Showing papers on "Substrate (chemistry) published in 2002"

Enzyme dynamics during catalysis.

Abstract: Internal protein dynamics are intimately connected to enzymatic catalysis. However, enzyme motions linked to substrate turnover remain largely unknown. We have studied dynamics of an enzyme during catalysis at atomic resolution using nuclear magnetic resonance relaxation methods. During catalytic action of the enzyme cyclophilin A, we detect conformational fluctuations of the active site that occur on a time scale of hundreds of microseconds. The rates of conformational dynamics of the enzyme strongly correlate with the microscopic rates of substrate turnover. The present results, together with available structural data, allow a prediction of the reaction trajectory.

Crystal structure of a four-copper laccase complexed with an arylamine: insights into substrate recognition and correlation with kinetics.

Abstract: Laccases are multicopper oxidases that catalyze the oxidation of a wide range of phenols or arylamines, and their use in industrial oxidative processes is increasing. We purified from the white rot fungus Trametes versicolor a laccase that exists as five different isozymes, depending on glycosylation. The 2.4 A resolution structure of the most abundant isozyme of the glycosylated enzyme was solved. The four copper atoms are present, and it is the first crystal structure of a laccase in its active form. The crystallized enzyme binds 2,5-xylidine, which was used as a laccase inducer in the fungus culture. This arylamine is a very weak reducing substrate of the enzyme. The cavity enclosing 2,5-xylidine is rather wide, allowing the accommodation of substrates of various sizes. Several amino acid residues make hydrophobic interactions with the aromatic ring of the ligand. In addition, two charged or polar residues interact with its amino group. The first one is an histidine that also coordinates the copper that functions as the primary electron acceptor. The second is an aspartate conserved among fungal laccases. The purified enzyme can oxidize various hydroxylated compounds of the phenylurea family of herbicides that we synthesized. These phenolic substrates have better affinities at pH 5 than at pH 3, which could be related to the 2,5-xylidine binding by the aspartate. This is the first high-resolution structure of a multicopper oxidase complexed to a reducing substrate. It provides a model for engineering laccases that are either more efficient or with a wider substrate specificity.

Transport of Amino Acid-Related Compounds Mediated by L-Type Amino Acid Transporter 1 (LAT1): Insights Into the Mechanisms of Substrate Recognition

Abstract: The L-type amino acid transporter 1 (LAT1) is an Na(+)-independent neutral amino acid transporter subserving the amino acid transport system L. Because of its broad substrate selectivity, system L has been proposed to be responsible for the permeation of amino acid-related drugs through the plasma membrane. To understand the mechanisms of substrate recognition, we have examined the LAT1-mediated transport using a Xenopus laevis oocyte expression system. LAT1-mediated [(14)C]phenylalanine uptake was strongly inhibited in a competitive manner by aromatic-amino acid derivatives including L-dopa, alpha-methyldopa, melphalan, triiodothyronine, and thyroxine, whereas phenylalanine methyl ester, N-methyl phenylalanine, dopamine, tyramine, carbidopa, and droxidopa did not inhibit [(14)C]phenylalanine uptake. Gabapentin, a gamma-amino acid, also exerted a competitive inhibition on LAT1-mediated [(14)C]phenylalanine uptake. Although most of the compounds that inhibited LAT1-mediated uptake were able to induce the efflux of [(14)C]phenylalanine preloaded to the oocytes expressing LAT1 through the obligatory exchange mechanism, melphalan, triiodothyronine, and thyroxine did not induce the significant efflux. Based on the experimental and semiempirical computational analyses, it is proposed that, for an aromatic amino acid to be a LAT1 substrate, it must have a free carboxyl and an amino group. The carbonyl oxygen closer to the amino group needs a computed charge of -0.55 approximately -0.56 and must not participate in hydrogen bonding. In addition, the hydrophobic interaction between the substrate side chain and the substrate binding site of LAT1 seems to be crucial for the substrate binding. A substrate, however, becomes a blocker once Connolly accessible areas become large and/or the molecule has a high calculated logP value, such as those for melphalan, triiodothyronine, and thyroxine.

