Shuffling Active Site Substate Populations Affects Catalytic Activity: The Case of Glucose Oxidase

Anti Helicobacter pylori activity and gastrointestinal protective effects of Terminalia bellirica: Mechanistic insights from in vitro and in vivo studies

ETHNOPHARMACOLOGICAL RELEVANCE

Terminalia bellirica (Gaertn.) Roxb. (Combretaceae) (T. bellirica) is a longstanding medicinal plant traditionally referenced in both Indian and Tibetan medical practices. Currently, approximately 50% of the global population is infected with Helicobacter pylori (H. pylori). To curb antibiotic overuse, asymptomatic patients might require alternative therapy to mitigate the intestinal side effects commonly associated with excessive antibiotic usage.

AIM OF THE STUDY

Preliminary screening conducted by our team revealed that T. bellirica had excellent anti-H. pylori action in vitro. However, further research elucidating the mechanism behind T. bellirica's impact on H. pylori infection and its protective effects against related gastrointestinal diseases is yet to be explored.

MATERIALS AND METHODS

To assess the specific effect and underlying mechanism, we employed a comprehensive range of methodologies, including UPLC-MS/MS, in vitro and in vivo antibacterial assays, 5R 16S, molecular dynamics simulation and RT-qPCR.

RESULTS

Phytochemical analysis revealed abundant phenolic contents in T. bellirica, including chebulagic acid, chebulinic acid, corilagin, gallic acid, and ellagic acid. In vitro antibacterial evaluations demonstrated significant efficacy of T. bellirica against H. pylori, with a minimum inhibitory concentration (MIC) of 160 μg/mL, effectively inhibiting critical bacterial defense such as urease, adhesion and gene vacA. In vivo animal experiments showed that in addition to its anti-H. pylori effect, T. bellirica exhibited mild influence on gastric microbiota, with the composition restoring to normal levels after administration.

CONCLUSIONS

T. bellirica exerts potent anti-H. pylori activity both in vitro and in vivo, indicating its potential as an alternative therapeutic strategy for managing H. pylori infections while exerting minimal impact on gastric microbial balance. Further studies are warranted to elucidate additional pathways involved and to validate its clinical applications.

FAD binding and dissociation in GMC-oxidoreductases

The glucose-methanol-choline (GMC)-oxidoreductase superfamily comprises a large group of flavoenzymes such as glucose oxidase, glucose dehydrogenase and cellobiose dehydrogenase, which have been extensively studied and applied in biocatalysis and biosensors. Since the applicability of recombinant flavoenzymes is compromised by divergent glycosylation patterns and substoichiometric FAD occupancy, this study employed experimental and computational methods to analyze the deflavination and reconstitution of three GMC-oxidoreductases from a structural perspective. The results demonstrated that the amount of glycosylation of flavoenzymes is critical for both processes. FAD dissociation constants for glucose oxidase, glucose dehydrogenase and cellobiose dehydrogenase were determined by three different methods, showing Kd values in the range of 10 to 47 nM. Both, the presence of FAD and N-glycosides increase the thermal stability of the flavoenzymes. Steered molecular dynamics simulations revealed differences in the FAD binding of the three enzymes and indicated an undiscovered route of the FAD to dissociate from GMC-oxidoreductases by movement of a loop-and-lid structure on the enzyme surface. This work provides new insights into the mechanism of FAD binding and dissociation in GMC-oxidoreductases and offers strategies for their recombinant production.

Artificial-Cofactor-Mediated Hydrogen and Electron Transfer Endows AuFe/Polydopamine Superparticles with Enhanced Glucose Oxidase-Like Activity

Various applications related to glucose catalysis have led to the development of functional nanozymes with glucose oxidase (GOX)-like activity. However, the unsatisfactory catalytic activity of nanozymes is a major challenge for their practical applications due to their inefficient hydrogen and electron transfer. Herein, we present the synthesis of AuFe/polydopamine (PDA) superparticles that exhibit photothermal-enhanced GOX-like activity. Experimental investigations and theoretical calculations reveal that the glucose oxidation process catalyzed by AuFe/PDA follows an artificial-cofactor-mediated hydrogen atom transfer mechanism, which facilitates the generation of carbon-centered radical intermediates. Rather than depending on charged Au surfaces for thermodynamically unstable hydride transfer, Fe(III)-coordinated PDA with abundant amino and phenolic hydroxyl groups serves as cofactor mimics, facilitating both hydrogen atom and electron transfer in the catalytic process. Finally, leveraging the photothermal-enhanced GOX-like and catalase-like activities of AuFe/PDA, we establish a highly sensitive and accurate point-of-care testing blood glucose determination with exceptional anti-jamming capabilities.

