Sabatier Principle for Interfacial (Heterogeneous) Enzyme Catalysis

Transition Metal-Modified Co4 Clusters Supported on Graphdiyne as an Effective Nitrogen Reduction Reaction Electrocatalyst

Conversion of N₂ into NH₃ through the electrochemical nitrogen reduction reaction (NRR) under ambient conditions represents a novel green ammonia synthesis method. The main obstacle for NRR is lack of efficient, stable, and cost-effective catalysts. In this work, by using density functional theory calculations, 16 transition metal-modified Co₄ clusters supported on graphdiyne (GDY) as potential NRR catalysts were systematically screened. Through the examinations of stability, N₂ activation, selectivity, and activity, Ti-, V-, Cr-, Mn-, and Zr-Co₃@GDY were identified as the promising candidates toward NRR. Further explorations on the NRR mechanisms and the Pourbaix diagrams suggest that Ti-Co₃@GDY was the most promising candidate catalyst, as it has the lowest limiting potential and high stability under the working conditions. The high activities originate from the synergy effect, where the Co₃ cluster acts as the electron donor and the heteroatom serves as the single active site throughout the NRR process. Our results offer a new perspective for advancing sustainable NH₃ production.

Synthesis of N-Heterocycles via Oxidant-Free Dehydrocyclization of Alcohols Using Heterogeneous Catalysts

N-Heterocycles, such as pyrroles, pyrimidines, quinazolines, and quinoxalines, are important building blocks for organic chemistry and the fine-chemical industry. For their synthesis, catalytic borrowing hydrogen and acceptorless dehydrogenative coupling reactions of alcohols as sustainable reagents have received significant attention in recent years. To overcome the problems of product separation and catalyst reusability, several metal-based heterogeneous catalysts have been reported to achieve these transformations with good yields and selectivity. In this Minireview, we summarize recent developments using both noble and non-noble metal-based heterogeneous catalysts to synthesize N-heterocycles from alcohols and N-nucleophiles via acceptorless dehydrogenation or borrowing hydrogen methodologies. Furthermore, this Minireview introduces strategies for the preparation and functionalization of the corresponding heterogeneous catalysts, discusses the reaction mechanisms and the roles of metal electronic states, and the influence of support Lewis acid-base properties on these reactions.

Single-Atom (Iron-Based) Catalysts: Synthesis and Applications

Supported single-metal atom catalysts (SACs) are constituted of isolated active metal centers, which are heterogenized on inert supports such as graphene, porous carbon, and metal oxides. Their thermal stability, electronic properties, and catalytic activities can be controlled via interactions between the single-metal atom center and neighboring heteroatoms such as nitrogen, oxygen, and sulfur. Due to the atomic dispersion of the active catalytic centers, the amount of metal required for catalysis can be decreased, thus offering new possibilities to control the selectivity of a given transformation as well as to improve catalyst turnover frequencies and turnover numbers. This review aims to comprehensively summarize the synthesis of Fe-SACs with a focus on anchoring single atoms (SA) on carbon/graphene supports. The characterization of these advanced materials using various spectroscopic techniques and their applications in diverse research areas are described. When applicable, mechanistic investigations conducted to understand the specific behavior of Fe-SACs-based catalysts are highlighted, including the use of theoretical models.

Development and validation of a label-free method for measuring the collagen hydrolytic activity of protease

Collagen is the most abundant fibrous structural protein, and therefore, the quantitative evaluation of the effect of protease on collagen has a profound influence on enzyme application. In this research, unlabeled native bovine hide powder was utilized to detect collagen hydrolytic activity of the protease. The optimum conditions of the determination method were as follows: 30 mg/mL substrate concentration, 30 min reaction time, and 2-9 U/mL enzyme concentration. Then, several typical industrial protease preparations were chosen to measure collagenolytic activities at different temperatures and pH values, whose change trends were quite distinct from those of proteolytic activity assay method based on casein or dye-labeled hide powder substrate. Especially, in the pH 5-7, casein hydrolytic activities of these proteases showed sharper peaks with relative activity from 6% to 100%, whereas, their collagen hydrolytic activities based on native hide powder exhibited 30-100% with broader peaks. And collagen hydrolytic activities resulted from using dye-labeled substrate reached a lower optimum pH value than that of other methods. Besides, the results of these measurements displayed a moderate degree of reproducibility. This method is more reasonable than the protease assay method using casein or labeled hide powder as the substrate in many fields.

