufficiently strong coupling. Our findings suggest that, despite their molecular scale, enzymes can be cooperative and improve their performance in metabolic clusters.

A simple theory for molecular chemotaxis driven by specific binding interactions

Recent experiments have suggested that enzymes and other small molecules chemotax toward their substrates. However, the physical forces driving this chemotaxis are currently debated. In this work, we consider a simple thermodynamic theory for molecular chemotaxis that is based on the McMillan-Mayer theory of dilute solutions and Schellman's theory for macromolecular binding. Even in the absence of direct interactions, the chemical binding equilibrium introduces a coupling term into the relevant free energy, which then reduces the chemical potential of both enzymes and their substrates. Assuming a local thermodynamic equilibrium, this binding contribution to the chemical potential generates an effective thermodynamic force that promotes chemotaxis by driving each solute toward its binding partner. Our numerical simulations demonstrate that, although small, this thermodynamic force is qualitatively consistent with several experimental studies. Thus, our study may provide additional insight into the role of the thermodynamic binding free energy for molecular chemotaxis.

Oxygen Generation Using Catalytic Nano/Micromotors

Gaseous oxygen plays a vital role in driving the metabolism of living organisms and has multiple agricultural, medical, and technological applications. Different methods have been discovered to produce oxygen, including plants, oxygen concentrators and catalytic reactions. However, many such approaches are relatively expensive, involve challenges, complexities in post-production processes or generate undesired reaction products. Catalytic oxygen generation using hydrogen peroxide is one of the simplest and cleanest methods to produce oxygen in the required quantities. Chemically powered micro/nanomotors, capable of self-propulsion in liquid media, offer convenient and economic platforms for on-the-fly generation of gaseous oxygen on demand. Micromotors have opened up opportunities for controlled oxygen generation and transport under complex conditions, critical medical diagnostics and therapy. Mobile oxygen micro-carriers help better understand the energy transduction efficiencies of micro/nanoscopic active matter by careful selection of catalytic materials, fuel compositions and concentrations, catalyst surface curvatures and catalytic particle size, which opens avenues for controllable oxygen release on the level of a single catalytic microreactor. This review discusses various micro/nanomotor systems capable of functioning as mobile oxygen generators while highlighting their features, efficiencies and application potentials in different fields.

Stable and Temporary Enzyme Complexes and Metabolons Involved in Energy and Redox Metabolism

Significance: Alongside well-characterized permanent multimeric enzymes and multienzyme complexes, relatively unstable transient enzyme-enzyme assemblies, including metabolons, provide an important mechanism for the regulation of energy and redox metabolism. Critical Issues: Despite the fact that enzyme-enzyme assemblies have been proposed for many decades and experimentally analyzed for at least 40 years, there are very few pathways for which unequivocal evidence for the presence of metabolite channeling, the most frequently evoked reason for their formation, has been provided. Further, in contrast to the stronger, permanent interactions for which a deep understanding of the subunit interface exists, the mechanism(s) underlying transient enzyme-enzyme interactions remain poorly studied. Recent Advances: The widespread adoption of proteomic and cell biological approaches to characterize protein-protein interaction is defining an ever-increasing number of enzyme-enzyme assemblies as well as enzyme-protein interactions that likely identify factors which stabilize such complexes. Moreover, the use of microfluidic technologies provided compelling support of a role for substrate-specific chemotaxis in complex assemblies. Future Directions: Embracing current and developing technologies should render the delineation of metabolons from other enzyme-enzyme complexes more facile. In parallel, attempts to confirm that the findings reported in microfluidic systems are, indeed, representative of the cellular situation will be critical to understanding the physiological circumstances requiring and evoking dynamic changes in the levels of the various transient enzyme-enzyme assemblies of the cell. Antioxid. Redox Signal. 35, 788-807.