Method of film deposition using activated precursor gases

Abstract: A method for depositing a film on a substrate is provided. In one aspect, the method includes providing a metal-containing precursor to an activation zone, and activating the metal-containing precursor to form an activated precursor. The activated precursor gas is transported to a reaction chamber, and a film is deposited on the substrate using a cyclical deposition process, wherein the activated precursor gas and a reducing gas are alternately adsorbed on the substrate. Also provided is a method of depositing a film on a substrate using an activated reducing gas.

Cellulase adsorption and an evaluation of enzyme recycle during hydrolysis of steam-exploded softwood residues.

Abstract: The sugar yield and enzyme adsorption profile obtained during the hydrolysis of SO2-catalyzed steam-exploded Douglas-fir and posttreated steam-exploded Douglas-fir substrates were determined. After hot alkali peroxide posttreatment, the rates and yield of hydrolysis attained from the posttreated Douglas-fir were significantly higher, even at lower enzyme loadings, than those obtained with the corresponding steam-exploded Douglas-fir. The enzymatic adsorption profiles observed during hydrolysis of the two substrates were significantly different. Ultrafiltration was employed to recover enzyme in solution (supernatant) and reused in subsequent hydrolysis reactions with added, fresh substrate. These recycle findings suggested that the enzyme remained relatively active for three rounds of recycle. It is likely that enzyme recovery and reuse during the hydrolysis of posttreated softwood substrates could lead to reductions in the need for the addition of fresh enzyme during softwood-based bioconversion processes.

Production of tuna waste hydrolysates by a commercial neutral protease preparation

Abstract: The fish protein hydrolysates (FPH) are of increasing interest due to their potential applications as a source of bioactive peptides or as nitrogenous substrates for the fermentation media. A waste product from the canning industry was hydrolysed using a commercial protease “Umamizyme”. Enzymatic hydrolysis was investigated in a 1-l batch reactor at pH 7 and 45 °C. The influence of the process variables (enzyme/protein substrate ratio ranging from 0.1 to 1.5% (w/w) protein) was studied with regards to the extent of the proteolytic degradation, the nitrogen released and the molecular weight distribution of the peptides. A degree of hydrolysis up to 22.5% was obtained with an enzyme/substrate ratio of 1.5%, after 4 h of hydrolysis. A linear correlation was found to exist between the hydrolysis degree and the nitrogen recovery. The limiting factor of hydrolysis was deduced from a set of experiments conducted at 45 °C and pH 7 where the effects of intermediate substrate and enzyme addition were studied. Results showed that the protease “Umamizyme” performed as effectively as Alcalase ® 2, 4L for the tuna waste solubilisation. However, the Umamizyme stability is lower than Alcalase ® 2, 4L.

Peptide Microarrays for the Determination of Protease Substrate Specificity

Abstract: A method is described for the preparation of substrate microarrays that allow for the rapid determination of protease substrate specificity. Peptidyl coumarin substrates, synthesized on solid support using standard techniques, are printed onto glass slides using DNA microarraying equipment. The linkage from the peptide to the slide is formed through a chemoselective reaction, resulting in an array of uniformly displayed fluorogenic substrates. The arrays can be treated with proteases to yield substrate specificity profiles. Standard instrumentation for visualization of microarrays can be used to obtain comparisons of the specificity constants for all of the prepared substrates. The utility of these arrays is demonstrated by the selective cleavage of preferred substrates with trypsin, thrombin, and granzyme B, and by assessing the extended substrate specificity of thrombin using a microarray of 361 different peptidyl coumarin substrates.

A model explaining declining rate in hydrolysis of lignocellulose substrates with cellobiohydrolase I (cel7A) and endoglucanase I (cel7B) of Trichoderma reesei.

