Unique Catalytic Functions Research Articles

Modular Weaving DNAzyme in Skeleton of DNA Nanocages for Photoactivatable Catalytic Activity Regulation.

DNAzymes exhibit tremendous application potentials in the field of biosensing and gene regulation due to its unique catalytic function. However, spatiotemporally controlled regulation of DNAzyme activity remains a daunting challenge, which may cause nonspecific signal leakage or gene silencing of the catalytic systems. Here, we report a photochemical approach via modular weaving active DNAzyme into the skeleton of tetrahedral DNA nanocages (TDN) for light-triggered on-demand liberation of DNAzyme and thus conditional control of gene regulation activity. We demonstrate that the direct encoding of DNAzyme in TDN could improve the biostability of DNAzyme and ensure the delivery efficiency, comparing with the conventional surface anchoring strategy. Furthermore, the molecular weaving of the DNA nanostructures allows remote control of DNAzyme-mediated gene regulation with high spatiotemporal precision of light. In addition, we demonstrate that the approach is applicable for controlled regulation of the gene editing functions of other functional nucleic acids.

Modular Weaving DNAzyme in Skeleton of DNA Nanocages for Photoactivatable Catalytic Activity Regulation

AbstractDNAzymes exhibit tremendous application potentials in the field of biosensing and gene regulation due to its unique catalytic function. However, spatiotemporally controlled regulation of DNAzyme activity remains a daunting challenge, which may cause nonspecific signal leakage or gene silencing of the catalytic systems. Here, we report a photochemical approach via modular weaving active DNAzyme into the skeleton of tetrahedral DNA nanocages (TDN) for light‐triggered on‐demand liberation of DNAzyme and thus conditional control of gene regulation activity. We demonstrate that the direct encoding of DNAzyme in TDN could improve the biostability of DNAzyme and ensure the delivery efficiency, comparing with the conventional surface anchoring strategy. Furthermore, the molecular weaving of the DNA nanostructures allows remote control of DNAzyme‐mediated gene regulation with high spatiotemporal precision of light. In addition, we demonstrate that the approach is applicable for controlled regulation of the gene editing functions of other functional nucleic acids.

Catalytic Mechanism of Nonglycosidic C-N Bond Formation by the Pseudoglycosyltransferase Enzyme VldE.

The pseudoglycosyltransferase (PsGT) enzyme VldE is a homologue of the retaining glycosyltransferase (GT) trehalose 6-phosphate synthase (OtsA) that catalyzes a coupling reaction between two pseudo-sugar units, GDP-valienol and validamine 7-phosphate, to give a product with α,α-N-pseudo-glycosidic linkage. Despite its biological importance and unique catalytic function, the molecular bases for its substrate specificity and reaction mechanism are still obscure. Here, we report a comparative mechanistic study of VldE and OtsA using various engineered chimeric proteins and point mutants of the enzymes, X-ray crystallography, docking studies, and kinetic isotope effects. We found that the distinct substrate specificities between VldE and OtsA are most likely due to topological differences within the hot spot amino acid regions of their N-terminal domains. We also found that the Asp158 and His182 residues, which are in the active site, play a significant role in the PsGT function of VldE. They do not seem to be directly involved in the catalysis but may be important for substrate recognition or contribute to the overall architecture of the active site pocket. Moreover, results of the kinetic isotope effect experiments suggest that VldE catalyzes a C-N bond formation between GDP-valienol and validamine 7-phosphate via an SNi-like mechanism. The study provides new insights into the substrate specificity and catalytic mechanism of a member of the growing family of PsGT enzymes, which may be used as a basis for developing new PsGTs from GTs.

Preparation of CdS and its Photocalytic behaviour for Dye Degradation

A short time ago, transition metal sulphides like CdS has been arduously studied because it has unique catalytic functions. This disclosed that CdS nanocrystals are good photocatalysts because it can quickly generate electron-hole pairs by photo-excitation. In the present work, CdS is prepared by hydrothermal process. Prepared samples were characterized by X-ray diffractions (XRD), SEM, Optical study, and for evaluation of photophysical properties, UV/VIS spectra were recorded. By UV irradiation and photocatalytic decay of dyes, the photoactivity of synthesised CdS was accessed. The CdS shows higher catalytic activity.

