Controlling Redox Enzyme Orientation at Planar Electrodes

Use of genomics & proteomics in studying lipase producing microorganisms & its application

In biotechnological applications, lipases are recognized as the most widely utilized and versatile enzymes, pivotal in biocatalytic processes, predominantly produced by various microbial species. Utilizing omics technology, natural sources can be meticulously screened to find microbial flora which are responsible for oil production. Lipases are versatile biocatalysts. They are used in a variety of bioconversion reactions and are receiving a lot of attention because of the quick development of enzyme technology and its usefulness in industrial operations. This article offers recent insights into microbial lipase sources, including fungi, bacteria, and yeast, alongside traditional and modern methods of purification such as precipitation, immunopurification and chromatographic separation. Additionally, it explores innovative methods like the reversed micellar system, aqueous two-phase system (ATPS), and aqueous two-phase flotation (ATPF). The article deals with the use of microbial lipases in a variety of sectors, including the food, textile, leather, cosmetics, paper, detergent, while also critically analyzing lipase-producing microbes. Moreover, it highlights the role of lipases in biosensors, biodiesel production, tea processing, bioremediation, and racemization. This review provides the concept of the use of omics technique in the mechanism of screening of microbial species those are capable of producing lipase and also find the potential applications.

Adsorption of cytochrome c on different self-assembled monolayers: The role of surface chemistry and charge density

In this work, the adsorption behavior of cytochrome c (Cyt-c) on five different self-assembled monolayers (SAMs) (i.e., CH3-SAM, OH-SAM, NH2-SAM, COOH-SAM, and OSO3--SAM) was studied by combined parallel tempering Monte Carlo and molecular dynamics simulations. The results show that Cyt-c binds to the CH3-SAM through a hydrophobic patch (especially Ile81) and undergoes a slight reorientation, while the adsorption on the OH-SAM is relatively weak. Cyt-c cannot stably bind to the lower surface charge density (SCD, 7% protonation) NH2-SAM even under a relatively high ionic strength condition, while a higher SCD of 25% protonation promotes Cyt-c adsorption on the NH2-SAM. The preferred adsorption orientations of Cyt-c on the negatively-charged surfaces are very similar, regardless of the surface chemistry and the SCD. As the SCD increases, more counterions are attracted to the charged surfaces, forming distinct counterion layers. The secondary structure of Cyt-c is well kept when adsorbed on these SAMs except the OSO3--SAM surface. The deactivation of redox properties for Cyt-c adsorbed on the highly negatively-charged surface is due to the confinement of heme reorientation and the farther position of the central iron to the surfaces, as well as the relatively larger conformation change of Cyt-c adsorbed on the OSO3--SAM surface. This work may provide insightful guidance for the design of Cyt-c-based bioelectronic devices and controlled enzyme immobilization.

Ultrathin Film Antimony-Doped Tin Oxide Prevents [NiFe] Hydrogenase Inactivation at High Electrode Potentials

For hydrogenases to serve as effective electrocatalysts in hydrogen biotechnological devices, such as enzymatic fuel cells, it is imperative to design electrodes that facilitate stable and functional enzyme immobilization, efficient substrate accessibility, and effective interfacial electron transfer. Recent years have seen considerable advancements in this area, particularly concerning hydrogenases. However, a significant limitation remains: the inactivation of hydrogenases at high oxidative potentials across most developed electrodes. Addressing this issue necessitates a thorough understanding of the interactions between the enzyme and the electrode surface. In this study, we employ ATR-IR spectroscopy combined with electrochemistry in situ to investigate the interaction mechanisms, electrocatalytic behavior, and stability of the oxygen-tolerant membrane-bound [NiFe] hydrogenase from Cupriavidus necator (MBH), which features a His-tag on its small subunit C-terminus. Antimony-doped tin oxide (ATO) thin films were selected as electrodes due to their protein compatibility, suitable potential window, conductivity, and transparency, making them an ideal platform for spectroelectrochemical measurements. Our comprehensive examination of the physiological and electrochemical processes of [NiFe] MBH on ATO thin film electrodes demonstrates that by tuning the electron transport properties of the ATO thin film, we can prevent MBH inactivation at extended oxidative potentials while maintaining direct electron transfer between the enzyme and the electrode.

Emerging Trends of Bilirubin Oxidases at the Bioelectrochemical Interface: Paving the Way for Self-Powered Electrochemical Devices and Biosensors

Bilirubin oxidases (BODs) [EC 1.3.3.5 - bilirubin: oxygen oxido-reductase] are enzymes that belong to the multicopper oxidase family and can oxidize bilirubin, diphenols, and aryl amines and reduce the oxygen by direct four-electron transfer from the electrode with almost no electrochemical overpotential. Therefore, BOD is a promising bioelectrocatalyst for (self-powered) biosensors and/or enzymatic fuel cells. The advantages of electrochemically active BOD enzymes include selective biosensing, biocatalysis for efficient energy conversion, and electrosynthesis. Owing to the rise in publications and patents, as well as the expanding interest in BODs for a range of physiological conditions, this Review analyzes scientific literature reports on BOD enzymes and current hypotheses on their bioelectrocatalysis. This Review evaluates the specific research outcomes of the BOD in enzyme (protein) engineering, immobilization strategies, and challenges along with their bioelectrochemical properties, limitations, and applications in the fields of (i) biosensors, (ii) self-powered biosensors, and (iii) biofuel cells for powering bioelectronics.

Biofluid-Activated Biofuel Cells, Batteries, and Supercapacitors: A Comprehensive Review

Recent developments in wearable and implanted devices have resulted in numerous, unprecedented capabilities that generate increasingly detailed information about a user's health or provide targeted therapy. However, options for powering such systems remain limited to conventional batteries which are large and have toxic components and as such are not suitable for close integration with the human body. This work provides an in-depth overview of biofluid-activated electrochemical energy devices, an emerging class of energy sources judiciously designed for biomedical applications. These unconventional energy devices are composed of biocompatible materials that harness the inherent chemistries of various biofluids to produce useable electrical energy. This work covers examples of such biofluid-activated energy devices in the form of biofuel cells, batteries, and supercapacitors. Advances in materials, design engineering, and biotechnology that form the basis for high-performance, biofluid-activated energy devices are discussed. Innovations in hybrid manufacturing and heterogeneous integration of device components to maximize power output are also included. Finally, key challenges and future scopes of this nascent field are provided.

Electrochemistry in sensing of molecular interactions of proteins and their behavior in an electric field

Electrochemical methods can be used not only for the sensitive analysis of proteins but also for deeper research into their structure, transport functions (transfer of electrons and protons), and sensing their interactions with soft and solid surfaces. Last but not least, electrochemical tools are useful for investigating the effect of an electric field on protein structure, the direct application of electrochemical methods for controlling protein function, or the micromanipulation of supramolecular protein structures. There are many experimental arrangements (modalities), from the classic configuration that works with an electrochemical cell to miniaturized electrochemical sensors and microchip platforms. The support of computational chemistry methods which appropriately complement the interpretation framework of experimental results is also important. This text describes recent directions in electrochemical methods for the determination of proteins and briefly summarizes available methodologies for the selective labeling of proteins using redox-active probes. Attention is also paid to the theoretical aspects of electron transport and the effect of an external electric field on the structure of selected proteins. Instead of providing a comprehensive overview, we aim to highlight areas of interest that have not been summarized recently, but, at the same time, represent current trends in the field.

