Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje

Two archaeal Holliday junction resolving enzymes, Holliday junction cleavage (Hjc) and Holliday junction endonuclease (Hje), have been characterized. Both are members of a nuclease superfamily that includes the type II restriction enzymes, although their DNA cleaving activity is highly specific for four-way junction structure and not nucleic acid sequence. Despite 28% sequence identity, Hje and Hjc cleave junctions with distinct cutting patterns—they cut different strands of a four-way junction, at different distances from the junction centre. We report the high-resolution crystal structure of Hje from Sulfolobus solfataricus. The structure provides a basis to explain the differences in substrate specificity of Hje and Hjc, which result from changes in dimer organization, and suggests a viral origin for the Hje gene. Structural and biochemical data support the modelling of an Hje:DNA junction complex, highlighting a flexible loop that interacts intimately with the junction centre. A highly conserved serine residue on this loop is shown to be essential for the enzyme's activity, suggesting a novel variation of the nuclease active site. The loop may act as a conformational switch, ensuring that the active site is completed only on binding a four-way junction, thus explaining the exquisite specificity of these enzymes.

Crowded Diphosphinomethane Ligands in Catalysis: [(R2PCH2PR′2-κ2P)-NiR″]+ Cations for Ethylene Polymerization without Activators

The preparation of a series of nickel dichloride complexes with bulky diphosphinomethane chelate ligands R2PCH2PR′2 is reported. Reaction with the appropriate Grignard reagent leads to the corresponding dimethyl and dibenzyl complexes. Cationic monomethyl and mono-η3-benzyl complexes are generated from these dialkyl complexes by protonation with [H(OEt2)2]+[B(3,5-(CF3)2C6H3)4]−, while the complex [(dtbpm κ2P)Ni(η3-CH(CH2Ph)Ph]+[B(3,5-(CF3)2C6H3)4]−is obtained from protonation of the Ni(0) olefin complex (dtbpm-κ2P)N(η2-trans-stilbene). Crystal structures of examples of dichlorides, dimethyl, dibenzyl, cationic methyl, and cationic η3-benzyl complexes are reported. Solutions of the cations polymerize ethylene under mild conditions and without the necessity of an activating agent, to form polyethylene having high molecular weights and low degrees of chain branching. In comparison to the Ni methyl cations, the η3-benzyl cation complexes are more stable and somewhat less active but still very efficient in C2H4 polymerization. The effect on the resulting polyethylene of varying the substituents R, R′ on the phosphine ligand has been examined, and a clear trend for longer chain PE with less branching in the presence of more bulky substituents on the diphosphine has been found. Density functional calculations have been used to examine the rapid suprafacial η3 to η3 haptotropic shift processes of the[(R2PCH2PR′2)Ni] fragment and the η3−η1 change of the coordination mode of the benzyl group required for polymerization in those cations.

Observations on catalysis by hammerhead ribozymes are consistent with a two-divalent-metal-ion mechanism

Significant cleavage by hammerhead ribozymes requires activation by divalent metal ions. Several models have been proposed to account for the influence of metal ions on hammerhead activity. A number of recent papers have presented data that have been interpreted as supporting a one-metal-hydroxide-ion mechanism. In addition, a solvent deuterium isotope effect has been taken as evidence against a proton transfer in the rate-limiting step of the cleavage reaction. We propose that these data are more easily explained by a two-metal-ion mechanism that does not involve a metal hydroxide, but does involve a proton transfer in the rate-limiting step.

Non-covalent surface modification of boron nitride nanotubes for enhanced catalysis

Boron nitride nanotubes were functionalized by microperoxidase-11 in aqueous media, showing improved catalytic performance due to a strong electron coupling 10 between the active centre of microperoxidase-11 and boron nitride nanotubes. One main application challenge of enzymes as biocatalysts is molecular aggregation in the aqueous solution. This issue is addressed by immobilization of enzymes on solid supports which 15 can enhance enzyme stability and facilitate separation, and recovery for reuse while maintaining catalytic activity and selectivity. The protein-nanoparticle interactions play a key role in bio-nanotechnology and emerge with the development of nanoparticle-protein “corona”. Bio-molecular coronas provide a 20 unique biological identity of nanosized materials.1, 2 As a structural analogue to carbon nanotubes (CNTs), Boron nitride nanotubes have boron and nitrogen atoms distributed equally in hexagonal rings and exhibit excellent mechanical strength, unique physical properties, and chemical stability at high-temperatures. 25 The chemical inertness of BN materials suits to work in hazardous environments, making them an optimal candidate in practical applications in biological and medical field.3, 4

Formation of nanostructured porous Cu-Au surfaces : the influence of cationic sites on (electro)-catalysis