Substrate Turnover Dynamics Guide Ketol-Acid Reductoisomerase Redesign for Increased Specific Activity

The task of adapting enzymes for specific applications is often hampered by our incomplete ability to tune and tailor catalytic functions, particularly when seeking increased activity. Here, we develop and demonstrate a rational approach to address this challenge, applied to ketol-acid reductoisomerase (KARI), which has uses in industrial-scale isobutanol production. While traditional structure-based computational enzyme redesign strategies typically focus on the enzyme-bound ground state (GS) and transition state (TS), we postulated that additionally treating the underlying dynamics of complete turnover events that connect and pass through both states could further elucidate the structural properties affecting catalysis and help identify mutations that lead to increased catalytic activity. To examine the dynamics of substrate conversion with atomistic detail, we adapted and applied computational methods based on path sampling techniques to gather thousands of QM/MM simulations of attempted substrate turnover events by KARI: both productive (reactive) and unproductive (nonreactive) attempts. From these data, machine learning models were constructed and used to identify specific conformational features (interatomic distances, angles, and torsions) associated with successful, productive catalysis. Multistate protein redesign techniques were then used to select mutations that stabilized reactive-like structures over nonreactive-like ones while also meeting additional criteria consistent with enhanced specific activity. This procedure resulted in eight high-confidence enzyme mutants with a significant improvement in calculated specific activity relative to wild type (WT), with the fastest variant's increase in calculated k cat being (2 ± 1) × 104-fold. Collectively, these results suggest that introducing mutations designed to increase the population of reaction-promoting conformations of the enzyme-substrate complex before it reaches the barrier can provide an effective approach to engineering improved enzyme catalysts.

Hypersecretory production of glucose oxidase in Pichia pastoris through combinatorial engineering of protein properties, synthesis, and secretion

Glucose oxidase (EC 1.1.3.4, GOD) is a widely used industrial enzyme. To construct a GOD-hyperproducing Pichia pastoris strain, combinatorial strategies have been applied to improve GOD activity, synthesis, and secretion. First, wild-type GOD was subjected to saturation mutagenesis to obtain an improved variant, MGOD1 (V20W/T30S), with 1.7-fold higher kcat /KM . Subsequently, efficient signal peptides were screened, and the copy number of MGOD1 was optimized to generate a high-producing strain, 8GM1, containing eight copies of AOX1 promoter-GAS1 signal peptide-MGOD1 expression cassette. Finally, the vesicle trafficking of 8GM1 was engineered to obtain the hyperproducing strain G1EeSe co-expressing the trafficking components EES and SEC. 22, and the EES gene (PAS_chr3_0685) was found to facilitate both protein secretion and production for the first time. Using these strategies, GOD secretion was enhanced 65.2-fold. In the 5-L bioreactor, conventional fed-batch fermentation without any process optimization resulted in up to 7223.0 U/mL extracellular GOD activity (3.3-fold higher than the highest level reported to date), with almost only GOD in the fermentation supernatant at a protein concentration of 30.7 g/L. Therefore, a GOD hyperproducing strain for industrial applications was developed, and this successful case can provide a valuable reference for the construction of high-producing strains for other industrial enzymes.

Untangling the Effects of Doping Carbon with Diverse Heteroatoms on the Bioelectrochemistry of Glucose Oxidase

Great enthusiasm for doping carbon materials with nonmetallic heteroatoms for promoting electrical contact of redox enzymes with electrodes in bioelectronics has been aroused. However, systematic studies of different heteroatoms on enzyme activities are still lacking. Herein, choosing glucose oxidase (GOD) as a model enzyme, carbon nanotubes (CNTs) are used as electron carriers to evaluate the effects of heteroatoms' species on the direct electron transfer and catalytic activities of GOD. Experimental data demonstrate that phosphorus (P)-doped CNTs provide the most intimate electrical contact with GOD compared to other elements (B, N, and S) doping, delivering a 3-fold increase in rate constant (k_s, 2.1 s^-1) and an enhanced turnover rate (k_cat, 2.74 × 10^-9 M cm^-2 s^-1) in comparison with CNTs. Meanwhile, theoretical modeling clarifies that the active center of GOD interacts more strongly with P-doped CNTs and maintains their conformation well compared to other CNTs. This study will help to understand the mechanism of heteroatom doping of carbon on the enzymatic electron transfer and shed light on the design of efficient bioelectrocatalytic interfaces.

Understanding the activity of glucose oxidase after exposure to organic solvents

Long-term stability of enzymes in organic solvents is one of the most challenging problems in modern biotechnology and chemical industries. However, the resistance of enzymes to organic solvents is not very well understood so far. Herein, the effects of apolar, chlorinated, and polar organic solvents on the activity and structure of glucose oxidase from Aspergillus niger were systemically investigated using spectrophotometric activity assay of this enzyme and absorption and chiroptical spectroscopy. Molecular dynamics simulations and correlation of the activity with properties of the organic solvents were employed to understand the effects of organic solvents on the enzyme. The experimental and theoretical results showed that apolar solvents reduce the enzyme activity because they facilitate its aggregation through inter-enzymatic salt bridges. Moreover, polar solvents strongly coordinate with amino acid residues in the glucose binding pocket and prevent binding of the substrates. We found that this enzyme is stable in pure apolar and chlorinated solvents and these solvents can be used for the functionalization of its residues. This work provides an in depth understanding at the molecular level of the impact of various pure organic solvents on the structure and dynamics of glucose oxidase and the regulation of its catalytic activity.