Synthetic styrene-based bioinspired model of the [FeFe]-hydrogenase active site for electrocatalytic hydrogen evolution

Integration of molecular catalysts inside polymeric scaffolds has gained substantial attention over the past decade, as it provides a path towards generating systems with enhanced stability as well as enzyme-like morphologies and properties. In the context of solar fuels research and chemical energy conversion, this approach has been found to improve both rates and energy efficiencies of a range of catalytic reactions. However, system performance still needs to be improved to reach technologically relevant currents and stability, parameters that are heavily influenced by the nature of the incorporated molecular catalyst. Here, we have focused on the integration of a biomimetic {Fe2(μ-adt)(CO)6} (-CH2NHCH2S-, azadithiolate or adt2-) based active site ("[2Fe2S]adt"), inspired by the catalytic cofactor of [FeFe] hydrogenases, within a synthetic polymeric scaffold using free radical polymerization. The resulting metallopolymers [2Fe2S]adtk[DMAEMA]l[PyBMA]m (DMAEMA = dimethylaminoethyl methacrylate as water soluble monomer; PyBMA = 4-(pyren-1-yl)-butyl methacrylate as hydrophobic anchor for heterogenization) were found to be active for electrochemical H2 production in neutral aqueous media. The pyrene content was varied to optimize durability and activity. Following immobilization on multiwalled carbon nanotubes (MWNT) the most active metallopolymer, containing ∼2.3 mol% of PyBMA, could reach a turnover number for hydrogen production (TONH2) of ∼0.4 ×105 over 20 hours of electrolysis at an overpotential of 0.49 V, two orders of magnitude higher than the isolated catalyst counterpart. The study provides a synthetic methodology for incorporating catalytic units featuring second coordination sphere functional groups, and highlights the benefit of the confinement within the polymer matrix for catalytic performance.

Immobilization of Enzyme Electrochemical Biosensors and Their Application to Food Bioprocess Monitoring

Electrochemical biosensors based on immobilized enzymes are among the most popular and commercially successful biosensors. The literature in this field suggests that modification of electrodes with nanomaterials is an excellent method for enzyme immobilization, which can greatly improve the stability and sensitivity of the sensor. However, the poor stability, weak reproducibility, and limited lifetime of the enzyme itself still limit the requirements for the development of enzyme electrochemical biosensors for food production process monitoring. Therefore, constructing sensing technologies based on enzyme electrochemical biosensors remains a great challenge. This article outlines the construction principles of four generations of enzyme electrochemical biosensors and discusses the applications of single-enzyme systems, multi-enzyme systems, and nano-enzyme systems developed based on these principles. The article further describes methods to improve enzyme immobilization by combining different types of nanomaterials such as metals and their oxides, graphene-related materials, metal-organic frameworks, carbon nanotubes, and conducting polymers. In addition, the article highlights the challenges and future trends of enzyme electrochemical biosensors, providing theoretical support and future perspectives for further research and development of high-performance enzyme chemical biosensors.

DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion

The elucidation of structural interfaces between proteins and inorganic surfaces is a crucial aspect of bionanotechnology development. Despite its significance, the interfacial structures between proteins and metallic surfaces are yet to be fully understood, and the lack of experimental investigation has impeded the development of many devices. To overcome this limitation, we suggest considering the generation of protein/surface structures as a molecular docking problem with a homogenous plan as the target. To this extent, we propose a new software, DockSurf, which aims to quickly propose reliable protein/surface structures. Our approach considers the conformational exploration with Euler's angles, which provide a cartography instead of a unique structure. Interaction energies were derived from quantum mechanics computations for a set of small molecules that describe protein atom types and implemented in a Derjaguin, Landau, Verwey, and Overbeek potential for the consideration of large systems such as proteins. The validation of DockSurf software was conducted with molecular dynamics for corona proteins with gold surfaces and provided enthusiastic results. This software is implemented in the RPBS platform to facilitate widespread access to the scientific community.

Molecular Insights of Cellobiose Dehydrogenase Adsorption on Self-Assembled Monolayers

Cellobiose dehydrogenase (CDH) is capable of direct electron transfer (DET) on electrodes and is a promising redox enzyme for bioelectrochemical applications. Its unique two-domain structure makes the function of CDH adsorbed on the surface of the electrode deeply affected by the external environment, such as ion species, strength, pH, and surface charge density. To date, however, the exact mechanism of how the external environment tailors the structure and dynamics of CDH adsorbed on the electrode surface still remains poorly understood. Here, multiscale simulations were performed to look for insight into the effect of Na⁺ and Ca²⁺ ions on the activation of CDH on oppositely charged self-assembled monolayer (NH₂-SAM and COOH-SAM) surfaces with different surface charge densities (SCDs). Both Na⁺ and Ca²⁺ can promote CDH conformation switch from the open state to the closed state, while the promotion effect of Ca²⁺ is stronger than that of Na⁺ at the same conditions. However, the high ionic strength (IS) of Ca²⁺ renders the cytochrome (CYT) domain of CDH away from the NH₂-SAM with low SCD. In contrast, whatever the IS, the NH₂-SAM surface with high SCD can not only enhance the CYT-surface interaction but also achieve a closed-state conformation due to a similar role of Ca²⁺. Overall, this study gains molecular-level insights into the role of ion species and surface charge in modulating the structure and conformation of CDH on the SAM surface, thereby tailoring its activity.

Hierarchically-structured laccase@Ni3(PO4)2 hybrid nanoflowers for antibiotic degradation: Application in real wastewater effluent and toxicity evaluation

Laccase@Ni₃(PO₄)₂ hybrid nanoflowers (HNFs) were prepared by the anisotropic growth of biomineralized nickel phosphate. The immobilization yield was 77.5 ± 3.6 %, and the immobilized enzyme retained 50 % of its initial activity after 18 reusability cycles. The immobilized and free enzymes lost 80 % of their activity after 18 and 6 h incubation in municipal wastewater effluent (MWWE), respectively. The increase in α-helix content (8 %) following immobilization led to a more rigid enzyme structure, potentially contributing to its improved stability. The removal of ciprofloxacin from MWWE by laccase@Ni₃(PO₄)₂·HNFs/p-coumaric acid oxidation system was optimized using a Box-Behnken design. Under the optimized conditions [initial laccase activity (0.05 U mL^-1), the concentration of p-coumaric acid (2.9 mM), and treatment time (4.9 h)], the biocatalyst removed 90 % of ciprofloxacin (10 mg L^-1) from MWWE. The toxicity of ciprofloxacin against some G⁺ and G^- bacteria was reduced by 35-70 %, depending on their strain. The EC₅₀ of ciprofloxacin for the alga Raphidocelis subcapitata reduced from 3.08 to 1.07 mg L^-1 (p-value <0.05) after the bioremoval. Also, the acute and chronic toxicity of identified biodegradation products was lower than ciprofloxacin at three trophic levels, as predicted by ECOSAR software.

Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator

Comprising at least a bipartite architecture, the large subunit of [NiFe]-hydrogenase harbors the catalytic nickel-iron site while the small subunit houses an array of electron-transferring Fe-S clusters. Recently, some [NiFe]-hydrogenase large subunits have been isolated showing an intact and redox active catalytic cofactor. In this computational study we have investigated one of these metalloproteins, namely the large subunit HoxG of the membrane-bound hydrogenase from Cupriavidus necator (CnMBH), targeting its conformational and mechanical stability using molecular modelling and long all-atom Gaussian accelerated molecular dynamics (GaMD). Our simulations predict that isolated HoxG is stable in aqueous solution and preserves a large portion of its mechanical properties, but loses rigidity in regions around the active site, in contrast to the MBH heterodimer. Inspired by biochemical data showing dimerization of the HoxG protein and IR measurements revealing an increased stability of the [NiFe] cofactor in protein preparations with higher dimer content, corresponding simulations of homodimeric forms were also undertaken. While the monomeric subunit contains several flexible regions, our data predicts a regained rigidity in homodimer models. Furthermore, we computed the electrostatic properties of models obtained by enhanced sampling with GaMD, which displays a significant amount of positive charge at the protein surface, especially in solvent-exposed former dimer interfaces. These data offer novel insights on the way the [NiFe] core is protected from de-assembly and provide hints for enzyme anchoring to surfaces, which is essential information for further investigations on these minimal enzymes.

Gold Nanoparticles Are an Immobilization Platform for Active and Stable Acetylcholinesterase: Demonstration of a General Surface Protein Functionalization Strategy

Immobilizing enzymes onto abiological surfaces is a key step for developing protein-based technologies that can be useful for applications such as biosensors and biofuel cells. A central impediment for the advancement of this effort is a lack of generalizable strategies for functionalizing surfaces with proteins in ways that prevent unfolding, aggregation, and uncontrolled binding, requiring surface chemistries to be developed for each surface-enzyme pair of interest. In this work, we demonstrate a significant advancement toward addressing this problem using a gold nanoparticle (AuNP) as an initial scaffold for the chemical bonding of the enzyme acetylcholinesterase (AChE), forming the conjugate AuNP-AChE. This can then be placed onto chemically and structurally distinct surfaces (e.g., metals, semiconductors, plastics, etc.), thereby bypassing the need to develop surface functionalization strategies for every substrate or condition of interest. Carbodiimide crosslinker chemistry was used to bind surface lysine residues in AChE to AuNPs functionalized with ligands containing carboxylic acid tails. Using amino acid analysis, we found that on average, 3.3 ± 0.1 AChE proteins were bound per 5.22 ± 1.25 nm AuNP. We used circular dichroism spectroscopy to measure the structure of the bound protein and determined that it remained essentially unchanged after binding. Finally, we performed Michaelis-Menten kinetics to determine that the enzyme retained 18.2 ± 2.0% of its activity and maintained that activity over a period of at least three weeks after conjugation to AuNPs. We hypothesize that structural changes to the peripheral active site of AChE are responsible for the differences in activity of bound AChE and unbound AChE. This work is a proof-of-concept demonstration of a generalizable method for placing proteins onto chemically and structurally diverse substrates and materials without the need for surface functionalization strategies.

Structural design of anthraquinone bridges in direct electron transfer of fructose dehydrogenase

Multi-functional small molecules attached to an electrode surface can bind non-covalently to the redox enzyme fructose dehydrogenase (FDH) to ensure efficient electrochemical electron transfer (ET) and electrocatalysis of the enzyme in both mediated (MET) and direct (DET) ET modes. The present work investigates the potential of exploiting secondary, electrostatic and hydrophobic interactions between substituents on a small molecular bridge and the local FDH surfaces. Such interactions ensure alignment of the enzyme in an orientation favourable for both MET and DET. We have used a group of novel synthesized anthraquinones as the small molecule bridge, functionalised with electrostatically neutral, anionic, or cationic substituents. Particularly, we investigated the immobilisation of FDH on a nanoporous gold (NPG) electrode decorated with the novel synthesised anthraquinones using electrochemical methods. The best DET-capable fraction out of four anthraquinone derivatives tested is achieved for an anthraquinone functionalised with an anionic sulphonate group. Our study demonstrates, how the combination of chemical design and bioelectrochemistry can be brought to control alignment of enzymes in productive orientations on electrodes, a paradigm for thiol modified surfaces in biosensors and bioelectronics.

Modeling of the Electrostatic Interaction and Catalytic Activity of [NiFe] Hydrogenases on a Planar Electrode

Hydrogenases are a group of enzymes that have caught the interest of researchers in renewable energies, due to their ability to catalyze the redox reaction of hydrogen. The exploitation of hydrogenases in electrochemical devices requires their immobilization on the surface of suitable electrodes, such as graphite. The orientation of the enzyme on the electrode is important to ensure a good flux of electrons to the catalytic center, through an array of iron-sulfur clusters. Here we present a computational approach to determine the possible orientations of a [NiFe] hydrogenase (PDB 1e3d) on a planar electrode, as a function of pH, salinity, and electrode potential. The calculations are based on the solution of the linearized Poisson-Boltzmann equation, using the PyGBe software. The results reveal that electrostatic interactions do not truly immobilize the enzyme on the surface of the electrode, but there is instead a dynamic equilibrium between different orientations. Nonetheless, after averaging over all thermally accessible orientations, we find significant differences related to the solution's salinity and pH, while the effect of the electrode potential is relatively weak. We also combine models for the protein adsoption-desorption equilibria and for the electron transfer between the proteins and the electrode to arrive at a prediction of the electrode's activity as a function of the enzyme concentration.

Biosensing Dopamine and L-Epinephrine with Laccase (Trametes pubescens) Immobilized on a Gold Modified Electrode

Engineering electrode surfaces through the electrodeposition of gold may provide a range of advantages in the context of biosensor development, such as greatly enhanced surface area, improved conductivity and versatile functionalization. In this work we report on the development of an electrochemical biosensor for the laccase-catalyzed assay of two catecholamines—dopamine and L-epinephrine. Variety of electrochemical techniques—cyclic voltammetry, differential pulse voltammetry, electrochemical impedance spectroscopy and constant potential amperometry have been used in its characterization. It has been demonstrated that the laccase electrode is capable of sensing dopamine using two distinct techniques—differential pulse voltammetry and constant potential amperometry, the latter being suitable for the assay of L-epinephrine as well. The biosensor response to both catecholamines, examined by constant potential chronoamperometry over the potential range from 0.2 to −0.1 V (vs. Ag|AgCl, sat KCl) showed the highest electrode sensitivity at 0 and −0.1 V. The dependencies of the current density on either catecholamine’s concentration was found to follow the Michaelis—Menten kinetics with apparent constants K_M^app = 0.116 ± 0.015 mM for dopamine and K_M^app = 0.245 ± 0.031 mM for L-epinephrine and linear dynamic ranges spanning up to 0.10 mM and 0.20 mM, respectively. Calculated limits of detection for both analytes were found to be within the sub-micromolar concentration range. The biosensor applicability to the assay of dopamine concentration in a pharmaceutical product was demonstrated (with recovery rates between 99% and 106%, n = 3).