Enzyme aggregation and fragmentation induced by catalysis relevant species

It is usually assumed that enzymes retain their native structure during catalysis. However, the aggregation and fragmentation of proteins can be difficult to detect and sometimes conclusions are drawn based on the assumption that the protein is in its native form. We have examined three model enzymes, alkaline phosphatase (AkP), hexokinase (HK) and glucose oxidase (GOx). We find that these enzymes aggregate or fragment after addition of chemical species directly related to their catalysis. We used several independent techniques to study this behavior. Specifically, we found that glucose oxidase and hexokinase fragment in the presence of D-glucose but not L-glucose, while hexokinase aggregates in the presence of Mg²⁺ ion and either ATP or ADP at low pH. Alkaline phosphatase aggregates in the presence of Zn²⁺ ion and inorganic phosphate. The aggregation of hexokinase and alkaline phosphatase does not appear to attenuate their catalytic activity. Our study indicates that specific multimeric structures of native enzymes may not be retained during catalysis and suggests pathways for different enzymes to associate or separate over the course of substrate turnover.

Nanoscale Catalyst Chemotaxis Can Drive the Assembly of Functional Pathways

Recent experiments demonstrate molecular chemotaxis or altered diffusion rates of enzymes in the presence of their own substrates. We show here an important implication, namely, that if a nanoscale catalyst A produces a small-molecule ligand product L which is the substrate of another catalyst B, the two catalysts will attract each other. We explore this nonequilibrium producer recruitment force (ProRec) in a reaction-diffusion model. The predicted cat-cat association will be the strongest when A is a fast producer of L and B is a tight binder to it. ProRec is a force that could drive a mechanism (the catpath mechanism) by which catalysts could become spatially localized into functional pathways, such as in the biochemical networks in cells, which can achieve complex goals.

Conformation-changing enzymes and macromolecular crowding

We study how crowding affects the activity and catalysis-enhanced diffusion of enzymes and passive tracers by employing a fluctuating-dumbbell model of conformation-changing enzymes. Our Brownian dynamics simulations reveal that the diffusion of enzymes depends qualitatively on the type of crowding. If only enzymes are present in the system, the catalysis-induced enhancement of the enzyme diffusion - somewhat counter-intuitively - increases with crowding, while it decreases if crowding is due to inert particles. For the tracers, the diffusion enhancement increases with increasing the enzyme concentration. We also show how the enzyme activity is reduced by crowding and propose a simple expression to describe this reduction. Our results highlight subtle effects at play concerning enzymatic activity and macromolecular transport in crowded systems, such as, e.g., the interior of living cells.

Chemically-powered swimming and diffusion in the microscopic world

The past decade has seen intriguing reports and heated debates concerning the chemically-driven enhanced motion of objects ranging from small molecules to millimetre-size synthetic robots. These objects, in solutions in which chemical reactions were occurring, were observed to diffuse (spread non-directionally) or swim (move directionally) at rates exceeding those expected from Brownian motion alone. The debates have focused on whether observed enhancement is an experimental artefact or a real phenomenon. If the latter were true, then we would also need to explain how the chemical energy is converted into mechanical work. In this Perspective, we summarize and discuss recent observations and theories of active diffusion and swimming. Notably, the chemomechanical coupling and magnitude of diffusion enhancement are strongly size-dependent and should vanish as the size of the swimmers approaches the molecular scale. We evaluate the reliability of common techniques to measure diffusion coefficients and finish by considering the potential applications and chemical to mechanical energy conversion efficiencies of typical nanoswimmers and microswimmers.

Simultaneously monitoring endogenous MAPK members in single living cells by multi-channel fluorescence correlation spectroscopy

