Sabatier Principle for Interfacial (Heterogeneous) Enzyme Catalysis

SPOCK Tool for Constructing Empirical Volcano Diagrams from Catalytic Data

Volcano plots, stemming from the Sabatier principle, visualize descriptor-performance relationships, allowing rational catalyst design. Manually drawn volcanoes originating from experimental studies are potentially prone to human bias as no guidelines or metrics exist to quantify the goodness of fit. To address this limitation, we introduce a framework called SPOCK (systematic piecewise regression for volcanic kinetics) and validate it using experimental data from heterogeneous, homogeneous, and enzymatic catalysis to fit volcano-like relationships. We then generalize this approach to DFT-derived volcanoes and evaluate the tool's robustness against noisy kinetic data and in identifying false-positive volcanoes, i.e., cases where studies claim a volcano-like relationship exists, but such correlations are not statistically significant. Once the SPOCK's functional features are established, we demonstrate its potential to identify descriptor-performance relationships, exemplified via the ceria-promoted water-gas shift and single-atom-catalyzed electrocatalytic carbon dioxide reduction reactions. In both cases, the model uncovers descriptors previously unreported, revealing insights that are not easily recognized by human experts. Finally, we showcase SPOCK's capabilities to formulate multivariable descriptors, an emerging topic in catalysis research. Our work pioneers an automated and standardized tool for volcano plot construction and validation, and we release the model as an open-source web application for greater accessibility and knowledge generation in catalysis.

Mechanism analysis for the differences in multi-level structure, enzyme accessibility and pasting properties of starch granules caused by different hydrolysis pathways of maltogenic α-amylase

The effect of pores distribution on the multi-scale structure, enzyme accessibility, and pasting properties of the waxy maize starch granules with the same degree of hydrolysis were examined. Increased maltogenic α-amylase (MA) dosage obviously increased the shallow pores number and the roughness, whereas extended time increased the holes depth. Despite achieving the same hydrolysis degree and specific surface area, samples with numerous shallow holes exhibited a higher mass fractal dimension, a lower, peak viscosity, final viscosity and setback. Besides, increased dosage prompted a sustained decrease in the number of short chains with DP 10-17; whereas prolonging time encouraged the continuous catalyzation in the same chains. Enzymatic probe profiles showed MA was more accessible to the amorphous region on the periphery of starch granules, rather than the inside. This finding provides a more valuable understanding of the catalytic mechanism for MA in heterogeneous systems and an accurate guidance for the industrial production.

Regulating the production distribution in Ni-Cu nanoparticle mediated nitrile hydrogenation

The selective hydrogenation of nitrile compounds represents a pivotal area of research within both industrial and academic catalysis. In this study, we prepared Ni-Cu bimetallic catalysts through a co-deposition-crystallization sequence, aimed at the efficient production of primary and secondary amines. The enhanced selectivity for primary amines is attributed to the downshift of the d-band center of Ni0.1Cu, which weakens the adsorption of key imine intermediates. Consequently, the synthesized Ni-Cu catalysts demonstrated exceptional catalytic performance in the selective hydrogenation of nitrile compounds, including those with reduction-sensitive functional groups such as -Cl and -Br, achieving 100 % conversion efficiency and significant yields ranging from 80 % to 99 %. The reaction conditions were comprehensively optimized, taking into account factors such as temperature, solvent, time, additives, and hydrogen pressure. Furthermore, the catalytic performance of Ni0.1Cu and Ni0.4Cu in the selective hydrogenation of nitriles was sustained over at least five reaction cycles. Temperature-programmed desorption results elucidated the structure-activity relationship, revealing that a strong interaction site prevails in Ni0.4Cu, while a weaker or moderate interaction site in Ni0.1Cu is responsible for the formation of primary amines. Theoretical calculations indicate that the reaction proceeds via an imine mechanism, with benzylideneimine serving as a key intermediate. This work may stimulate further research into the development of bimetallic nano-catalysts for selective nitrile hydrogenation in industrial catalytic processes.

Phase Engineering Modulates the Electronic Structure of the IrO2/MoS2 Heterojunction for Efficient and Stable Water Splitting

The engineering of dual-functional catalytic systems capable of driving complete water dissociation in acidic environments represents a critical requirement for advancing proton exchange membrane electrolyzer technology, yet significant challenges remain. In this work, we investigate an IrO2/MoS2/CNT heterostructure catalyst demonstrating enhanced bifunctional performance for both the oxygen evolution reaction (OER) and hydrogen evolution reaction (HER) under acidic conditions. Strategic incorporation of IrO2 into the MoS2/CNT heterojunction induces a partial phase transformation from 2H to the metastable 1T configuration in MoS2, thereby modulating the electronic structure of IrO2 and improving the catalytic performance for overall water splitting. The optimized IrO2/MoS2/CNT catalyst exhibited exceptional overpotentials of 9 mV (HER) and 182 mV (OER) at a current density of 10 mA cm-2 in acidic media. Full-cell evaluations further confirmed its practical potential, showing a 1.47 V operation voltage that outperforms standard Pt/C||IrO2 counterparts by 120 mV. The experimental results revealed that the n-n heterojunction between IrO2/CNT and MoS2/CNT generates a built-in electric field, enhancing charge redistribution and electron transport. Moreover, density functional theory simulations further identify iridium centers as dominant catalytic loci, with a metastable 1T-MoS2 phase mediating charge equilibration at atomic interfaces. This modification facilitates *OH adsorption and *OOH deprotonation and lowers the kinetic barrier during the water-splitting process.

Hyper-production and Characterization of Exoglucanase Through Physical, Chemical, and Combined Mutagenesis in Indigenous Strain of Thermophilic Aspergillus fumigatus

The present study explored the optimization of exoglucanase production from waste cellulosic biomaterials using microbial cellulases, focusing on enhancing enzyme efficiency through mutagenesis techniques. Research illustrated the hyper-production and quantitative characterization of an exoglucanase from a thermophilic Aspergillus fumigatus strain via physical and chemical mutagenesis under optimized fermentation conditions. Physical mutagenesis via UV irradiation (15-min exposure) yielded the highest activity (96.57 U/mL), while chemical mutagenesis with ethyl methane sulfonates (250 µg/mL) resulted in 69.61 U/mL activity. Combined mutagenesis using EMS (250 µg/mL) concentration with 15-min UV exposure significantly enhanced exoglucanase production to 136.19 U/mL as compared to the native enzyme 52.46 U/mL. Among various cellulosic substrates, peanut shells exhibited superior suitability for exoglucanase production reaching a maximum activity of 202.41 U/mL. Fermentation parameters including pH, temperature, incubation period, and inoculum size were optimized, leading to a substantial increase in exoglucanase activity of 285.28 U/mL using response surface methodology followed by gel filtration chromatography. The mutant exoglucanase was characterized by its enhanced activities with a higher Vmax (0.6515) and lower Km (0.3142) than those of native enzyme. The characterization has confirmed the temperature and pH tolerance of the mutant enzyme, as well as its tolerance to metal ions and substrate concentrations. This study showed how mutagenesis-driven optimization could provide a means to enhance exoglucanase production from cellulosic biomass, with a rational insight toward enzyme kinetics and applications toward bioenergy generation.