Physical constraints and functional plasticity of cellulases

Enzyme reactions, both in Nature and technical applications, commonly occur at the interface of immiscible phases. Nevertheless, stringent descriptions of interfacial enzyme catalysis remain sparse, and this is partly due to a shortage of coherent experimental data to guide and assess such work. In this work, we produced and kinetically characterized 83 cellulases, which revealed a conspicuous linear free energy relationship (LFER) between the substrate binding strength and the activation barrier. The scaling occurred despite the investigated enzymes being structurally and mechanistically diverse. We suggest that the scaling reflects basic physical restrictions of the hydrolytic process and that evolutionary selection has condensed cellulase phenotypes near the line. One consequence of the LFER is that the activity of a cellulase can be estimated from its substrate binding strength, irrespectively of structural and mechanistic details, and this appears promising for in silico selection and design within this industrially important group of enzymes.

Kinetic Study on Enzymatic Hydrolysis of Cellulose in an Open, Inhibition-Free System

Due to the complexity of cellulases and the requirement of enzyme adsorption on cellulose prior to reactions, it is difficult to evaluate their reaction with a general mechanistic scheme. Nevertheless, it is of great interest to come up with an approximate analytic description of a valid model for the purpose of developing an intuitive understanding of these complex enzyme systems. Herein, we used the surface plasmonic resonance method to monitor the action of a cellobiohydrolase by itself, as well as its mixture with a synergetic endoglucanase, on the surface of a regenerated model cellulose film, under continuous flow conditions. We found a phenomenological approach by taking advantage of the long steady state of cellulose hydrolysis in the open, inhibition-free system. This provided a direct and reliable way to analyze the adsorption and reaction processes with a minimum number of fitting parameters. We investigated a generalized Langmuir-Michaelis-Menten model to describe a full set of kinetic results across a range of enzyme concentrations, compositions, and temperatures. The overall form of the equations describing the pseudo-steady-state kinetics of the flow-system shares some interesting similarities with the Michaelis-Menten equation. The use of familiar Michaelis-Menten parameters in the analysis provides a unifying framework to study cellulase kinetics. The strategy may provide a shortcut for approaching a quantitative while intuitive understanding of enzymatic degradation of cellulose from top to bottom. The open system approach and the kinetic analysis should be applicable to a variety of cellulases and reaction systems to accelerate the progress in the field.

Secondary Nucleation and the Conservation of Structural Characteristics of Amyloid Fibril Strains

Amyloid fibrils are ordered protein aggregates and a hallmark of many severe neurodegenerative diseases. Amyloid fibrils form through primary nucleation from monomeric protein, grow through monomer addition and proliferate through fragmentation or through the nucleation of new fibrils on the surface of existing fibrils (secondary nucleation). It is currently still unclear how amyloid fibrils initially form in the brain of affected individuals and how they are amplified. A given amyloid protein can sometimes form fibrils of different structure under different solution conditions in vitro, but often fibrils found in patients are highly homogeneous. These findings suggest that the processes that amplify amyloid fibrils in vivo can in some cases preserve the structural characteristics of the initial seed fibrils. It has been known for many years that fibril growth by monomer addition maintains the structure of the seed fibril, as the latter acts as a template that imposes its fold on the newly added monomer. However, for fibrils that are formed through secondary nucleation it was, until recently, not clear whether the structure of the seed fibril is preserved. Here we review the experimental evidence on this question that has emerged over the last years. The overall picture is that the fibril strain that forms through secondary nucleation is mostly defined by the solution conditions and intrinsic structural preferences, and not by the seed fibril strain.