Construction of Covalent Organic Framework Capsule-Based Nanoreactor for Sensitive Glucose Detection

Enzyme immobilization is critical to boosting its application in various areas. Covalent organic frameworks (COFs) are ideal hosts for enzyme immobilization due to their porous and predesignable structures. Nevertheless, the construction of COFs-based enzyme immobilization systems with high activity via existing immobilization methods (including covalent linkages and channel entrapment) remains a considerable challenge. Herein, a versatile approach was introduced to encapsulate enzymes within hollow COF capsule (named enzyme@COF) using metal-organic frameworks (including ZPF-1(C8H11N4O4.5Zn), ZIF-8(C8H10N4Zn), and ZIF-90(C8H6N4O2Zn)) as sacrificial templates. The obtained porous COF capsule could not only facilitate the efficient mass transfer of enzymatic reactions but also protect enzymes against the incompatible conditions, resulting in enhanced activity and stability of the encapsulated enzymes. Moreover, this approach offered an opportunity to spatially organize multienzymes in COF capsule to construct enzyme cascade system. For instance, glucose oxidase (GOx) and cytochrome c (Cyt c) were coencapsulated within COF capsule to construct GOx-Cyt c cascade. The integration of GOx and Cyt c within COF capsule achieved ∼1.6-fold improvement in catalytic activity than that of free enzymes and the resultant GOx-Cyt c@COF was successfully adopted as a nanoreactor for the sensitive determination of glucose in serum. This work provided a new insight into the design of COFs-based enzyme immobilization systems.

Molecular Dynamics Simulation of E412 Catalytic Residue Mutation of GOx-IPBCC

The enzyme glucose oxidase from Aspergillus niger has a homodimeric structure, consisting of two identical subunits with a molecular weight of 150,000 Daltons. In this study, we used the structure of the enzyme glucose oxidase from Aspergillus niger IPBCC.08.610 (GOx-IPBCC), this enzyme had a total activity of 92.87 U (μmol/min) and a Michaelis-Menten constant (Km) of 2.9 mM (millimolar). This study was conducted to predict the molecular dynamics of E412 (Glu412) residue catalytic mutation belonging to the GOx-IPBCC enzyme was determine the effect of changes in the catalytic residue on substrate binding (β-D-glucose). The results of molecular docking of 19 mutant structures, six E412 mutant homologous structures were selected (E412C, E412K, E412Q, E412T, E412, E412V, and E412W), which were evaluated using molecular dynamics simulation for 50 ns. The results showed a decrease in ∆G values in two mutant structures is E412C and E412T, and there is one mutant structure that increased ∆G values, namely E412W, these three mutant structures showed the best stability, bond interaction, and salt bridge profile according to molecular dynamics simulation.

Regulation of different protonated states of two intimate histidine residues on the reductive half-reaction of glucose oxidase

Glucose oxidase (GOx) can catalyze the oxidation of β-D-glucose under mild conditions to directly convert biological energy into electrical energy, which has great potential for applications in the fields of enzyme biofuel cells and glucose biosensors. In enzymatic biofuel cells, GOx is often used as an anodic catalyst to improve the performance. The important role of two intimate histidine residues, His505 and His548 (PDB code 4YNU), in the GOx active center has been highlighted in the catalytic oxidation of β-D-glucose, but there is still a lack of systematic examination on the influence of different protonated states of His505 and His548 on the catalytic oxidation of β-D-glucose in GOx. Therefore, in the present work, the GOx active center under the possible protonated states of His548 and His505 is systematically examined by using ONIOM calculations, as well as the influence of remote Arg210 is considered. The calculations reveal that the intimate His505 and His548 can modulate the interaction of the β-D-glucose substrate with isoalloxazine and then control the deprotonization of the hydroxyl group bound to the anomeric carbon of β-D-glucose like controllers. The remote Arg210 provides the driving force for the transfer of two electrons from β-D-glucose to isoalloxazine of FAD via the long-range electrostatic attraction like a horse. Specially, the protonated His505 can serve as a good helper of Arg210 to promote the occurring of the two-proton-coupled two-electron transfer from β-D-glucose to isoalloxazine and His548 in the active center of GOx. These findings provide much insight into the catalytic reactions of GOx in a low pH environment, which may be beneficial to expand the applications of GOx.