Tailoring the Selective Oxidation of Hydroxyl-Containing Compounds via Precisely Tuning the Hydrogen-Bond Strength of Catalyst H-Bond Acceptors

The unique performance of the enzyme is mainly achieved via weak interactions between the "outer coordination sphere" and the substrate. Inspired by this process, we developed 3D encapsulated-structure catalysts with hydrogen-bond engineering on the shell, which mimics the "outer coordination sphere" of an enzyme. Various hydrogen bond acceptors (C=O, S=O, and N-O groups) are imparted in the shell. Concentration-dependent 1H NMR, inverse-phase gas Chromatography (IGC) measurements, and DFT calculations underscore that the hydrogen bond strength between the acceptor groups and alcohol follows the order of C=O < S=O < N-O. The hydroxyl compound oxidation rate vs the hydrogen bond strength follows a volcano behavior, reminiscent of Sabatier's principle. The performance variation among catalysts is attributed to the adsorption strength of the substrate. The proposed bioinspired design principle expands the scope of encapsulated catalysts, enabling fine regulation of catalytic activity through precise microenvironment control via weak interactions with substrates.

Toward a Circular Economy of Heteroatom Containing Plastics: A Focus on Heterogeneous Catalysis in Recycling

Plastics play a vital role in modern society, but their accumulation in landfills and the environment presents significant risks to ecosystems and human health. In addition, the discarding of plastic waste constitutes to a loss of valuable material. While the usual mechanical recycling method often results in reduced material quality, chemical recycling offers exciting opportunities to valorize plastic waste into compounds of interest. Its versatility leans on the broad horizon of chemical reactions applicable, such as hydrogenolysis, hydrolysis, alcoholysis, or aminolysis. The development of heterogeneous and supported organocatalysts has enormous potential to enhance the economic and industrial viability of these technologies, reducing the cost of the process and mitigating its global environmental impact. This review summarizes the challenges and opportunities of chemically recycling heteroatom-containing plastics through heterogeneous catalysis, covering widely used plastics such as polyesters (notably PET and PLA), BPA-polycarbonate (BPA-PC), polyurethane (PU), polyamide (PA), and polyether. It examines the potential and limitations of various solid catalysts, including clays, zeolites, and metal-organic frameworks as well as supported organocatalysts and immobilized enzymes (heterogeneous biocatalysts), for reactions that facilitate the recovery of high-value products. By reintroducing these high-value products into the economy as precursors, this approach supports a more sustainable lifecycle for plastics, aligning with the principles of a circular economy.

Structure-Activity Relationships for s-Block Metal/Co(III) Heterodinuclear Catalysts in Cyclohexene Oxide Ring-Opening Copolymerizations

In homogeneous catalysis, uncovering structure-activity relationships remains very rare but invaluable to understand and rationally improve performances. Here, generalizable structure-activity relationships apply to a series of heterodinuclear polymerization catalysts featuring Co(III) and s-block metals M(I/II) (M=Na(I), K(I), Ca(II), Sr(II), Ba(II)). These are shown to apply to polycarbonate production by the ring-opening copolymerizations (ROCOP) of cyclohexene oxide (CHO) and carbon dioxide (CO2), conducted at high (20 bar) and low (1 bar) CO2 pressures, and to polyester production by copolymerization of cyclohexene oxide and phthalic anhydride (PA). For the CHO/PA and high-pressure CHO/CO2 copolymerizations, activity increases exponentially with s-block metal acidity peaking at the Co(III)K(I) catalyst, whilst for the low-pressure CHO/CO2 copolymerization it increases linearly to the same metal combination. The polymerization kinetics fit second order rate laws and the correlations support dinuclear metallate mechanistic hypotheses. These relationships help understand and identify key metal complex structural features in synergic polymerization catalysis.

Molecular Details of Polyester Decrystallization via Molecular Simulation

Waste polyesters are a potential feedstock for recycled and upcycled products. These polymers are generally semicrystalline, which presents a challenge for chemical and biological recycling to monomers, and thus the thermodynamic work associated with polyester decrystallization is an important consideration in some depolymerization strategies. Here, we use molecular dynamics simulations to calculate the free energy required to decrystallize a single chain from the crystal surface of five commercially and scientifically important, semiaromatic polyesters (PET, PTT, PBT, PEN, and PEF) in water. Our results indicate the decrystallization work ranges from approximately 15 kcal/mol (PEN) to 8 kcal/mol (PEF) per repeat unit for chains in the middle of a crystal surface. The insight gained into the molecular interactions that form the structural basis of semicrystalline synthetic polyesters can guide the pursuit of more efficient plastic processing, which could include catalyst development, optimizing recycling conditions including pretreatment, enzyme and solvent selections, and design of new materials.

Applying the Sabatier Principle to Decipher the Surface-Structure-Dependent Catalysis of Different Starch Granules by Pullulanase

Interfacial enzyme catalysis is widespread in both nature and industry. Granular starch is a sustainable and abundant raw material for which a rigorous correlation of the surface structure with enzymatic degradation is lacking. Here pullulanase-catalyzed debranching of 12 granular starches varying in amylopectin contents and branch chain contents and lengths is shown to present a biphasic relationship characteristic of the Sabatier principle. Introducing normalization of the specific rate (v 0/E 0) by a substrate-dependent constant C, related to the Arrhenius prefactor of k cat, reveals that optimal activity according to the Sabatier principle occurs at moderate substrate binding strength. The density of pullulanase attack sites (kinΓmax), determined using combined conventional and inverse Michaelis-Menten kinetics, was increased by branching enzyme treatment. Medium kinΓmax and branch chain length conferred the highest activity depending on substrate load. Correlation analysis demonstrated that starch granular crystallinity, surface order, and average branch chain length influence the enzymatic degradation by affecting the C constant. Therefore, C should be considered together with the enzyme binding strength to understand the degradation of starch granules. The Sabatier principle could serve as a diagnostic tool to characterize enzyme performance on substrates having different surface structures and guide rational modification of granular starches for specific purposes.

Balanced Adsorption Toward Highly Selective Electrochemical Reduction of CO2 to Formate

Tin-based materials have been designed as potential catalysts for the electrochemical conversion of CO2 into a single product. However, such tin-based materials still face the challenges of unsatisfactory selectivity, because the rate-determining step is situated within the slow desorption step. In this work, a variety of tin-based materials are synthesized using the electrospinning technique in an effort to control the adsorption strength during electrochemical reduction, therefore improving the selectivity of CO2 reduction toward formate. The optimized SnS material exhibits moderate adsorption strength to *OCHO and *HCOOH, and the appropriate atomic distance of Sn-Sn maintained the balanced adsorption posture of both intermediate. Therefore, the rate-determining step can be shifted from the slow desorption of the *HCOOH step (Sn) to the first hydrogenation of the *OCHO species step (SnS). Due to this shift, the SnS/C electrode demonstrated excellent selectivity, with a Faradaic efficiency of 96% for the production of formate. A maximum current density of -12.5 mA cm-2 for formate is also achieved for a period of 33 h.

Single-atom Pd directly anchored on biphenylene: a promising bifunctional electrocatalyst for overall water splitting

The development of bifunctional single-atom catalysts (SACs) for overall water splitting is crucial for clean energy production in the context of sustainable development. Using first-principles calculations, the catalytic capability of different transition metal (TM) atoms supported on biphenylene (Bip) monolayers (TM@Bip, TM = V-Cu, Ru-Ag, and Ir-Au) is comprehensively investigated. Bip can directly anchor TM atoms without engineered vacancies or nitrogen defects. Among the screened SACs, Pd@Bip is found to be an excellent bifunctional catalyst for both the hydrogen evolution reaction (HER) and the oxygen evolution reaction (OER). The overpotentials for the HER and the OER were calculated to be 0.05 and 0.50 V, respectively, which are even superior to the commercialized catalysts like Pt and IrO2. Furthermore, adjusting the d-band center of TM atoms effectively modulates the catalytic activity, and the optimal OER performance of TM-Bip can be achieved with a d-band center of -2.32 eV, which can serve as a principle to design Bip-based SACs. Our findings may serve as a practical theoretical guide for the exploration of effective bifunctional SACs for overall water splitting.