Functional diversity of three tandem C-terminal carbohydrate-binding modules of a β-mannanase

Carbohydrate active enzymes, such as those involved in plant cell wall and storage polysaccharide biosynthesis and deconstruction, often contain repeating noncatalytic carbohydrate-binding modules (CBMs) to compensate for low-affinity binding typical of protein–carbohydrate interactions. The bacterium Saccharophagus degradans produces an endo-β-mannanase of glycoside hydrolase family 5 subfamily 8 with three phylogenetically distinct family 10 CBMs located C-terminally from the catalytic domain (SdGH5_8-CBM10x3). However, the functional roles and cooperativity of these CBM domains in polysaccharide binding are not clear. To learn more, we studied the full-length enzyme, three stepwise CBM family 10 (CBM10) truncations, and GFP fusions of the individual CBM10s and all three domains together by pull-down assays, affinity gel electrophoresis, and activity assays. Only the C-terminal CBM10-3 was found to bind strongly to microcrystalline cellulose (dissociation constant, K_d = 1.48 μM). CBM10-3 and CBM10-2 bound galactomannan with similar affinity (K_d = 0.2–0.4 mg/ml), but CBM10-1 had 20-fold lower affinity for this substrate. CBM10 truncations barely affected specific activity on carob galactomannan and konjac glucomannan. Full-length SdGH5_8-CBM10x3 was twofold more active on the highly galactose-decorated viscous guar gum galactomannan and crystalline ivory nut mannan at high enzyme concentrations, but the specific activity was fourfold to ninefold reduced at low enzyme and substrate concentrations compared with the enzyme lacking CBM10-2 and CBM10-3. Comparison of activity and binding data for the different enzyme forms indicates unproductive and productive polysaccharide binding to occur. We conclude that the C-terminal-most CBM10-3 secures firm binding, with contribution from CBM10-2, which with CBM10-1 also provides spatial flexibility.

A Review on the Design and Hydration Properties of Natural Polymer-Based Hydrogels

Hydrogels are hydrophilic 3D networks that are able to ingest large amounts of water or biological fluids, and are potential candidates for biosensors, drug delivery vectors, energy harvester devices, and carriers or matrices for cells in tissue engineering. Natural polymers, e.g., cellulose, chitosan and starch, have excellent properties that afford fabrication of advanced hydrogel materials for biomedical applications: biodegradability, biocompatibility, non-toxicity, hydrophilicity, thermal and chemical stability, and the high capacity for swelling induced by facile synthetic modification, among other physicochemical properties. Hydrogels require variable time to reach an equilibrium swelling due to the variable diffusion rates of water sorption, capillary action, and other modalities. In this study, the nature, transport kinetics, and the role of water in the formation and structural stability of various types of hydrogels comprised of natural polymers are reviewed. Since water is an integral part of hydrogels that constitute a substantive portion of its composition, there is a need to obtain an improved understanding of the role of hydration in the structure, degree of swelling and the mechanical stability of such biomaterial hydrogels. The capacity of the polymer chains to swell in an aqueous solvent can be expressed by the rubber elasticity theory and other thermodynamic contributions; whereas the rate of water diffusion can be driven either by concentration gradient or chemical potential. An overview of fabrication strategies for various types of hydrogels is presented as well as their responsiveness to external stimuli, along with their potential utility in diverse and novel applications. This review aims to shed light on the role of hydration to the structure and function of hydrogels. In turn, this review will further contribute to the development of advanced materials, such as "injectable hydrogels" and super-adsorbents for applications in the field of environmental science and biomedicine.

Manipulating Interfaces of Electrocatalysts Down to Atomic Scales: Fundamentals, Strategies, and Electrocatalytic Applications

Raising electrocatalysis by rationally devising catalysts plays a core role in almost all renewable energy conversion and storage systems. The principal catalytic properties can be controlled and improved well by manipulation of interfaces, ascribed to the interactions among different components/players at the interfaces. In particular, manipulating interfaces down to atomic scales is becoming increasingly attractive, not only because those atoms at around the interface are the key players during electrocatalysis, but also, understandings on the atomic level electrocatalysis allow one to gain deep insights into the reaction mechanism. With the feature down-sizing to atomic scales, there is a timely need to redefine the interfaces, as some of them have gone beyond the conventionally perceived interfacial concept. In this overview, the key active players participating in the interfacial manipulation of electrocatalysts are examined, from a new angle of "atomic interface," including those individual atoms, defects, and their interactions, together with the essential characterization techniques for them. The specific approaches and pathways to engineer better atomic interfaces are investigated, and thus to enable the unique electrocatalysis for targeted applications. Looking beyond recent progress, the challenges and prospects of the atomic level interfacial engineering are also briefly visited.

