Showing papers on "Substrate (chemistry) published in 2010"

Graphene Oxide as a Matrix for Enzyme Immobilization

Abstract: Graphene oxide (GO), having a large specific surface area and abundant functional groups, provides an ideal substrate for study enzyme immobilization. We demonstrated that the enzyme immobilization on the GO sheets could take place readily without using any cross-linking reagents and additional surface modification. The atomically flat surface enabled us to observe the immobilized enzyme in the native state directly using atomic force microscopy (AFM). Combining the AFM imaging results of the immobilized enzyme molecules and their catalytic activity, we illustrated that the conformation of the immobilized enzyme is mainly determined by interactions of enzyme molecules with the functional groups of GO.

The biological significance of substrate inhibition: a mechanism with diverse functions.

Abstract: Many enzymes are inhibited by their own substrates, leading to velocity curves that rise to a maximum and then descend as the substrate concentration increases Substrate inhibition is often regarded as a biochemical oddity and experimental annoyance We show, using several case studies, that substrate inhibition often has important biological functions In each case we discuss, the biological significance is different Substrate inhibition of tyrosine hydroxylase results in a steady synthesis of dopamine despite large fluctuations in tyrosine due to meals Substrate inhibition of acetylcholinesterase enhances the neural signal and allows rapid signal termination Substrate inhibition of phosphofructokinase ensures that resources are not devoted to manufacturing ATP when it is plentiful In folate metabolism, substrate inhibition maintains reactions rates in the face of substantial folate deprivation Substrate inhibition of DNA methyltransferase serves to faithfully copy DNA methylation patterns when cells divide while preventing de novo methylation of methyl-free promoter regions

Substrate catalysis enhances single-enzyme diffusion.

Abstract: We show that diffusion of single urease enzyme molecules increases in the presence of urea in a concentration-dependent manner and calculate the force responsible for this increase. Urease diffusion measured using fluorescence correlation spectroscopy increased by 16-28% over buffer controls at urea concentrations ranging from 0.001 to 1 M. This increase was significantly attenuated when urease was inhibited with pyrocatechol, demonstrating that the increase in diffusion was the result of enzyme catalysis of urea. Local molecular pH changes as measured using the pH-dependent fluorescence lifetime of SNARF-1 conjugated to urease were not sufficient to explain the increase in diffusion. Thus, a force generated by self-electrophoresis remains the most plausible explanation. This force, evaluated using Brownian dynamics simulations, was 12 pN per reaction turnover. These measurements demonstrate force generation by a single enzyme molecule and lay the foundation for a further understanding of biological force generation and the development of enzyme-driven nanomotors.

Substrate Size-Selective Catalysis with Zeolite-Encapsulated Gold Nanoparticles

Abstract: Over the years, many strategies have been developed to address the problem of sintering of nanoparticle catalysts, including encapsulating metal nanoparticles in protective shells, and trapping nanoparticles in the cavities of certain zeolites in post-synthesis steps. In general, materials that contain metal nanoparticles that are only accessible via zeolite micropores are intriguing, specifically, but not exclusively, for catalytic applications. The encapsulation of carbon nanoparticles during zeolite crystallization is a well-known approach for making carbon–zeolite composites that afford mesoporous zeolites after combustion. Herein, we show that metal nanoparticles can also be encapsulated during zeolite crystallization, as exemplified by silicalite-1 crystals that are embedded with circa 1–2 nm-sized gold nanoparticles that remain stable and catalytically active after calcination in air at 550 8C. Moreover, we show that the encapsulated gold nanoparticles are only are accessible through the micropores of the zeolite, which makes this material a substrate-size selective oxidation catalyst. Currently, more than 175 different zeolite structures have been reported, and these can be tuned according to the desired acidity and/or redox properties. Expanding the scope from pure zeolites to hybrid materials, by combining the properties of zeolites with other components, significantly widens the field of zeolite materials design. Aside from posttreatment methods, two types of approaches have been pursued for preparing hybrid zeolite–nanoparticle materials. The first type of approach involves crystallization of the zeolite from a gel that contains metal ions that are immobilized in the zeolite during crystallization. With this kind of approach, it is very difficult to control the properties of the non-zeolite component in terms of, for example, particle size. The other type of approach is to first synthesize the nonzeolite component and subsequently encapsulate this in the individual zeolite crystals during crystallization. Indeed, this strategy is also well-known and an entire family of materials, known as mesoporous or hierarchical zeolite crystals, are based on the embedding of carbon nanoparticles, nanofibers, nanotubes, or other nanostructures during zeolite crystallization (and subsequent combustion) in a process known as carbon templating. 15, 16] Concerning the embedding of metal nanoparticles in zeolites, Hashimoto et al. reported a top down approach that features downsizing gold flakes to approximately 40 nm particles by laser ablation, and subsequent encapsulation of these particles during crystallization. A reduction in particle size by one order of magnitude is necessary for an efficient use of costly noble metals in catalytic applications. However, a reduction of the particle size enhances the tendency for sintering, owing to the increase in surface free energy. To mitigate this problem, we report herein a bottom-up approach for the preparation of hybrid zeolite-nanoparticle materials that contain small metal nanoparticles, dispersed throughout the zeolite crystals. This synthetic approach comprises three steps (Figure 1): First, a metal nanoparticle colloid is prepared with suitable anchor points for the generation of a silica shell. Second, the particles are encapsulated in an amorphous silica matrix. Third, the silica nanoparticle precursor is subjected to hydrothermal conditions in order for zeolite crystallization to take place. Using this approach, we successfully prepared a material that consisted predominantly of circa 1–2 nm sized gold particles that were embedded in silicalite-1 crystals. X-ray diffraction revealed that the material contained exclusively gold as well as MFI-structured material (generalized silicalite-1 crystal structure type). Figure 2 shows scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images of the hybrid material that consists of gold nanoparticles embedded in silicalite-1 crystals. The SEM image reveals that the material is mainly composed of circa 1–2 mm long coffinshaped crystals, with a minor fraction of intergrown coffin[*] A. B. Laursen, K. T. Højholt, L. F. Lundegaard, S. B. Simonsen, S. Helveg, Prof. C. H. Christensen, K. Egeblad Haldor Topsøe A/S Nymøllevej 55, 2800 Kgs. Lyngby (Denmark) E-mail: chc@topsoe.dk kreg@topsoe.dk