The mitogen-activated protein kinase (MAPK) pathway is a major module for cellular signal transduction. The dysregulation of the MAPK pathway has been involved in the pathogenesis of multiple diseases ranging from cancers to chronic inflammations. So far, we have not fully understood the influences of external factors and signaling networks on the MAPK pathway due to the lack of in situ methods for simultaneous detection of multiple kinases in the pathway in living cells. Herein, we present a new strategy for in situ and simultaneously monitoring MAPK pathway kinases in single living cells combining multi-channel fluorescence correlation spectroscopy (FCS) with affinity fluorescent probes. We chose rapidly growing fibrosarcoma kinase (RAF), mitogen-activated protein kinase (MEK), and extracellular signal-regulated kinase (ERK) as representative members in the MAPK pathway. We designed and synthesized three fluorescent affinity probes and experimental results demonstrated that the three probes specifically targeted endogenous BRAF, MEK1/2, and ERK1/2 in living cells. Based on the multi-channel FCS system, we studied the influences of biological substances, drugs and oxidative stress on the activities of endogenous MAPK kinases and the cross-talk between the MAPK and PI3K-mTOR pathways. We have found that serum, sorafenib, and hydrogen peroxide can regulate multiple MAPK kinases and the effects of external stimuli can transmit to the MAPK pathway; furthermore, we have observed that the MAPK pathway can be activated by modulating the PI3K-mTOR pathway. Our results illustrated the complexity of a cellular signal network and the necessity of in situ and simultaneous determination of biomolecules in living cells.

Revealing Conformational Transition Dynamics of Photosynthetic Proteins in Single-Molecule Electrical Circuits

The function of proteins depends on their structural flexibility and conformational change. By utilizing silicon-nanowire-based single-molecule electrical circuits, here we present a label-free real-time measurement method that can directly monitor conformational changes of a photosynthetic LH1-RC complex, reaching the ultimate goal of analytic chemistry. These results manifest that the conformation of the LH1-RC complex vibrates among four conformations with strong temperature dependence. At the optimal temperature, States 2 and 3 occupy the main conformations of the LH1-RC complex, and its conformational variation mostly emerges as anharmonic vibration modes, which contributes to photon acquisition and heat transmission. The influence of light activation on occurrence percentage is observed, resulting from light-driven quivering of pigments. Therefore, this avenue proves to be an efficient platform for revealing the fundamental mechanisms of various biological processes in vitro.

Spectroscopic and in silico investigation of the interaction between GH1 β-glucosidase and ginsenoside Rb1

The function and application of β-glucosidase attract attention nowadays. β-glucosidase was confirmed of transforming ginsenoside Rb1 to rare ginsenoside, but the interaction mechanism remains not clear. In this work, β-glucosidase from GH1 family of Paenibacillus polymyxa was selected, and its gene sequence bglB was synthesized by codon. Then, recombinant plasmid was transferred into Escherichia coli BL21 (DE3) and expressed. The UV-visible spectrum showed that ginsenoside Rb1 decreased the polarity of the corresponding structure of hydrophobic aromatic amino acids (Trp) in β-glucosidase and increased new π-π* transition. The fluorescence quenching spectrum showed that ginsenoside Rb1 inhibited intrinsic fluorescence, formed static quenching, reduced the surface hydrophobicity of β-glucosidase, and KSV was 8.37 × 103 L/M (298K). Circular dichroism (CD) showed that secondary structure of β-glucosidase was changed by the binding action. Localized surface plasmon resonance (LSPR) showed that β-glucosidase and Rb1 had strong binding power which KD value was 5.24 × 10-4 (±2.35 × 10-5) M. Molecular docking simulation evaluated the binding site, hydrophobic force, hydrogen bond, and key amino acids of β-glucosidase with ginsenoside Rb1 in the process. Thus, this work could provide basic mechanisms of the binding and interaction between β-glucosidase and ginsenoside Rb1.

Experimental insight into enzyme catalysis and dynamics: A review on applications of state of art spectroscopic methods

Enzymes are dynamic in nature and understanding their activity depends on exploring their overall structural fluctuation as well as transformation at the active site in free state as well as turnover conditions. In this chapter, the application of several different spectroscopy techniques viz. single molecule spectroscopy, ultrafast spectroscopy and Raman spectroscopy in the context of enzyme dynamics and catalysis are discussed. The importance of such studies are significant in the understanding of new discoveries of drugs, cure for some lethal diseases, gene modification as well as in industrial applications.