Tuned selectivity and enhanced activity of CO2 methanation over Ru catalysts by modified metal-carbonate interfaces

Carbonate-modified metal-support interfaces allow Ru/MnCO3 catalyst to exhibit over 99% selectivity, great specific activity and long-term anti-CO poisoning stability in atmospheric CO2 methanation. As a contrast, Ru/MnO catalyst with metal-oxide interfaces prefers reverse water–gas shift rather than methanation route, along with a remarkably lower activity and a less than 15% CH4 selectivity. The carbonate-modified interfaces are found to stabilize the Ru species and activate CO2 and H2 molecules. Ru-CO* species are identified as the reaction intermediates steadily formed from CO2 dissociation, which show moderate adsorption strength and high reactivity in further hydrogenation to CH4. Furthermore, carbonates of Ru/MnCO3 are found to be consumed by hydrogenation to form CH4 and replenished by exchange with CO2, which are in a dynamic equilibrium during the reaction. Modification with surface carbonates is proved as an efficient strategy to endow metal-support interfaces of Ru-based catalysts with unique catalytic functions for selective CO2 hydrogenation.

Operando Dual Beam FTIR Study of Hydroxyl Groups and Zn Species over Defective HZSM-5 Zeolite Supported Zinc Catalysts

A series of defective ZSM-5 zeolites (~300 nm, SiO2/Al2O3 ratio of 55, 100, 480 and 950) were systematically studied by XRD, SEM, 29Si MAS NMR, argon physisorption, NH3-TPD and FT-IR technologies. The nature, the amount and the accessibility of the acid sites of defective ZSM-5 zeolites are greatly different from reported ZSM-5 zeolites with a perfect crystal structure. The Brønsted acid sites (Si(OH)Al) with strong acid strength and the Brønsted acid sites (hydroxyl nests) with weak acid strength co-existed over defective ZSM-5 zeolites, which leads to a unique catalytic function. Zn(C2H5)2 was grafted onto defective ZSM-5 zeolites through the chemical liquid deposition (CLD) method. Interestingly, FT-IR spectroscopic studies found that Zn(C2H5)2 was preferentially grafted on the hydroxyl nests with weak acid strength rather than the Si(OH)Al groups with strong acid strength over different defective ZSM-5 zeolites. In particular, home-built operando dual beam FTIR-MS was applied to study the catalytic performance of Zn species located in different sites of defective ZSM-5 zeolites under real n-hexane transformation conditions. Results show that Zn species grafted over hydroxyl nests obtain better dehydrogenative aromatization performance than Zn species over Si(OH)Al groups. This study provides guidance for the rational design of highly efficient alkane dehydrogenative aromatization catalysts.

New mechanistic insights into the Claisen rearrangement of chorismate – a Unified Reaction Valley Approach study

ABSTRACTThe Bacillus subtilis chorismate mutase catalysed Claisen rearrangement of chorismate to prephenate is one of the few pericyclic processes in biology, and as such provides a rare opportunity for understanding how Nature promotes such rearrangements so successfully. The major focus of this work is on (i) Exploring the hypothesis that the mechanism of the chorismate rearrangement is the same in the gas phase, in the aqueous solution and in the enzyme; (ii) Investigating current suggestions that the enzyme lowers the barrier via transition state stabilisation rather than via space confinement; and (iii) A comparison of Nature's way of catalysing the reaction with a gold(I) catalysed chorismate rearrangement. Based the Unified Reaction Valley Approach (URVA), for the first time, a detailed one-to-one comparison of the rearrangement in the gas phase, in the aqueous solution and in the enzyme is presented. URVA confirms that the actual chemical process of CO bond breaking and CC bond forming is the same for all media and unravels the unique catalytic function of the enzyme as a combination of shortening the process of positioning the enolpyruvyl side chain over the cyclohexadienyl ring by space confinement in concert with facilitating CO cleavage by enhanced charge polarisation. The transition state does not play a signifiant role for the rearrangement. In contrast, the gold catalyst changes the chemical process. The rearrangement is split into two steps by switching between Au[I]-π and Au[I]-σ complexation, thus avoiding the energy consuming CO breakage in the first step. Suggestions are made for metalloenzyme analogues combining both strategies.

Effect of anodes decoration with metal and metal oxides nanoparticles on pharmaceutically active compounds removal and power generation in microbial fuel cells

