Nonconventional amide bond formation catalysis: programming enzyme specificity with substrate mimetics

This article reports on the design and characteristics of substrate mimetics in protease-catalyzed reactions. Firstly, the basis of protease-catalyzed peptide synthesis and the general advantages of substrate mimetics over common acyl donor components are described. The binding behavior of these artificial substrates and the mechanism of catalysis are further discussed on the basis of hydrolysis, acyl transfer, protein-ligand docking, and molecular dynamics studies on the trypsin model. The general validity of the substrate mimetic concept is illustrated by the expansion of this strategy to trypsin-like, glutamic acid-specific, and hydrophobic amino acid-specific proteases. Finally, opportunities for the combination of the substrate mimetic strategy with the chemical solid-phase peptide synthesis and the use of substrate mimetics for non-peptide organic amide synthesis are presented.

Enzyme Microheterogeneous Hydration and Stabilization in Supercritical Carbon Dioxide

Supercritical carbon dioxide is a promising green-chemistry solvent for many enzyme-catalyzed chemical reactions, yet the striking stability of some enzymes in such unconventional environments is not well understood. Here, we investigate the stabilization of the Candida antarctica Lipase B (CALB) in supercritical carbon dioxide-water biphasic systems using molecular dynamics simulations. The preservation of the enzyme structure and optimal activity depend on the presence of small amounts of water in the supercritical dispersing medium. When the protein is at least partially hydrated, water molecules bind to specific sites on the enzyme surface and prevent carbon dioxide from penetrating its catalytic core. Strikingly, water and supercritical carbon dioxide cover the protein surface quite heterogeneously. In the first solvation layer, the hydrophilic residues at the surface of the protein are able to pin down patches of water, whereas carbon dioxide solvates preferentially hydrophobic surface residues. In the outer solvation shells, water molecules tend to cluster predominantly on top of the larger water patches of the first solvation layer instead of spreading evenly around the remainder of the protein surface. For CALB, this exposes the substrate-binding region of the enzyme to carbon dioxide, possibly facilitating diffusion of nonpolar substrates into the catalytic funnel. Therefore, by means of microheterogeneous solvation, enhanced accessibility of hydrophobic substrates to the active site can be achieved, while preserving the functional structure of the enzyme. Our results provide a molecular picture on the nature of the stability of proteins in nonaqueous media.

A windows program for the derivation of steady-state equations in enzyme systems

Despite the number of computer-assisted methods described for the derivation of steady-state equations of enzyme systems, most of them are focused on strict steady-state conditions or are not able to solve complex reaction mechanisms. Moreover, many of them are based on computer programs that are either not readily available or have limitations. We present here a computer program called WinStes, which derives equations for both strict steady-state systems and those with the assumption of rapid equilibrium, for branched or unbranched mechanisms, containing both reversible and irreversible conversion steps. It solves reaction mechanisms involving up to 255 enzyme species, connected by up to 255 conversion steps. The program provides all the advantages of the Windows programs, such as a user-friendly graphical interface, and has a short computation time. WinStes is available free of charge on request from the authors. (c) 2006 Elsevier Inc. All rights reserved.

UniPathway: a resource for the exploration and annotation of metabolic pathways.

UniPathway (http://www.unipathway.org) is a fully manually curated resource for the representation and annotation of metabolic pathways. UniPathway provides explicit representations of enzyme-catalyzed and spontaneous chemical reactions, as well as a hierarchical representation of metabolic pathways. This hierarchy uses linear subpathways as the basic building block for the assembly of larger and more complex pathways, including species-specific pathway variants. All of the pathway data in UniPathway has been extensively cross-linked to existing pathway resources such as KEGG and MetaCyc, as well as sequence resources such as the UniProt KnowledgeBase (UniProtKB), for which UniPathway provides a controlled vocabulary for pathway annotation. We introduce here the basic concepts underlying the UniPathway resource, with the aim of allowing users to fully exploit the information provided by UniPathway.

Managanese and dicopper complexes for bioinspired oxidation reactions: catalytic and mechanistic studies on C-H and C=C oxidations

Enzymes are high-weight molecules which catalyze most of the metabolic processes in living organisms. Very often, these proteins contain one or more 1st row transition metal ions in their active center (Fe, Cu, Co, Mn, Zn, etc.), and are known as metalloenzymes or metalloproteins. Among these, metalloenzymes that activate molecular oxygen and use it as terminal oxidant stand out because of the wide range of catalyzed reactions and their exquisite selectivity. In this PhD dissertation we develop low-weight synthetic bioinspired complexes that can mimic structural and/or functional features of the active center of oxigenases. In the first part, we describe the use of unsymmetric dinuclear Cu complexes which are capable of performing the oxidation of phenols and phenolates in a analogous manner of the tyrosinase protein. In the second part, we describe the use of mononuclear manganese complexes in the oxidation of alcanes and alquenes.

Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution

Background: Glucosamine 6-phosphate deaminase from Escherichia coli is an allosteric hexameric enzyme which catalyzes the reversible conversion of D-glucosamine 6-phosphate into D-fructose 6-phosphate and ammonium ion and is activated by N-acetyl-D-glucosamine 6-phosphate. Mechanistically, it belongs to the group of aldose-ketose isomerases, but its reaction also accomplishes a simultaneous amination/deamination. The determination of the structure of this protein provides fundamental knowledge for understanding its mode of action and the nature of allosteric conformational changes that regulate its function. Results: The crystal structure of glucosamine 6-phosphate deaminase with bound phosphate ions is presented at 2.1 Å resolution together with the refined structures of the enzyme in complexes with its allosteric activator and with a competitive inhibitor. The protein fold can be described as a modified NAD-binding domain. Conclusions: From the similarities between the three presented structures, it is concluded that these represent the enzymatically active R state conformer. A mechanism for the deaminase reaction is proposed. It comprises steps to open the pyranose ring of the substrate and a sequence of general base-catalyzed reactions to bring about isomerization and deamination, with Asp72 playing a key role as a proton exchanger.

A pentacyclic reaction intermediate of riboflavin synthase

The S41A mutant of riboflavin synthase from Escherichia coli catalyzes the formation of riboflavin from 6,7-dimethyl-8-ribityllumazine at a very low rate. Quenching of presteady-state reaction mixtures with trifluoroacetic acid afforded a compound with an absorption maximum at 412 nm (pH 1.0) that can be converted to a mixture of riboflavin and 6,7-dimethyl-8-ribityllumazine by treatment with wild-type riboflavin synthase. The compound was shown to qualify as a kinetically competent intermediate of the riboflavin synthase-catalyzed reaction. Multinuclear NMR spectroscopy, using various 13C- and 15N-labeled samples, revealed a pentacyclic structure arising by dimerization of 6,7-dimethyl-8-ribityllumazine. Enzyme-catalyzed fragmentation of this compound under formation of riboflavin can occur easily by a sequence of two elimination reactions.

Isolation, characterisation and application of novel microbial protein cross-linking enzymes

Microbial transglutaminase is favoured for use in industry over the mammalian isoform, and hence has been utilized, to great effect, as an applied biocatalyst in many industrial areas including the food and textiles industries. There are currently only a limited number of microbial TGase sources known. A number of organisms have been screened for transglutaminase activity using biochemical assays directed towards TGase catalyzed reactions (amine incorporation and peptide cross-linking assay). Of those organisms screened, TGase was identified in a number of isolates including members of the Bacillus and Streptomyces families. In addition, a protein capable of performing a TGase-like reaction was identified in the organism Pseudomonas putida that was deemed immunologically distinct from previously described TGase isoforms, though further work would be required to purify the protein responsible. The genuses Streptoverticillium and Streptomyces are known to be closely related. A number of micro-organisms relating to Streptomyces mobaraensis (formerly Streptoverticillium mobaraensis) have been identified as harboring a TGase enzyme. The exact biological role of Streptomyces TGase is not well understood, though from work undertaken here it would appear to be involved in cell wall growth. Comparison of the purified Streptomyces TGase proteins showed them to exhibit marginally different characteristics in relation to enzymatic activity and pH dependency upon comparison with Streptomyces mobaraensis TGase. In addition, TGase was identified in the organism Saccharomonospora viridis that was found to be genetically identical to that from S. mobaraensis raising questions about the enzymes dissemination in nature. TGase from S. baldaccii was found to be most diverse with respect to enzymatic characteristics whilst still retaining comparable E(y-glutamyl) lysine bond formation to S. mobaraensis TGase. As such S. baldaccii TGase was cloned into an expression vector enabling mass production of the enzyme thereby providing a viable alternative to S. mobaraensis TGase for many industrial processes.