Abstract: It is commonly observed that the rate of enzymatic hydrolysis of solid cellulose substrates declines markedly with time. In this work the mechanism behind the rate reduction was investigated using two dominant cellulases of Trichoderma reesei: exoglucanase Cel7A (formerly known as CBHI) and endoglucanase Cel7B (formerly EGI). Hydrolysis of steam-pretreated spruce (SPS) was performed with Cel7A and Cel7B alone, and in reconstituted mixtures. Throughout the 48-h hydrolysis, soluble products, hydrolysis rates, and enzyme adsorption to the substrate were measured. The hydrolysis rate for both enzymes decreases rapidly with hydrolysis time. Both enzymes adsorbed rapidly to the substrate during hydrolysis. Cel7A and Cel7B cooperate synergistically, and synergism was approximately constant during the SPS hydrolysis. Thermal instability of the enzymes and product inhibition was not the main cause of reduced hydrolysis rates. Adding fresh substrate to substrate previously hydrolyzed for 24 h with Cel7A slightly increased the hydrolysis of SPS; however, the rate increased even more by adding fresh Cel7A. This suggests that enzymes become inactivated while adsorbed to the substrate and that unproductive binding is the main cause of hydrolysis rate reduction. The strongest increase in hydrolysis rate was achieved by adding Cel7B. An improved model is proposed that extends the standard endo-exo synergy model and explains the rapid decrease in hydrolysis rate. It appears that the processive action of Cel7A becomes hindered by obstacles in the lignocellulose substrate. Obstacles created by disordered cellulose chains can be removed by the endo activity of Cel7B, which explains some of the observed synergism between Cel7A and Cel7B. The improved model is supported by adsorption studies during hydrolysis.

Catalytic activity of mesoporous silicate-immobilized chloroperoxidase

Abstract: A versatile enzyme, FeHeme chloroperoxidase (CPO) from Caldariomyces fumago, is immobilized in the mesoporous silicate material, mesocellular foam (MCF). MCF is a promising material for immobilizing enzymes, due to its large pore structure and high loading capacity compared to other mesoporous materials, such as MCM-48, SBA-16 and SBA-15. The immobilized CPO in MCF retains its activity. The optimal pH at which the maximum amount of enzyme is immobilized was determined to be pH 3.4, slightly below the isoelectric point of the enzyme. A weak ionic interaction between the enzyme and the surface of the inorganic substrate is thought to be critical in maintaining the activity of the immobilized enzyme. The loading capacity of MCF is 122 mg protein per 1 g of MCF. We demonstrate the advantage of MCF as an inorganic substrate for immobilization of enzymes.

Design and characterization of immobilized enzymes in microfluidic systems.

Abstract: Herein we report the fabrication, characterization, and use of total analytical microsystems containing surface-immobilized enzymes. Streptavidin-conjugated alkaline phosphatase was linked to biotinylated phospholipid bilayers coated inside poly(dimethylsiloxane) microchannels and borosilicate microcapillary tubes. Rapid determination of enzyme kinetics at many different substrate concentrations was made possible by carrying out laminar flow-controlled dilution on-chip. This allowed Lineweaver−Burk analysis to be performed from a single experiment with all the data collected simultaneously. The results revealed an enzyme turnover number of 51.1 ± 3.2 s-1 for this heterogeneous system. Furthermore, the same enzyme immobilization strategy was extended to demonstrate that multiple chemical reactions could be performed in sequence by immobilizing various enzymes in series. Specifically, the presence of glucose was detected by two coupled steps employing immobilized avidinD-conjugated glucose oxidase and strep...

Effect of a dispersion of interfacial electron transfer rates on steady state catalytic electron transport in [NiFe]-hydrogenase and other enzymes

Abstract: Redox enzymes can be adsorbed onto electrode surfaces such that there is a rapid and efficient direct electron transfer (ET) between the electrode and the enzyme's active site, along with high catalytic activity. In an idealized way, this may be analogous to protein−protein ET or, more significantly, the nonrigid interface between different domains of membrane-bound enzymes. The catalytic current that is obtained when substrate is added to the solution is directly proportional to the enzyme's turnover rate and its dependence on the electrode potential reports on the energetics and kinetics of the entire catalytic cycle. Although the current is expected to reach a limiting value as the electrode potential is varied to increase the driving force, a residual slope in voltammograms is often observed. This slope is significant, as it is unexpected from all simple considerations of electrochemical kinetics. A particularly remarkable result is obtained in experiments carried out with the [NiFe]-hydrogenase from ...