Photochemical and Molecular Dynamics Studies of Halide Binding in Flavoenzyme Glucose Oxidase

Glucose oxidase (GOX), a characteristic flavoprotein oxidase with widespread industrial applications, binds fluoride (F - ) and chloride (Cl - ). We investigated binding properties of halide inhibitors of GOX through time-resolved spectral characterization of flavin-related photochemical processes and molecular dynamic simulations. Cl - and F - bind differently to the protein active site and have substantial but opposite effects on the population and decay of the flavin excited state. Cl - binds closer to the flavin, whose excited-state decays in <100 fs due to anion-π interactions. Such interactions appear absent in F - binding, which, however, significantly increases the active-site rigidity leading to more homogeneous, picosecond fluorescence decay kinetics. These findings are discussed in relation to the mechanism of halide inhibition of GOX by occupying the  accommodation site of catalytic intermediates and increasing the active-site rigidity.

Review of glucose oxidase as a feed additive: production, engineering, applications, growth-promoting mechanisms, and outlook

The regulation and prohibition of antibiotics used as growth promoters (AGP) in the feed field are increasing because they cause antimicrobial resistance and drug residue issues and threaten community health. Recently, glucose oxidase (GOx) has attracted increasing interest in the feed industry as an alternative to antibiotics. GOx specifically catalyzes the production of gluconic acid (GA) and hydrogen peroxide (H₂O₂) by consuming molecular oxygen, and plays an important role in relieving oxidative stress, preserving health, and promoting animal growth. To expand the application of GOx in the feed field, considerable efforts have been made to mine new genetic resources. Efforts have also been made to heterologously overexpress relevant genes to reduce production costs and to engineer proteins by modifying enzyme properties, both of which are bottleneck problems that limit industrial feed applications. Herein, the: different sources, diverse biochemical properties, distinct structural features, and various strategies of GOx engineering and heterologous overexpression are summarized. The mechanism through which GOx promotes growth in animal production, including the improvement of antioxidant capacity, maintenance of intestinal microbiota homeostasis, and enhancement of gut function, are also systematically addressed. Finally, a new perspective is provided for the future development of GOx applications in the feed field.

Molecular Docking Study of IPBCC.08.610 Glucose Oxidase Mutant for Increasing Gluconic Acid Production

Glucose oxidase (GOD) is an oxidoreductase enzyme that catalyzes the oxidation of glucose to gluconolactone and hydrogen peroxide. Then, gluconolactone will be hydrolyzed to gluconic acid. The wide application of gluconic acid in various industries has increased production demand. However, glucose concentrations higher than 40% (w/w) inhibited the conversion of glucose to gluconic acid due to a decrease in the oxygen solubility concentration at pH 6, 30℃, and 1 bar pressure. Therefore, decreasing the value of Km is predicted to reduce saturation and enhance gluconic acid production. This study aimed to analyze the interaction between the IPBCC.08.610 GOD mutant with β-D-Glucose in improving gluconic acid production by decreasing the Km value. Mutations were performed in silico using Chimera and then docked using AutoDock Vina. The mutations resulted in distinct ligand poses in the binding pocket, different -OH conformations of the ligands, and changes in the T554M/D578P mutant’s hydrophobicity index (554 mutated from threonine to methionine, and 578 mutated from aspartate to proline), and decreased ΔG and Km values in the H559D mutant (559 mutated from histidine to aspartate), D578P and T554M/D578P. This decrease might strengthen the ligand-receptor interaction, increasing gluconic acid production. The H559D was the best mutant to increase production based on the ΔG, Km value, and stability due to the addition of hydrogen bonds.

Kinetically restrained oxygen reduction to hydrogen peroxide with nearly 100% selectivity

Hydrogen peroxide has been synthesized mainly through the electrocatalytic and photocatalytic oxygen reduction reaction in recent years. Herein, we synthesize a single-atom rhodium catalyst (Rh₁/NC) to mimic the properties of flavoenzymes for the synthesis of hydrogen peroxide under mild conditions. Rh₁/NC dehydrogenates various substrates and catalyzes the reduction of oxygen to hydrogen peroxide. The maximum hydrogen peroxide production rate is 0.48 mol g_catalyst^-1 h^-1 in the phosphorous acid aerobic oxidation reaction. We find that the selectivity of oxygen reduction to hydrogen peroxide can reach 100%. This is because a single catalytic site of Rh₁/NC can only catalyze the removal of two electrons per substrate molecule; thus, the subsequent oxygen can only obtain two electrons to reduce to hydrogen peroxide through the typical two-electron pathway. Similarly, due to the restriction of substrate dehydrogenation, the hydrogen peroxide selectivity in commercial Pt/C-catalyzed enzymatic reactions can be found to reach 75%, which is 30 times higher than that in electrocatalytic oxygen reduction reactions.

