Enzyme function and evolution through the lens of bioinformatics.

Enzymes have been shaped by evolution over billions of years to catalyse the chemical reactions that support life on earth. Dispersed in the literature, or organised in online databases, knowledge about enzymes can be structured in distinct dimensions, either related to their quality as biological macromolecules, such as their sequence and structure, or related to their chemical functions, such as the catalytic site, kinetics, mechanism, and overall reaction. The evolution of enzymes can only be understood when each of these dimensions is considered. In addition, many of the properties of enzymes only make sense in the light of evolution. We start this review by outlining the main paradigms of enzyme evolution, including gene duplication and divergence, convergent evolution, and evolution by recombination of domains. In the second part, we overview the current collective knowledge about enzymes, as organised by different types of data and collected in several databases. We also highlight some increasingly powerful computational tools that can be used to close gaps in understanding, in particular for types of data that require laborious experimental protocols. We believe that recent advances in protein structure prediction will be a powerful catalyst for the prediction of binding, mechanism, and ultimately, chemical reactions. A comprehensive mapping of enzyme function and evolution may be attainable in the near future.

Dual single atomic Ni sites constructing Janus hollow graphene for boosting electrochemical sensing of glucose.

Single atom catalysts (SACs) have attracted attention due to their excellent catalysis activity under specific reactions and conditions. However, the low density of SACs greatly limits catalytic performance. The three-dimensional graphene hollow nanospheres (GHSs) with very thin shell structure can be used as excellent carrier materials. Not only can its outer surface be used to anchor metal single atoms, but its inner surface can also provide rich sites. Here, a novel step-by-step assembly strategy is reported to anchor nickel single atoms (Ni SAs) on the inner and outer surfaces of GHSs (Ni SAs/GHSs/Ni SAs), which significantly increases the loading capacity of Ni SAs (4.8 wt%). Compared to conventional materials that only anchor Ni SAs to the outer surface of the carrier (Ni SAs/GHSs), Ni SAs/GHSs/Ni SAs exhibits significantly higher electrocatalytic activity toward glucose oxidation in alkaline media. The sensitivity of Ni SAs/GHSs/Ni SAs/GCE is nearly five times higher than that of Ni SAs/GHSs/GCE. Moreover, the sensor based on Ni SAs/GHSs/Ni SAs can detect glucose in a wide concentration range of 0.8 µM-1.1244 mM with a low detection limit of 0.19 µM (S/N = 3). This study not only provides an effective sensing material for glucose detection, but also opens a new avenue to construct high-density metal SACs.

Pd/Ni bimetallic modification of SrTiO3for enhancement of photocatalytic water splitting.

This paper investigates the impact of Pd/Ni modification on the photocatalytic hydrogen production performance of SrTiO3(STO). STO catalysts were synthesized using a hydrothermal method, and Pd/Ni modification was applied on the surface of STO through chemical deposition. Experimental results demonstrate that the hydrogen evolution rate of Pd/Ni-modified STO (Pd/Ni-STO) reaches 2232.14µmol g-1h-1. X-ray absorption fine structure spectroscopy analysis reveals substitutional doping of Ni with Ti and coordination of Pd with surface O. X-ray photoelectron spectroscopy analysis indicates the introduction of oxygen vacancies due to Pd/Ni doping. Density functional theory calculations suggest that Ni doping activates neighboring Ti atoms, leading to the formation of bimetallic catalytic sites composed of oxygen vacancies and Ti atoms, greatly enhancing the photocatalytic hydrogen evolution performance. This study not only provides an effective catalyst for photocatalytic applications but also offers insights into the underlying mechanism, which may stimulate the development of metal-doped catalytic materials and have implications for a range of other applications.

Covalent Organic Frameworks Containing Dual O2 Reduction Centers for Overall Photosynthetic Hydrogen Peroxide Production.