The fabrication of nanostructured bimetallic materials through electrochemical routes offers the ability to control the composition and shape of the final material that can then be effectively applied as (electro)-catalysts. In this work a clean and transitory hydrogen bubble templating method is employed to generate porous Cu–Au materials with a highly anisotropic nanostructured interior. Significantly, the co-electrodeposition of copper and gold promotes the formation of a mixed bimetallic oxide surface which does not occur at the individually electrodeposited materials. Interestingly, the surface is dominated by Au(I) oxide species incorporated within a Cu2O matrix which is extremely effective for the industrially important (electro)-catalytic reduction of 4-nitrophenol. It is proposed that an aurophilic type of interaction takes place between both oxidized gold and copper species which stabilizes the surface against further oxidation and facilitates the binding of 4-nitrophenol to the surface and increases the rate of reaction. An added benefit is that very low gold loadings are required typically less than 2 wt% for a significant enhancement in performance to be observed. Therefore the ability to create a partially oxidized Cu–Au surface through a facile electrochemical route that uses a clean template consisting of only hydrogen bubbles should be of benefit for many more important reactions.

Effect of palygorskite clay on pyrolysis of rape straw : an in situ catalysis study

Biomass tar restricts the wide application and development of biomass gasification technology. In the present paper, palygorskite, a natural magnesium-containing clay mineral, was investigated for catalytic pyrolysis of rape straw in situ and compared with the dolomite researched widely. The two types of natural minerals were characterized with XRD and BET. The results showed that combustible gas derived from the pyrolysis increased with an increase in gasification temperature. The Hconversion and Cconversion increased to 44.7% and 31% for the addition of palygorskite and increased to 41.3% and 31.3% for the addition of dolomite at the gasification temperature of 800 °C, compared with 15.1% and 5.6% without addition of the two types of material. It indicated that more biomass was converted into combustible gases implying the decrease in biomass tar under the function of palygorskite or dolomite and palygorskite had a slightly better efficiency than that of dolomite in the experimental conditions.

Mechanisms of sulfide ion oxidation during cyanidation. Part II : Surface catalysis by pyrite

The mechanisms and the reaction products for the oxidation of sulfide ions in the presence of pyrite have been established. When the leach solution contains free sulfide ions, oxidation occurs via electron transfer from the sulfide ion to dissolved oxygen on the pyrite mineral surface, with polysulfides being formed as an intermediate oxidation product. In the absence of cyanide, the polysulfides are further oxidised to thiosulfate, whilst with cyanide present, thiocyanate and sulfite are also formed from the reaction of polysulfides with cyanide and dissolved oxygen. Polysulfide chain length has been shown to affect the final reaction products of polysulfide oxidation by dissolved oxygen. The rate of pyrite catalysed sulfide ion oxidation was found to be slower in cyanide solutions compared to cyanide free solutions. Mixed potential measurements indicated that the reduction of oxygen at the pyrite surface is hindered in the presence of cyanide. The presence of sulfide ions was also found to activate the pyrite surface, increasing its rate of oxidation by oxygen. This effect was particularly evident in the presence of cyanide; in the presence of sulfide the increase in total sulfur from pyrite oxidation was 2.3 mM in 7 h, compared to an increase of <1 mM in the absence of sulfide over 24 h.

Surface plasmon-enhanced zeolite catalysis under light irradiation and its correlation with molecular polarity of reactants

Enhanced catalytic performance of zeoltes via the plasmonic effect of gold nanoparticles has been discovered to be closely correlated with the molecular polarity of reactants. The intensified polarised electrostatic field of Na+ in NaY plays a critical role in stretching the C=O bond of aldehydes to improve the reaction rate.

The repertoire of nitrogen assimilation in Rhodococcus: Catalysis, pathways and relevance in biotechnology and bioremediation

The Rhodococcus genus exhibits diverse enzymatic activity that can be exploited in the conversion of natural and anthropogenic nitrogenous compounds. This catalytic response provides a selective advantage in terms of available nutrients while also serving to remove otherwise harmful xenobiotics. This review provides a critical assessment of the literature on bioconversion of organo-nitrogen compounds with a consideration of applications in bioremediation and commercial biotechnology. By examining the major nitro-organic compounds (amino acids, amines, nitriles, amides and nitroaromatics) in turn, the considerable repertoire of Rhodococcus spp. is established. The available published enzyme reaction data is coupled with genomic characterisation to provide a molecular basis for Rhodococcus enzyme activity with an assessment of the cellular properties that aid substrate accessibility and ensure stability. The metabolic gene clusters associated with the observed reaction pathways are identified and future directions in enzyme optimisation and metabolic engineering are assessed. © 2014 Society of Chemical Industry.