Glucose Oxidase, an Enzyme "Ferrari": Its Structure, Function, Production and Properties in the Light of Various Industrial and Biotechnological Applications

Glucose oxidase (GOx) is an important oxidoreductase enzyme with many important roles in biological processes. It is considered an "ideal enzyme" and is often called an oxidase "Ferrari" because of its fast mechanism of action, high stability and specificity. Glucose oxidase catalyzes the oxidation of β-d-glucose to d-glucono-δ-lactone and hydrogen peroxide in the presence of molecular oxygen. d-glucono-δ-lactone is sequentially hydrolyzed by lactonase to d-gluconic acid, and the resulting hydrogen peroxide is hydrolyzed by catalase to oxygen and water. GOx is presently known to be produced only by fungi and insects. The current main industrial producers of glucose oxidase are Aspergillus and Penicillium. An important property of GOx is its antimicrobial effect against various pathogens and its use in many industrial and medical areas. The aim of this review is to summarize the structure, function, production strains and biophysical and biochemical properties of GOx in light of its various industrial, biotechnological and medical applications.

Ultrafast photooxidation of protein-bound anionic flavin radicals

Flavoproteins are colored proteins involved in a large variety of biochemical reactions. They can perform photochemical reactions, which are increasingly exploited for bioengineering new protein-derived photocatalysts. In particular, light-induced reduction of the resting oxidized state of the flavin by close-lying amino acids or substrates is extensively studied. Here, we demonstrate that the reverse and previously unknown reaction photooxidation of the anionic semireduced flavin radical, a short-lived reaction intermediate in many biochemical reactions, efficiently occurs in flavoprotein oxidases. We anticipate that this finding will allow photoreduction of external reactants and lead to exploration of novel photocatalytic pathways.

The photophysical properties of anionic semireduced flavin radicals are largely unknown despite their importance in numerous biochemical reactions. Here, we studied the photoproducts of these intrinsically unstable species in five different flavoprotein oxidases where they can be stabilized, including the well-characterized glucose oxidase. Using ultrafast absorption and fluorescence spectroscopy, we unexpectedly found that photoexcitation systematically results in the oxidation of protein-bound anionic flavin radicals on a time scale of less than ∼100 fs. The thus generated photoproducts decay back in the remarkably narrow 10- to 20-ps time range. Based on molecular dynamics and quantum mechanics computations, positively charged active-site histidine and arginine residues are proposed to be the electron acceptor candidates. Altogether, we established that, in addition to the commonly known and extensively studied photoreduction of oxidized flavins in flavoproteins, the reverse process (i.e., the photooxidation of anionic flavin radicals) can also occur. We propose that this process may constitute an excited-state deactivation pathway for protein-bound anionic flavin radicals in general. This hitherto undocumented photochemical reaction in flavoproteins further extends the family of flavin photocycles.

Tailored enzymes as next-generation food-packaging tools

Enzymes have the potential for biotransformation in the food industry. Engineering tools can be used to develop tailored enzymes for food-packaging systems that perform well and retain their activity under adverse conditions. Consequently, novel tailored enzymes have been produced to improve or include new and useful characteristics for intelligent food-packaging systems. This review discusses the protein-engineering tools applied to create new functionality in food-packaging enzymes. The challenges in applications and anticipated directions for future developments are also highlighted. The development and discovery of tailored enzymes for smart food packaging is a promising way to ensure safe and high-quality food products.

Fuel-Driven and Enzyme-Regulated Redox-Responsive Supramolecular Hydrogels

Chemical reaction networks (CRN) embedded in hydrogels can transform responsive materials into complex self-regulating materials that generate feedback to counter the effect of external stimuli. This study presents hydrogels containing the β-cyclodextrin (CD) and ferrocene (Fc) host-guest pair as supramolecular crosslinks where redox-responsive behavior is driven by the enzyme-fuel couples horse radish peroxidase (HRP)-H2 O2 and glucose oxidase (GOx)-d-glucose. The hydrogel can be tuned from a responsive to a self-regulating supramolecular system by varying the concentration of added reduction fuel d-glucose. The onset of self-regulating behavior is due to formation of oxidation fuel in the hydrogel by a cofactor intermediate GOx[FADH2 ]. UV/Vis spectroscopy, rheology, and kinetic modeling were employed to understand the emergence of out-of-equilibrium behavior and reveal the programmable negative feedback response of the hydrogel, including the adaptation of its elastic modulus and its potential as a glucose sensor.

Two β-Lactamase Variants with Reduced Clavulanic Acid Inhibition Display Different Millisecond Dynamics

The β-lactamase of Mycobacterium tuberculosis, BlaC, is susceptible to inhibition by clavulanic acid. The ability of this enzyme to escape inhibition through mutation was probed using error-prone PCR combined with functional screening in Escherichia coli. The variant that was found to confer the most inhibitor resistance, K234R, as well as variant G132N that was found previously were characterized using X-ray crystallography and nuclear magnetic resonance (NMR) relaxation experiments to probe structural and dynamic properties. The G132N mutant exists in solution in two almost equally populated conformations that exchange with a rate of ca. 88 s-1. The conformational change affects a broad region of the enzyme. The crystal structure reveals that the Asn132 side chain forces the peptide bond between Ser104 and Ile105 in a cis-conformation. The crystal structure suggests multiple conformations for several side chains (e.g., Ser104 and Ser130) and a short loop (positions 214 to 216). In the K234R mutant, the active-site dynamics are significantly diminished with respect to the wild-type enzyme. These results show that multiple evolutionary routes are available to increase inhibitor resistance in BlaC and that active-site dynamics on the millisecond time scale are not required for catalytic function.