Are cellulases slow? Kinetic and thermodynamic limitations for enzymatic breakdown of cellulose

Cellulases are of paramount interest for upcoming biorefineries that utilize residue from agriculture and forestry to produce sustainable fuels and chemicals. Specifically, cellulases are used for the conversion of recalcitrant plant biomass to fermentable sugars in a so-called saccharification process. The vast literature on enzymatic saccharification frequently refers to low catalytic rates of cellulases as a main bottleneck for industrial implementation, but such statements are rarely supported by kinetic or thermodynamic considerations. In this perspective, we first discuss activation barriers and equilibrium conditions for the hydrolysis of cellulose and how these parameters influence enzymatic turnover. Next, we propose a simple framework for kinetic description of cellulolytic enzyme reactions and show how this can pave the way for comparative biochemical analyses of cellulases acting on their native, insoluble substrate. This latter analysis emphasizes that cellulases are characterized by extraordinarily low off-rate constants, while other kinetic parameters including specificity constants and rate constants for association and bond cleavage are quite like parameters reported for related enzymes acting on soluble substrates.

Design of Plastic Binding Lytic Polysaccharide Monooxygenases via Modular Engineering

The worldwide accumulation of plastic waste in the environment, along with its lifespan of hundreds of years, represents a serious threat to ecosystems. Enzymatic recycling of plastic waste offers a promising solution, but the high chemical inertness and hydrophobicity of plastics pose several challenges to enzymes. In nature, lytic polysaccharide monooxygenases (LPMOs) can act at the surface of recalcitrant biopolymers, taking advantage of their solvent-exposed active sites and appended carbohydrate-binding modules (CBMs). LPMOs can disrupt the densely packed chains of polysaccharides (e.g., cellulose) by the oxidation of C-H bonds. Given the similarities between these natural and artificial polymers, we aimed here at promoting plastic-binding properties to LPMOs, by swapping their CBM with three natural, surface-active accessory modules displaying different amphipathic properties. The polymer binding capacity of the resulting LPMO chimeras was assessed on a library of synthetic polymers, including polyester, polyamide, and polyolefin substrates. We demonstrated that the plastic binding properties of these engineered LPMOs are polymer-dependent and can be tuned by playing on the nature of the accessory module and reaction conditions. Remarkably, we gained full binding for some chimera LPMOs with striking results for polyhydroxyalkanoates (PHA). In the long term perspective of harnessing the unique copper chemistry of LPMOs to degrade plastics, we also provided the first evidence of LPMO-dependent modification of the PHA polymer, as supported by enzyme assays, gel permeation chromatography, and scanning electron microscopy. Altogether, our study provides the first roadmap for engineering plastic-binding ability in LPMOs, constituting a crucial first step on the evolutionary path toward efficient interfacial catalysis of plastic-active enzymes.

A theoretical investigation on the OER and ORR activity of graphene-based TM-N3 and TM-N2X (X = B, C, O, P) single atom catalysts by density functional theory calculations

Single-atom catalysts (SACs) have shown promising activity in electrocatalysis, such as CO2 reduction (CO2RR), the oxygen evolution reaction (OER) and the oxygen reduction reaction (ORR). Transition-metal-embedded N-doped graphene (M-N-C) with TM-N4 active sites (where TM represents a transition metal) is a representative SAC family that has attracted the most attention in both experimental and theoretical studies. However, TM-N3 type M-N-C has received less attention than TM-N4, although some experimental studies have reported its excellent activity in OER and CO2RR. To fully explore the electrocatalytic activity of TM-N3 type M-N-C, in this work we systematically investigate the OER and ORR activity of TM-N3 (TM = Ti, V, Cr, Mn, Fe, Co, Ni, Cu) and TM-N2X (X = B, C, O, P) using density functional theory (DFT) calculation. We examine the formation energies, OER/ORR free energy diagrams, overpotentials, charge density, d-band center and electronic structure of each candidate. Our computational screening shows that CuN3 is a promising bifunctional electrocatalyst for both OER and ORR with low overpotentials of 0.31 V (OER) and 0.44 V (ORR), while CrN3 and CuN2B are predicted to be promising OER catalysts, with overpotentials of 0.26 V and 0.50 V, respectively. A volcano plot derived from the scaling relationships suggests that substituting one nitrogen atom with a hetero atom significantly affects the potential-limiting step in OER/ORR, leading to worse activity in most cases. Density of states and d-band center analyses indicate that the change in OER/ORR activity is strongly correlated with the binding strength of *OH, which is dominated by the location of the d-band center. Our simulation results introduce a comprehensive insight into the activity of the TM-N3 site in TM-N-C, which could benefit the further development of graphene-based SACs for fuel cells and renewable energy applications.

Ni3C/Ni3S2 Heterojunction Electrocatalyst for Efficient Methanol Oxidation via Dual Anion Co-modulation Strategy

Enhancing active states on the catalyst surface by modulating the adsorption-desorption properties of reactant species is crucial to optimizing the electrocatalytic activity of transition metal-based nanostructured materials. In this work, an efficient optimization strategy is proposed by co-modulating the dual anions (C and S) in Ni3C/Ni3S2, the heterostructured electrocatalyst, which is prepared via a simple hot-injection method. The presence of Ni3C/Ni3S2 heterojunctions accelerates the charge carrier transfer and promotes the generation of active sites, enabling the heterostructured electrocatalyst to achieve current densities of 10/100 mA cm-2 at 1.37 V/1.53 V. The Faradaic efficiencies for formate production coupled with hydrogen evolution approach 100%, accompanied with a stability record of 350 h. Additionally, operando electrochemical impedance spectroscopy (EIS), in situ Raman spectroscopy, and density functional theory (DFT) calculations further demonstrate that the creation of Ni3C/Ni3S2 heterointerfaces originating from dual anions' (C and S) differentiation is effective in adjusting the d-band center of active Ni atoms, promoting the generation of active sites, as well as optimizing the adsorption and desorption of reaction intermediates. This dual anions co-modulation strategy to stable heterostructure provides a general route for constructing high-performance transition metal-based electrocatalysts.

PdMoPtCoNi High Entropy Nanoalloy with d Electron Self-Complementation-Induced Multisite Synergistic Effect for Efficient Nanozyme Catalysis

Engineering multimetallic nanocatalysts with the entropy-mediated strategy to reduce reaction activation energy is regarded as an innovative and effective approach to facilitate efficient heterogeneous catalysis. Accordingly, conformational entropy-driven high-entropy alloys (HEAs) are emerging as a promising candidate to settle the catalytic efficiency limitations of nanozymes, attributed to their versatile active site compositions and synergistic effects. As proof of the high-entropy nanozymes (HEzymes) concept, elaborate PdMoPtCoNi HEA nanowires (NWs) with abundant active sites and tuned electronic structures, exhibiting peroxidase-mimicking activity comparable to that of natural horseradish peroxidase are reported. Density functional theory calculations demonstrate that the enhanced electron abundance of HEA NWs near the Fermi level (EF) is facilitated via the self-complementation effect among the diverse transition metal sites, thereby boosting the electron transfer efficiency at the catalytic interface through the cocktail effect. Subsequently, the HEzymes are integrated with a portable electronic device that utilizes Internet of Things-driven signal conversion and wireless transmission functions for point-of-care diagnosis to validate their applicability in digital biosensing of urinary biomarkers. The proposed HEzymes underscore significant potential in enhancing nanozymes catalysis through tunable electronic structures and synergistic effects, paving the way for reformative advancements in nano-bio analysis.