Anodes modified with MnO2, Pd and Fe3O4 nanoparticles were used in microbial fuel cells (MFCs) and their effects on pharmaceutically active compounds (PhACs) removal and power generation were investigated. Results showed that anode decoration with MnO2, Fe3O4 and Pd led to different performance in removing PhACs from MFCs. Diclofenac (DCF), ibuprofen (IBF) and carbamazepine (CBZ) were more effectively removed in the MFCs with the MnO2, Fe3O4 or Pd anode compared to that with the carbon black (CB) modified control anode, with a removal of 81.5%–84.0% for CBZ, 48.7%–52.6% for DCF and 18.8%–20.1% for IBF, while the corresponding parts attained with the CB anode were 71.0%–78.5% for CBZ, 28.8% for DCF and 14.6% for IBF. Iohexol (IOX) was hardly removed in all the MFCs. When common non-conductive carrier (nonwoven) was used as the anode of MFCs, PhACs were less removed compared to the MFC systems, suggesting MFCs possess specially advantages over PhACs removal. The MFCs with the Pd, MnO2 and Fe3O4 anodes generated a maximum power density of 824 ± 36, 782 ± 37 and 728 ± 33 mW m−2, respectively, higher than that with the control anode (680 ± 28 mW m−2). High-throughput sequencing results showed that the MnO2 and Fe3O4 modified anodes especially enriched the exoelectrogen Geobacter (72.1%), while the Pd decorated anode enriched a high abundance of Geobacter (38.5%) and Sphaerochaeta (16.1%). Enhanced electron transfer, specially enriched microbial community, unique catalytic functions of the metal or metal oxides deposited on the anodes, may contribute to the enhanced performance of MFCs on power generation and PhACs removal.

Inter-molecular crosslinking activity is engendered by the dimeric form of transglutaminase 2.

Transglutaminase 2 (TGase 2) catalyzes a crosslink between protein bound-glutamine and -lysine. We proposed the mechanism of TGase 2 activation depends on conformation change from unfolded monomer to unfolded dimer. We found that TGase 2 has temperature-sensitive conformation change system at 30°C. Small-angle X-ray scattering analysis showed that the enzyme was maintained as an unfolded monomer at temperatures below 30°C, but changed to an unfolded dimer at over 30°C. Mass analysis revealed that the C-terminus of TGase 2 was the critical region for dimerization. Furthermore, this conformational switch creates new biochemical reactivity that catalyzed inter-molecular crosslink at above 30°C as an unfolded dimer of TGase 2 while catalyzed intra-molecular crosslink at below 30°C as an unfolded monomer of TGase 2. The mechanism of TGase 2 activation depends on temperature-sensitive conformation change from unfolded monomer to unfolded dimer at over 30°C. Furthermore, inter-molecular crosslinking activity is generated by the dimeric form of TGase 2. TGase 2 switches its conformation from a monomer to a dimer following a change in temperature, which engendered unique catalytic function of enzyme as inter-molecular crosslinking activity with calcium.

Structure-Function Analysis of a Broad Specificity Populus trichocarpa Endo-β-glucanase Reveals an Evolutionary Link between Bacterial Licheninases and Plant XTH Gene Products

The large xyloglucan endotransglycosylase/hydrolase (XTH) gene family continues to be the focus of much attention in studies of plant cell wall morphogenesis due to the unique catalytic functions of the enzymes it encodes. The XTH gene products compose a subfamily of glycoside hydrolase family 16 (GH16), which also comprises a broad range of microbial endoglucanases and endogalactanases, as well as yeast cell wall chitin/β-glucan transglycosylases. Previous whole-family phylogenetic analyses have suggested that the closest relatives to the XTH gene products are the bacterial licheninases (EC 3.2.1.73), which specifically hydrolyze linear mixed linkage β(1→3)/β(1→4)-glucans. In addition to their specificity for the highly branched xyloglucan polysaccharide, XTH gene products are distinguished from the licheninases and other GH16 enzyme subfamilies by significant active site loop alterations and a large C-terminal extension. Given these differences, the molecular evolution of the XTH gene products in GH16 has remained enigmatic. Here, we present the biochemical and structural analysis of a unique, mixed function endoglucanase from black cottonwood (Populus trichocarpa), which reveals a small, newly recognized subfamily of GH16 members intermediate between the bacterial licheninases and plant XTH gene products. We postulate that this clade comprises an important link in the evolution of the large plant XTH gene families from a putative microbial ancestor. As such, this analysis provides new insights into the diversification of GH16 and further unites the apparently disparate members of this important family of proteins.