The evolution and engineering of enzyme activity through tuning conformational landscapes

Proteins are dynamic molecules whose structures consist of an ensemble of conformational states. Dynamics contribute to protein function and a link to protein evolution has begun to emerge. This increased appreciation for the evolutionary impact of conformational sampling has grown from our developing structural biology capabilities and the exploration of directed evolution approaches, which have allowed evolutionary trajectories to be mapped. Recent studies have provided empirical examples of how proteins can evolve via conformational landscape alterations. Moreover, minor conformational substates have been shown to be involved in the emergence of new enzyme functions as they can become enriched through evolution. The role of remote mutations in stabilizing new active site geometries has also granted insight into the molecular basis underpinning poorly understood epistatic effects that guide protein evolution. Finally, we discuss how the growth of our understanding of remote mutations is beginning to refine our approach to engineering enzymes.

Structure and function relationships of sugar oxidases and their potential use in biocatalysis

Several sugar oxidases that catalyze the oxidation of sugars have been isolated and characterized. These enzymes can be classified as flavoenzyme due to the presence of flavin adenine dinucleotide (FAD) as a cofactor. Sugar oxidases have been proposed to be the key biocatalyst in biotransformation of carbohydrates which can potentially convert sugars to provide a pool of intermediates for synthesis of rare sugars, fine chemicals and drugs. Moreover, sugar oxidases have been applied in biosensing of various biomolecules in food industries, diagnosis of diseases and environmental pollutant detection. This review provides the discussions on general properties, current mechanistic understanding, structural determination, biocatalytic application, and biosensor integration of representative sugar oxidase enzymes, namely pyranose 2-oxidase (P2O), glucose oxidase (GO), hexose oxidase (HO), and oligosaccharide oxidase. The information regarding the relationship between structure and function of these sugar oxidases points out the key properties of this particular group of enzymes that can be modified by engineering, which had resulted in a remarkable economic importance.

Harnessing Conformational Plasticity to Generate Designer Enzymes

Recent years have witnessed an explosion of interest in understanding the role of conformational dynamics both in the evolution of new enzymatic activities from existing enzymes and in facilitating the emergence of enzymatic activity de novo on scaffolds that were previously non-catalytic. There are also an increasing number of examples in the literature of targeted engineering of conformational dynamics being successfully used to alter enzyme selectivity and activity. Despite the obvious importance of conformational dynamics to both enzyme function and evolvability, many (although not all) computational design approaches still focus either on pure sequence-based approaches or on using structures with limited flexibility to guide the design. However, there exist a wide variety of computational approaches that can be (re)purposed to introduce conformational dynamics as a key consideration in the design process. Coupled with laboratory evolution and more conventional existing sequence- and structure-based approaches, these techniques provide powerful tools for greatly expanding the protein engineering toolkit. This Perspective provides an overview of evolutionary studies that have dissected the role of conformational dynamics in facilitating the emergence of novel enzymes, as well as advances in computational approaches that allow one to target conformational dynamics as part of enzyme design. Harnessing conformational dynamics in engineering studies is a powerful paradigm with which to engineer the next generation of designer biocatalysts.

Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations

Guanylate binding proteins (GBPs) belong to the dynamin-related superfamily and exhibit various functions in the fight against infections. The functions of the human guanylate binding protein 1 (hGBP1) are tightly coupled to GTP hydrolysis and dimerization. Despite known crystal structures of the hGBP1 monomer and GTPase domain dimer, little is known about the dynamics of hGBP1. To gain a mechanistic understanding of hGBP1, we performed sub-millisecond multi-resolution molecular dynamics simulations of both the hGBP1 monomer and dimer. We found that hGBP1 is a highly flexible protein that undergoes a hinge motion similar to the movements observed for other dynamin-like proteins. Another large-scale motion was observed for the C-terminal helix α13, providing a molecular view for the α13-α13 distances previously reported for the hGBP1 dimer. Most of the loops of the GTPase domain were found to be flexible, revealing why GTP binding is needed for hGBP1 dimerization to occur.