Computational screening of transition metal atom doped ZnS and ZnSe nanostructures as promising bifunctional oxygen electrocatalysts

The design of bifunctional oxygen electrocatalysts showing high catalytic performance for the oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) is of great significance for developing new renewable energy storage and conversion technologies. Herein, based on the first principles calculations, we systematically explored the electrocatalytic activity of a series of transition metal atom (Fe, Co, Ni, Cu, Pd and Pt)-doped ZnS and ZnSe nanostructures for OER and ORR. The calculated results revealed that Ni- and Pt-doped ZnS and ZnSe nanostructures exhibit promising electrocatalytic performance for both OER and ORR in comparison to the pristine ZnS and ZnSe nanostructures. Especially, the OER/ORR overpotentials of Ni-doped ZnS and ZnSe nanostructures are estimated to be 0.28/0.30 and 0.31/0.31 V, respectively, disclosing their great potential as bifunctional oxygen electrocatalysts. Moreover, it is found that Ni-doped ZnS and ZnSe nanostructures for OER and ORR are on the top of the volcano plots, evincing promising catalytic performance. Our results provide theoretical insights into a feasible strategy to synthesize highly efficient ZnS- and ZnSe-based bifunctional oxygen electrocatalysts in the future.

Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes

Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.

The lignocellulosic biorefinery concept is sound: a commentary on Zhao et al

In the opinion paper by Zhao et al. 'Making the biochemical conversion of lignocellulose more robust', the authors claim that '…lignocellulose biorefinery is conceptually wrong'. In response, we argue that this claim itself has already been proved wrong by several companies.

Rationalizing the Influence of the Binding Affinity on the Activity of Phosphoserine Phosphatases

The Sabatier principle states that catalytic activity can be maximized when the substrate binding affinity is neither too strong nor too weak. Recent studies have shown that the activity of several hydrolases is maximized at intermediate values of the binding affinity (Michaelis-Menten constant: Km ). However, it remains unclear whether this concept of artificial catalysis is applicable to enzymes in general, especially for those which have evolved under different reaction environments. Herein, we show that the activity of phosphoserine phosphatase is also enhanced at an intermediate Km value of approximately 0.5 mM. Within our dataset, the variation of Km by three orders of magnitude accounted for a roughly 18-fold variation in the activity. Owing to the high phylogenetic and physiological diversity of our dataset, our results support the importance of optimizing Km for enzymes in general. On the other hand, a 77-fold variation in the activity was attributed to other physicochemical parameters, such as the Arrhenius prefactor of kcat , and could not be explained by the Sabatier principle. Therefore, while tuning the binding affinity according to the Sabatier principle is an important consideration, the Km value is only one of many physicochemical parameters which must be optimized to maximize enzymatic activity.

Recent advances in microbial and enzymatic engineering for the biodegradation of micro- and nanoplastics

This review examines the escalating issue of plastic pollution, specifically highlighting the detrimental effects on the environment and human health caused by microplastics and nanoplastics. The extensive use of synthetic polymers such as polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS) has raised significant environmental concerns because of their long-lasting and non-degradable characteristics. This review delves into the role of enzymatic and microbial strategies in breaking down these polymers, showcasing recent advancements in the field. The intricacies of enzymatic degradation are thoroughly examined, including the effectiveness of enzymes such as PETase and MHETase, as well as the contribution of microbial pathways in breaking down resilient polymers into more benign substances. The paper also discusses the impact of chemical composition on plastic degradation kinetics and emphasizes the need for an approach to managing the environmental impact of synthetic polymers. The review highlights the significance of comprehending the physical characteristics and long-term impacts of micro- and nanoplastics in different ecosystems. Furthermore, it points out the environmental and health consequences of these contaminants, such as their ability to cause cancer and interfere with the endocrine system. The paper emphasizes the need for advanced analytical methods and effective strategies for enzymatic degradation, as well as continued research and development in this area. This review highlights the crucial role of enzymatic and microbial strategies in addressing plastic pollution and proposes methods to create effective and environmentally friendly solutions.

Engineering of glycoside hydrolase family 7 cellobiohydrolases directed by natural diversity screening

Protein engineering and screening of processive fungal cellobiohydrolases (CBHs) remain challenging due to limited expression hosts, synergy-dependency, and recalcitrant substrates. In particular, glycoside hydrolase family 7 (GH7) CBHs are critically important for the bioeconomy and typically difficult to engineer. Here, we target the discovery of highly active natural GH7 CBHs and engineering of variants with improved activity. Using experimentally assayed activities of genome mined CBHs, we applied sequence and structural alignments to top performers to identify key point mutations linked to improved activity. From ∼1500 known GH7 sequences, an evolutionarily diverse subset of 57 GH7 CBH genes was expressed in Trichoderma reesei and screened using a multiplexed activity screening assay. Ten catalytically enhanced natural variants were identified, produced, purified, and tested for efficacy using industrially relevant conditions and substrates. Three key amino acids in CBHs with performance comparable or superior to Penicillium funiculosum Cel7A were identified and combinatorially engineered into P. funiculosum cel7a, expressed in T. reesei, and assayed on lignocellulosic biomass. The top performer generated using this combined approach of natural diversity genome mining, experimental assays, and computational modeling produced a 41% increase in conversion extent over native P. funiculosum Cel7A, a 55% increase over the current industrial standard T. reesei Cel7A, and 10% improvement over Aspergillus oryzae Cel7C, the best natural GH7 CBH previously identified in our laboratory.

Multienzyme-Like Nanozymes: Regulation, Rational Design, and Application

Nanomaterials with more than one enzyme-like activity are termed multienzymic nanozymes, and they have received increasing attention in recent years and hold huge potential to be applied in diverse fields, especially for biosensing and therapeutics. Compared to single enzyme-like nanozymes, multienzymic nanozymes offer various unique advantages, including synergistic effects, cascaded reactions, and environmentally responsive selectivity. Nevertheless, along with these merits, the catalytic mechanism and rational design of multienzymic nanozymes are more complicated and elusive as compared to single-enzymic nanozymes. In this review, the multienzymic nanozymes classification scheme based on the numbers/types of activities, the internal and external factors regulating the multienzymatic activities, the rational design based on chemical, biomimetic, and computer-aided strategies, and recent progress in applications attributed to the advantages of multicatalytic activities are systematically discussed. Finally, current challenges and future perspectives regarding the development and application of multienzymatic nanozymes are suggested. This review aims to deepen the understanding and inspire the research in multienzymic nanozymes to a greater extent.