Induction of Cytochrome P450 1A5 mRNA, Protein and Enzymatic Activities by Dioxin-Like Compounds, and Congener-Specific Metabolism and Sequestration in the Liver of Wild Jungle Crow (Corvus macrorhynchos) from Tokyo, Japan

This study presents concentrations of polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), and dioxin-like coplanar PCBs (Co-PCBs) in the liver and breast muscle of jungle crows (JCs; Corvus macrorhynchos) collected from Tokyo, Japan. 2,3,7,8-Tetrachlorodibenzo-p-dioxin toxic equivalents (TEQs) derived by WHO bird-TEF were in the range of 23 to 280 pg/g (lipid) in the liver, which are lower or comparable to the lowest-observed-effect-level of CYP induction in chicken, and 5.6-78 pg/g (lipid) in the pectoral muscle. Cytochrome P450 (CYP) 1A-, 2B-, 2C-, and 3A-like proteins were detected using anti-rat CYP polyclonal antibodies in hepatic microsomal fractions. Significant (p < 0.05) positive correlations between hepatic TEQs and CYP1A or CYP3A-like protein expression levels were noticed, implying induction of these CYP isozymes by TEQs. On the other hand, there was no significant positive correlation between muscle TEQ and any one of analyzed CYP isozyme expression levels. CYP1A- and CYP3A-like protein expression levels represented better correlations with pentoxy- and benzyloxyresorufin-O-dealkylase activities rather than methoxy- and ethoxyresorufin-O-dealkylase activities, indicating unique catalytic functions of these CYPs in JCs. Furthermore, we succeeded in isolating CYP1A5 cDNA from the liver of JC, having an open reading frame of 531 amino acid residues with a predicted molecular mass of 60.3 kDa. JC CYP1A5 mRNA expression measured by real-time RT-PCR had a significant positive correlation with hepatic TEQs, suggesting induction of CYP1A5 at the transcriptional level. Ratios of several Co-PCB congeners to CB-169 in the liver of JCs revealed significant negative correlations with CYP1A protein or CYP1A5 mRNA expression levels, implying metabolism of these congeners by the induced CYP1A. The liver/breast muscle concentration (L/M) ratios of PCDDs/DFs and CB-169 increased with an increase in hepatic CYP1A protein or CYP1A5 mRNA expression levels, suggesting congener-specific hepatic sequestrations by the induced CYP1A. The present study provides insights into the propensity of CYP1A induction to the exposure of dioxin-like chemicals, and unique metabolic and sequestration capacities of CYP1A in JC.

Mass Production and High Photocatalytic Activity of ZnS Nanoporous Nanoparticles

Environmental problems associated with organic pollutants and toxic water pollutants provide the impetus for sustained fundamental and applied research in the area of environmental remediation. Semiconductor photocatalysis offers the potential for complete elimination of toxic chemicals through its efficiency and potentially broad applicability. [1] Various new compounds and materials for photocatalysis have been synthesized in the past few decades. A successful example is TiO2, a metal oxide often used as a catalyst in photochemistry, electrochemistry, environmental protection, and in the battery industry. [2] Recently, transition-metal sulfides, in particular ZnS and CdS, have been intensively studied because of their unique catalytic functions compared to those of TiO2. [2, 3] These studies have revealed that ZnS nanocrystals (NCs) are good photocatalysts as a result of the rapid generation of electron– hole pairs by photoexcitation and the highly negative reduction potentials of excited electrons. The photocatalytic properties occur not only in the photoreductive production of H2 from water and the photoreduction of CO2, [4] but also in the phototransformation of various organic substrates such as the oxidative formation of carbon–carbon bonds from organic electron donors, cis–trans photoisomerization of alkenes, and the photoreduction of aldehydes and their derivatives. [5] The notable finding in nonmetalized ZnS photocatalysis is an irreversible two-electron-transfer photoreduction of organic substrates. [6] A favorable shift of the optical response into the visible region occurs subsequent to the doping of transition metal or rare-earth metal ions, such as Ni 2+ and Cu 2+ ; therefore, ZnS NCs can also be used as effective catalysts for photocatalytic evolution of H2 and photoreduction of toxic ions under visible-light irradiation. [7] An important application of ZnS is as a photocatalyst in environmental protection through the removal of organic

Type II phosphoinositide 5-phosphatases have unique sensitivities towards fatty acid composition and head group phosphorylation

The catalytic properties of the type II phosphoinositide 5-phosphatases of Lowe's oculocerebrorenal syndrome, INPP5B, Synaptojanin1, Synaptojanin2 and SKIP were analysed with respect to their substrate specificity and enzymological properties. Our data reveal that all phosphatases have unique substrate specificities as judged by their corresponding K M and V Max values. They also possessed an exclusive sensitivity towards fatty acid composition, head group phosphorylation and micellar presentation. Thus, the biological function of these enzymes will not just be determined by their corresponding regulatory domains, but will be distinctly influenced by their catalytic properties as well. This suggests that the phosphatase domains fulfil a unique catalytic function that cannot be fully compensated by other phosphatases.

Mechanistic insights into Sky1p, a yeast homologue of the mammalian SR protein kinases.