Analyses of p73 Protein Oligomerization and p73-MDM2 Interaction in Single Living Cells Using In Situ Single Molecule Spectroscopy

Protein oligomerization and protein-protein interaction are crucial to regulate protein functions and biological processes. p73 protein is a very important transcriptional factor and can promote apoptosis and cell cycle arrest, and its transcriptional activity is regulated by p73 oligomerization and p73-MDM2 interaction. Although extracellular studies on p73 oligomerization and p73-MDM2 interaction have been carried out, it is unclear how p73 oligomerization and p73-MDM2 interaction occur in living cells. In our study, we described an in situ method for studying p73 oligomerization and p73-MDM2 interaction in living cells by combining fluorescence cross-correlation spectroscopy with a fluorescent protein labeling technique. Lentiviral transfection was used to transfect cells with a plasmid for either p73 or MDM2, each fused to a different fluorescent protein. p73 oligomerization was evaluated using brightness per particle, and the p73-MDM2 interaction was quantified using the cross-correlation value. We constructed a series of p73 mutants in three domains (transactivation domain, DNA binding domain, and oligomerization domain) and MDM2 mutants. We systematically studied p73 oligomerization and the effects of p73 oligomerization and the p73 and MDM2 structures on the p73-MDM2 interaction in single living cells. We have found that the p73 protein can form oligomers and that the p73 structure changes in the oligomerization domain significantly influence its oligomerization. p73 oligomerization and the structure changes significantly affect the p73-MDM2 interaction. Furthermore, the effects of inhibitors on p73 oligomerization and p73-MDM2 interaction were studied.

Comment on “Boosted molecular mobility during common chemical reactions”

The apparent “boosted mobility” observed by Wang et al. (Reports, 31 July 2020, p. 537) is the result of a known artifact. When signal intensities are changing during a nuclear magnetic resonance (NMR) diffusion measurement for reasons other than diffusion, the use of monotonically increasing gradient amplitudes produces erroneous diffusion coefficients. We show that no boosted molecular mobility is observed when shuffled gradient amplitudes are applied.

Selective analysis of newly synthesized proteins by combining fluorescence correlation spectroscopy with bioorthogonal non-canonical amino acid tagging

FCS with the BONCAT strategy is a promising approach for analysis of newly synthesized proteins and also be extended to further application for studying physiological or pathological processes related to proteins or other metabolic molecular changes.

Fundamentals and applications of enzyme powered micro/nano-motors

Micro/nanomotors (MNMs) are miniaturized machines that can convert many kinds of energy into mechanical motion. Over the past decades, a variety of driving mechanisms have been developed, which have greatly extended the application scenarios of MNMs. Enzymes exist in natural organisms which can convert chemical energy into mechanical force. It is an innovative attempt to utilize enzymes as biocatalyst providing driving force for MNMs. The fuels for enzymatic reactions are biofriendly as compared to traditional counterparts, which makes enzyme-powered micro/nanomotors (EMNMs) of great value in biomedical field for their nature of biocompatibility. Until now, EMNMs with various shapes can be propelled by catalase, urease and many others. Also, they can be endowed with multiple functionalities to accomplish on-demand tasks. Herein, combined with the development process of EMNMs, we are committed to present a comprehensive understanding of EMNMs, including their types, propelling principles, and potential applications. In this review, we will introduce single enzyme that can be used as motor, enzyme powered molecule motors and other micro/nano-architectures. The fundamental mechanism of energy conversion process of EMNMs and crucial factors that affect their movement behavior will be discussed. The current progress of proof-of-concept applications of EMNMs will also be elaborated in detail. At last, we will summarize and prospect the opportunities and challenges that EMNMs will face in their future development.

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Clear classification and description of different enzyme-powered micro/nanomotors (EMNMs).

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Discussion of the fundamental mechanism of energy conversion process of EMNMs and their movement influence factors.

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Introduction of the current progress of proof-of-concept applications of EMNMs.