Substrate processing apparatus, substrate processing method, and storage medium storing program for implementing the method

Abstract: A substrate processing apparatus that enables an oxide layer and an organic layer to be removed efficiently. A substrate formed at its surface with an organic layer covered with the oxide layer is housed in a chemical reaction processing apparatus of the substrate processing apparatus, in which the oxide layer is subjected to chemical reaction with gas molecules, and thus a product is produced on the substrate surface. The substrate is heated in a chamber of a heat treatment apparatus of the substrate processing apparatus, whereby the product is vaporized and the organic layer is exposed. Microwaves are then introduced into the chamber into which oxygen gas is supplied, whereby there are produced oxygen radicals that decompose and remove the organic layer.

What Factors Influence the Rate Constant of Substrate Epoxidation by Compound I of Cytochrome P450 and Analogous Iron(IV)-Oxo Oxidants?

Abstract: The cytochromes P450 are a versatile range of mono-oxygenase enzymes that catalyze a variety of different chemical reactions, of which the key reactions include aliphatic hydroxylation and C═C double bond epoxidation. To establish the fundamental factors that govern substrate epoxidation by these enzymes we have done a systematic density functional theory study on substrate epoxidation by the active species of P450 enzymes, namely the iron(IV)-oxo porphyrin cation radical oxidant or Compound I. We show here, for the first time, that the rate constant of substrate epoxidation, and hence the activation energy, correlates with the ionization potential of the substrate as well as with intrinsic electronic properties of the active oxidant such as the polarizability volume. To explain these findings we present an electron-transfer model for the reaction mechanism that explains the factors that determine the barrier heights and developed a valence bond (VB) curve crossing mechanism to rationalize the observed tr...

The effects of substrate composition, quantity, and diversity on microbial activity

Abstract: Variation in organic matter inputs caused by differences in plant community composition has been shown to affect microbial activity, although the mechanisms controlling these effects are not entirely understood. In this study we determine the effects of variation in substrate composition, quantity, and diversity on soil extracellular enzyme activity and respiration in laboratory microcosms. Microbial respiration responded predictably to substrate composition and quantity and was maximized by the addition of labile substrates and greater substrate quantity. However, there was no effect of substrate diversity on respiration. Substrate composition significantly affected enzyme activity. Phosphatase activity was maximized with addition of C and N together, supporting the common notion that addition of limiting resources increases investment in enzymes to acquire other limiting nutrients. Chitinase activity was maximized with the addition of chitin, suggesting that some enzymes may be stimulated by the addition of the substrate they degrade. In contrast, activities of glucosidase and peptidase were maximized by the addition of the products of these enzymes, glucose and alanine, respectively, for reasons that are unclear. Substrate diversity and quantity also stimulated enzyme activity for three and four of the six enzymes assayed, respectively. We found evidence of complementary (i.e., non-additive) effects of additions of different substrates on activity for three of the six enzymes assayed; for the remaining enzymes, effects of adding a greater diversity of substrates appeared to arise from the substrate-specific effects of those substrates included in the high-diversity treatment. Finally, in a comparison of measures of microbial respiration and enzyme activity, we found that labile C and nutrient-acquiring enzymes, not those involved in the degradation of recalcitrant compounds, were the best predictors of respiration rates. These results suggest that while composition, quantity, and diversity of inputs to microbial communities all affect microbial enzyme activity, the mechanisms controlling these relationships are unique for each particular enzyme.

Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands

Abstract: Enzyme catalysis can be described as progress over a multi-dimensional energy landscape where ensembles of interconverting conformational substates channel the enzyme through its catalytic cycle. We applied NMR relaxation dispersion to investigate the role of bound ligands in modulating the dynamics and energy landscape of Escherichia coli dihydrofolate reductase to obtain insights into the mechanism by which the enzyme efficiently samples functional conformations as it traverses its reaction pathway. Although the structural differences between the occluded substrate binary complexes and product ternary complexes are very small, there are substantial differences in protein dynamics. Backbone fluctuations on the micros-ms timescale in the cofactor binding cleft are similar for the substrate and product binary complexes, but fluctuations on this timescale in the active site loops are observed only for complexes with substrate or substrate analog and are not observed for the binary product complex. The dynamics in the substrate and product binary complexes are governed by quite different kinetic and thermodynamic parameters. Analogous dynamic differences in the E:THF:NADPH and E:THF:NADP(+) product ternary complexes are difficult to rationalize from ground-state structures. For both of these complexes, the nicotinamide ring resides outside the active site pocket in the ground state. However, they differ in the structure, energetics, and dynamics of accessible higher energy substates where the nicotinamide ring transiently occupies the active site. Overall, our results suggest that dynamics in dihydrofolate reductase are exquisitely "tuned" for every intermediate in the catalytic cycle; structural fluctuations efficiently channel the enzyme through functionally relevant conformational space.

A novel approach for development of surface nanocomposite by friction stir processing

Abstract: A new approach was used to produce Al–10%Al2O3 surface nanocomposite on Al2024 substrate. This novel approach involved air plasma spraying of Al–10%Al2O3 powder to produce Al–10%Al2O3 coating on substrate. The coated material was then subjected to friction stir processing (FSP) to distribute Al2O3 particles into the substrate. Microstructure and mechanical properties of samples were investigated by optical microscopy (OM), scanning electron microscopy (SEM), micro-hardness and wear measurements. As a result, it was found that the Al2O3 particles were distributed uniformly inside the substrate with an average penetration depth of about 600 μm. The surface nanocomposites produced in this way had excellent bonding with the substrate. The micro-hardness of the surface nanocomposite was ∼230 Hv, much higher than ∼90 Hv for Al2024 substrate. The surface nanocomposites also exhibited lower friction coefficient and wear rate. It was found that the addition of Al2O3 nanoparticles to the Al2024 matrix alloy affect the mechanism of wear.

Poly(ethylene glycol) adlayers immobilized to metal oxide substrates through catechol derivatives: influence of assembly conditions on formation and stability.

Abstract: We have investigated Five different poly(ethylene glycol) (PEG, 5 kDa) catechol derivatives in terms of their spontaneous surface assembly from aqueous solution, adlayer stability, and resistance to nonspecific blood serum adsorption as a function of the type of catechol-based anchor, assembly conditions (temperature, pH), and type of substrate (SiO2, TiO2, Nb2O5), Variable-angle spectroscopic ellipsometry (VASE) was used for layer thickness evaluation, X-ray photoelectron spectroscopy (XPS) for layer composition, and ultraviolet-visible optical spectroscopy (UV-vis) for cloud point determination. Polymer surface coverage was influenced by the type of catechol anchor, type of the substrate, as well as pH and temperature (7) of the assembly solution. Furthermore, it was found to be highest for T close to the cloud point (T-CP) and pH of the assembly solution close to pK(a1) (dissociation constant of the first catechol hydroxy group) of the polymer and to the isoelectric point (1EP) of the substrate. T-CP turned out to depend on not only the ionic strength of the assembly solution, but also the type of catechol derivative and pH. PEG-coating dry thickness above 10 angstrom correlated with low serum adsorption. We therefore conclude that optimum coating protocols for catechol-based polymer assembly at metal oxide interfaces have to take into account specific physicochemical properties of the polymer, anchor, and substrate.

Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics

Abstract: Nature often colocalizes successive steps in a metabolic pathway. Such organization is predicted to increase the effective concentration of pathway intermediates near their recipient active sites and to enhance catalytic efficiency. Here, the pathway of a two-step reaction is modeled using a simple spherical approximation for the enzymes and substrate particles. Brownian dynamics are used to simulate the trajectory of a substrate particle as it diffuses between the active site zones of two different enzyme spheres. The results approximate distances for the most effective reaction pathways, indicating that the most effective reaction pathway is one in which the active sites are closely aligned. However, when the active sites are too close, the ability of the substrate to react with the first enzyme was hindered, suggesting that even the most efficient orientations can be improved for a system that is allowed to rotate or change orientation to optimize the likelihood of reaction at both sites.

Formation of catalytic silver nanoparticles supported on branched polyethyleneimine derivatives.

Abstract: A new and straightforward method for screening highly catalytically active silver nanoparticle-polymer composites derived from branched polyethyleneimine (PEI) is reported. The one-step systematic derivatization of the PEI scaffold with alkyl (butyl or octyl) and ethanolic groups led to a structural diversity correlated to the stabilization of silver nanoparticles and catalysis. Analysis of PEI derivative libraries identified a silver nanoparticle-polymer composite that was able to efficiently catalyze the p-nitrophenol reduction by NaBH(4) in water with a rate constant normalized to the surface area of the nanoparticles per unit volume (k(1)) of 0.57 s(-1) m(-2) L. Carried out in the presence of excess NaBH(4), the catalytic reaction was observed to follow pseudo-first-order kinetics and the apparent rate constant was linearly dependent on the total surface area of the silver nanoparticles (Ag-NPs), indicating that catalysis takes place on the surface of the nanoparticles. All reaction kinetics presented induction periods, which were dependent on the concentration of substrates, the total surface of the nanoparticles, and the polymer composition. All data indicated that this induction time is related to the resistance to substrate diffusion through the polymer support. Hydrophobic effects are also assumed to play an important role in the catalysis, through an increase in the local substrate concentration.

Plasma etching method and apparatus thereof

Abstract: A method of etching a substrate includes positioning the substrate on a substrate support within a chamber, etching a formation in the substrate in the presence of plasma within the chamber, decreasing a positive charge within the formation, and further etching the formation in the substrate in the presence of plasma after decreasing the positive charge within the formation.

Crystal structures of a Populus tomentosa 4-coumarate:CoA ligase shed light on its enzymatic mechanisms.

Abstract: 4-Coumaric acid:CoA ligase (4CL) is the central enzyme of the plant-specific phenylpropanoid pathway. It catalyzes the synthesis of hydroxycinnamate-CoA thioesters, the precursors of lignin and other important phenylpropanoids, in two-step reactions involving the formation of hydroxycinnamate-AMP anhydride and then the nucleophilic substitution of AMP by CoA. In this study, we determined the crystal structures of Populus tomentosa 4CL1 in the unmodified (apo) form and in forms complexed with AMP and adenosine 5'-(3-(4-hydroxyphenyl)propyl)phosphate (APP), an intermediate analog, at 2.4, 2.5, and 1.9 A resolution, respectively. 4CL1 consists of two globular domains connected by a flexible linker region. The larger N-domain contains a substrate binding pocket, while the C-domain contains catalytic residues. Upon binding of APP, the C-domain rotates 81° relative to the N-domain. The crystal structure of 4CL1-APP reveals its substrate binding pocket. We identified residues essential for catalytic activities (Lys-438, Gln-443, and Lys-523) and substrate binding (Tyr-236, Gly-306, Gly-331, Pro-337, and Val-338) based on their crystal structures and by means of mutagenesis and enzymatic activity studies. We also demonstrated that the size of the binding pocket is the most important factor in determining the substrate specificities of 4CL1. These findings shed light on the enzymatic mechanisms of 4CLs and provide a solid foundation for the bioengineering of these enzymes.