Computing Cellulase Kinetics with a Two-Domain Linear Interaction Energy Approach

While heterogeneous enzyme reactions play an essential role in both nature and green industries, computational predictions of their catalytic properties remain scarce. Recent experimental work demonstrated the applicability of the Sabatier principle for heterogeneous biocatalysis. This provides a simple relationship between binding strength and the catalytic rate and potentially opens a new way for inexpensive computational determination of kinetic parameters. However, broader implementation of this approach will require fast and reliable prediction of binding free energies of complex two-phase systems, and computational procedures for this are still elusive. Here, we propose a new framework for the assessment of the binding strengths of multidomain proteins, in general, and interfacial enzymes, in particular, based on an extended linear interaction energy (LIE) method. This two-domain LIE (2D-LIE) approach was successfully applied to predict binding and activation free energies of a diverse set of cellulases and resulted in robust models with high accuracy. Overall, our method provides a fast computational screening tool for cellulases that have not been experimentally characterized, and we posit that it may also be applicable to other heterogeneously acting biocatalysts.

Molecular origins of reduced activity and binding commitment of processive cellulases and associated carbohydrate-binding proteins to cellulose III

Efficient enzymatic saccharification of cellulosic biomass into fermentable sugars can enable production of bioproducts like ethanol. Native crystalline cellulose, or cellulose I, is inefficiently processed via enzymatic hydrolysis but can be converted into the structurally distinct cellulose III allomorph that is processed via cellulase cocktails derived from Trichoderma reesei up to 20-fold faster. However, characterization of individual cellulases from T. reesei, like the processive exocellulase Cel7A, shows reduced binding and activity at low enzyme loadings toward cellulose III. To clarify this discrepancy, we monitored the single-molecule initial binding commitment and subsequent processive motility of Cel7A enzymes and associated carbohydrate-binding modules (CBMs) on cellulose using optical tweezers force spectroscopy. We confirmed a 48% lower initial binding commitment and 32% slower processive motility of Cel7A on cellulose III, which we hypothesized derives from reduced binding affinity of the Cel7A binding domain CBM1. Classical CBM-cellulose pull-down assays, depending on the adsorption model fitted, predicted between 1.2- and 7-fold reduction in CBM1 binding affinity for cellulose III. Force spectroscopy measurements of CBM1-cellulose interactions, along with molecular dynamics simulations, indicated that previous interpretations of classical binding assay results using multisite adsorption models may have complicated analysis, and instead suggest simpler single-site models should be used. These findings were corroborated by binding analysis of other type-A CBMs (CBM2a, CBM3a, CBM5, CBM10, and CBM64) on both cellulose allomorphs. Finally, we discuss how complementary analytical tools are critical to gain insight into the complex mechanisms of insoluble polysaccharides hydrolysis by cellulolytic enzymes and associated carbohydrate-binding proteins.

Reduced type-A carbohydrate-binding module interactions to cellulose I leads to improved endocellulase activity

Dissociation of nonproductively bound cellulolytic enzymes from cellulose is hypothesized to be a key rate-limiting factor impeding cost-effective biomass conversion to fermentable sugars. However, the role of carbohydrate-binding modules (CBMs) in enabling nonproductive enzyme binding is not well understood. Here, we examine the subtle interplay of CBM binding and cellulose hydrolysis activity for three models type-A CBMs (Families 1, 3a, and 64) tethered to multifunctional endoglucanase (CelE) on two distinct cellulose allomorphs (i.e., cellulose I and III). We generated a small library of mutant CBMs with varying cellulose affinity, as determined by equilibrium binding assays, followed by monitoring cellulose hydrolysis activity of CelE-CBM fusion constructs. Finally, kinetic binding assays using quartz crystal microbalance with dissipation were employed to measure CBM adsorption and desorption rate constants k on and k off , respectively, towards nanocrystalline cellulose derived from both allomorphs. Overall, our results indicate that reduced CBM equilibrium binding affinity towards cellulose I alone, resulting from increased desorption rates ( k off ) and reduced effective adsorption rates ( nk on ), is correlated to overall improved endocellulase activity. Future studies could employ similar approaches to unravel the role of CBMs in nonproductive enzyme binding and develop improved cellulolytic enzymes for industrial applications.