Covalent organic frameworks (COFs) are highly desirable for achieving high-efficiency overall photosynthesis of hydrogen peroxide (H2 O2 ) via molecular design. However, precise construction of COFs toward overall photosynthetic H2 O2 remains a great challenge. Herein, we report the crystalline s-heptazine-based COFs (HEP-TAPT-COF and HEP-TAPB-COF) with separated redox centers for efficient H2 O2 production from O2 and pure water. The spatially and orderly separated active sites in HEP-COFs can efficiently promote charge separation and enhance photocatalytic H2 O2 production. Compared with HEP-TAPB-COF, HEP-TAPT-COF exhibits higher H2 O2 production efficiency for integrating dual O2 reduction active centers of s-heptazine and triazine moieties. Accordingly, HEP-TAPT-COF bearing dual O2 reduction centers exhibits a remarkable solar-to-chemical energy efficiency of 0.65 % with a high apparent quantum efficiency of 15.35 % at 420 nm, surpassing previously reported COF-based photocatalysts.

Catalytic Linkage Engineering of Covalent Organic Frameworks for the Oxygen Reduction Reaction.

Metal-free covalent organic frameworks (COFs) have been employed to catalyze the oxygen reduction reaction (ORR). To achieve high activity and selectivity, various building blocks containing heteroatoms and groups linked by imine bonds were used to create catalytic COFs. However, the roles of linkages of COFs in ORR have not been investigated. In this work, the catalytic linkage engineering has been employed to modulate the catalytic behaviors. To create single catalytic sites while avoiding other possible catalytic sites, we synthesized COFs from benzene units linked by various bonds, such as imine, amide, azine, and oxazole bonds. Among these COFs, the oxazole-linkage in COFs enables to catalyze the ORR with the highest activity, which achieved a half-wave potential of 0.75 V and a limited current density of 5.5 mA cm-2 . Moreover, the oxazole-linked COF achieved a conversion frequency (TOF) value of 0.0133 S-1 , which were 1.9, 1.3, and 7.4-times that of azine-, amide- and imine-COFs, respectively. The theoretical calculation showed that the carbon atoms in oxazole linkages facilitated the formation of OOH* and promoted protonation of O* to form the OH*, thus advancing the catalytic activity. This work guides us on which linkages in COFs are suitable for ORR.

CoN5 Sites Constructed by Anchoring Co Porphyrins on Vinylene-Linked Covalent Organic Frameworks for Electroreduction of Carbon Dioxide.

Developing effective electrocatalysts for CO2 reduction (CO2 RR) is of critical importance for producing carbon-neutral fuels. Covalent organic frameworks (COFs) are an ideal platform for constructing catalysts toward CO2 RR, because of their controllable skeletons and ordered pores. However, most of these COFs are synthesized from Co-porphyrins or phthalocyanines-based monomers, and the available building units and resulting catalytic centers in COFs are still limited. Herein, Co-N5 sites are first developed through anchoring Co porphyrins on an olefin-linked COF, where the Co active sites are uniformly distributed in the hexagonal networks. The strong electronic coupling between Co porphyrins and COF is disclosed by various characterizations such as X-ray absorption spectroscopy (XAS) and density functional theory calculation (DFT). Thanks to the CoN5 sites, the catalytic COF shows remarkable catalytic activity with Faraday efficiencies (FECO ) of 84.2-94.3% at applied potentials between -0.50 and -0.80 V (vs RHE), and achieves a turnover frequency of 4578 h-1 at -1.0 V. Moreover, the theoretical calculation further reveals that the CoN5 sites enable a decrease in the overpotential for the formation COOH*. This work provides a design strategy to employ COFs as scaffold for fabricating efficient CO2 electrocatalysts.

Local frustration around enzyme active sites.

Conflicting biological goals often meet in the specification of protein sequences for structure and function. Overall, strong energetic conflicts are minimized in folded native states according to the principle of minimal frustration, so that a sequence can spontaneously fold, but local violations of this principle open up the possibility to encode the complex energy landscapes that are required for active biological functions. We survey the local energetic frustration patterns of all protein enzymes with known structures and experimentally annotated catalytic residues. In agreement with previous hypotheses, the catalytic sites themselves are often highly frustrated regardless of the protein oligomeric state, overall topology, and enzymatic class. At the same time a secondary shell of more weakly frustrated interactions surrounds the catalytic site itself. We evaluate the conservation of these energetic signatures in various family members of major enzyme classes, showing that local frustration is evolutionarily more conserved than the primary structure itself.