Modulating the adsorption orientation of methionine-rich laccase by tailoring the surface chemistry of single-walled carbon nanotubes

Achieving fast electron transfer process between oxidoreductase and electrodes is pivotal for the biocathode of enzymatic biofuel cells (EBFCs). However, in-depth understanding of the interplay mechanism between enzymes and electrode materials remains challenging when designing and constructing EBFCs. Herein, atomic-scale insight into the direct electron transfer (DET) behavior of Thermus thermophilus laccase (TtLac) with a special methionine-rich β-hairpin motif adsorbed on the carboxyl-functionalized carbon nanotube (COOH-CNT) and amino-functionalized carbon nanotube (NH₂-CNT) surfaces were disclosed by multi-scale molecular simulations. Simulation results reveal that electrostatic modification is an effective way to tune the DET behavior for TtLac on the modified-CNTs electrode surface. Surprisingly, the positively charged TtLac can be attracted by both negatively charged COOH-CNT and positively charged NH₂-CNT surfaces, yet only the latter is capable to trigger the DET process due to the 'lying-on' adsorption orientation. Specifically, the T1 copper site is near the methionine-rich β-hairpin motif, which is the key binding site for TtLac binding onto the NH₂-CNT surface via electrostatic interaction, π-π stacking and cation-π interaction. Moreover, TtLac on the NH₂-CNT surface undergoes less conformational changes than those on the COOH-CNT surface, which allows the laccase stability and catalytic efficiency to be well preserved. These findings provide a fundamental guidance for future design and fabrication of methionine-rich laccase-based EBFCs with high power output and long lifespan.

Predicting the Orientation of Adsorbed Proteins Steered with Electric Fields Using a Simple Electrostatic Model

Under the most common experimental conditions, the adsorption of proteins to solid surfaces is a spontaneous process that leads to a rather compact layer of randomly oriented molecules. However, controlling such orientation is critically important for the development of catalytic surfaces. In this regard, the use of electric fields is one of the most promising alternatives. Our work is motivated by experimental observations that show important differences in catalytic activity of a trypsin-covered surface, which depended on the applied potential during the adsorption. Even though adsorption results from the combination of several processes, we were able to determine that (under the selected conditions) mean-field electrostatics play a dominant role, determining the orientation and yielding a difference in catalytic activity. We simulated the electrostatic potential numerically, using an implicit-solvent model based on the linearized Poisson-Boltzmann equation. This was implemented in an extension of the code PyGBe that included an external electric field, and rendered the electrostatic component of the solvation free energy. Our model (extensions available at the Github repository) allowed estimating the overall affinity of the protein with the surface, and their most likely orientation as a function of the potential applied. Our results show that the active sites of trypsin are, on average, more exposed when the electric field is negative, which agrees with the experimental results of catalytic activity, and confirm the premise that electrostatic interactions can be used to control the orientation of adsorbed proteins.

Between Two Walls: Modeling the Adsorption Behavior of β-Glucosidase A on Bare and SAM-Functionalized Gold Surfaces

The efficient immobilization of enzymes on surfaces remains a complex but central issue in the biomaterials field, which requires us to understand this process at the atomic level. Using a multiscale approach combining all-atom molecular dynamics and coarse-grain Brownian dynamics simulations, we investigated the adsorption behavior of β-glucosidase A (βGA) on bare and self-assembled monolayer (SAM)-functionalized gold surfaces. We monitored the enzyme position and orientation during the molecular dynamics (MD) trajectories and measured the contacts it forms with both surfaces. While the adsorption process has little impact on the protein conformation, it can nonetheless perturb its mechanical properties and catalytic activity. Our results show that compared to the SAM-functionalized surface, the adsorption of βGA on bare gold is more stable, but less specific, and more likely to disrupt the enzyme's function. This observation emphasizes the fact that the structural organization of proteins at the solid interface is a key point when designing devices based on enzyme immobilization, as one must find an acceptable stability-activity trade-off.

Effect of Oriented Electric Fields on Biologically Relevant Iron-Sulfur Clusters: Tuning Redox Reactivity for Catalysis

Enzyme-based iron-sulfur clusters, exemplified in families such as hydrogenases, nitrogenases, and radical S-adenosylmethionine enzymes, feature in many essential biological processes. The functionality of biological iron-sulfur clusters extends beyond simple electron transfer, relying primarily on the redox activity of the clusters, with a remarkable diversity for different enzymes. The active-site structure and the electrostatic environment in which the cluster resides direct this redox reactivity. Oriented electric fields in enzymatic active sites can be significantly strong, and understanding the extent of their effect on iron-sulfur cluster reactivity can inform first steps toward rationally engineering their reactivity. An extensive systematic density functional theory-based screening approach using OPBE/TZP has afforded a simple electric field-effect representation. The results demonstrate that the orientation of an external electric field of strength 28.8 MV cm^-1 at the center of the cluster can have a significant effect on its relative stability in the order of 35 kJ mol^-1. This shows clear implications for the reactivity of iron-sulfur clusters in enzymes. The results also demonstrate that the orientation of the electric field can alter the most stable broken-symmetry state, which further has implications on the directionality of initiated electron-transfer reactions. These insights open the path for manipulating the enzymatic redox reactivity of iron-sulfur cluster-containing enzymes by rationally engineering oriented electric fields within the enzymes.

Ceruloplasmin in flatland: the relationship between enzyme catalytic activity and surface hydrophilicity

The effective immobilization of the enzyme on the substrate surface plays a key role especially in biocatalysis, medicine or industry. Herein, we showed the influence of substrate hydrophilicity on the activity of the physically immobilized ceruloplasmin. To control the hydrophilicity of the substrate, thiols with various terminal groups were used. We have found that the effectiveness of the catalytic process of multimeric protein is the highest in the situation of application of the highly hydrophilic substrate. In the case of physical adsorption, the orientation of the enzyme is random, however the application of the appropriate modifying layer enforces the desired enzyme orientation. The quartz crystal microbalance with dissipation (QCM-D) results showed that the crucial parameter for the highest and most durable catalytic activity of the enzyme is the orientation, not the amount of the physically adsorbed enzyme.

Surface hydrophilicity – the way to control the activity of the immobilized enzyme.

Peptide sequence-driven direct electron transfer properties and binding behaviors of gold-binding peptide-fused glucose dehydrogenase on electrode

Oriented enzyme immobilization on electrodes is crucial for interfacial electrical coupling of direct electron transfer (DET)-based enzyme-electrode systems. As inorganic-binding peptides are introduced as molecular binders and enzyme-orienting agents, inorganic-binding peptide-fused enzymes should be designed and constructed to achieve efficient DET. In this study, it is aimed to compare the effects of various gold-binding peptides (GBPs) fused to enzymes on electrocatalytic activity, bioactivity, and material-binding behaviors. Here, GBPs with identical gold-binding properties but different amino acid sequences were fused to the FAD-dependent glucose dehydrogenase gamma-alpha complex (GDHγα) to generate four GDHγα variants. The structural, biochemical, mechanical, and bioelectrochemical properties of these GDHγα variants immobilized on electrode were determined by their fused GBPs. Our results confirmed that the GBP type is vital in the design, construction, and optimization of GBP-fused enzyme-modified electrodes for facile interfacial DET and practical DET-based enzyme-electrode systems.