The SRPK family is distinguished from typical eukaryotic protein kinases by several unique structural features recently elucidated by X-ray diffraction methods [Nolen et al. (2001) Nat. Struct. Biol. 8, 176-183]. To determine whether these features impart unique catalytic function, the phosphorylation of the physiological Sky1p substrate, Npl3p, was monitored using steady-state and pre-steady-state kinetic techniques. While Sky1p has a low apparent affinity for ATP compared to other protein kinases, it binds Npl3p with very high affinity. The latter is achieved through a combination of local and distal factors in the protein substrate. The phosphoryl donor ATP has access to the nucleotide pocket in the absence or presence of Npl3p, indicating that a large protein substrate does not enforce an ordered addition of ligands. Sky1p binds two Mg(2+)-the first is essential whereas the second further enhances catalysis. While the turnover number is low (0.5 s(-1)), Npl3p is rapidly phosphorylated in the active site (40 s(-1)) based on single turnover experiments. These results indicate that Sky1p employs a catalytic pathway involving fast phosphoryl transfer followed by slow net release of products. These studies represent the first kinetic investigation of a member of the SRPK family and the first pre-steady-state kinetic study of a protein kinase using a natural protein substrate.

New approach to block copolymerization of ethylene with polar monomers by the unique catalytic function of organolanthanide complexes

New approach to block copolymerization of ethylene with polar monomers by the unique catalytic function of organolanthanide complexes

New approach to block copolymerization of ethylene with polar monomers by the unique catalytic function of organolanthanide complexes

This paper describes the first examples of ABA- and AB-type block copolymerizations of a nonpolar monomer, in this case ethylene, with polar monomers, such as methyl methacrylate (MMA), ϵ-caprolactone (CL), and 2,2-dimethyltrimethylene carbonate (DTC), initiated by the unique catalytic function of rare earth metal complexes [Sm(II) and Ln(III) (Ln = Y, Sm)] as initiators. The Sm(II) species conducts the ABA-type triblock copolymerization, leading to poly(MMA-co-ethylene-co-MMA), poly(CL-co-ethylene-co-CL), or poly(DTC-co-ethylene-co-DTC) by the efficient catalysis of racemic Me2Si(C5H2-2-Me3Si-4-tBu)2Sm(THF)2 (1) or meso Me2Si(Me2SiOSiMe2)(C5H2-3-tBu)Sm(THF) (2b). The resulting block copolymers are completely insoluble in THF and CHCl3, but the homopolymers of MMA, CL, and DTC are freely soluble in these solvents. TEM profiles provide direct evidence for the block copolymerizations, where the spheric morphology of homogeneously dispersed polar polymers was observed. Ln(III) species, such as racemic Me2Si(C5H2-2-Me3Si-4-tBuMe2Si)YH (5) and Me2Si(C5H2-2-Me3Si-4-tBu)SmH (6), afford AB-type block copolymers between ethylene and MMA or CL, whose TEM images reveal the homogeneous dispersion of poly(MMA) or poly(CL) units in the polyethylene region. The ABA- and AB-type block copolymers demonstrate high break stress and high tensile modulus as compared with their corresponding blended polymers. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 4095–4109, 2000

Stoichiometry, organisation and catalytic function of protein X of the pyruvate dehydrogenase complex from bovine heart.

Mammalian pyruvate dehydrogenase complex (PDC) contains a subunit, protein X, which mediates high-affinity binding of dihydrolipoamide dehydrogenase (E3)to the dihydrolipoamide acetyltransferase (E2) core. Precise stoichiometric determinations on bovine heart PDC, by means of two approaches, indicate the presence of 12 mol protein X/mol PDC and 60 mol E2/mol PDC. Studies of the organisation of collagenase-modified PDC by means of covalent cross-linking of N,N'-1,2-phenylenedimaleimide to lipoamide thiols on protein X, reveal that the main cross-linked products have Mr values corresponding to homodimers of protein X. However, significant formation of higher-Mr aggregates indicates that lipoyl domains of protein X can form an interacting network independent of E2 lipoyl domains. These data suggest that either 12 interacting X monomers or 6 interacting X dimers are involved in the binding of six E3 homodimers to the E2/X core. The presence of 60 E2 subunits/complex also supports proposals for a non-integrated external position of protein X. Collagenase-treated PDC possesses residual activity (15 %), indicating that protein-X-linked lipoamide groups can substitute for the lipoyl domains of E2 in overall complex catalysis. Protein-X-mediated diacetylation of dihydrolipoamide moieties is also performed by the modified complex which raises the possibility of a unique catalytic function for protein X.