Tug-of-War between Two Distinct Catalytic Sites Enables Fast and Selective Ring-Opening Copolymerizations.

Ring-opening copolymerizations have emerged as a powerful approach towards the creation of sustainable polymers. Typical H-bonding catalysts for ring-opening are subject to a single catalytic site. Here we describe a H-bond-donor/Lewis-acidic-boron organocatalyst featuring two distinct catalytic sites in one molecule. The ring-opening copolymerization of epoxides with anhydride mediated by these modular, and tunable catalysts achieves high selectivity (>99 % polyester selectivity) and markedly higher activity compared to either of the di-thiourea analogues or any combinations of them. Calculations and experimental studies reveal that the superior catalytic performance arises from tug-of-war between two differentiated catalytic sites: thiourea pulls off the propagating chain-end from boron center, simultaneously enhancing the role of monomer activation and also nucleophilicity of the propagation intermediates.

An Atom-Pair Design Strategy for Optimizing the Synergistic Electron Effects of Catalytic Sites in NO Selective Reduction.

Effective adsorption and speedy surface reactions are vital requirements for efficient active sites in catalysis, but it remains challenging to maximize these two functions simultaneously. We present a solution to this issue by designing a series of atom-pair catalytic sites with tunable electronic interactions. As a case study, NO selective reduction occurring on V1 -W1 /TiO2 is chosen. Experimental and theoretical results reveal that the synergistic electron effect present between the paired atoms enriches high-energy spin charge around the Fermi level, simultaneously rendering reactant (NH3 or O2 ) adsorption more effective and subsequent surface reactions speedier as compared with single V or W atom alone, and hence higher reaction rates. This strategy enables us to rationally design a high-performance V1 -Mo1 /TiO2 catalyst with optimized vanadium(IV)-molybdenum(V) electronic interactions, which has exceptional activity significantly higher than the commercial or reported catalysts.

Engineering Functional Interface with Built-in Catalytic and Self-Oxidation Sites for Highly Stable Lithium-Sulfur Batteries.

Lithium-sulfur (Li-S) batteries have attracted great attention due to their high theoretical energy density. The rapid redox conversion of lithium polysulfides (LiPS) is effective for solving the serious shuttle effect and improving the utilization of active materials. The functional design of the separator interface with fast charge transfer and active catalytic sites is desirable for accelerating the conversion of intermediates. Herein, a graphene-wrapped MnCO3 nanowire (G@MC) was prepared and utilized to engineer the separator interface. G@MC with active Mn2+ sites can effectively anchor the LiPS by forming the Mn-S chemical bond according to our theoretical calculation results. In addition, the catalytic Mn2+ sites and conductive graphene layer of G@MC could accelerate the reversible conversion of LiPS via the spontaneous "self-redox" reaction and the rapid electron transfer in electrochemical process. As a result, the G@MC-based battery exhibits only 0.038 % capacity decay (per cycle) after 1000 cycles at 2.0 C. This work affords new insights for designing the integrated functional interface for stable Li-S batteries.

Atomic-Level Fe-N-C Coupled with Fe3 C-Fe Nanocomposites in Carbon Matrixes as High-Efficiency Bifunctional Oxygen Catalysts.