Master curve of boosted diffusion for 10 catalytic enzymes

The literature is inconsistent regarding evidence for boosted molecular mobility during enzyme catalysis, a phenomenon that challenges the common tenet that enzyme mobility is governed solely by Brownian motion. This paper surveys 10 different catalytic enzymes and shows that magnitude of enhanced diffusion scales with energy release rate, the Gibbs free energy of reaction multiplied by the Michaelis–Menten reaction rate. A practical implication is that boosted effective diffusivity can be used to determine the energetics associated with enzyme action, since effective enzyme diffusivity is simply proportional to the change in free energy associated with the biochemical conversion. This master curve to predict the magnitude of boosted molecular mobility may be useful for estimating the effect in as-yet untested enzymes.

Molecular agitation more rapid than thermal Brownian motion is reported for cellular environments, motor proteins, synthetic molecular motors, enzymes, and common chemical reactions, yet that chemical activity coupled to molecular motion contrasts with generations of accumulated knowledge about diffusion at equilibrium. To test the limits of this idea, a critical testbed is the mobility of catalytically active enzymes. Sentiment is divided about the reality of enhanced enzyme diffusion, with evidence for and against. Here a master curve shows that the enzyme diffusion coefficient increases in proportion to the energy release rate—the product of Michaelis-Menten reaction rate and Gibbs free energy change (ΔG)—with a highly satisfactory correlation coefficient of 0.97. For 10 catalytic enzymes (urease, acetylcholinesterase, seven enzymes from the glucose cascade cycle, and one other), our measurements span from a roughly 40% enhanced diffusion coefficient at a high turnover rate and negative ΔG to no enhancement at a slow turnover rate and positive ΔG. Moreover, two independent measures of mobility show consistency, provided that one avoids undesirable fluorescence photophysics. The master curve presented here quantifies the limits of both ideas, that enzymes display enhanced diffusion and that they do not within instrumental resolution, and has possible implications for understanding enzyme mobility in cellular environments. The striking linear dependence of ΔG for the exergonic enzymes (ΔG <0), together with the vanishing effect for endergonic enzyme (ΔG >0), are consistent with a physical picture in which the mechanism boosting the diffusion is an active one, utilizing the available work from the chemical reaction.

Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments

Recent experiments have suggested that the energy released by a chemical reaction can propel its enzyme catalyst (for example, alkaline phosphatase). However, this topic remains controversial, partially due to the indirect and ensemble nature of existing measurements. Here, we used recently developed single-molecule approaches to monitor directly the motions of individual proteins in aqueous solution and find that single alkaline phosphatase enzymes do not diffuse faster under catalysis. Instead, we demonstrate that interactions between the fluorescent dye and the enzyme’s substrate can produce the signature of apparent diffusion enhancement in fluorescence correlation spectroscopy, the standard ensemble assay currently used to study enzyme diffusion and indicate that single-molecule approaches provide a more robust means to investigate diffusion at the nanoscale.

Theoretical and experimental observations that catalysis enhances the diffusion of enzymes have generated exciting implications about nanoscale energy flow, molecular chemotaxis, and self-powered nanomachines. However, contradictory claims on the origin, magnitude, and consequence of this phenomenon continue to arise. To date, experimental observations of catalysis-enhanced enzyme diffusion have relied almost exclusively on fluorescence correlation spectroscopy (FCS), a technique that provides only indirect, ensemble-averaged measurements of diffusion behavior. Here, using an anti-Brownian electrokinetic (ABEL) trap and in-solution single-particle tracking, we show that catalysis does not increase the diffusion of alkaline phosphatase (ALP) at the single-molecule level, in sharp contrast to the ∼20% enhancement seen in parallel FCS experiments using p-nitrophenyl phosphate (pNPP) as substrate. Combining comprehensive FCS controls, ABEL trap, surface-based single-molecule fluorescence, and Monte Carlo simulations, we establish that pNPP-induced dye blinking at the ∼10-ms timescale is responsible for the apparent diffusion enhancement seen in FCS. Our observations urge a crucial revisit of various experimental findings and theoretical models––including those of our own––in the field, and indicate that in-solution single-particle tracking and ABEL trap are more reliable means to investigate diffusion phenomena at the nanoscale.