Development of Enzyme-Based Approaches for Recycling PET on an Industrial Scale

Pollution by plastics such as polyethylene (PE), polypropylene (PP), polyvinyl chloride (PVC), polyurethane (PUR), polyamide (PA), polystyrene (PS), and poly(ethylene terephthalate) (PET) is now gaining worldwide attention as a critical environmental issue, closely linked to climate change. Among them, PET is particularly prone to hydrolysis, breaking down into its constituents, ethylene glycol (EG) and terephthalate (TPA). Biorecycling or bioupcycling stands out as one of the most promising methods for addressing PET pollution. For dealing with pollution by the macrosize PET, a French company Carbios has developed a pilot-scale plant for biorecycling waste PET beverage bottles into new bottles using derivatives of thermophilic leaf compost cutinase (LCC). However, this system still provides significant challenges in its practical implementation. For the micro- or nanosize PET pollution that poses significant human health risks, including cancer, no industrial-scale approach has been established so far, despite the need to develop such technologies. In this Perspective, we explore the enhancement of the low activity and thermostability of the enzyme PETase to match that of LCC, along with the potential application of microbes and enzymes for the treatment of waste PET as microplastics. Additionally, we discuss the shortcomings of the current biorecycling protocols from a life cycle assessment perspective, covering aspects such as the diversity of PET-hydrolyzing enzymes in nature, the catalytic mechanism for crystallized PET, and more. We also provide an overview of the Ideonella sakaiensis system, highlighting its ability to operate and grow at moderate temperatures, in contrast to high-temperature processes.

Highly Accessible Co-Nx Active Sites-Doped Carbon Framework with Uniformly Dispersed Cobalt Nanoparticles for the Oxygen Reduction Reaction in Alkaline and Neutral Electrolytes

Porous carbon materials with nitrogen-coordinated transition metal active sites have been widely regarded as appealing alternatives to replace noble metal catalysts in oxygen-based electrochemical reaction activities. However, improving the electrocatalytic activity of transition-metal-based catalysts remains a challenge for widespread application in renewable devices. Herein, we use a simple one-step pyrolysis method to construct a Co nanoparticles/Co-Nx-decorated carbon framework catalyst with a near-total external surface structure and uniform dispersion nanoparticles, which displays promising catalytic activity and superior stability for oxygen reduction reactions in both alkaline and neutral electrolytes, as evidenced by the positive shift of half-wave potential by 44 and 11 mV compared to 20% Pt/C. Excellent electrochemical performance originates from highly accessible Co nanoparticles/Co-Nx active sites at the external surface structure (this is, exposing active sites). The thus-assembled liquid zinc-air battery using the synthesized electrocatalyst as the cathode material delivers a maximum power density of 178 mW cm-2 with an open circuit potential of 1.48 V and long-term discharge stability over 150 h.

Functional Roles of N-Terminal Domains in Pullulanase from Human Gut Lactobacillus acidophilus

Pullulanases are multidomain α-glucan debranching enzymes with one or more N-terminal domains (NTDs) including carbohydrate-binding modules (CBMs) and domains of unknown function (DUFs). To elucidate the roles of NTDs in Lactobacillus acidophilus NCFM pullulanase (LaPul), two truncated variants, Δ41-LaPul (lacking CBM41) and Δ(41+DUFs)-LaPul (lacking CBM41 and two DUFs), were produced recombinantly. LaPul recognized 1.3- and 2.2-fold more enzyme attack-sites on starch granules compared to Δ41-LaPul and Δ(41+DUFs)-LaPul, respectively, as measured by interfacial kinetics. Δ41-LaPul displayed markedly lower affinity for starch granules and β-cyclodextrin (10- and >21-fold, respectively) in comparison to LaPul, showing substrate binding mainly stems from CBM41. Δ(41+DUFs)-LaPul exhibited a 12 °C lower melting temperature than LaPul and Δ41-LaPul, indicating that the DUFs are critical for LaPul stability. Notably, Δ41-LaPul exhibited a 14-fold higher turnover number (kcat) and 9-fold higher Michaelis constant (KM) compared to LaPul, while Δ(41+DUFs)-LaPul's values were close to those of LaPul, possibly due to the exposure of aromatic by truncation.

Transition Metal High-Entropy Nanozyme: Multi-Site Orbital Coupling Modulated High-Efficiency Peroxidase Mimics

Strong substrate affinity and high catalytic efficiency are persistently pursued to generate high-performance nanozymes. Herein, with unique surface atomic configurations and distinct d-orbital coupling features of different metal components, a class of highly efficient MnFeCoNiCu transition metal high-entropy nanozymes (HEzymes) is prepared for the first time. Density functional theory calculations demonstrate that improved d-orbital coupling between different metals increases the electron density near the Fermi energy level (EF ) and shifts the position of the overall d-band center with respect to EF , thereby boosting the efficiency of site-to-site electron transfer while also enhancing the adsorption of oxygen intermediates during catalysis. As such, the proposed HEzymes exhibit superior substrate affinities and catalytic efficiencies comparable to that of natural horseradish peroxidase (HRP). Finally, HEzymes with superb peroxidase (POD)-like activity are used in biosensing and antibacterial applications. These results suggest that HEzymes have great potential as new-generation nanozymes.

Genomic analysis of lignocellulolytic enzyme producing novel Streptomyces sp.MS2A for the bioethanol applications

The conversion of lignocellulosic waste to energy offers a cost-effective biofuel. The current study discusses the utilization of cellulose in rice husks by lichen-associated Streptomyces sp. MS2A via carbohydrate metabolism. Out of 39 actinobacteria, one actinobacterial strain MS2A, showed CMCase, FPase, and cellobiohydrolase activity. The whole genome analysis of Streptomyces sp. MS2A showed maximum similarity with Streptomyces sp. CCM_MD2014. The genome analysis confirmed the presence of cellulose-degrading genes along with xylan-degrading genes that code for GH3, GH6, GH9, GH11, GH43, GH51, and 15 other GH families with glycosyl transferase, carbohydrate-binding modules, and energy metabolism groups. Protein family analysis corroborates the enzyme family. Among the 19,402 genes of Streptomyces sp. MS2A, approximately 70 GH family codes for lignocellulose degradation enzymes. The structure of cellulase was modeled and validated. Scanning electron microscopy and gas chromatography-mass spectrometry (GCMS) was performed to analyze the lignocellulosic degradation of rice husk and the end product bioethanol.

Supercharging carbohydrate-binding module alone enhances endocellulase thermostability, binding, and activity on cellulosic biomass

Lignocellulosic biomass recalcitrance to enzymatic degradation necessitates high enzyme loadings incurring large processing costs for industrial-scale biofuels or biochemicals production. Manipulating surface charge interactions to minimize non-productive interactions between cellulolytic enzymes and plant cell wall components (e.g., lignin or cellulose) via protein supercharging has been hypothesized to improve biomass biodegradability, but with limited demonstrated success to date. Here we characterize the effect of introducing non-natural enzyme surface mutations and net charge on cellulosic biomass hydrolysis activity by designing a library of supercharged family-5 endoglucanase Cel5A and its native family-2a carbohydrate binding module (CBM) originally belonging to an industrially relevant thermophilic microbe Thermobifida fusca . A combinatorial library of 33 mutant constructs containing different CBM and Cel5A designs spanning a net charge range of -52 to 37 was computationally designed using Rosetta macromolecular modelling software. Activity for all mutants was rapidly characterized as soluble cell lysates and promising mutants (containing mutations either on the CBM, Cel5A catalytic domain, or both CBM and Cel5A domains) were then purified and systematically characterized. Surprisingly, often endocellulases with mutations on the CBM domain alone resulted in improved activity on cellulosic biomass, with three top-performing supercharged CBM mutants exhibiting between 2-5-fold increase in activity, compared to native enzyme, on both pretreated biomass enriched in lignin (i.e., corn stover) and isolated crystalline/amorphous cellulose. Furthermore, we were able to clearly demonstrate that endocellulase net charge can be selectively fine-tuned using protein supercharging protocol for targeting distinct substrates and maximizing biocatalytic activity. Additionally, several supercharged CBM containing endocellulases exhibited a 5-10 °C increase in optimal hydrolysis temperature, compared to native enzyme, which enabled further increase in hydrolytic yield at higher operational reaction temperatures. This study demonstrates the first successful implementation of enzyme supercharging of cellulolytic enzymes to increase hydrolytic activity towards complex lignocellulosic biomass derived substrates.