Highly active and durable bifunctional oxygen electrocatalysts are of pivotal importance for clean and renewable energy conversion devices, but the lack of earth-abundant electrocatalysts to improve the intrinsic sluggish kinetic process of oxygen reduction/evolution reactions (ORR/OER) is still a challenge. Fe-N-C catalysts with abundant natural merits are considered as promising alternatives to noble-based catalysts, yet further improvements are urgently needed because of their poor stability and unclear catalytic mechanism. Here, an atomic-level Fe-N-C electrocatalyst coupled with low crystalline Fe3 C-Fe nanocomposite in 3D carbon matrix (Fe-SAs/Fe3 C-Fe@NC) is fabricated by a facile and scalable method. Versus atomically FeNx species and crystallized Fe3 C-Fe nanoparticles, Fe-SAs/Fe3 C-Fe@NC catalyst, abundant in vertical branched carbon nanotubes decorated on intertwined carbon nanofibers, exhibits high electrocatalytic activities and excellent stabilities both in ORR (E1/2 , 0.927 V) and OER (EJ=10 , 1.57 V). This performance benefits from the strong synergistic effects of multicomponents and the unique structural advantages. In-depth X-ray absorption fine structure analysis and density functional theory calculation further demonstrate that more extra charges derived from modified Fe clusters decisively promote the ORR/OER performance for atomically FeN4 configurations by enhanced oxygen adsorption energy. These insightful findings inspire new perspectives for the rational design and synthesis of economical-practical bifunctional oxygen electrocatalysts.

A computational method to characterize the missense mutations in the catalytic domain of GAA protein causing Pompe disease.

Pompe disease is an autosomal recessive lysosomal storage disease caused by acid α-glucosidase (GAA) deficiency, resulting in intralysosomal accumulation of glycogen, including cardiac, skeletal, and smooth muscle cells. The GAA gene is located on chromosome 17 (17q25.3), the GAA protein consists of 952 amino acids; of which 378 amino acids (347-726) falls within the catalytic domain of the protein and comprises of active sites (518 and 521) and binding sites (404, 600, 616, and 674). In this study, we used several computational tools to classify the missense mutations in the catalytic domain of GAA for their pathogenicity and stability. Eight missense mutations (R437C, G478R, N573H, Y575S, G605D, V642D, L705P, and L712P) were predicted to be pathogenic and destabilizing to the protein structure. These mutations were further subjected to phenotyping analysis using SNPeffect 4.0 to predict the chaperone binding sites and structural stability of the protein. The mutations R437C and G478R were found to compromise the chaperone-binding activity with GAA. Molecular docking analysis revealed that the G478R mutation to be more significant and hinders binding to the DNJ (Miglustat) compared with the R437C. Further molecular dynamic analysis for the two mutations demonstrated that the G478R mutation was acquired higher deviation, fluctuation, and lower compactness with decreased intramolecular hydrogen bonds compared to the mutant R437C. These data are expected to serve as a platform for drug design against Pompe disease and will serve as an ultimate tool for variant classification and interpretations.

Phosphorus Incorporation into Co9 S8 Nanocages for Highly Efficient Oxygen Evolution Catalysis.

The improvement of activity of electrocatalysts lies in the increment of the density of active sites or the enhancement of intrinsic activity of each active site. A common strategy to realize dual active sites is the use of bimetal compound catalysts, where each metal atom contributes one active site. In this work, a new concept is presented to realize dual active sites with tunable electron densities in monometal compound catalysts. Dual Co2+ tetrahedral (Co2+ (Td )) and Co3+ octahedral (Co3+ (Oh )) coordination active sites are developed and adjustable electron densities on the Co2+ (Td ) and Co3+ (Oh ) are further achieved by phosphorus incorporation (P-Co9 S8 ). The experimental results and density functional theory calculations show that the nonmetal P doping can systematically modulate charge density of Co2+ (Td ) and Co3+ (Oh ) in P-Co9 S8 and simultaneously improve the electrical conductivity of Co9 S8 , which substantially enhances oxygen evolution reaction performance of P-Co9 S8 .

A Phthalocyanine-Based Layered Two-Dimensional Conjugated Metal-Organic Framework as a Highly Efficient Electrocatalyst for the Oxygen Reduction Reaction.