Self-Propelled Micro/Nanomotors for On-Demand Biomedical Cargo Transportation

Micro/nanomotors (MNMs) are miniaturized machines that can perform assigned tasks at the micro/nanoscale. Over the past decade, significant progress has been made in the design, preparation, and applications of MNMs that are powered by converting different sources of energy into mechanical force, to realize active movement and fulfill on-demand tasks. MNMs can be navigated to desired locations with precise controllability based on different guidance mechanisms. A considerable research effort has gone into demonstrating that MNMs possess the potential of biomedical cargo loading, transportation, and targeted release to achieve therapeutic functions. Herein, the recent advances of self-propelled MNMs for on-demand biomedical cargo transportation, including their self-propulsion mechanisms, guidance strategies, as well as proof-of-concept studies for biological applications are presented. In addition, some of the major challenges and possible opportunities of MNMs are identified for future biomedical applications in the hope that it may inspire future research.

Cooperatively enhanced reactivity and "stabilitaxis" of dissociating oligomeric proteins

Many functional units in biology, such as enzymes or molecular motors, are composed of several subunits that can reversibly assemble and disassemble. This includes oligomeric proteins composed of several smaller monomers, as well as protein complexes assembled from a few proteins. By studying the generic spatial transport properties of such proteins, we investigate here whether their ability to reversibly associate and dissociate may confer on them a functional advantage with respect to nondissociating proteins. In uniform environments with position-independent association-dissociation, we find that enhanced diffusion in the monomeric state coupled to reassociation into the functional oligomeric form leads to enhanced reactivity with localized targets. In nonuniform environments with position-dependent association-dissociation, caused by, for example, spatial gradients of an inhibiting chemical, we find that dissociating proteins generically tend to accumulate in regions where they are most stable, a process that we term "stabilitaxis."

Visualization photofragmentation-induced rhodamine B release from gold nanorod delivery system by combination two-photon luminescence imaging with correlation spectroscopy

Plasmon-enhanced gold nanorod (AuNR) with high photothermal conversion efficiency is a promising light-controllable nanodrug delivery system for cancer therapy. Understanding the mechanism for the light-controllable drug release of AuNR delivery systems is important for the development of nanomedicine. In this study, the rhodamine B (RB) released from AuNR-RB nanodelivery system was quantitated and visualized by using two-photon luminescence (TPL) imaging combined with correlation spectroscopy. The photofragmentation of AuNR induced by femtosecond pulsed laser was revealed by TPL correlation spectroscopy when the laser energy was above the thermal damage threshold of AuNR, and the RB released from this nanodrug delivery system was visualized by TPL imaging. Furthermore, the photofragmentation-induced release of RB from AuNR-RB nanodelivery system was visualized in living MCF-7 breast cancer cells by TPL imaging combined with correlation spectroscopy. These results provided a novel optical approach to quantify the release of drugs from gold nanocarriers in complex biological media.

Enhanced Diffusion and Chemotaxis of Enzymes

Many enzymes appear to diffuse faster in the presence of substrate and to drift either up or down a concentration gradient of their substrate. Observations of these phenomena, termed enhanced enzyme diffusion (EED) and enzyme chemotaxis, respectively, lead to a novel view of enzymes as active matter. Enzyme chemotaxis and EED may be important in biology and could have practical applications in biotechnology and nanotechnology. They are also of considerable biophysical interest; indeed, their physical mechanisms are still quite uncertain. This review provides an analytic summary of experimental studies of these phenomena and of the mechanisms that have been proposed to explain them and offers a perspective on future directions for the field.