Recent Advances in Nanozyme-Mediated Strategies for Pathogen Detection and Control

Pathogen detection and control have long presented formidable challenges in the domains of medicine and public health. This review paper underscores the potential of nanozymes as emerging bio-mimetic enzymes that hold promise in effectively tackling these challenges. The key features and advantages of nanozymes are introduced, encompassing their comparable catalytic activity to natural enzymes, enhanced stability and reliability, cost effectiveness, and straightforward preparation methods. Subsequently, the paper delves into the detailed utilization of nanozymes for pathogen detection. This includes their application as biosensors, facilitating rapid and sensitive identification of diverse pathogens, including bacteria, viruses, and plasmodium. Furthermore, the paper explores strategies employing nanozymes for pathogen control, such as the regulation of reactive oxygen species (ROS), HOBr/Cl regulation, and clearance of extracellular DNA to impede pathogen growth and transmission. The review underscores the vast potential of nanozymes in pathogen detection and control through numerous specific examples and case studies. The authors highlight the efficiency, rapidity, and specificity of pathogen detection achieved with nanozymes, employing various strategies. They also demonstrate the feasibility of nanozymes in hindering pathogen growth and transmission. These innovative approaches employing nanozymes are projected to provide novel options for early disease diagnoses, treatment, and prevention. Through a comprehensive discourse on the characteristics and advantages of nanozymes, as well as diverse application approaches, this paper serves as a crucial reference and guide for further research and development in nanozyme technology. The expectation is that such advancements will significantly contribute to enhancing disease control measures and improving public health outcomes.

Thermodynamic principle to enhance enzymatic activity using the substrate affinity

Understanding how to tune enzymatic activity is important not only for biotechnological applications, but also to elucidate the basic principles guiding the design and optimization of biological systems in nature. So far, the Michaelis-Menten equation has provided a fundamental framework of enzymatic activity. However, there is still no concrete guideline on how the parameters should be optimized towards higher activity. Here, we demonstrate that tuning the Michaelis-Menten constant ([Formula: see text]) to the substrate concentration ([Formula: see text]) enhances enzymatic activity. This guideline ([Formula: see text]) was obtained mathematically by assuming that thermodynamically favorable reactions have higher rate constants, and that the total driving force is fixed. Due to the generality of these thermodynamic considerations, we propose [Formula: see text] as a general concept to enhance enzymatic activity. Our bioinformatic analysis reveals that the [Formula: see text] and in vivo substrate concentrations are consistent across a dataset of approximately 1000 enzymes, suggesting that even natural selection follows the principle [Formula: see text].

Tetraphenylporphyrin electrocatalysts for the hydrogen evolution reaction: applicability of molecular volcano plots to experimental operating conditions

Recent years have seen an increasing interest in molecular electrocatalysts for the hydrogen evolution reaction (HER). Efficient hydrogen evolution would play an important role in a sustainable fuel economy, and molecular systems could serve as highly specific and tunable alternatives to traditional noble metal surface catalysts. However, molecular catalysts are currently mostly used in homogeneous setups, where quantitative evaluation of catalytic activity is non-standardized and cumbersome, in particular for multistep, multielectron processes. The molecular design community would therefore be well served by a straightforward model for prediction and comparison of the efficiency of molecular catalysts. Recent developments in this area include attempts at applying the Sabatier principle and the volcano plot concept - popular tools for comparing metal surface catalysts - to molecular catalysis. In this work, we evaluate the predictive power of these tools in the context of experimental operating conditions, by applying them to a series of tetraphenylporphyrins employed as molecular electrocatalysts of the HER. We show that the binding energy of H and the redox chemistry of the porphyrins depend solely on the electron withdrawing ability of the central metal ion, and that the thermodynamics of the catalytic cycle follow a simple linear free energy relation. We also find that the catalytic efficiency of the porphyrins is almost exclusively determined by reaction kinetics and therefore cannot be explained by thermodynamics alone. We conclude that the Sabatier principle, linear free energy relations and molecular volcano plots are insufficient tools for predicting and comparing activity of molecular catalysts, and that experimentally useful information of catalytic performance can still only be obtained through detailed knowledge of the catalytic pathway for each individual system.

A multi-enzyme machine polymerizes the Haemophilus influenzae type b capsule

Bacterial capsules have critical roles in host-pathogen interactions. They provide a protective envelope against host recognition, leading to immune evasion and bacterial survival. Here we define the capsule biosynthesis pathway of Haemophilus influenzae serotype b (Hib), a Gram-negative bacterium that causes severe infections in infants and children. Reconstitution of this pathway enabled the fermentation-free production of Hib vaccine antigens starting from widely available precursors and detailed characterization of the enzymatic machinery. The X-ray crystal structure of the capsule polymerase Bcs3 reveals a multi-enzyme machine adopting a basket-like shape that creates a protected environment for the synthesis of the complex Hib polymer. This architecture is commonly exploited for surface glycan synthesis by both Gram-negative and Gram-positive pathogens. Supported by biochemical studies and comprehensive 2D nuclear magnetic resonance, our data explain how the ribofuranosyltransferase CriT, the phosphatase CrpP, the ribitol-phosphate transferase CroT and a polymer-binding domain function as a unique multi-enzyme assembly.

Interfacial Catalysis during Amylolytic Degradation of Starch Granules: Current Understanding and Kinetic Approaches

Enzymatic hydrolysis of starch granules forms the fundamental basis of how nature degrades starch in plant cells, how starch is utilized as an energy resource in foods, and develops efficient, low-cost saccharification of starch, such as bioethanol and sweeteners. However, most investigations on starch hydrolysis have focused on its rates of degradation, either in its gelatinized or soluble state. These systems are inherently more well-defined, and kinetic parameters can be readily derived for different hydrolytic enzymes and starch molecular structures. Conversely, hydrolysis is notably slower for solid substrates, such as starch granules, and the kinetics are more complex. The main problems include that the surface of the substrate is multifaceted, its chemical and physical properties are ill-defined, and it also continuously changes as the hydrolysis proceeds. Hence, methods need to be developed for analyzing such heterogeneous catalytic systems. Most data on starch granule degradation are obtained on a long-term enzyme-action basis from which initial rates cannot be derived. In this review, we discuss these various aspects and future possibilities for developing experimental procedures to describe and understand interfacial enzyme hydrolysis of native starch granules more accurately.

Computational screening of effective g-C3N4 based single atom electrocatalysts for the selective conversion of CO2

Two-dimensional (2D) material-based single-atom catalysts (SACs) have demonstrated their potential in electrochemical reduction reactions but exploring suitable 2D material-based SACs for the CO₂ reduction reaction (CO₂RR) by experiments is still a formidable task. In this study, theoretical screening of transition metal (TM)-doped graphitic carbon nitride (g-C₃N₄) materials as catalysts for the CO₂RR was systematically performed based on density functional theory (DFT) calculations. An indicator for the selective formation of one carbon (C1) products was developed to screen catalysts that are active and selective in the CO₂RR. The results indicated that Ti- and Ag-g-C₃N₄ demonstrate excellent catalytic activity and selectivity for the formation of CO and HCOOH, with limiting potentials of -0.330 and -0.096 V, respectively, while Cr-g-C₃N₄ exhibits the highest catalytic activity for yielding CH₃OH and CH₄ (-0.355 and -0.420 V, respectively), but none of the screened catalysts have been identified as ideal candidates for the selective production of CH₃OH and CH₄. Furthermore, Bader charge analysis suggested that excessive electron transfer from TM leads to stronger adsorption of intermediates and high limiting potentials, which subsequently result in lower catalytic activity. This work provides theoretical insights into the effective screening of active and selective 2D material-based SACs which has the potential to significantly reduce the time and resources required for the discovery of novel electrocatalysts for the controlled formation of various products.