Tackling the Challenges of Enzymatic (Bio)Fuel Cells

The ever-increasing demands for clean and sustainable energy sources combined with rapid advances in biointegrated portable or implantable electronic devices have stimulated intensive research activities in enzymatic (bio)fuel cells (EFCs). The use of renewable biocatalysts, the utilization of abundant green, safe, and high energy density fuels, together with the capability of working at modest and biocompatible conditions make EFCs promising as next generation alternative power sources. However, the main challenges (low energy density, relatively low power density, poor operational stability, and limited voltage output) hinder future applications of EFCs. This review aims at exploring the underlying mechanism of EFCs and providing possible practical strategies, methodologies and insights to tackle these issues. First, this review summarizes approaches in achieving high energy densities in EFCs, particularly, employing enzyme cascades for the deep/complete oxidation of fuels. Second, strategies for increasing power densities in EFCs, including increasing enzyme activities, facilitating electron transfers, employing nanomaterials, and designing more efficient enzyme-electrode interfaces, are described. The potential of EFCs/(super)capacitor combination is discussed. Third, the review evaluates a range of strategies for improving the stability of EFCs, including the use of different enzyme immobilization approaches, tuning enzyme properties, designing protective matrixes, and using microbial surface displaying enzymes. Fourth, approaches for the improvement of the cell voltage of EFCs are highlighted. Finally, future developments and a prospective on EFCs are envisioned.

Enzymatic self-wiring in nanopores and its application in direct electron transfer biofuel cells

A synthetic enzymatic activity in nanopores leading to the direct fabrication of modified electrodes applicable as biosensors and/or biofuel cell elements is reported. We demonstrate the heterogeneous enzymatic implanting of platinum nanoclusters, PtNCs, in glucose oxidase, GOx, immobilized on mesoporous carbon nanoparticles, MPCNP-modified surface. As the pores confine the growth of the clusters, the PtNC@GOx/MPCNP assembly becomes electrically wired to the matrix, demonstrating direct electron transfer, DET, bioelectrocatalytic properties that correlate with the applied duration of synthesis and cluster size. This inside-out nanocluster growth from the cofactor to the matrix is investigated and further compared to a reversed outside-in strategy which follows the electrochemical deposition of the Pt clusters inside the pores and their electrically induced expansion towards the FAD center of the enzyme. While the inside-out and outside-in methodologies provide, for the first time, synthetic bidirectional direct wiring routes of an enzyme to a surface, we highlight an asymmetry in the wiring efficiency associated with the different assemblies. The results indicate the existence of a shorter gap between the FAD cofactor and the PtNCs in the enzymatically implanted assembly, resulting in elevated bioelectrocatalytic currents, lower overpotential, and a higher turnover rate, 2580 e^- s^-1. The implanted assembly is then coupled to a bilirubin oxidase-adsorbed MPCNP cathode to yield an all-DET biofuel cell. Due to the superior electrical contact of the inside-out-synthesized anode, this cell demonstrates enhanced discharge potential and power outputs as compared to similar systems employing electrochemically synthesized outside-in-grown PtNC-GOx/MPCNPs or even GOx-modified MPCNPs diffusionally mediated by ferrocenemethanol.

Protein engineers turned evolutionists-the quest for the optimal starting point

The advent of laboratory directed evolution yielded a fruitful crosstalk between the disciplines of molecular evolution and bio-engineering. Here, we outline recent developments in both disciplines with respect to how one can identify the best starting points for directed evolution, such that highly efficient and robust tailor-made enzymes can be obtained with minimal optimization. Directed evolution studies have highlighted essential features of engineer-able enzymes: highly stable, mutationally robust enzymes with the capacity to accept a broad range of substrates. Robust, evolvable enzymes can be inferred from the natural sequence record. Broad substrate spectrum relates to conformational plasticity and can also be predicted by phylogenetic analyses and/or by computational design. Overall, an increasingly powerful toolkit is becoming available for identifying optimal starting points including network analyses of enzyme superfamilies and other bioinformatics methods.

The evolution of multiple active site configurations in a designed enzyme

Developments in computational chemistry, bioinformatics, and laboratory evolution have facilitated the de novo design and catalytic optimization of enzymes. Besides creating useful catalysts, the generation and iterative improvement of designed enzymes can provide valuable insight into the interplay between the many phenomena that have been suggested to contribute to catalysis. In this work, we follow changes in conformational sampling, electrostatic preorganization, and quantum tunneling along the evolutionary trajectory of a designed Kemp eliminase. We observe that in the Kemp Eliminase KE07, instability of the designed active site leads to the emergence of two additional active site configurations. Evolutionary conformational selection then gradually stabilizes the most efficient configuration, leading to an improved enzyme. This work exemplifies the link between conformational plasticity and evolvability and demonstrates that residues remote from the active sites of enzymes play crucial roles in controlling and shaping the active site for efficient catalysis.

Molecular modeling of conformational dynamics and its role in enzyme evolution

With increasing computational power, biomolecular simulations have become an invaluable tool for understanding enzyme mechanisms and the origins of enzyme catalysis. More recently, computational studies have started to focus on understanding how enzyme activity itself evolves, both in terms of enhancing the native or new activities on existing enzyme scaffolds, or completely de novo on previously non-catalytic scaffolds. In this context, both experiment and molecular modeling provided strong evidence for an important role of conformational dynamics in the evolution of enzyme functions. This contribution will present a brief overview of the current state of the art for computationally exploring enzyme conformational dynamics in enzyme evolution, and, using several showcase studies, illustrate the ways molecular modeling can be used to shed light on how enzyme function evolves, at the most fundamental molecular level.