Tuning the activity of catechol oxidase model complexes by geometric changes of the dicopper core

Abstract: Dicopper(II) complexes of a series of different pyrazolate-based dinucleating ligands [L1](-)-[L4](-) have been synthesized and characterized structurally and spectroscopically. A major difference between the four complexes is the individual metal-metal separation that is enforced by the chelating side arms of the pyrazolate ligand scaffold: it varies from 3.45 A in 2 x (BF4)4 to 4.53 A in 4 x (ClO4)2. All complexes have been evaluated as model systems for the catechol oxidase enzyme by using 3,5-di-tert-butylcatechole (DTBC) as the test substrate. They were shown to exhibit very different catecholase activities ranging from very efficient to poor catalysts (k(obs) between 2430+/-202 and 22.8+/-1.2 h(-1)), with an order of decreasing activity 2 x (ClO4)4 > 1 x (ClO4)2 > 3 x (ClO4)2 >> 4 x (ClO4)2. A correlation of the catecholase activities with the variation in Cu...Cu distances, as well as other effects resulting from the distinct redox potentials, neighboring groups, and the individual coordination spheres are discussed. Saturation behavior for the rate dependence on substrate concentration was observed in only two cases, that is, for the most active 2 x (ClO4)4 and for the least active 4 x (ClO4)2, whereas a catalytic rate that is almost independent of substrate concentration (within the range studied) was observed for 1 x (ClO4)2 and 3 x (ClO4)2. H2O2 was detected as the product of O2 reduction in the catecholase reaction of the three most active systems. The structures of the adducts of "L3Cu2" and "L4Cu2" with a substrate analogue (tetrachlorocatecholate, TCC) suggest a bidentate substrate coordination to only one of the copper ions for those catalysts that feature short ligand side arms and correspondingly exhibit larger metal-metal separations; this possibly contributes to the lower activity of these systems. TCC binding is supported by several H-bonding interactions to water molecules at the adjacent copper or to ligand-side-arm N-donors; this emphasizes the importance of functional groups in proximity to the bimetallic active site.

AN OVERVIEW OF THE MECHANISM, SUBSTRATE SPECIFICITIES, AND STRUCTURE OF FMOs

Abstract: Kinetic studies carried out over the past three decades, primarily with purified pig liver flavin-containing monooxygenase (FMO1), demonstrated that the mechanism of this flavoenzyme was distinctly different from other widely studied flavin-dependent monooxygenases in that reduction of O2 by nicotinamide-adenine-dinucleotide-phosphate reduced (NADPH) occurred before the addition of the xenobiotic substrate. Compounds bearing a soft nucleophilic heteroatom show substrate activity provided they could contact the enzyme-bound 4a-hydroperoxy flavin. Structure–activity studies suggest that in addition to nucleophilicity, size and charge of potential substrates are important parameters limiting access to the enzyme-bound hydroxylating intermediate form of the enzyme. The mechanism of FMO 1, 2, 3, and 4 are similar and differences in the substrate specificities of these isoforms can be attributed almost entirely to differences in the dimensions of the cleft or channel limiting access to the 4a-hydroperoxy flavin...

Exploring the Active Site of Amine:Pyruvate Aminotransferase on the Basis of the Substrate Structure−Reactivity Relationship: How the Enzyme Controls Substrate Specificity and Stereoselectivity

Abstract: An active site model of the amine:pyruvate aminotransferase (APA) from Vibrio fluvialis JS17 was constructed on the basis of the relationship between substrate structure and reactivity. Due to the broad substrate specificity of the APA, various amino donors (chiral and achiral amine, amino acid, and amino acid derivative) and amino acceptors (keto acid, keto ester, aldehyde, and ketone) were used to explore the active site structure. The result suggested a two-binding site model consisting of two pockets, one large (L) and the other small (S). The difference in the size of each binding pocket and strong repulsion for a carboxylate in the S pocket were key determinants to control its substrate specificity and stereoselectivity. The L pocket showed dual recognition mode for both hydrophobic and carboxyl groups as observed in the side-chain pockets of aspartate aminotransferase and aromatic aminotransferase. Comparison of the model with those of other aminotransferases revealed that the L and S pockets corresponded to carboxylate trap and side-chain pocket, respectively. The active site model successfully explains the observed substrate specificity as well as the stereoselectivity of the APA.