The role of lysine-41 in RNase A catalysis - A quantum chemical study on the active site ligand complex

Several mechanisms have been proposed to explain the action of enzymes at the atomic level. Among them, the recent proposals involving short hydrogen bonds as a step in catalysis by Gerlt and Gassman [1] and proton transfer through low barrier hydrogen bonds (LBHBs) [2, 3] have attracted attention. There are several limitations to experimentally testing such hypotheses, Recent developments in computational methods facilitate the study of active site-ligand complexes to high levels of accuracy, Our previous studies, which involved the docking of the dinucleotide substrate UpA to the active site of RNase A [4, 5], enabled us to obtain a realistic model of the ligand-bound active site of RNase A. From these studies, based on empirical potential functions, we were able to obtain the molecular dynamics averaged coordinates of RNase A, bound to the ligand UpA. A quantum mechanical study is required to investigate the catalytic process which involves the cleavage and formation of covalent bonds. In the present study, we have investigated the strengths of some of the hydrogen bonds between the active site residues of RNase A and UpA at the ab initio quantum chemical level using the molecular dynamics averaged coordinates as the starting point. The 49 atom system and other model systems were optimized at the 3-21G level and the energies of the optimized systems were obtained at the 6-31G* level. The results clearly indicate the strengthening of hydrogen bonds between neutral residues due to the presence of charged species at appropriate positions. Such a strengthening manifests itself in the form of short hydrogen bonds and a low barrier for proton transfer. In the present study, the proton transfer between the 2'-OH of ribose (from the substrate) and the imidazole group from the H12 of RNase A is influenced by K41, which plays a crucial role in strengthening the neutral hydrogen bond, reducing the barrier for proton transfer.

Vanadium Catalysis in Bromoperoxidation Reaction

Peroxidative bromination of phenol red to its tetrabromo derivative, bromophenol blue, required vanadate in addition to H2O2 when carried out in the pH range of 5-7. Excess H2O2, with ratio of H2O2:vanadate of 2:1 and above, prevented the reaction. Diperoxovanadate, known to be formed in such reaction mixtures, was ineffective by itself and needed uncomplexed vanadate (V-v) or vanadyl (V-iv) to support bromination. Bromide-assisted reduction of the excess vanadate to vanadyl appeared to be an essential secondary reaction. In the absence of phenol red oxygen was released, and concomitantly bromide was oxidized to a form competent to brominate phenol red added after termination of oxygen release. These findings indicated participation of reactions leading to an intermediate derived from vanadyl and diperoxovanadate, previously described from this laboratory (Arch. Biochem. Biophys. 316, 319-326, 1995). Continuous bromination of phenol red occurred when glucose oxidase-glucose system was used as a source of continuous flow of H2O2. A scheme of reactions involving peroxovanadates (mono-, di-, mu-, and bromo-) is proposed for the formation and utilization of an active brominating species and for the recycling of the product, mono-peroxovanadate, by H2O2, which explains the catalytic role of vanadium in the bromoperoxidation reaction.

Catalysis and mechanism of malonyl transferase activity in type II fatty acid biosynthesis acyl carrier proteins

One of the unexplored, yet important aspects of the biology of acyl carrier proteins (ACPs) is the self-acylation and malonyl transferase activities dedicated to ACPs in polyketide synthesis. Our studies demonstrate the existence of malonyl transferase activity in ACPs involved in type II fatty acid biosynthesis from Plasmodium falciparum and Escherichia coli. We also show that the catalytic malonyl transferase activity is intrinsic to an individual ACP. Mutational analysis implicates an arginine/lysine in loop II and an arginine/glutamine in helix III as the catalytic residues for transferase function. The hydrogen bonding properties of these residues appears to be indispensable for the transferase reaction. Complementation of fabD(Ts) E. coli highlights the putative physiological role of this process. Our studies thus shed light on a key aspect of ACP biology and provide insights into the mechanism involved therein.

Catalysis for NOx abatement

Research in the field of NOx abatement has grown significantly in the past two decades. The general trend has been to develop new catalysts with complex materials in order to meet the stringent environmental regulations. This review discusses briefly about the different sources of NOx and its adverse effect on the ecosystem. The main portion of the review discusses the progress and development of various catalysts for NOx removal from exhaust by NO decomposition, NO reduction by CO or H-2 or NH3 or hydrocarbons. The importance of understanding the mechanism of NO decomposition and reduction in presence of metal ion substituted catalysts is emphasized. Some conclusions are made on the various catalytic approaches to NOx abatement.

Robust nanostructured silver and copper fabrics with localized surface plasmon resonance property for effective visible light induced reductive catalysis

Inspired by high porosity, absorbency, wettability and hierarchical ordering on the micrometer and nanometer scale of cotton fabrics, a facile strategy is developed to coat visible light active metal nanostructures of copper and silver on cotton fabric substrates. The fabrication of nanostructured Ag and Cu onto interwoven threads of a cotton fabric by electroless deposition creates metal nanostructures that show a localized surface plasmon resonance (LSPR) effect. The micro/nanoscale hierarchical ordering of the cotton fabrics allows access to catalytically active sites to participate in heterogeneous catalysis with high efficiency. The ability of metals to absorb visible light through LSPR further enhances the catalytic reaction rates under photoexcitation conditions. Understanding the mode of electron transfer during visible light illumination in Ag@Cotton and Cu@Cotton through electrochemical measurements provides mechanistic evidence on the influence of light in promoting electron transfer during heterogeneous catalysis for the first time. The outcomes presented in this work will be helpful in designing new multifunctional fabrics with the ability to absorb visible light and thereby enhance light-activated catalytic processes.