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The four GBP sequences are genetically fused to catalytic subunit of GDHγα complex

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The cofactor-surface interface was investigated with 3D models of fusion enzymes

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The four systems exhibit diverse electrochemical results depending on GBP type

Enhanced Performance of Bioelectrodes Made with Amination-Modified Glucose Oxidase Immobilized on Carboxyl-Functionalized Ordered Mesoporous Carbon

This research reveals the improved performance of bioelectrodes made with amination-modified glucose oxidase (GOx-NH2) and carboxyl-functionalized mesoporous carbon (OMC-COOH). Results showed that when applied with 10 mM EDC amination, the functional groups of NH2 were successfully added to GOx, according to the analysis of 1H-NMR, elemental composition, and FTIR spectra. Moreover, after the aminated modification, increased enzyme immobilization (124.01 ± 1.49 mg GOx-NH2/g OMC-COOH; 2.77-fold increase) and enzyme activity (1.17-fold increase) were achieved, compared with those of non-modified GOx. Electrochemical analysis showed that aminated modification enhanced the peak current intensity of Nafion/GOx-NH2/OMC-COOH (1.32-fold increase), with increases in the charge transfer coefficient α (0.54), the apparent electron transfer rate constant ks (2.54 s-1), and the surface coverage Γ (2.91 × 10-9 mol·cm-2). Results showed that GOx-NH2/OMC-COOH exhibited impressive electro-activity and a favorable anodic reaction.

A glucose biosensor based on glucose oxidase fused to a carbohydrate binding module family 2 tag that specifically binds to the cellulose-modified electrode

The method of immobilization of glucose oxidase (GOD) on electrodes is especially important for the fabrication and performance of glucose biosensors. In this study, a carbohydrate binding module family 2 (CBM2) was successfully fused to the C terminal of GOD with a natural linker (NL) in endo-β-xylanase by genetic recombination, and a fusion GOD (GOD-NL-CBM2) was obtained. The CBM2 was used as an affinity adsorption tag for immobilization of the GOD-NL-CBM2 on a cellulose modified electrode. The specific activity of GOD-NL-CBM2 was comparable to that of the wild type GOD. In addition, the CBM2 tag of fusion GOD almost maintained its highest binding capacity under optimal catalytic conditions (pH 5.0, 50 °C). The morphology and composition analysis of the cellulose film reacted with and without GOD or GOD-NL-CBM2 confirmed the immobilization of GOD-NL-CBM2. The electrochemical properties of the GOD-NL-CBM2/cellulose film bioelectrode, with a characteristic peak of H₂O₂ at +0.6 V in the presence of glucose, revealed the capability of the immobilized GOD-NL-CBM2 to efficiently catalyze glucose and produce H₂O₂. Additionally, the current signal response of the biosensor to glucose was linear in the concentration range from 1.25 to 40 mM (r² ≥ 0.99). The sensitivity and detection limit of the GOD-NL-CBM2/cellulose film bioelectrode were 466.7 μA mol^-1 L cm^-2 and 0.475 mM (S/N = 3), respectively. Moreover, the glucose biosensor exhibited a rapid current change (< 5 s), high reproducibility (Relative standard deviation, RSD < 5%), substrate selectivity and stability, and retained about 80 % of the original current response after 2 months. The affinity adsorption-based immobilization strategy for GOD provides a promising approach to develop a high performance glucose biosensor.

Site directed confinement of laccases in a porous scaffold towards robustness and selectivity

We immobilized a fungal laccase with only two spatially close lysines available for functionalization into macrocellular Si(HIPE) monoliths for the purpose of continuous flow catalysis. Immobilization (30-45 % protein immobilization yields) was obtained using a covalent bond forming reaction between the enzyme and low glutaraldehyde (0.625 % (w/w)) functionalized foams. Testing primarily HBT-mediated RB5 dye decolorization in continuous flow reactors, we show that the activity of the heterogeneous catalyst is comparable to its homogeneous counterpart. More, its operational activity remains as high as 60 % after twelve consecutive decolorization cycles as well as after one-year storage, performances remarkable for such a material. We further immobilized two variants of the laccase containing a unique lysine: one located in the vicinity of the substrate oxidation site (K157) and one at the opposite side of this oxidation site (K71) to study the effect of the proximity of the Si(HIPE) surface on enzyme activity. Comparing activities on different substrates for monoliths with differentially oriented catalysts, we show a twofold discrimination for ABTS relative to ascorbate. This study provides ground for the development of neo-functionalized materials that beyond allowing stability and reusability will become synergic partners in the catalytic process.

Amperometric Biosensors Based on Direct Electron Transfer Enzymes

The accurate determination of analyte concentrations with selective, fast, and robust methods is the key for process control, product analysis, environmental compliance, and medical applications. Enzyme-based biosensors meet these requirements to a high degree and can be operated with simple, cost efficient, and easy to use devices. This review focuses on enzymes capable of direct electron transfer (DET) to electrodes and also the electrode materials which can enable or enhance the DET type bioelectrocatalysis. It presents amperometric biosensors for the quantification of important medical, technical, and environmental analytes and it carves out the requirements for enzymes and electrode materials in DET-based third generation biosensors. This review critically surveys enzymes and biosensors for which DET has been reported. Single- or multi-cofactor enzymes featuring copper centers, hemes, FAD, FMN, or PQQ as prosthetic groups as well as fusion enzymes are presented. Nanomaterials, nanostructured electrodes, chemical surface modifications, and protein immobilization strategies are reviewed for their ability to support direct electrochemistry of enzymes. The combination of both biosensor elements-enzymes and electrodes-is evaluated by comparison of substrate specificity, current density, sensitivity, and the range of detection.

Probing Selective Self-Assembly of Putrescine Oxidase with Controlled Orientation Using a Genetically Engineered Peptide Tag

Controlling enzyme orientation and location on surfaces is a critical step for their successful deployment in diverse applications from biosensors to lab-on-a-chip devices. Functional activity of the enzymes on the surface will largely depend on the spatial arrangement and orientation. Solid binding peptides have been proven to offer versatility for immobilization of biomolecules on inorganic materials including metals, oxides, and minerals. Previously, we demonstrated the utility of a gold binding peptide genetically incorporated into the enzyme putrescine oxidase (PutOx-AuBP), enabling self-enzyme assembly on gold substrates. PutOx is an attractive biocatalyst among flavin oxidases, using molecular oxygen as an electron acceptor without requiring a dissociable coenzyme. Here, we explore the selective self-assembly of this enzyme on a range of surfaces using atomic force microscopy (AFM) along with the assessment of functional activity. This work probes the differences in surface coverage, distribution, size, shape, and activity of PutOx-AuBP in comparison to those of native putrescine oxidase (PutOx) on multiple surfaces to provide insight for material-selective enzymatic assembly. Surfaces investigated include metal (templated-stripped gold (TSG)), oxide (native SiO₂ on Si(111)), minerals (mica and graphite), and self-assembled monolayers (SAMs) with a range of hydrophobicity and charge. Supported by both the coverage and the dimensions of immobilized enzymes, our results indicate that of the surfaces investigated, material-selective binding takes place with orientation control only for PutOx-AuBP onto the TSG substrate. These differences are consistent with the measurements of surface-bound enzymatic activities. Substrate-dependent differences observed indicate significant variations in enzyme-surface interactions ranging from peptide-directed self-assembly to enzyme aggregation. The implications of this study provide insight for the fabrication of enzymatic patterns directed by self-assembling peptide tags onto localized surface regions. Enabling functional enzyme-based nanoscale materials offers a fascinating path for utilization of sustainable biocatalysts integrated into multiscale devices.