Catalytic oxidations of steroid substrates by artificial cytochrome p-450 enzymes.

Abstract: Catalysts comprising manganese-porphyrins carrying cyclodextrin binding groups are able to perform hydroxylations with substrate selectivity and regio- and stereoselectivity and high catalytic turnovers. The geometries of the catalyst/substrate complexes override intrinsic substrate reactivities, permitting attack on geometrically accessible saturated carbons of steroids in the presence of secondary carbinol groups and carbon-carbon double bonds, as in enzymatic reactions. Selective hydroxylations of steroid carbon 9 positions are of particular practical interest.

The 2.0 Å crystal structure of catalase-peroxidase from Haloarcula marismortui

Abstract: Catalase-peroxidase is a member of the class I peroxidase superfamily. The enzyme exhibits both catalase and peroxidase activities to remove the harmful peroxide molecule from the living cell. The 2.0 A crystal structure of the catalase-peroxidase from Haloarcula marismortui (HmCP) reveals that the enzyme is a dimer of two identical subunits. Each subunit is composed of two structurally homologous domains with a topology similar to that of class I peroxidase. The active site of HmCP is in the N-terminal domain. Although the arrangement of the catalytic residues and the cofactor heme b in the active site is virtually identical to that of class I peroxidases, the heme moiety is buried inside the domain, similar to that in a typical catalase. In the vicinity of the active site, novel covalent bonds are formed among the side chains of three residues, including that of a tryptophan on the distal side of the heme. Together with the C-terminal domain, these covalent bonds fix two long loops on the surface of the enzyme that cover the substrate access channel to the active site. These features provide an explanation for the dual activities of this enzyme.

Alkaline phosphatase revisited: hydrolysis of alkyl phosphates.

Abstract: Escherichia coli alkaline phosphatase (AP) is the prototypical two metal ion catalyst with two divalent zinc ions bound approximately 4 A apart in the active site. Studies spanning half a century have elucidated many structural and mechanistic features of this enzyme, rendering it an attractive model for investigating the potent catalytic power of bimetallic centers. Unfortunately, fundamental mechanistic features have been obscured by limitations with the standard assays. These assays generate concentrations of inorganic phosphate (P(i)) in excess of its inhibition constant (K(i) approximately 1 muM). This tight binding by P(i) has affected the majority of published kinetic constants. Furthermore, binding limits k(cat)/K(m) for reaction of p-nitrophenyl phosphate, the most commonly employed substrate. We describe a sensitive (32)P-based assay for hydrolysis of alkyl phosphates that avoids the complication of product inhibition. We have revisited basic mechanistic features of AP with these alkyl phosphate substrates. The results suggest that the chemical step for phosphorylation of the enzyme limits k(cat)/K(m). The pH-rate profile and additional results suggest that the serine nucleophile is active in its anionic form and has a pK(a) of < or = 5.5 in the free enzyme. An inactivating pK(a) of 8.0 is observed for binding of both substrates and inhibitors, and we suggest that this corresponds to ionization of a zinc-coordinated water molecule. Counter to previous suggestions, inorganic phosphate dianion appears to bind to the highly charged AP active site at least as strongly as the trianion. The dependence of k(cat)/K(m) on the pK(a) of the leaving group follows a Bronsted correlation with a slope of beta(lg) = -0.85 +/- 0.1, differing substantially from the previously reported value of -0.2 obtained from data with a less sensitive assay. This steep leaving group dependence is consistent with a largely dissociative transition state for AP-catalyzed hydrolysis of phosphate monoesters. The new (32)P-based assay employed herein will facilitate continued dissection of the AP reaction by providing a means to readily follow the chemical step for phosphorylation of the enzyme.