Protein-plastic interactions: The driving forces behind the high affinity of a carbohydrate-binding module for polyethylene terephthalate

Polyethylene terephthalate (PET) waste is a common pollutant in the environment, mainly due to resistance of the plastic to bio-degradation. Nevertheless, hydrolytic enzymes have been identified with activity on this substrate, which are continually being engineered to increase activity. Some insoluble biological polymers are degraded by enzymes with a multi-domain architecture, comprising of a catalytic domain, and a substrate-binding domain, such as a carbohydrate-binding module (CBM). Enzymes that degrade PET have been shown to have a higher activity when fused with these CBMs, indicating a promising route for engineering better enzymes for plastic bioprocessing. However, no detailed study of the affinity and binding mechanism of these domains on PET has yet been made. Here, we perform an in depth analysis of a binding domain from CBM family 2 on PET, showing that the affinity of the protein for the plastic is highly dependent on temperature and crystallinity of the plastic. We also investigate the mechanism of the interaction, and show how affinity may be engineered in both directions. CBM affinity for other synthetic polymers is also demonstrated for the first time. Our results demonstrate that the substrate affinity of fusion enzymes with binding modules can be tuned to the desired level.

Enhanced Peroxidase-Like and Antibacterial Activity of Ir-CoatedPd-Pt Nanodendrites as Nanozyme

To inhibit the growth of bacteria, the DA-PPI nanozyme with enhanced peroxidase-like activity was synthesized. The DA-PPI nanozyme was obtained by depositing high-affinity element iridium (Ir) on the surface of Pd-Pt dendritic structures. The morphology and composition of DA-PPI nanozyme were characterized using SEM, TEM, and XPS. The kinetic results showed that the DA-PPI nanozyme possessed a higher peroxidase-like activity than that of Pd-Pt dendritic structures. The PL, ESR, and DFT were employed to explain the high peroxidase activity. As a proof of concept, the DA-PPI nanozyme could effectively inhibit E. coli (G^-) and S. aureus (G⁺) due to its high peroxidase-like activity. The study provides a new idea for the design of high active nanozymes and their application in the field of antibacterial.

Engineering cellulases for conversion of lignocellulosic biomass

Lignocellulosic biomass is a renewable source of energy, chemicals and materials. Many applications of this resource require the depolymerization of one or more of its polymeric constituents. Efficient enzymatic depolymerization of cellulose to glucose by cellulases and accessory enzymes such as lytic polysaccharide monooxygenases is a prerequisite for economically viable exploitation of this biomass. Microbes produce a remarkably diverse range of cellulases, which consist of glycoside hydrolase (GH) catalytic domains and, although not in all cases, substrate-binding carbohydrate-binding modules (CBMs). As enzymes are a considerable cost factor, there is great interest in finding or engineering improved and robust cellulases, with higher activity and stability, easy expression, and minimal product inhibition. This review addresses relevant engineering targets for cellulases, discusses a few notable cellulase engineering studies of the past decades and provides an overview of recent work in the field.

CelS-Catalyzed Processive Cellulose Degradation and Cellobiose Extraction for the Production of Bioethanol

Bacterial cellulase enzymes are potent candidates for the efficient production of bioethanol, a promising alternative to fossil fuels, from cellulosic biomass. These enzymes catalyze the breakdown of cellulose in plant biomass into simple sugars and then to bioethanol. In the absence of the enzyme, the cellulosic biomass is recalcitrant to decomposition due to fermentation-resistant lignin and pectin coatings on the cellulose surface, which make them inaccessible for hydrolysis. Cellobiohydrolase CelS is a microbial enzyme that binds to cellulose fiber and efficiently cleaves it into a simple sugar (cellobiose) by a repeated processive chopping mechanism. The two contributing factors to the catalytic reaction rate and the yield of cellobiose are the efficient product expulsion from the product binding site of CelS and the movement of the substrate or cellulose chain into the active site. Despite progress in understanding product expulsion in other cellulases, much remains to be understood about the molecular mechanism of processive action of these enzymes. Here, nonequilibrium molecular dynamics simulations using suitable reaction coordinates are carried out to investigate the energetics and mechanism of the substrate dynamics and product expulsion in CelS. The calculated free energy barrier for the product expulsion is three times lower than that for the processive action indicating that product removal is relatively easier and faster than the sliding of the substrate to the catalytic active site. The water traffic near the active site in response to the product expulsion and the processive action is also explored.

On the impact of carbohydrate-binding modules (CBMs) in lytic polysaccharide monooxygenases (LPMOs)

Lytic polysaccharide monooxygenases (LPMOs) have revolutionized our understanding of how enzymes degrade insoluble polysaccharides. Compared with the substantial knowledge developed on the structure and mode of action of the catalytic LPMO domains, the (multi)modularity of LPMOs has received less attention. The presence of other domains, in particular carbohydrate-binding modules (CBMs), tethered to LPMOs has profound implications for the catalytic performance of the full-length enzymes. In the last few years, studies on LPMO modularity have led to advancements in elucidating how CBMs, other domains, and linker regions influence LPMO structure and function. This mini review summarizes recent literature, with particular focus on comparative truncation studies, to provide an overview of the diversity in LPMO modularity and the functional implications of this diversity.

The Sabatier principle as a tool for discovery and engineering of industrial enzymes

The recent breakthrough in all-atom, protein structure prediction opens new avenues for a range of computational approaches in enzyme design. These new approaches could become instrumental for the development of technical biocatalysts, and hence our transition toward more sustainable industries. Here, we discuss one approach, which is well-known within inorganic catalysis, but essentially unexploited in biotechnology. Specifically, we review examples of linear free-energy relationships (LFERs) for enzyme reactions and discuss how LFERs and the associated Sabatier Principle may be implemented in algorithms that estimate kinetic parameters and enzyme performance based on model structures.

Model of Processive Catalysis with Site Clustering and Blocking and Its Application to Cellulose Hydrolysis

Interactions between particles moving on a linear track and their possible blocking by obstacles can lead to crowding, impeding the particles' transport kinetics. When the particles are enzymes processively catalyzing a reaction along a linear polymeric substrate, these crowding and blocking effects may substantially reduce the overall catalytic rate. Cellulose hydrolysis by exocellulases processively moving along cellulose chains assembled into insoluble cellulose particles is an example of such a catalytic transport process. The details of the kinetics of cellulose hydrolysis and the causes of the often observed reduction of hydrolysis rate over time are not yet fully understood. Crowding and blocking of enzyme particles are thought to be one of the important factors affecting the cellulose hydrolysis, but its exact role and mechanism are not clear. Here, we introduce a simple model based on an elementary transport process that incorporates the crowding and blocking effects in a straightforward way. This is achieved by making a distinction between binding and non-binding sites on the chain. The model reproduces a range of experimental results, mainly related to the early phase of cellulose hydrolysis. Our results indicate that the combined effects of clustering of binding sites together with the occupancy pattern of these sites by the enzyme molecules play a decisive role in the overall kinetics of cellulose hydrolysis. It is suggested that periodic desorption and rebinding of enzyme molecules could be a basis of a strategy to partially counter the clustering of and blocking by the binding sites and so enhance the rate of cellulose hydrolysis. The general nature of the model means that it could be applicable also to other transport processes that make a distinction between binding and non-binding sites, where crowding and blocking are expected to be relevant.