Self-Powered Detection of Glucose by Enzymatic Glucose/Oxygen Fuel Cells on Printed Circuit Boards

Monitoring glucose levels in physiological fluids can help prevent severe complications associated with hypo- and hyper-glycemic events. Current glucose-monitoring systems require a three-electrode setup and a power source to function, which can hamper the system miniaturization to the patient discomfort. Enzymatic fuel cells (EFCs) offer the opportunity to develop self-powered and minimally invasive glucose sensors by eliminating the need for an external power source. Nevertheless, practical applications demand for cost-effective and mass-manufacturable EFCs compatible with integration strategies. In this study, we explore for the first time the use of gold electrodes on a printed circuit board (PCB) for the development of an EFC and demonstrate its application in saliva. To increase the specific surface area, the PCB gold-plated electrodes were modified with porous gold films. At the anode, glucose oxidase is immobilized with an osmium redox polymer that serves as an electron-transfer mediator. At the cathode, bilirubin oxidase is adsorbed onto the porous gold surface with a blocking agent that prevents parasitic reactions while maintaining the enzyme catalytic activity. The resulting EFC showed a linear response to glucose in phosphate buffer within the range 50 μM to 1 mM, with a sensitivity of 14.13 μA cm-2 mM-1. The sensor was further characterized in saliva, showing the linear range of detection of 0.75 to 2 mM, which is within the physiological range, and sensitivity of 21.5 μA cm-2 mM-1. Overall, this work demonstrates that PCBs are suitable platforms for EFCs, paving the way for the development of fully integrated systems in a seamless and miniaturized device.

Orientated Immobilization of FAD-Dependent Glucose Dehydrogenase on Electrode by Carbohydrate-Binding Module Fusion for Efficient Glucose Assay

The discovery or engineering of fungus-derived FAD-dependent glucose 1-dehydrogenase (FAD-GDH) is especially important in the fabrication and performance of glucose biosensors. In this study, a novel FAD-GDH gene, phylogenetically distantly with other FAD-GDHs from Aspergillus species, was identified. Additionally, the wild-type GDH enzyme, and its fusion enzyme (GDH-NL-CBM2) with a carbohydrate binding module family 2 (CBM2) tag attached by a natural linker (NL), were successfully heterogeneously expressed. In addition, while the GDH was randomly immobilized on the electrode by conventional methods, the GDH-NL-CBM2 was orientationally immobilized on the nanocellulose-modified electrode by the CBM2 affinity adsorption tag through a simple one-step approach. A comparison of the performance of the two electrodes demonstrated that both electrodes responded linearly to glucose in the range of 0.12 to 40.7 mM with a coefficient of determination R² > 0.999, but the sensitivity of immobilized GDH-NL-CBM2 (2.1362 × 10⁻² A/(M*cm²)) was about 1-fold higher than that of GDH (1.2067 × 10⁻² A/(M*cm²)). Moreover, a lower detection limit (51 µM), better reproducibility (<5%) and stability, and shorter response time (≈18 s) and activation time were observed for the GDH-NL-CBM2-modified electrode. This facile and easy immobilization approach used in the preparation of a GDH biosensor may open up new avenues in the development of high-performance amperometric biosensors.

From Enzyme Stability to Enzymatic Bioelectrode Stabilization Processes

Bioelectrocatalysis using redox enzymes appears as a sustainable way for biosensing, electricity production, or biosynthesis of fine products. Despite advances in the knowledge of parameters that drive the efficiency of enzymatic electrocatalysis, the weak stability of bioelectrodes prevents large scale development of bioelectrocatalysis. In this review, starting from the understanding of the parameters that drive protein instability, we will discuss the main strategies available to improve all enzyme stability, including use of chemicals, protein engineering and immobilization. Considering in a second step the additional requirements for use of redox enzymes, we will evaluate how far these general strategies can be applied to bioelectrocatalysis.

Enhancement of direct electron transfer in graphene bioelectrodes containing novel cytochrome c553 variants with optimized heme orientation

The highly efficient bioelectrodes based on single layer graphene (SLG) functionalized with pyrene self-assembled monolayer and novel cytochromec₅₅₃(cytc₅₅₃)peptide linker variants were rationally designed to optimize the direct electron transfer (DET) between SLG and the heme group of cyt. Through a combination of photoelectrochemical and quantum mechanical (QM/MM) approaches we show that the specific amino acid sequence of a short peptide genetically inserted between the cytc₅₅₃holoprotein and thesurface anchoring C-terminal His₆-tag plays a crucial role in ensuring the optimal orientation and distance of the heme group with respect to the SLG surface. Consequently, efficient DET occurring between graphene and cyt c₅₅₃ leads to a 20-fold enhancement of the cathodic photocurrent output compared to the previously reported devices of a similar type. The QM/MM modeling implies that a perpendicular or parallel orientation of the heme group with respect to the SLG surface is detrimental to DET, whereas the tilted orientation favors the cathodic photocurrent generation. Our work confirms the possibility of fine-tuning the electronic communication within complex bio-organic nanoarchitectures and interfaces due to optimization of the tilt angle of the heme group, its distance from the SLG surface and optimal HOMO/LUMO levels of the interacting redox centers.

Recent Advances in the Direct Electron Transfer-Enabled Enzymatic Fuel Cells

Direct electron transfer (DET), which requires no mediator to shuttle electrons from enzyme active site to the electrode surface, minimizes complexity caused by the mediator and can further enable miniaturization for biocompatible and implantable devices. However, because the redox cofactors are typically deeply embedded in the protein matrix of the enzymes, electrons generated from oxidation reaction cannot easily transfer to the electrode surface. In this review, methods to improve the DET rate for enhancement of enzymatic fuel cell performances are summarized, with a focus on the more recent works (past 10 years). Finally, progress on the application of DET-enabled EFC to some biomedical and implantable devices are reported.

Electrocatalysis by Heme Enzymes—Applications in Biosensing

Heme proteins take part in a number of fundamental biological processes, including oxygen transport and storage, electron transfer, catalysis and signal transduction. The redox chemistry of the heme iron and the biochemical diversity of heme proteins have led to the development of a plethora of biotechnological applications. This work focuses on biosensing devices based on heme proteins, in which they are electronically coupled to an electrode and their activity is determined through the measurement of catalytic currents in the presence of substrate, i.e., the target analyte of the biosensor. After an overview of the main concepts of amperometric biosensors, we address transduction schemes, protein immobilization strategies, and the performance of devices that explore reactions of heme biocatalysts, including peroxidase, cytochrome P450, catalase, nitrite reductase, cytochrome c oxidase, cytochrome c and derived microperoxidases, hemoglobin, and myoglobin. We further discuss how structural information about immobilized heme proteins can lead to rational design of biosensing devices, ensuring insights into their efficiency and long-term stability.