Metal-organic framework based bifunctional oxygen electrocatalysts for rechargeable zinc-air batteries: current progress and prospects

Zinc-air batteries (ZABs) are regarded as ideal candidates for next-generation energy storage equipment due to their high energy density, non-toxicity, high safety, and environmental friendliness. However, the slow oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) kinetics on the air cathode limit their efficiency and the development of highly efficient, low cost and stable bifunctional electrocatalysts is still challenging. Metal-Organic Framework (MOF) based bifunctional oxygen electrocatalysts have been demonstrated as promising alternative catalysts due to the regular structure, tunable chemistry, high specific surface area, and simple and easy preparation of MOFs, and great progress has been made in this area. Herein, we summarize the latest research progress of MOF-based bifunctional oxygen electrocatalysts for ZABs, including pristine MOFs, derivatives of MOFs and MOF composites. The effects of the catalysts' composites, morphologies, specific surface areas and active sites on catalytic performances are specifically addressed to reveal the underlying mechanisms for different catalytic activity of MOF based catalysts. Finally, the main challenges and prospects for developing advanced MOF-based bifunctional electrocatalysts are proposed.

Structural and Functional Studies of a Klebsiella Phage Capsule Depolymerase Tailspike: Mechanistic Insights into Capsular Degradation

Capsule polysaccharide is a major virulence factor of Klebsiella pneumoniae, a nosocomial pathogen associated with a wide range of infections. It protects bacteria from harsh environmental conditions, immune system response, and phage infection. To access cell wall-located receptors, some phages possess tailspike depolymerases that degrade the capsular polysaccharide. Here, we present the crystal structure of a tailspike against Klebsiella, KP32gp38, whose primary sequence shares no similarity to other proteins of known structure. In the trimeric structure of KP32gp38, each chain contains a flexible N-terminal domain, a right-handed parallel β helix domain and two β sandwiches with carbohydrate binding features. The crystal structure and activity assays allowed us to locate the catalytic site. Also, our data provide experimental evidence of a branching architecture of depolymerases in KP32 Klebsiella viruses, as KP32gp38 displays nanomolar affinity to another depolymerase from the same phage, KP32gp37. Results provide a structural framework for enzyme engineering to produce serotype-broad-active enzyme complexes against K. pneumoniae.

Substrate binding in the processive cellulase Cel7A: Transition state of complexation and roles of conserved tryptophan residues

Cellobiohydrolases effectively degrade cellulose and are of biotechnological interest because they can convert lignocellulosic biomass to fermentable sugars. Here, we implemented a fluorescence-based method for real-time measurements of complexation and decomplexation of the processive cellulase Cel7A and its insoluble substrate, cellulose. The method enabled detailed kinetic and thermodynamic analyses of ligand binding in a heterogeneous system. We studied WT Cel7A and several variants in which one or two of four highly conserved Trp residues in the binding tunnel had been replaced with Ala. WT Cel7A had on/off-rate constants of 1 × 105 m-1 s-1 and 5 × 10-3 s-1, respectively, reflecting the slow dynamics of a solid, polymeric ligand. Especially the off-rate constant was many orders of magnitude lower than typical values for small, soluble ligands. Binding rate and strength both were typically lower for the Trp variants, but effects of the substitutions were moderate and sometimes negligible. Hence, we propose that lowering the activation barrier for complexation is not a major driving force for the high conservation of the Trp residues. Using so-called Φ-factor analysis, we analyzed the kinetic and thermodynamic results for the variants. The results of this analysis suggested a transition state for complexation and decomplexation in which the reducing end of the ligand is close to the tunnel entrance (near Trp-40), whereas the rest of the binding tunnel is empty. We propose that this structure defines the highest free-energy barrier of the overall catalytic cycle and hence governs the turnover rate of this industrially important enzyme.