Layered two-dimensional (2D) conjugated metal-organic frameworks (MOFs) represent a family of rising electrocatalysts for the oxygen reduction reaction (ORR), due to the controllable architectures, excellent electrical conductivity, and highly exposed well-defined molecular active sites. Herein, we report a copper phthalocyanine based 2D conjugated MOF with square-planar cobalt bis(dihydroxy) complexes (Co-O4 ) as linkages (PcCu-O8 -Co) and layer-stacked structures prepared via solvothermal synthesis. PcCu-O8 -Co 2D MOF mixed with carbon nanotubes exhibits excellent electrocatalytic ORR activity (E1/2 =0.83 V vs. RHE, n=3.93, and jL =5.3 mA cm-2 ) in alkaline media, which is the record value among the reported intrinsic MOF electrocatalysts. Supported by in situ Raman spectro-electrochemistry and theoretical modeling as well as contrast catalytic tests, we identified the cobalt nodes as ORR active sites. Furthermore, when employed as a cathode electrocatalyst for zinc-air batteries, PcCu-O8 -Co delivers a maximum power density of 94 mW cm-2 , outperforming the state-of-the-art Pt/C electrocatalysts (78.3 mW cm-2 ).

Characterisation of the Carboxypeptidase G2 Catalytic Site and Design of New Inhibitors for Cancer Therapy.

The enzyme carboxypeptidase G2 (CPG2) is used in antibody-directed enzyme prodrug therapy (ADEPT) to catalyse the formation of an active drug from an inert prodrug. Free CPG2 in the bloodstream must be inhibited before administration of the prodrug in order to avoid a systemic reaction in the patient. Although a few small-molecule CPG2 inhibitors have been reported, none has been taken forward thus far. This lack of progress is due in part to a lack of structural understanding of the CPG2 active site as well as the absence of small molecules that can block the active site whilst targeting the complex for clearance. The work described here aimed to address both areas. We report the structural/functional impact of extensive point mutation across the putative CPG2 catalytic site and adjacent regions for the first time, revealing that residues outside the catalytic region (K208A, S210A and T357A) are crucial to enzyme activity. We also describe novel molecules that inhibit CPG2 whilst maintaining the accessibility of galactosylated moieties aimed at targeting the enzyme for clearance. This work acts as a platform for the future development of high-affinity CPG2 inhibitors that occupy new chemical space and will advance the safe application of ADEPT in cancer treatment.

Enabling Visible-Light-Driven Selective CO2 Reduction by Doping Quantum Dots: Trapping Electrons and Suppressing H2 Evolution.

Quantum dots (QDs), a class of promising candidates for harvesting visible light, generally exhibit low activity and selectivity towards photocatalytic CO2 reduction. Functionalizing QDs with metal complexes (or metal cations through ligands) is a widely used strategy for improving their catalytic activity; however, the resulting systems still suffer from low selectivity and stability in CO2 reduction. Herein, we report that doping CdS QDs with transition-metal sites can overcome these limitations and provide a system that enables highly selective photocatalytic reactions of CO2 with H2 O (100 % selectivity to CO and CH4 ), with excellent durability over 60 h. Doping Ni sites into the CdS lattice leads to effective trapping of photoexcited electrons at surface catalytic sites and substantial suppression of H2 evolution. The method reported here can be extended to various transition-metal sites, and offers new opportunities for exploring QD-based earth-abundant photocatalysts.

Oxygen-Molecule Adsorption and Dissociation on BCN Graphene: A First-Principles Study.

Boron and nitrogen co-doped (BCN) graphene is an attractive material for use as a metal-free oxygen reduction reaction electrocatalyst and as other catalysts due to its unique structure and electronic properties. Reported here is the structure, determined by using density functional theory, of the active O2 -dissociation site of BCN graphene containing different types of BN cluster. The results show that the edge termination and shape of substitutional BN clusters are two important factors that determine the catalytic activity of BCN graphene for the dissociation of molecular oxygen. N-Terminated triangular BN (t-BN) cluster doping can reduce the energy barrier more effectively compared to a t-BN with a B edge or quadrangular BN cluster. Interestingly, the B atom neighboring the N edge, only in the case of N-terminated t-BN doping, is determined to be the most active site for O2 dissociation due to the barrier being as low as 0.08 eV. The electronic structure calculations reveal that in addition to the large positive charge densities, the catalytic activity of graphene enhanced by B,N doping is also attributed to the increased density of states of the π* states of the active site around the Fermi level.