Potential Enzyme Cost Reduction with the Addition of Surfactant during the Hydrolysis of Pretreated Softwood

Abstract: The potential economic benefits of surfactants addition on enzymatic hydrolysis of steam-exploded lodgepole pine (SELP) and ethanol-pretreated lodgepole pine (EPLP) were investigated in this study. Free cellulase readsorption on fresh substrate was used to recover and recycle cellulase enzymes during the hydrolysis of SELP and EPLP substrate. Supplementing Tween 80 during the hydrolysis could facilitate enzyme recycling for EPLP substrate. A logarithmic correlation was established between surfactant concentration and free cellulase content after lignocellulosic hydrolysis, which was used to compute enzyme cost savings over various Tween 80 concentrations. A simple economic analysis of enzyme cost savings versus the cost of surfactant was undertaken. The results indicated that the addition of Tween 80 (priced at US $0.25/kg) during the hydrolysis of the EPLP substrate could save 60% of the total enzyme cost at concentrations in the 0.025% to 0.2% range. The addition of Tween for the hydrolysis of the SELP substrate significantly reduced the material cost by 24% per 1 gal of ethanol produced, and the ethanol production cost could be reduced by 8.6% with the addition of Tween and enzymes recycle for the hydrolysis of SELP substrate. A schematic concept of recycling enzyme and surfactant was also presented with a recirculation of process streams during hydrolysis. Further analysis indicated a 66% reduction in total enzyme cost could potentially be achieved under the concept.

Effects of lignin-metal complexation on enzymatic hydrolysis of cellulose.

Abstract: This study investigated the inhibition of enzymatic hydrolysis by unbound lignin (soluble and insoluble) with or without the addition of metal compounds. Sulfonated, Organosolv, and Kraft lignin were added in aqueous enzyme-cellulose systems at different concentrations before hydrolysis. The measured substrate enzymatic digestibility (SED) of cellulose was decreased by 15% when SL was added to a concentration of 0.1 g/L due to nonproductive adsorption of enzymes onto lignin. Cu(II) and Fe(III) were found to inhibit enzymatic cellulose hydrolysis in the presence of lignin. Ca(II) and Mg(II) were found to reduce or eliminate nonproductive enzyme adsorption by the formation of lignin-metal complex. The addition of Ca(II) or Mg(II) to a concentration of 10 mM can almost completely eliminate the reduction in SED caused by the nonproductive enzyme adsorption onto the lignins studied (SL, OL, or KL at concentration of 0.1 g/L). Ca(II) was also found to reduce the inhibitive effect of bound lignin in pretreated wood substrate, suggesting that Ca(II) can also form complex with bound lignin on pretreated solid lignocelluloses. Significant improvement in SED of about over 27% of a eucalyptus substrate produced by sulfite pretreatment to overcome recalcitrance of lignocellulose (SPORL) was achieved with the application of Ca(II).

Experimental Identification of Chemical Effects in Surface Enhanced Raman Scattering of 4-Aminothiophenol

Abstract: We report on the experimental identification of Raman modes that are enhanced through the chemical effect in surface enhanced Raman spectroscopy of 4-aminothiophenol (also known as p-mercaptoaniline) adsorbed on gold substrate. Introduction of a thin spacer layer between the metal and the sample can prevent any possible chemical bonding between metal atoms and sample molecules, hence such a sample shows only those Raman modes that are enhanced through the electromagnetic effect. Alternatively, a significant increase in the chemical effect could be observed in the presence of halide ions as compared to their absence. This result provides another way to experimentally identify those Raman modes that undergo chemical enhancement. In addition, apart from the electromagnetic-based resonance in SERS, chemical enhancement also shows a resonance with varying wavelength of the excitation light, which provides yet another way to experimentally identify chemically enhanced Raman modes in SERS. Some new chemically enhanced modes could be observed when the sample molecules were sandwiched between gold substrate and a gold nanotip.

Photochemical Reactivity of Titania Films on BaTiO3 Substrates: Origin of Spatial Selectivity

Abstract: Titania films, 15−100 nm thick, have been grown on BaTiO3 substrates and used to photochemically reduce Ag+ to Ag0 and oxidize Pb2+ to Pb4+ under ultraviolet illumination. Atomic force microscopy was used to show that the reactions are spatially selective and that the pattern of products on the film surface reproduces the pattern of products on the bare substrate. The influence of the substrate on the pattern of reactants is diminished as the film thickness increases and is quenched when the film is donor-doped with Nb. The results indicate that for thin (15 nm) films, dipolar fields from the ferroelectric domains cause carriers generated in the substrate to travel through the film to react on the surface.

Conductance Anisotropy in Epitaxial Graphene Sheets Generated by Substrate Interactions

Abstract: We present the first microscopic transport study of epitaxial graphene on SiC using an ultrahigh vacuum four-probe scanning tunneling microscope. Anisotropic conductivity is observed that is caused by the interaction between the graphene and the underlying substrate. These results can be explained by a model where charge buildup at the step edges leads to local scattering of charge carriers. This highlights the importance of considering substrate effects in proposed devices that utilize nanoscale patterning of graphene on electrically isolated substrates.