Ultrathin 2D-MOFs for dual-enzyme cascade biocatalysis with sensitive glucose detection performances

In recent years, two-dimensional nanosheet metal-organic frameworks (2D MOFs) have been widely considered as promising carriers for enzyme immobilization owing to their large surface area, designable and tunable structures, and other properties that enhance enzyme loading and modulate interactions with enzymes. In this study, a series of ultrathin 2D M-TCPP (M = Co, Ni, Zn, Cu) nanosheets were synthesized employing a surfactant-assisted bottom-up approach, and the effect of solvent ratio on the morphology and properties of 2D MOFs was explored. After systematic characterization, Cu-based 2D MOFs with large specific surface areas and excellent water stability was selected as the carrier for the co-immobilization of glucose oxidase (GOx) and horseradish peroxidase (HRP). The effects of adsorption and covalent immobilization strategies on bis-enzyme loading and enzyme activity, as well as their applications in rapid glucose detection, were systematically investigated. The results showed that A-CTGH and C-CTGH owned enzyme loadings of 187.9 and 249.1 mg/g, respectively, and exhibited superior enzymatic activity when exposed to harsh environments compared to free enzymes. In addition, the covalently immobilized biocatalyst based on GOx demonstrated a more sensitive glucose detection performance, including a wide linear range from 5.0 to 16 μM with a detection limit of 0.6 μM.

Electrochemical Zero-Mode Waveguide Potential-Dependent Fluorescence of Glutathione Reductase at Single-Molecule Occupancy

Understanding functional states of individual redox enzymes is important because electron-transfer reactions are fundamental to life, and single-enzyme molecules exhibit molecule-to-molecule heterogeneity in their properties, such as catalytic activity. Zero-mode waveguides (ZMW) constitute a powerful tool for single-molecule studies, enabling investigations of binding reactions up to the micromolar range due to the ability to trap electromagnetic radiation in zeptoliter-scale observation volumes. Here, we report the potential-dependent fluorescence dynamics of single glutathione reductase (GR) molecules using a bimodal electrochemical ZMW (E-ZMW), where a single-ring electrode embedded in each of the nanopores of an E-ZMW array simultaneously serves to control electrochemical potential and to confine optical radiation within the nanopores. Here, the redox state of GR is manipulated using an external potential control of the Au electrode in the presence of a redox mediator, methyl viologen (MV). Redox-state transitions in GR are monitored by correlating electrochemical and spectroscopic signals from freely diffusing MV/GR in 60 zL effective observation volumes at single GR molecule average pore occupancy, ⟨n⟩ ∼ 0.8. Fluorescence intensities decrease (increase) at reducing (oxidizing) potentials for MV due to the MV-mediated control of the GR redox state. The spectroelectrochemical response of GR to the enzyme substrate, i.e., glutathione disulfide (GSSG), shows that GSSG promotes GR oxidation via enzymatic reduction. The capabilities of E-ZMWs to probe spectroelectrochemical phenomena in zL-scale-confined environments show great promise for the study of single-enzyme reactions and can be extended to important technological applications, such as those in molecular diagnostics.

Non-Markovian intracellular transport with sub-diffusion and run-length dependent detachment rate

Intracellular transport of organelles is fundamental to cell function and health. The mounting evidence suggests that this transport is in fact anomalous. However, the reasons for the anomaly is still under debate. We examined experimental trajectories of organelles inside a living cell and propose a mathematical model that describes the previously reported transition from sub-diffusive to super-diffusive motion. In order to explain super-diffusive behaviour at long times, we introduce non-Markovian detachment kinetics of the cargo: the rate of detachment is inversely proportional to the time since the last attachment. Recently, we observed the non-Markovian detachment rate experimentally in eukaryotic cells. Here we further discuss different scenarios of how this effective non-Markovian detachment rate could arise. The non-Markovian model is successful in simultaneously describing the time averaged variance (the time averaged mean squared displacement corrected for directed motion), the mean first passage time of trajectories and the multiple peaks observed in the distributions of cargo velocities. We argue that non-Markovian kinetics could be biologically beneficial compared to the Markovian kinetics commonly used for modelling, by increasing the average distance the cargoes travel when a microtubule is blocked by other filaments. In turn, sub-diffusion allows cargoes to reach neighbouring filaments with higher probability, which promotes active motion along the microtubules.