A Solvent-Based Strategy for Tuning the Internal Structure of Metallo-Folded Single-Chain Nanoparticles.

Controlling the spatial distribution of catalytic sites in metallo-folded single-chain nanoparticles (SCNPs) is a first step toward the rational design of improved catalytic soft nano-objects. Here an unexplored pathway is reported for tuning the internal structure of metallo-folded SCNPs. Unlike the conventional SCNP synthesis in good solvent (protocol I), the proposed new route (protocol II) is based on the use of amphiphilic random copolymers and transfer, after SCNP formation, from selective to good (nonselective) solvent conditions. The size and morphology of the SCNPs obtained by the two protocols, and the corresponding spatial distribution of the catalytic sites, have been determined by combining results from size exclusion chromatography with triple detection, small-angle X-ray scattering and molecular dynamics (MD) simulations. Remarkably, the use of these protocols allows the tuning of the internal structure of the metallo-folded SCNPs, as supported by MD simulations results. While the conventional protocol I yields a homogeneous distribution of the catalytic sites in the SCNP, these are arranged into clusters in the case of protocol II.

Efficacious bioconversion of alginate/cellulose to value-added oligosaccharides by alginate-degrading GH5 endoglucanase from Trichoderma asperellum.

Enzymatic degradation of lignocellulosic biomass provides an eco-friendly approach to produce value-added macromolecules, e.g., bioactive polysaccharides. A novel acidophilic GH5 ß-1,4-endoglucanase (termed TaCel5) from Trichoderma asperellum ND-1 was efficiently expressed in Komagataella phaffii (∼1.5-fold increase, 38.42 U/mL). TaCel5 displayed both endoglucanase (486.3 U/mg) and alginate lyase (359.5 U/mg) enzyme activities. It had optimal pH 3.0 and strong pH stability (exceed 86 % activity retained over pH range 3.0-5.0). 80 % activity (both endoglucanase and alginate lyase) was retained in the presence of 15 % ethanol or 3.42 M NaCl. Analysis of action mode revealed that hydrolytic activity of TaCel5 required at least three glucose (cellotriose) residues, yielding mainly cellobiose. Glu241 and Glu352 are essential catalytic residues, while Asp106, Asp277 and Asp317 play auxiliary roles in cellulose degradation. TaCel5 displayed high hydrolysis efficiency for glucan and alginate substrates. ESI-MS analysis indicated that the enzymatic hydrolysates of alginate mainly contained disaccharides and heptasaccharides. This is the first detailed report of a bifunctional GH5 endoglucanase/alginate lyase enzyme from T. asperellum. Thus TaCel5 has strong potential in food and feed industries as a catalyst for bioconversion of cellulose- and alginate-containing waste materials into value-added products oligosaccharides, which was of great benefit both for the economy and environment.

Transformation of corncob into high-value xylooligosaccharides using glycoside hydrolase families 10 and 11 xylanases from Trichoderma asperellum ND-1.

Effective production of xylooligosaccharides (XOS) with lower proportion of xylose entails unique and robust xylanases. In this study, two novel xylanases from Trichoderma asperellum ND-1 belonging to glycoside hydrolase families 10 (XynTR10) and 11 (XynTR11) were over-expressed in Komagataella phaffii X-33 and characterized to be robust enzymes with high halotolerance and ethanol tolerant. Both enzymes displayed strict substrate specificity towards beechwood xylan and wheat arabinoxylan. (Glu153/Glu258) and (Glu161/Glu252) were key catalytic sites for XynTR10 and XynTR11. Notably, XynTR11 could rapidly degrade xylan/XOS into xylobiose without xylose via transglycosylation. Direct degradation of corncob using XynTR10 and XynTR111 displayed that while XynTR10 yielded 77% xylobiose and 25% xylose, XynTR11 yielded much less xylose (11%) and comparable amounts of xylobiose (63%). XynTR10 or XynTR111 has great potential as a catalyst for bioconversion of xylan-containing agricultural waste into high-value products (biofuel or XOS), which is of significant benefit for the economy and environment.