Self-Propulsion Strategies for Artificial Cell-Like Compartments

Reconstitution of life-like properties in artificial cells is a current research frontier in synthetic biology. Mimicking metabolism, growth, and sensing are active areas of investigation; however, achieving motility and directional taxis are also challenging in the context of artificial cells. To tackle this problem, recent progress has been made that leverages the tools of active matter physics in synthetic biology. This review surveys the most significant achievements in designing motile cell-like compartments. In this context, strategies for self-propulsion are summarized, including, compartmentalization of catalytically active particles, phoretic propulsion of vesicles and emulsion droplet motion driven by Marangoni flows. This work showcases how the realization of motile protocells may impact biomedical engineering while also aiming at answering fundamental questions in locomotion of prebiotic cells.

Robustness of FCS (Fluorescence Correlation Spectroscopy) with Quenchers Present

Inspired by recent publications doubtful of the FCS technique, we scrutinize how irreversible ("static") and reversible ("dynamic") quenching can influence the interpretation of such data. Textbook presentations often emphasize only how to analyze data in extremes, the absence of quenching or the presence of substantial quenching. Here, we consider intermediate cases where the assessment of photophysics (static quenching, blinking-like triplet-state relaxation) influence on autocorrelation curves can be delicate if dye-labeled objects diffuse on comparably rapid time scales. We used the amino acid, tryptophan, as the quencher. As our example of small-molecule dye that diffuses rapidly, we mix the quencher with the fluorescence dye, Alexa 488. The translational diffusion coefficient, inferred from fit to the standard one-component Fickian diffusion model, speeds up without the loss of quality of fit, but quenching is reflected in the fact that the data become exceptionally noisy. This reflects the bidisperse population of quenched and unquenched dyes when the time scales overlap between the processes of translational diffusion, quenching, and blinking. As our example of the large-molecule dye-labeled object that diffuses relatively slowly, we mixed the quencher with dye-labeled BSA, bovine serum albumin. Diffusion, static quenching, and blinking time scales are now separated. In spite of quenching contribution to the autocorrelation function when the delay time is relatively short, the inferred translational diffusion coefficient now depends weakly on the presence of a quencher. We conclude that when the diffusing molecule is substantially slower to diffuse than the time scale of photophysical processes of the fluorescent dye to which it is attached, the influence of quenching is self-evident and the FCS autocorrelation curves give an appropriate diffusion coefficient if correct fitting functions are chosen in the analysis.

Direct Single Molecule Imaging of Enhanced Enzyme Diffusion

Recent experimental results have shown that enzymes can diffuse faster when they are in the presence of their reactants (substrate). This faster diffusion has been termed enhanced diffusion. Fluorescence correlation spectroscopy (FCS), which has been employed as the only method to make these measurements, relies on analyzing the fluctuations in fluorescence intensity to measure the diffusion coefficient of particles. Recently, artifacts in FCS measurements due to its sensitivity to environmental conditions have been evaluated, calling prior enhanced diffusion results into question. It behooves us to adopt complementary and direct methods to measure the mobility of enzymes. Herein, we use a technique of direct single molecule imaging to observe the diffusion of individual enzymes in solution. This technique is less sensitive to intensity fluctuations and deduces the diffusion coefficient directly based on the trajectory of the enzyme. Our measurements recapitulate that enzyme diffusion is enhanced in the presence of its substrate and find that the relative increase in diffusion of a single enzyme is even higher than those previously reported using FCS. We also use this complementary method to test if the total enzyme concentration affects the relative increase in diffusion and if the enzyme oligomerization state changes during its catalytic turnover. We find that the diffusion increase is independent of the total concentration of enzymes and the presence of substrate does not change the oligomerization state of enzymes.

Motility of Enzyme-Powered Vesicles

Autonomous nanovehicles powered by energy derived from chemical catalysis have potential applications as active delivery agents. For in vivo applications, it is necessary that the engine and its fuel, as well as the chassis itself, be biocompatible. Enzyme molecules have been shown to display enhanced motility through substrate turnover and are attractive candidates as engines; phospholipid vesicles are biocompatible and can serve as cargo containers. Herein, we describe the autonomous movement of vesicles with membrane-bound enzymes in the presence of the substrate. We find that the motility of the vesicles increases with increasing enzymatic turnover rate. The enhanced diffusion of these enzyme-powered systems was further substantiated in real time by tracking the motion of the vesicles using optical microscopy. The membrane-bound protocells that move by transducing chemical energy into mechanical motion serve as models for motile living cells and are key to the elucidation of the fundamental mechanisms governing active membrane dynamics and cellular movement.