Interfacial molecular interactions of cellobiohydrolase Cel7A and its variants on cellulose

BACKGROUND

Molecular-scale mechanisms of the enzymatic breakdown of cellulosic biomass into fermentable sugars are still poorly understood, with a need for independent measurements of enzyme kinetic parameters. We measured binding times of cellobiohydrolase Trichoderma reesei Cel7A (Cel7A) on celluloses using wild-type Cel7A (WT_intact), the catalytically deficient mutant Cel7A E212Q (E212Q_intact) and their proteolytically isolated catalytic domains (CD) (WT_core and E212Q_core, respectively). The binding time distributions were obtained from time-resolved, super-resolution images of fluorescently labeled enzymes on cellulose obtained with total internal reflection fluorescence microscopy.

RESULTS

Binding of WT_intact and E212Q_intact on the recalcitrant algal cellulose (AC) showed two bound populations: ~ 85% bound with shorter residence times of < 15 s while ~ 15% were effectively immobilized. The similarity between binding times of the WT and E212Q suggests that the single point mutation in the enzyme active site does not affect the thermodynamics of binding of this enzyme. The isolated catalytic domains, WT_core and E212Q_core, exhibited three binding populations on AC: ~ 75% bound with short residence times of ~ 15 s (similar to the intact enzymes), ~ 20% bound for < 100 s and ~ 5% that were effectively immobilized.

CONCLUSIONS

Cel7A binding to cellulose is driven by the interactions between the catalytic domain and cellulose. The cellulose-binding module (CBM) and linker increase the affinity of Cel7A to cellulose likely by facilitating recognition and complexation at the substrate interface. The increased affinity of Cel7A to cellulose by the CBM and linker comes at the cost of increasing the population of immobilized enzyme on cellulose. The residence time (or inversely the dissociation rates) of Cel7A on cellulose is not catalysis limited.

The dissociation mechanism of processive cellulases

Cellulase enzymes deconstruct recalcitrant cellulose into soluble sugars, making them a biocatalyst of biotechnological interest for use in the nascent lignocellulosic bioeconomy. Cellobiohydrolases (CBHs) are cellulases capable of liberating many sugar molecules in a processive manner without dissociating from the substrate. Within the complete processive cycle of CBHs, dissociation from the cellulose substrate is rate limiting, but the molecular mechanism of this step is unknown. Here, we present a direct comparison of potential molecular mechanisms for dissociation via Hamiltonian replica exchange molecular dynamics of the model fungal CBH, Trichoderma reesei Cel7A. Computational rate estimates indicate that stepwise cellulose dethreading from the binding tunnel is 4 orders of magnitude faster than a clamshell mechanism, in which the substrate-enclosing loops open and release the substrate without reversing. We also present the crystal structure of a disulfide variant that covalently links substrate-enclosing loops on either side of the substrate-binding tunnel, which constitutes a CBH that can only dissociate via stepwise dethreading. Biochemical measurements indicate that this variant has a dissociation rate constant essentially equivalent to the wild type, implying that dethreading is likely the predominant mechanism for dissociation.

A practical approach to steady-state kinetic analysis of cellulases acting on their natural insoluble substrate

Measurement of steady-state rates (v_SS) is straightforward in standard enzymology with soluble substrate, and it has been instrumental for comparative biochemical analyses within this area. For insoluble substrate, however, experimental values of v_ss remain controversial, and this has strongly limited the amount and quality of comparative analyses for cellulases and other enzymes that act on the surface of an insoluble substrate. In the current work, we have measured progress curves over a wide range of conditions for two cellulases, TrCel6A and TrCel7A from Trichoderma reesei, acting on their natural, insoluble substrate, cellulose. Based on this, we consider practical compromises for the determination of experimental v_SS values, and propose a basic protocol that provides representative reaction rates and is experimentally simple so that larger groups of enzymes and conditions can be readily assayed with standard laboratory equipment. We surmise that the suggested experimental approach can be useful in comparative biochemical studies of cellulases; an area that remains poorly developed.