Enzyme Synergy in Transient Clusters of Endo- and Exocellulase Enables a Multilayer Mode of Processive Depolymerization of Cellulose

Biological degradation of cellulosic materials relies on the molecular-mechanistic principle that internally chain-cleaving endocellulases work synergistically with chain end-cleaving exocellulases in polysaccharide chain depolymerization. How endo-exo synergy becomes effective in the deconstruction of a solid substrate that presents cellulose chains assembled into crystalline material is an open question of the mechanism, with immediate implications on the bioconversion efficiency of cellulases. Here, based on single-molecule evidence from real-time atomic force microscopy, we discover that endo- and exocellulases engage in the formation of transient clusters of typically three to four enzymes at the cellulose surface. The clusters form specifically at regular domains of crystalline cellulose microfibrils that feature molecular defects in the polysaccharide chain organization. The dynamics of cluster formation correlates with substrate degradation through a multilayer-processive mode of chain depolymerization, overall leading to the directed ablation of single microfibrils from the cellulose surface. Each multilayer-processive step involves the spatiotemporally coordinated and mechanistically concerted activity of the endo- and exocellulases in close proximity. Mechanistically, the cooperativity with the endocellulase enables the exocellulase to pass through its processive cycles ∼100-fold faster than when acting alone. Our results suggest an advanced paradigm of efficient multienzymatic degradation of structurally organized polymer materials by endo-exo synergetic chain depolymerization.

The optimal docking strength for reversibly tethered kinases

Many kinases use reversible docking interactions to augment the specificity of their catalytic domains. Such docking interactions are often structurally independent of the catalytic domain, which allow for a flexible combination of modules in evolution and in bioengineering. The affinity of docking interactions spans several orders of magnitude. This led us to ask how the affinity of the docking interaction affects enzymatic activity and how to pick the optimal interaction module to complement a given substrate. Here, we develop equations that predict the optimal binding strength of a kinase docking interaction and validate it using numerical simulations and steady-state phosphorylation kinetics for tethered protein kinase A. We show that a kinase-substrate pair has an optimum docking strength that depends on their enzymatic constants, the tether architecture, the substrate concentration, and the kinetics of the docking interactions. We show that a reversible tether enhances phosphorylation rates most when 1) the docking strength is intermediate, 2) the substrate is nonoptimal, 3) the substrate concentration is low, 4) the docking interaction has rapid exchange kinetics, and 5) the tether optimizes the effective concentration of the intramolecular reaction. This work serves as a framework for interpreting mutations in kinase docking interactions and as a design guide for engineering enzyme scaffolds.

Sabatier Principle for Rationalizing Enzymatic Hydrolysis of a Synthetic Polyester

Interfacial enzyme reactions are common in Nature and in industrial settings, including the enzymatic deconstruction of poly(ethylene terephthalate) (PET) waste. Kinetic descriptions of PET hydrolases are necessary for both comparative analyses, discussions of structure-function relations and rational optimization of technical processes. We investigated whether the Sabatier principle could be used for this purpose. Specifically, we compared the kinetics of two well-known PET hydrolases, leaf-branch compost cutinase (LCC) and a cutinase from the bacterium Thermobifida fusca (TfC), when adding different concentrations of the surfactant cetyltrimethylammonium bromide (CTAB). We found that CTAB consistently lowered the strength of enzyme-PET interactions, while its effect on enzymatic turnover was strongly biphasic. Thus, at gradually increasing CTAB concentrations, turnover was initially promoted and subsequently suppressed. This correlation with maximal turnover at an intermediate binding strength was in accordance with the Sabatier principle. One consequence of these results was that both enzymes had too strong intrinsic interaction with PET for optimal turnover, especially TfC, which showed a 20-fold improvement of k _cat at the maximum. LCC on the other hand had an intrinsic substrate affinity closer to the Sabatier optimum, and the turnover rate was 5-fold improved at weakened substrate binding. Our results showed that the Sabatier principle may indeed rationalize enzymatic PET degradation and support process optimization. Finally, we suggest that future discovery efforts should consider enzymes with weakened substrate binding because strong adsorption seems to limit their catalytic performance.

Construction of Pd Single Site Anchored on Nitrogen-Doped Porous Carbon and Its Application for Total Antioxidant Level Detection

Natural enzymes have excellent catalytic activity. However, due to their unstable nature and high cost, current research has turned to the synthesis and development of enzyme-like nanomaterials and single-atomic nanozymes. In this study, a single-atomic palladium-loaded nitrogen-doped porous carbon catalyst (SA-Pd/NPC) was prepared and used as a mimetic peroxidase to catalyze the substrates oxidation. The catalytic capability of the SA-Pd/NPC was tested by the TMB-H₂O₂ system, and it expressed a superior catalytic capability owing to the plentiful catalytic centers of the single-atom Pd, its high porosity, the large specific surface area, and the strong electron transfer capability of the NPC. For the color reaction of TMB, thiol antioxidants (e.g., glutathione, GSH) and non-thiol antioxidants (e.g., ascorbic acid, AA) are suitable for different inhibition mechanisms. GSH and AA are typical substances of these two main antioxidant types, respectively. Here, we demonstrate that this prepared catalyst could be used to simultaneously determine a variety of major known physiologically relevant thiol-containing and thiol-free antioxidants, accompanied by a blue color gradient change with UV-Vis spectra at 652 nm through the SA-Pd/NPC-catalyzed TMB-H₂O₂ system. Linear responses to GSH and AA could be obtained in the concentration ranges of 0.01-0.10 mM and 1-13 μM (both R² values were greater than 0.970), respectively, while the limits of detection were 3 μM and 0.3 μM, respectively. The ability of the nanozyme to detect overall antioxidant levels (TAL) was also confirmed in subsequent tests on artificial saliva and biological samples.

Mechanism-Based Design of Efficient PET Hydrolases

Polyethylene terephthalate (PET) is the most widespread synthetic polyester, having been utilized in textile fibers and packaging materials for beverages and food, contributing considerably to the global solid waste stream and environmental plastic pollution. While enzymatic PET recycling and upcycling have recently emerged as viable disposal methods for a circular plastic economy, only a handful of benchmark enzymes have been thoroughly described and subjected to protein engineering for improved properties over the last 16 years. By analyzing the specific material properties of PET and the reaction mechanisms in the context of interfacial biocatalysis, this Perspective identifies several limitations in current enzymatic PET degradation approaches. Unbalanced enzyme-substrate interactions, limited thermostability, and low catalytic efficiency at elevated reaction temperatures, and inhibition caused by oligomeric degradation intermediates still hamper industrial applications that require high catalytic efficiency. To overcome these limitations, successful protein engineering studies using innovative experimental and computational approaches have been published extensively in recent years in this thriving research field and are summarized and discussed in detail here. The acquired knowledge and experience will be applied in the near future to address plastic waste contributed by other mass-produced polymer types (e.g., polyamides and polyurethanes) that should also be properly disposed by biotechnological approaches.