Plasmon-Enhanced Single-Molecule Enzymology

We present a numerical study on plasmon-enhanced single-molecule enzymology. We combine Brownian dynamics and electromagnetic simulations to calculate the enhancement of fluorescence signals of fluorogenic substrate converted by an enzyme conjugated to a plasmonic particle. We simulate the Brownian motion of a fluorescent product away from the active site of the enzyme, and calculate the photon detection rate taking into account modifications of the excitation and emission processes by coupling to the plasmon. We show that plasmon enhancement can boost the signal-to-noise ratio (SNR) of single turnovers by up to 100 fold compared to confocal microscopy. This enhancement factor is a trade-off between the reduced residence time in the near-field of the particle, and the enhanced emission intensity due to coupling to the plasmon. The enhancement depends on the size, shape and material of the particle and the photophysical properties of the fluorescent product. Our study provides guidelines on how to enhance the SNR of single-molecule enzyme studies and may aid in further understanding and quantifying static and dynamic heterogeneity.

Slow domain reconfiguration causes power-law kinetics in a two-state enzyme

Protein dynamics are typically captured well by rate equations that predict exponential decays for two-state reactions. Here, we describe a remarkable exception. The electron-transfer enzyme quiescin sulfhydryl oxidase (QSOX), a natural fusion of two functionally distinct domains, switches between open- and closed-domain arrangements with apparent power-law kinetics. Using single-molecule FRET experiments on time scales from nanoseconds to milliseconds, we show that the unusual open-close kinetics results from slow sampling of an ensemble of disordered domain orientations. While substrate accelerates the kinetics, thus suggesting a substrate-induced switch to an alternative free energy landscape of the enzyme, the power-law behavior is also preserved upon electron load. Our results show that the slow sampling of open conformers is caused by a variety of interdomain interactions that imply a rugged free energy landscape, thus providing a generic mechanism for dynamic disorder in multidomain enzymes.

Shedding light on protein folding, structural and functional dynamics by single molecule studies

The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.

DNA replication at the single-molecule level

A cell can be thought of as a highly sophisticated micro factory: in a pool of billions of molecules - metabolites, structural proteins, enzymes, oligonucleotides - multi-subunit complexes assemble to perform a large number of basic cellular tasks, such as DNA replication, RNA/protein synthesis or intracellular transport. By purifying single components and using them to reconstitute molecular processes in a test tube, researchers have gathered crucial knowledge about mechanistic, dynamic and structural properties of biochemical pathways. However, to sort this information into an accurate cellular road map, we need to understand reactions in their relevant context within the cellular hierarchy, which is at the individual molecule level within a crowded, cellular environment. Reactions occur in a stochastic fashion, have short-lived and not necessarily well-defined intermediates, and dynamically form functional entities. With the use of single-molecule techniques these steps can be followed and detailed kinetic information that otherwise would be hidden in ensemble averaging can be obtained. One of the first complex cellular tasks that have been studied at the single-molecule level is the replication of DNA. The replisome, the multi-protein machinery responsible for copying DNA, is built from a large number of proteins that function together in an intricate and efficient fashion allowing the complex to tolerate DNA damage, roadblocks or fluctuations in subunit concentration. In this review, we summarize advances in single-molecule studies, both in vitro and in vivo, that have contributed to our current knowledge of the mechanistic principles underlying DNA replication.

Enzyme molecules in solitary confinement

Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.

INSIGHTS IN ENZYME FUNCTIONAL DYNAMICS AND ACTIVITY REGULATION BY SINGLE MOLECULE STUDIES

The advent of advanced single molecule measurements heralded the arrival of a wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways not deducible by conventional bulk assays. They offered the direct observation and quantification of the abundance and life time of multiple states and transient intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements, thus providing unprecedented insights into complex biological processes. Here we survey the current state of the art in single-molecule fluorescence microscopy methodology for studying the mechanism of enzymatic activity and the insights on protein functional dynamics. We will initially discuss the strategies employed to date, their limitations and possible ways to overcome them, and finally how single enzyme kinetics can advance our understanding on mechanisms underlying function and regulation of proteins.

[Formula: see text]Special Issue Comment: This review focuses on functional dynamics of individual enzymes and is related to the review on ion channels by Lu,44 the reviews on mathematical treatment of Flomenbom45 and Sach et al.,46 and review on FRET by Ruedas-Rama et al.41

Bacterial Enzyme Responsive Polymersomes: A Closer Look at the Degradation Mechanism of PEG-block-PLA Vesicles

Stimuli-responsive polymersomes that are selectively cleaved by enzymes of pathogenic bacteria are herein reported. The local disruption of the polyester wall in poly(ethylene glycol)-block-poly(lactic acid) (PEG-b-PLA) polymersomes filled with reporter dyes owing to enzymatic degradation by proteinase K was monitored by fluorescence lifetime imaging microscopy. Capsule opening occurred on timescales of minutes to hours, leading to the release of the dye, followed by a slow capsule disintegration, and finally cleavage into monomeric lactic acid over several weeks. These nanocontainers represent a promising element in novel theranostic systems for potential application in advanced wound dressings.