Theory of Nonequilibrium Free Energy Transduction by Molecular Machines

Biomolecular machines are protein complexes that convert between different forms of free energy. They are utilized in nature to accomplish many cellular tasks. As isothermal nonequilibrium stochastic objects at low Reynolds number, they face a distinct set of challenges compared with more familiar human-engineered macroscopic machines. Here we review central questions in their performance as free energy transducers, outline theoretical and modeling approaches to understand these questions, identify both physical limits on their operational characteristics and design principles for improving performance, and discuss emerging areas of research.

Enhanced Diffusion of Catalytically Active Enzymes

The past decade has seen an increasing number of investigations into enhanced diffusion of catalytically active enzymes. These studies suggested that enzymes are actively propelled as they catalyze reactions or bind with ligands (e.g., substrates or inhibitors). In this Outlook, we chronologically summarize and discuss the experimental observations and theoretical interpretations and emphasize the potential contradictions in these efforts. We point out that the existing multimeric forms of enzymes or isozymes may cause artifacts in measurements and that the conformational changes upon substrate binding are usually not sufficient to give rise to a diffusion enhancement greater than 30%. Therefore, more rigorous experiments and a more comprehensive theory are urgently needed to quantitatively validate and describe the enhanced enzyme diffusion.

A Thermodynamic Limit on the Role of Self-Propulsion in Enhanced Enzyme Diffusion

A number of enzymes reportedly exhibit enhanced diffusion in the presence of their substrates, with a Michaelis-Menten-like concentration dependence. Although no definite explanation of this phenomenon has emerged, a physical picture of enzyme self-propulsion using energy from the catalyzed reaction has been widely considered. Here, we present a kinematic and thermodynamic analysis of enzyme self-propulsion that is independent of any specific propulsion mechanism. Using this theory, along with biophysical data compiled for all enzymes so far shown to undergo enhanced diffusion, we show that the propulsion speed required to generate experimental levels of enhanced diffusion exceeds the speeds of well-known active biomolecules, such as myosin, by several orders of magnitude. Furthermore, the minimal power dissipation required to account for enzyme enhanced diffusion by self-propulsion markedly exceeds the chemical power available from enzyme-catalyzed reactions. Alternative explanations for the observation of enhanced enzyme diffusion therefore merit stronger consideration.

Absolute diffusion measurements of active enzyme solutions by NMR

The diffusion of enzymes is of fundamental importance for many biochemical processes. Enhanced or directed enzyme diffusion can alter the accessibility of substrates and the organization of enzymes within cells. Several studies based on fluorescence correlation spectroscopy report enhanced diffusion of enzymes upon interaction with their substrate or inhibitor. In this context, major importance is given to the enzyme fructose-bisphosphate aldolase, for which enhanced diffusion has been reported even though the catalysed reaction is endothermic. Additionally, enhanced diffusion of tracer particles surrounding the active aldolase enzymes has been reported. These studies suggest that active enzymes can act as chemical motors that self-propel and give rise to enhanced diffusion. However, fluorescence studies of enzymes can, despite several advantages, suffer from artefacts. Here, we show that the absolute diffusion coefficients of active enzyme solutions can be determined with Pulsed Field Gradient Nuclear Magnetic Resonance (PFG-NMR). The advantage of PFG-NMR is that the motion of the molecule of interest is directly observed in its native state without the need for any labelling. Furthermore, PFG-NMR is model-free and thus yields absolute diffusion constants. Our PFG-NMR experiments of solutions containing active fructose-bisphosphate aldolase from rabbit muscle do not show any diffusion enhancement for the active enzymes, nor the surrounding molecules. Additionally, we do not observe any diffusion enhancement of aldolase in the presence of its inhibitor pyrophosphate.