Top 5 Cited Papers in the Section of Biocatalysis

I have the honor of writing this editorial note on the top 5 cited papers published in 2018 in the section of Biocatalysis of the Catalyst journal [...]

Direct Electrochemical Enzyme Electron Transfer on Electrodes Modified by Self-Assembled Molecular Monolayers

Self-assembled molecular monolayers (SAMs) have long been recognized as crucial “bridges” between redox enzymes and solid electrode surfaces, on which the enzymes undergo direct electron transfer (DET)—for example, in enzymatic biofuel cells (EBFCs) and biosensors. SAMs possess a wide range of terminal groups that enable productive enzyme adsorption and fine-tuning in favorable orientations on the electrode. The tunneling distance and SAM chain length, and the contacting terminal SAM groups, are the most significant controlling factors in DET-type bioelectrocatalysis. In particular, SAM-modified nanostructured electrode materials have recently been extensively explored to improve the catalytic activity and stability of redox proteins immobilized on electrochemical surfaces. In this report, we present an overview of recent investigations of electrochemical enzyme DET processes on SAMs with a focus on single-crystal and nanoporous gold electrodes. Specifically, we consider the preparation and characterization methods of SAMs, as well as SAM applications in promoting interfacial electrochemical electron transfer of redox proteins and enzymes. The strategic selection of SAMs to accord with the properties of the core redox protein/enzymes is also highlighted.

Rational Surface Modification of Carbon Nanomaterials for Improved Direct Electron Transfer-Type Bioelectrocatalysis of Redox Enzymes

Interfacial electron transfer between redox enzymes and electrodes is a key step for enzymatic bioelectrocatalysis in various bioelectrochemical devices. Although the use of carbon nanomaterials enables an increasing number of redox enzymes to carry out bioelectrocatalysis involving direct electron transfer (DET), the role of carbon nanomaterials in interfacial electron transfer remains unclear. Based on the recent progress reported in the literature, in this mini review, the significance of carbon nanomaterials on DET-type bioelectrocatalysis is discussed. Strategies for the oriented immobilization of redox enzymes in rationally modified carbon nanomaterials are also summarized and discussed. Furthermore, techniques to probe redox enzymes in carbon nanomaterials are introduced.

Recent Progress in Applications of Enzymatic Bioelectrocatalysis

Bioelectrocatalysis has become one of the most important research fields in electrochemistry and provided a firm base for the application of important technology in various bioelectrochemical devices, such as biosensors, biofuel cells, and biosupercapacitors. The understanding and technology of bioelectrocatalysis have greatly improved with the introduction of nanostructured electrode materials and protein-engineering methods over the last few decades. Recently, the electroenzymatic production of renewable energy resources and useful organic compounds (bioelectrosynthesis) has attracted worldwide attention. In this review, we summarize recent progress in the applications of enzymatic bioelectrocatalysis.

Biocathode design with highly-oriented immobilization of multi-copper oxidase from Pyrobaculum aerophilum onto a single-walled carbon nanotube surface via a carbon nanotube-binding peptide

Biofuel cells generate electric energy using an enzyme as a catalyst for an electrode but their stability and low battery output pose problems for practical use. To solve these problems, this study aimed to build a long-lasting and high-output biocathode as a catalyst using a highly stable hyperthermophilic archaeal enzyme, multi-copper oxidase, from Pyrobaculum aerophilum (McoP). To increase output, McoP was oriented and immobilized on single-walled carbon nanotubes (SWCNT) with a high specific surface area, and the electrode interface was designed to achieve highly efficient electron transfer between the enzyme and electrode. Type 1 copper (T1Cu), an electron-accepting site in the McoP molecule, is located near the C-terminus. Therefore, McoP was prepared by genetically engineering a CNT-binding peptide with the sequence LLADTTHHRPWT, at the C-terminus of McoP (McoP-CBP). We then constructed an electrode using a complex in which McoP-CBP was aligned and immobilized on SWCNT, and then clarified the effect of CBP. The amounts of immobilized enzymes on McoP-SWCNT and (McoP-CBP)-SWCNT complexes were almost equal. CV measurement of the electrode modified with both complexes showed 5.4 times greater current density in the catalytic reaction of the (McoP-CBP)-SWCNT/GC electrode than in the McoP-SWCNT/GC electrode. This is probably because CBP fusion immobilize the enzyme on SWCNTs in an orientational manner, and T1Cu, the oxidation-reduction site in McoP, is close to the electrode, which improves electron transfer efficiency.

Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grained Representation

Surface immobilized enzymes play a key role in numerous biotechnological applications such as biosensors, biofuel cells, or biocatalytic synthesis. As a consequence, the impact of adsorption on the enzyme structure, dynamics, and function needs to be understood on the molecular level as it is critical for the improvement of these technologies. With this perspective in mind, we used a theoretical approach for investigating local protein flexibility on the residue scale that couples a simplified protein representation with an elastic network and Brownian dynamics simulations. The impact of protein adsorption on a solid surface is implicitly modeled via additional external constraints between the residues in contact with the surface. We first performed calculations on a redox enzyme, bilirubin oxidase (BOD) from M. verrucaria, to study the impact of adsorption on its mechanical properties. The resulting rigidity profiles show that, in agreement with the available experimental data, the mechanical variations observed in the adsorbed BOD will depend on its orientation and its anchor residues (i.e., residues that are in contact with the functionalized surface). Additional calculations on ribonuclease A and nitroreductase shed light on how seemingly stable adsorbed enzymes can nonetheless display an important decrease in their catalytic activity resulting from a perturbation of their mechanics and internal dynamics.

Microbial lipases and their industrial applications: a comprehensive review

Lipases are very versatile enzymes, and produced the attention of the several industrial processes. Lipase can be achieved from several sources, animal, vegetable, and microbiological. The uses of microbial lipase market is estimated to be USD 425.0 Million in 2018 and it is projected to reach USD 590.2 Million by 2023, growing at a CAGR of 6.8% from 2018. Microbial lipases (EC 3.1.1.3) catalyze the hydrolysis of long chain triglycerides. The microbial origins of lipase enzymes are logically dynamic and proficient also have an extensive range of industrial uses with the manufacturing of altered molecules. The unique lipase (triacylglycerol acyl hydrolase) enzymes catalyzed the hydrolysis, esterification and alcoholysis reactions. Immobilization has made the use of microbial lipases accomplish its best performance and hence suitable for several reactions and need to enhance aroma to the immobilization processes. Immobilized enzymes depend on the immobilization technique and the carrier type. The choice of the carrier concerns usually the biocompatibility, chemical and thermal stability, and insolubility under reaction conditions, capability of easy rejuvenation and reusability, as well as cost proficiency. Bacillus spp., Achromobacter spp., Alcaligenes spp., Arthrobacter spp., Pseudomonos spp., of bacteria and Penicillium spp., Fusarium spp., Aspergillus spp., of fungi are screened large scale for lipase production. Lipases as multipurpose biological catalyst has given a favorable vision in meeting the needs for several industries such as biodiesel, foods and drinks, leather, textile, detergents, pharmaceuticals and medicals. This review represents a discussion on microbial sources of lipases, immobilization methods increased productivity at market profitability and reduce logistical liability on the environment and user.