Single-molecule FRET studies of RNA folding: a Diels-Alderase ribozyme with photolabile nucleotide modifications

Enzymology at the single-molecule level by using fluorescence resonance energy transfer (smFRET) offers unprecedented insight into mechanistic aspects of catalytic reactions. Implementing spatiotemporal control of the reaction by using an external trigger is highly valuable in these challenging experiments. Here, we have incorporated a light-cleavable caging moiety into specific nucleotides of the Diels-Alderase (DAse) ribozyme. In this way, the folding energy landscape was significantly perturbed, and the catalytic activity was essentially suppressed. A careful smFRET efficiency histogram analysis at various Mg(2+) ion concentrations revealed an additional intermediate state that is not observed for the unmodified DAse ribozyme. We also observed that only a fraction of DAse molecules returns to the native state upon cleavage of the caged group by UV light. These constructs are attractive model RNA systems for further real-time single-molecule observation of the coupling between conformational changes and catalytic activity.

Allosteric inhibition of individual enzyme molecules trapped in lipid vesicles

Enzymatic inhibition by product molecules is an important and widespread phenomenon. We describe an approach to study product inhibition at the single-molecule level. Individual HRP molecules are trapped within surface-tethered lipid vesicles, and their reaction with a fluorogenic substrate is probed. While the substrate readily penetrates into the vesicles, the charged product (resorufin) gets trapped and accumulates inside the vesicles. Surprisingly, individual enzyme molecules are found to stall when a few tens of product molecules accumulate. Bulk enzymology experiments verify that the enzyme is noncompetitively inhibited by resorufin. The initial reaction velocity of individual enzyme molecules and the number of product molecules required for their complete inhibition are broadly distributed and dynamically disordered. The two seemingly unrelated parameters, however, are found to be substantially correlated with each other in each enzyme molecule and over long times. These results suggest that, as a way to counter disorder, enzymes have evolved the means to correlate fluctuations at structurally distinct functional sites.

Metallic-Nanostructure-Enhanced Fluorescence of Single Flavin Cofactor and Single Flavoenzyme Molecules

The enzyme cofactors are intrinsically fluorescent and participate directly in the single molecule enzymology studies. Due to photobleaching, one cannot follow kinetics continuously by cofactor fluorescence for more than several minutes typically. Modification of spectral properties of fluorophores, such as the amplification of emission intensity, can be achieved through coupling with surface plasmons in close proximity to metallic nanostructures. This process, referred to as metal-enhanced fluorescence, offers promise for a range of applications, including bioassays, sensor technology, microarrays, and single-molecule studies. Here, we demonstrated up to a 100-fold increase in the emission of the single cofactors and flavoenzymes near silver nanostructures. Amplified fluorescence of different types of flavins and flavoenzymes has been interpreted by using time-resolved single molecule fluorescence data. The results show considerable promise for the studies of enzyme kinetics using the intrinsic fluorescence from the cofactors.

Exploring both sequence detection and restriction endonuclease cleavage kinetics by recognition site via single-molecule microfluidic trapping

We demonstrate the feasibility of a single-molecule microfluidic approach to both sequence detection and obtaining kinetic information for restriction endonucleases on dsDNA. In this method, a microfluidic stagnation point flow is designed to trap, hold, and linearize double-stranded (ds) genomic DNA to which a restriction endonuclease has been pre-bound sequence-specifically. By introducing the cofactor magnesium, we determine the binding location of the enzyme by the cleavage process of dsDNA as in optical restriction mapping, however here the DNA need not be immobilized on a surface. We note that no special labeling of the enzyme is required, which makes it simpler than our previous scheme using stagnation point flows for sequence detection. Our accuracy in determining the location of the recognition site is comparable to or better than other single molecule techniques due to the fidelity with which we can control the linearization of the DNA molecules. In addition, since the cleavage process can be followed in real time, information about the cleavage kinetics, and subtle differences in binding and cleavage frequencies among the recognition sites, may also be obtained. Data for the five recognition sites for the type II restriction endonuclease EcoRI on λ-DNA are presented as a model system. While the roles of the varying fluid velocity and tension along the chain backbone on the measured kinetics remain to be determined, we believe this new method holds promise for a broad range of studies of DNA-protein interactions, including the kinetics of other DNA cleavage processes, the dissociation of a restriction enzyme from the cleaved substrate, and other macromolecular cleavage processes.