Catalytic oxidation of alcohols: recent advances

This review concerns metal-catalyzed reactions of oxidation of alcohols to the respective products, mainly ketones and aldehydes, mostly within the period of 2010–2014. Both conventional and unconventional systems, not only with usual reagents, but also with uncommon and prospective ones, are overviewed, with recently achieved developments.

Metabolic origin of δ15N values in nitrogenous compounds from Brassica napus L. leaves

Nitrogen isotope composition (δ15N) in plant organic matter is currently used as a natural tracer of nitrogen acquisition efficiency. However, the δ15N value of whole leaf material does not properly reflect the way in which N is assimilated because isotope fractionations along metabolic reactions may cause substantial differences among leaf compounds. In other words, any change in metabolic composition or allocation pattern may cause undesirable variability in leaf δ15N. Here, we investigated the δ15N in different leaf fractions and individual metabolites from rapeseed (Brassica napus) leaves. We show that there were substantial differences in δ15N between nitrogenous compounds (up to 30 ) and the content in (15N enriched) nitrate had a clear influence on leaf δ15N. Using a simple steady-state model of day metabolism, we suggest that the δ15N value in major amino acids was mostly explained by isotope fractionation associated with isotope effects on enzyme-catalysed reactions in primary nitrogen metabolism. δ15N values were further influenced by light versus dark conditions and the probable occurrence of alternative biosynthetic pathways. We conclude that both biochemical pathways (that fractionate between isotopes) and nitrogen sources (used for amino acid production) should be considered when interpreting the δ15N value of leaf nitrogenous compounds

Catalysis By Ferrites And Cobaltites For The Alkylation And Oxidation Of Organic Compounds

Catalysis is a very important process from an industrial point of view since the production of most industrially important chemicals involves catalysis.Solid acid catalysts are appealing since the nature of acid sites is known and their chemical behavior in acid catalyzed reactions can be rationalized by means of existing theories and models. Mixed oxides crystallizing in spinel structure are of special interest because the spinel lattice imparts extra stability to the catalyst under various reaction conditions so that theses systems have sustained activities for longer periods. The thesis entitled" Catalysis By Ferrites And Cobaltites For The Alkylation And Oxidation Of Organic Compounds " presents the preparation ,characterization ,and activity studies of the prepared spinels were modified by incorporating other ions and by changing the stoichiometry.The prepared spinels exhibiting better catalytic activity towards the studied reactions with good product selectivity.Acid-base properties and cation distribution of the spinels were found to control the catalytic activity.

Zur Synthese von alpha-Aminoaldehyden und Aminosäuren mit alpha-quartären Zentren durch Aziridinierung funktionalisierter Olefine

Ziel dieser Arbeit war, durch Aziridinierung homochiraler 5-Methyl-4H-1,3-dioxinen eine neue Methode zur Synthese von alpha-Aminoaldehyden und den ableitbaren Aminosäuren mit alpha-quartären Zentren zu entwickeln. Die chiralen 5-Methyl-4H-1,3-dioxine sind mit hohen Enantiomerenüberschüssen durch asymmetrische Doppelbindungsisomerisierung von 5-Methylen-1,3-dioxanen zugänglich. Die Metall-katalysierte Aziridinierung der 5-Methyl-4H-1,3-dioxine mit der Nitrenquelle (N-Tosylimino)phenyliodinan führte direkt zu N-Tosyl-geschützen 4-Methyl-1,3-oxazolidin-4-carbaldehyden. Vermutlich über ein Aziridin als nicht isolierbare Zwischenstufe werden über eine Ringöffnungs-/Ringverengungsreaktion die Oxazolidinderivate gebildet, vorzugsweise in Gegenwart von Cu(I)-Katalysatoren, während die Rhodium-katalysierte Reaktion ausschließlich zu Insertionsprodukten führt. In der Cu-katalysierten Aziridinierung ist das Verhältnis von Aziridinierung/Insertion abhängig von der Katalysatorkonzentration. Die Aziridinierung mit N-(p-Nitrobenzolsulfonyl)- und N-(Trimethylsilylethylsulfonyl)- substituierten Nitrenquellen führt zu Oxazolidinderivaten mit leichter abspaltbaren Schutzgruppen. Diese Nitrenquellen können in situ aus den korrespondierenden Sulfonamiden mit Iodosobenzol dargestellt werden. Bei dem Einsatz homochiraler 4H-1,3-Dioxine ist Erhalt der Stereoinformation abhängig vom Substituenten in 2-Position der Dioxine sowie von der Polarität des Lösungsmittels. Die höchsten Selektivitäten wurden in tert-Butylmethylether erzielt. In Falle des 2-tert-Butyl-4-methyl-3-(toluol-4-sulfonyl)-1,3-oxazolidin-4-carbaldehyds kristallisiert das Hauptdiastereomer in enantiomerenreiner Form. Die Absolutkonfiguration wurde durch Röntgenkristallstrukturanalyse ermittelt. Das Anwendungspotential dieser neuen Methode konnte durch Überführen der Serinale in Aminoalkohole und alpha-Methylserin-Derivate sowie in der Synthese der unnatürlichen Aminosäure alpha-Vinylalanin gezeigt werden.