Impact of Silane Monolayers on the Adsorption of Streptavidin on Silica and Its Subsequent Interactions with Biotin: Molecular Dynamics and Steered Molecular Dynamics Simulations

Protein adsorption on surfaces is used in analytical tools as an immobilization mean to trap the analyte to be detected. However, protein adsorption can lead to a conformational change in the protein structure, resulting in a loss of bioactivity. Here, we study adsorption of a streptavidin-biotin complex on amorphous SiO₂ surfaces functionalized with five different silane self-assembled monolayers by all-atom molecular dynamics simulations. We find that the streptavidin global conformational change, as well as the nature of residues with high mobility, depends on the alkyl chain length and head-group charge of silane molecules. Effects on interactions with biotin are further investigated by steered molecular dynamics (SMD) simulations, which mimics atomic force microscopy (AFM) with the biotin attached on the tip. We show the combined effects of adsorption-induced global conformational changes and of the position of residues with high mobility on the streptavidin-biotin rupture force. By comparing our results to experimental and SMD rupture forces obtained in water, without any surface, we conclude that silane with uncharged and short alkyl chains allows streptavidin immobilization, while keeping biotin interactions better than silanes with long alkyl chains or charged head groups.

Lignin nanoparticles are renewable and functional platforms for the concanavalin a oriented immobilization of glucose oxidase-peroxidase in cascade bio-sensing

Lignin nanoparticles (LNPs) acted as a renewable and efficient platform for the immobilization of horseradish peroxidase (HRP) and glucose oxidase (GOX) by a layer by layer procedure. The use of concanavalin A as a molecular spacer ensured the correct orientation and distance between the two enzymes as confirmed by Förster resonance energy transfer measurement. Layers with different chemo–physical properties tuned in a different way the activity and kinetic parameters of the enzymatic cascade, with cationic lignin performing as the best polyelectrolyte in the retention of the optimal Con A aggregation state. Electrochemical properties, temperature and pH stability, and reusability of the novel systems have been studied, as well as their capacity to perform as colorimetric biosensors in the detection of glucose using ABTS and dopamine as chromogenic substrates. A boosting effect of LNPs was observed during cyclovoltammetry analysis. The limit of detection (LOD) was found to be better than, or comparable to, that previously reported for other HRP–GOX immobilized systems, the best results being again obtained in the presence of a cationic lignin polyelectrolyte. Thus renewable lignin platforms worked as smart and functional devices for the preparation of green biosensors in the detection of glucose.

Lignin nanoparticles as functional renewable nanoplatform for the immobilization of cascade process in colorimetric biosensing of β-d-glucose.

Nanosecond Laser-Fabricated Monolayer of Gold Nanoparticles on ITO for Bioelectrocatalysis

Redox enzymes can be envisioned as biocatalysts in various electrocatalytic-based devices. Among factors that play roles in bioelectrochemistry limitations, the effect of enzyme-enzyme neighboring interaction on electrocatalysis has rarely been investigated, although critical in vivo. We report in this work an in-depth study of gold nanoparticles prepared by laser ablation in the ultimate goal of determining the relationship between activity and enzyme density on electrodes. Nanosecond laser interaction with nanometric gold films deposited on indium tin oxide support was used to generate in situ gold nanoparticles (AuNPs) free from any stabilizers. A comprehensive analysis of AuNP size and coverage, as well as total geometric surface vs. electroactive surface is provided as a function of the thickness of the treated gold layer. Using microscopy and electrochemistry, the long-term stability of AuNP-based electrodes in the atmosphere and in the electrolyte is demonstrated. AuNPs formed by laser treatment are then modified by thiol chemistry and their electrochemical behavior is tested with a redox probe. Finally, enzyme adsorption and bioelectrocatalysis are evaluated in the case of two enzymes, i.e., the Myrothecium verrucaria bilirubin oxidase and the Thermus thermophilus laccase. Behaving differently on charged surfaces, they allow demonstrating the validity of laser treated AuNPs for bioelectrocatalysis.

Enzyme-Based Biosensors: Tackling Electron Transfer Issues

This review summarizes the fundamentals of the phenomenon of electron transfer (ET) reactions occurring in redox enzymes that were widely employed for the development of electroanalytical devices, like biosensors, and enzymatic fuel cells (EFCs). A brief introduction on the ET observed in proteins/enzymes and its paradigms (e.g., classification of ET mechanisms, maximal distance at which is observed direct electron transfer, etc.) are given. Moreover, the theoretical aspects related to direct electron transfer (DET) are resumed as a guideline for newcomers to the field. Snapshots on the ET theory formulated by Rudolph A. Marcus and on the mathematical model used to calculate the ET rate constant formulated by Laviron are provided. Particular attention is devoted to the case of glucose oxidase (GOx) that has been erroneously classified as an enzyme able to transfer electrons directly. Thereafter, all tools available to investigate ET issues are reported addressing the discussions toward the development of new methodology to tackle ET issues. In conclusion, the trends toward upcoming practical applications are suggested as well as some directions in fundamental studies of bioelectrochemistry.

In Situ Fluorescence Tomography Enables a 3D Mapping of Enzymatic O2 Reduction at the Electrochemical Interface

Getting information about the fate of immobilized enzymes and the evolution of their environment during turnover is a mandatory step toward bioelectrode optimization for effective use in biodevices. We demonstrate here the proof-of-principle visual characterization of the reactivity at an enzymatic electrode thanks to fluorescence confocal laser scanning microscopy (FCLSM) implemented in situ during the electrochemical experiment. The enzymatic O₂ reduction involves proton-coupled electron transfers. Therefore, fluorescence variation of a pH-dependent fluorescent dye in the electrode vicinity enables reaction visualization. Simultaneous collection of electrochemical and fluorescence signals gives valuable space- and time-resolved information. Once the technical challenges of such a coupling are overcome, in situ FCLSM affords a unique way to explore reactivity at the electrode surface and in the electrolyte volume. Unexpected features are observed, especially the pH evolution of the enzyme environment, which is also indicated by a characteristic concentration profile within the diffusion layer. This coupled approach also gives access to a cartography of the electrode surface response (i.e., heterogeneity), which cannot be obtained solely by an electrochemical means.

Enzyme Immobilization for Solid-Phase Catalysis

The covalent immobilization of an enzyme to a solid support can broaden its applicability in various workflows. Immobilized enzymes facilitate catalyst re-use, adaptability to automation or high-throughput applications and removal of the enzyme without heat inactivation or reaction purification. In this report, we demonstrate a step-by-step procedure to carry out the bio-orthogonal immobilization of DNA modifying enzymes employing the self-labelling activity of the SNAP-tag to covalently conjugate the enzyme of interest to the solid support. We also demonstrate how modifying the surface functionality of the support can improve the activity of the immobilized enzyme. Finally, the utility of immobilized DNA-modifying enzymes is depicted through sequential processing of genomic DNA libraries for Illumina next-generation sequencing (NGS), resulting in improved read coverage across AT-rich sequences.