Production of carbon nanotubes

Abstract: A method of forming carbon nanotubes by plasma enhanced chemical vapour deposition using a carbon containing gas plasma, wherein the carbon nanotubes are not formed on a substrate at a temperature 300 °C or above.

Modulation of the enantioselectivity of Candida antarctica B lipase via conformational engineering. Kinetic resolution of (±)-α-hydroxy-phenylacetic acid derivatives

Abstract: The modulation, via immobilization and engineering the reaction medium, of the enantioselectivity exhibited by the lipase from Candida antarctica B (CABL) in the hydrolysis of α-hydroxy-phenylacetic acid derivatives is shown. The enzyme was purified and immobilized using different protocols to obtain immobilized enzyme preparations with different orientations and micro-environments. The catalytic properties (activity, specificity, enantioselectivity) of the resulting derivatives were found to be quite different from each other. The enantioselectivity ( E value) strongly depends on the type of derivative and the conditions employed. Thus, the enzyme immobilized on cyanogen bromide (CNBr) presented E =7.4, while the PEI derivative yielded E =67 in the hydrolysis of α-hydroxy-phenylacetic acid methyl ester under similar conditions. Moreover, the enantioselectivity of the PEI derivative decreased from 67 to 14 on lowering the reaction temperature from 25 to 4°C at pH 5, while the E of some other derivatives improved significantly under similar experimental changes. Similar changes in the E values were observed in the hydrolysis of ( RS )-2-butyroyl-2-phenylacetic acid. Using this substrate, the interfacially adsorbed enzyme (octadecyl) afforded an E value of only 2 at pH 5, while the glutaraldehyde derivative presented a high enantioselectivity ( E >400) under all conditions studied. The corresponding ( S )-ester and ( R )-acid were obtained with excellent enantiomeric excess using the glutaraldehyde derivative, while using the interfacially immobilized one there was no appreciable enantioselectivity. Thus, using differently immobilized derivatives and different experimental conditions, lipase enantioselectivity could vary from negligible to up to 400. The experimental conditions were also found to have varying effects on the different lipase derivatives.

Structural mechanism of enoyl-CoA hydratase: three atoms from a single water are added in either an E1cb stepwise or concerted fashion.

Abstract: We have determined the crystal structure of the enzyme enoyl-CoA hydratase (ECH) from rat liver with the bound substrate 4-(N,N-dimethylamino)cinnamoyl-CoA using X-ray diffraction data to a resolution of 2.3 A. In addition to the thiolester substrate, the catalytic water, which is added in the hydration reaction, has been modeled into well-defined electron density in each of the six active sites of the physiological hexamer within the crystallographic asymmetric unit. The catalytic water bridges Glu(144) and Glu(164) of the enzyme and has a lone pair of electrons poised to react with C(3) of the enzyme-bound alpha,beta-unsaturated thiolester. The water molecule, which bridges two glutamate residues, is reminiscent of the enolase active site. However, unlike enolase, which has a lysine available to donate a proton, there are no other sources of protons available from other active site residues in ECH. Furthermore, an analysis of the hydrogen-bonding network of the active site suggests that both Glu(144) and Glu(164) are ionized and carry a negative charge with no reasonable place to have a protonated carboxylate. This lack of hydrogen-bonding acceptors that could accommodate a source of a proton, other than from the water molecule, leads to a hypothesis that the three atoms from a single water molecule are added across the double bond to form the hydrated product. The structural results are discussed in connection with details of the mechanism, which have been elucidated from kinetics, site-directed mutagenesis, and spectroscopy of enzyme-substrate species, in presenting an atomic-resolution mechanism of the reaction. Contrary to the previous interpretation, the structure of the E-S complex together with previously determined kinetic isotope effects is consistent with either a concerted mechanism or an E1cb stepwise mechanism.