Electrochemical modified electrodes based on metal-salen complexes

A general view of the electroanalytical applications of metal-salen complexes is discussed in this review. The family of Schiff bases derived from ethylenediamine and ortho-phenolic aldehydes (N,N'-ethylenebis(salicylideneiminato) - salen) and their complexes of various transition metals, such as Al, Ce, Co, Cu, Cr, Fe, Ga, Hg, Mn, Mo, Ni, and V have been used in many fields of chemical research for a wide range of applications such as catalysts for the oxygenation of organic molecules, epoxidation of alkenes, oxidation of hydrocarbons and many other catalyzed reactions; as electrocatalyst for novel sensors development; and mimicking the catalytic functions of enzymes. A brief history of the synthesis and reactivity of metal-salen complexes will be presented. The potentialities and possibilities of metal-Salen complexes modified electrodes in the development of electrochemical sensors as well as other types of sensors, their construction and methods of fabrication, and the potential application of these modified electrodes will be illustrated and discussed.

Functional shikimate dehydrogenase from Mycobacterium tuberculosis H37Rv: Purification and characterization

Tuberculosis (TB) poses a major worldwide public health problem. The increasing prevalence of TB, the emergence of multi-drug-resistant strains of Mycobacterium tuberculosis, the causative agent of TB, and the devastating effect of co-infection with HIV have highlighted the urgent need for the development of new antimycobacterial agents. Analysis of the complete genome sequence of M. tuberculosis shows the presence of genes involved in the aromatic amino acid biosynthetic pathway. Experimental evidence that this pathway is essential for M. tuberculosis has been reported. The genes and pathways that are essential for the growth of the microorganisms make them attractive drug targets since inhibiting their function may kill the bacilli. We have previously cloned and expressed in the soluble form the fourth shikimate pathway enzyme of the M. tuberculosis, the aroE-encoded shikimate dehydrogenase (mtSD). Here, we present the purification of active recombinant aroE-encoded M. tuberculosis shikimate dehydrogenase (mtSD) to homogeneity, N-terminal sequencing, mass spectrometry, assessment of the oligomeric state by gel filtration chromatography, determination of apparent steady-state kinetic parameters for both the forward and reverse directions, apparent equilibrium constant, thermal stability, and energy of activation for the enzyme-catalyzed chemical reaction. These results pave the way for structural and kinetic studies, which should aid in the rational design of mtSD inhibitors to be tested as antimycobacterial agents. (c) 2005 Elsevier B.V. All rights reserved.

Dependence of divalent metal ions on phosphotransferase activity of osseous plate alkaline phosphatase

Kinetic evidence for the role of divalent metal ions in the phosphotransferase activity of polidocanol-solubilized alkaline phosphatase from osseous plate is reported. Ethylenediamine tetreacetate, 1,10-phenanthrolin, and Chelex-100 were used to prepare metal-depleted alkaline phosphatase. Except for Chelex-100, either irreversible inactivation of the enzyme or incomplete removal of metal ions occurred. After Chelex-100 treatment, full hydrolase activity of alkaline phosphatase was recovered upon addition of metal ions. on the other hand, only 20% of transferase activity was restored with 0.1 mu M ZnCl2, in the presence of 1.0 M diethanolamine as phosphate acceptor. In the presence of 0.1 mM MgCl2, the recovery of transferase activity increased to 63%. Independently of the phosphate acceptor used, the transferase activity of the metal-depleted alkaline phosphatase was fully restored by 8 mu M ZnCl2 plus 5 mM MgCl2. In the presence of diethanolamine as phosphate acceptor, manganese, cobalt, and calcium ions did nor stimulate the transferase activity. However, manganese and cobalt-enzyme catalyzed the transfer of phosphate to glycerol and glucose. (C) 1997 Elsevier B.V.