Conformational dynamics and enzyme evolution

Enzymes are dynamic entities, and their dynamic properties are clearly linked to their biological function. It follows that dynamics ought to play an essential role in enzyme evolution. Indeed, a link between conformational diversity and the emergence of new enzyme functionalities has been recognized for many years. However, it is only recently that state-of-the-art computational and experimental approaches are revealing the crucial molecular details of this link. Specifically, evolutionary trajectories leading to functional optimization for a given host environment or to the emergence of a new function typically involve enriching catalytically competent conformations and/or the freezing out of non-competent conformations of an enzyme. In some cases, these evolutionary changes are achieved through distant mutations that shift the protein ensemble towards productive conformations. Multifunctional intermediates in evolutionary trajectories are probably multi-conformational, i.e. able to switch between different overall conformations, each competent for a given function. Conformational diversity can assist the emergence of a completely new active site through a single mutation by facilitating transition-state binding. We propose that this mechanism may have played a role in the emergence of enzymes at the primordial, progenote stage, where it was plausibly promoted by high environmental temperatures and the possibility of additional phenotypic mutations.

Conformational Sampling of the Intrinsically Disordered C-Terminal Tail of DERA Is Important for Enzyme Catalysis

2-Deoxyribose-5-phosphate aldolase (DERA) catalyzes the reversible conversion of acetaldehyde and glyceraldehyde-3-phosphate into deoxyribose-5-phosphate. DERA is used as a biocatalyst for the synthesis of drugs such as statins and is a promising pharmaceutical target due to its involvement in nucleotide catabolism. Despite previous biochemical studies suggesting the catalytic importance of the C-terminal tyrosine residue found in several bacterial DERAs, the structural and functional basis of its participation in catalysis remains elusive because the electron density for the last eight to nine residues (i.e., the C-terminal tail) is absent in all available crystal structures. Using a combination of NMR spectroscopy and molecular dynamics simulations, we conclusively show that the rarely studied C-terminal tail of E. coli DERA (ecDERA) is intrinsically disordered and exists in equilibrium between open and catalytically relevant closed states, where the C-terminal tyrosine (Y259) enters the active site. Nuclear Overhauser effect distance restraints, obtained due to the presence of a substantial closed state population, were used to derive the solution-state structure of the ecDERA closed state. Real-time NMR hydrogen/deuterium exchange experiments reveal that Y259 is required for efficiency of the proton abstraction step of the catalytic reaction. Phosphate titration experiments show that, in addition to the phosphate-binding residues located near the active site, as observed in the available crystal structures, ecDERA contains previously unknown auxiliary phosphate-binding residues on the C-terminal tail which could facilitate in orienting Y259 in an optimal position for catalysis. Thus, we present significant insights into the structural and mechanistic importance of the ecDERA C-terminal tail and illustrate the role of conformational sampling in enzyme catalysis.

Biotechnological and protein-engineering implications of ancestral protein resurrection

Approximations to the sequences of ancestral proteins can be derived from the sequences of their modern descendants. Proteins encoded by such reconstructed sequences can be prepared in the laboratory and subjected to experimental scrutiny. These 'resurrected' ancestral proteins often display remarkable properties, reflecting ancestral adaptations to intra-cellular and extra-cellular environments that differed from the environments hosting modern/extant proteins. Recent experimental and computational work has specifically discussed high stability, substrate and catalytic promiscuity, conformational flexibility/diversity and altered patterns of interaction with other sub-cellular components. In this review, we discuss these remarkable properties as well as recent attempts to explore their biotechnological and protein-engineering potential.

Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation

Engineering high chemo-, regio-, and stereoselectivity is a prerequisite for enzyme usage in organic synthesis. Cytochromes P450 can oxidize a broad range of substrates, including macrocycles, which are becoming popular scaffolds for therapeutic agents. However, a large conformational space explored by macrocycles not only reduces the selectivity of oxidation but also impairs computational enzyme design strategies based on docking and molecular dynamics (MD) simulations. We present a novel design workflow that uses enhanced-sampling Hamiltonian replica exchange (HREX) MD and focuses on quantifying the substrate binding for suggesting the mutations to be made. This computational approach is applied to P450 BM3 with the aim to shift regioselectively toward one of the numerous possible positions during β-cembrenediol oxidation. The predictions are experimentally tested and the resulting product distributions validate our design strategy, as single mutations led up to 5-fold regioselectivity increases. We thus conclude that the HREX-MD-based workflow is a promising tool for the identification of positions for mutagenesis aiming at P450 enzymes with improved regioselectivity.