Role of the pyridine nitrogen in pyridoxal 5'-phosphate catalysis: activity of three classes of PLP enzymes reconstituted with deazapyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (PLP; vitamin B(6))-catalyzed reactions have been well studied, both on enzymes and in solution, due to the variety of important reactions this cofactor catalyzes in nitrogen metabolism. Three functional groups are central to PLP catalysis: the C4' aldehyde, the O3' phenol, and the N1 pyridine nitrogen. In the literature, the pyridine nitrogen has traditionally been assumed to be protonated in enzyme active sites, with the protonated pyridine ring providing resonance stabilization of carbanionic intermediates. This assumption is certainly correct for some PLP enzymes, but the structures of other active sites are incompatible with protonation of N1, and, consequently, these enzymes are expected to use PLP in the N1-unprotonated form. For example, aspartate aminotransferase protonates the pyridine nitrogen for catalysis of transamination, while both alanine racemase and O-acetylserine sulfhydrylase are expected to maintain N1 in the unprotonated, formally neutral state for catalysis of racemization and β-elimination. Herein, kinetic results for these three enzymes reconstituted with 1-deazapyridoxal 5'-phosphate, an isosteric analogue of PLP lacking the pyridine nitrogen, are compared to those for the PLP enzyme forms. They demonstrate that the pyridine nitrogen is vital to the 1,3-prototropic shift central to transamination, but not to reactions catalyzed by alanine racemase or O-acetylserine sulfhydrylase. Not all PLP enzymes require the electrophilicity of a protonated pyridine ring to enable formation of carbanionic intermediates. It is proposed that modulation of cofactor electrophilicity plays a central role in controlling reaction specificity in PLP enzymes.     

Metabolic Glycoengineering with N‐Acyl Side Chain Modified Mannosamines

In metabolic glycoengineering (MGE), cells or animals are treated with unnatural derivatives of monosaccharides. After entering the cytosol, these sugar analogues are metabolized and subsequently expressed on newly synthesized glycoconjugates. The feasibility of MGE was first discovered for sialylated glycans, by using N‐acyl‐modified mannosamines as precursor molecules for unnatural sialic acids. Prerequisite is the promiscuity of the enzymes of the Roseman–Warren biosynthetic pathway. These enzymes were shown to tolerate specific modifications of the N‐acyl side chain of mannosamine analogues, for example, elongation by one or more methylene groups (aliphatic modifications) or by insertion of reactive groups (bioorthogonal modifications). Unnatural sialic acids are incorporated into glycoconjugates of cells and organs. MGE has intriguing biological consequences for treated cells (aliphatic MGE) and offers the opportunity to visualize the topography and dynamics of sialylated glycans in vitro, ex vivo, and in vivo (bioorthogonal MGE).     

Modulating Mobility: a Paradigm for Protein Engineering?

Proteins are highly mobile structures. In addition to gross conformational changes occurring on, for example, ligand binding, they are also subject to constant thermal motion. The mobility of a protein varies through its structure and can be modulated by ligand binding and other events. It is becoming increasingly clear that this mobility plays an important role in key functions of proteins including catalysis, allostery, cooperativity, and regulation. Thus, in addition to an optimum structure, proteins most likely also require an optimal dynamic state. Alteration of this dynamic state through protein engineering will affect protein function. A dramatic example of this is seen in some inherited metabolic diseases where alternation of residues distant from the active site affects the mobility of the protein and impairs function. We postulate that using molecular dynamics simulations, experimental data or a combination of the two, it should be possible to engineer the mobility of active sites. This may be useful in, for example, increasing the promiscuity of enzymes. Thus, a paradigm for protein engineering is suggested in which the mobility of the active site is rationally modified. This might be combined with more “traditional” approaches such as altering functional groups in the active site.     

Polyelectrolyte complexes of carboxyl-containing polyanions: Stabilization of complexes in neutral and weakly acidic media and factors affecting this phenomenon

The stability of insoluble polyelectrolyte complexes formed by various carboxyl-containing polyanions with a positively charged partner—a linear polycation or protein—has been studied by means of turbidimetric titration. In most cases, acidification of the reaction medium leads to a significant strengthening of complexes against the action of the added salt in neutral or weakly acidic media. The data concerning the effect of the chemical nature of polymer components, the degree of polymerization, the density of charge, and the structure of their chains on the pH-dependent profiles of complex dissociation provide evidence that this effect is related to stabilization of the polyelectrolyte complex through the system of hydrogen bonds formed by carboxyl groups of a partially charged polyanion incorporated into the complex. Owing to a sharp and reversible change in the stability of systems at a pH and ionic strength of solution that are favorable for functioning of biopolymers (proteins, enzymes, antibodies, and nucleic acids), polycarboxylate polyelectrolyte complexes offer promise for solving practically important problems, for example, in biotechnology for separation of biological mixtures.     

Amperometric Biosensors Based on Direct Electron Transfer Enzymes

The accurate determination of analyte concentrations with selective, fast, and robust methods is the key for process control, product analysis, environmental compliance, and medical applications. Enzyme-based biosensors meet these requirements to a high degree and can be operated with simple, cost efficient, and easy to use devices. This review focuses on enzymes capable of direct electron transfer (DET) to electrodes and also the electrode materials which can enable or enhance the DET type bioelectrocatalysis. It presents amperometric biosensors for the quantification of important medical, technical, and environmental analytes and it carves out the requirements for enzymes and electrode materials in DET-based third generation biosensors. This review critically surveys enzymes and biosensors for which DET has been reported. Single- or multi-cofactor enzymes featuring copper centers, hemes, FAD, FMN, or PQQ as prosthetic groups as well as fusion enzymes are presented. Nanomaterials, nanostructured electrodes, chemical surface modifications, and protein immobilization strategies are reviewed for their ability to support direct electrochemistry of enzymes. The combination of both biosensor elements—enzymes and electrodes—is evaluated by comparison of substrate specificity, current density, sensitivity, and the range of detection.     

Metal and cofactor insertion

Cells require metal ions as cofactors for the assembly of metalloproteins. Principally one has to distinguish between metal ions that are directly incorporated into their cognate sites on proteins and those metal ions that have to become part of prosthetic groups, cofactors or complexes prior to insertion of theses moieties into target proteins. Molybdenum is only active as part of the molybdenum cofactor, iron can be part of diverse Fe-S clusters or of the heme group, while copper ions are directly delivered to their targets. We will focus in greater detail on molybdenum metabolism because molybdenum metabolism is a good example for demonstrating the role and the network of metals in metabolism: each of the three steps in the pathway of molybdenum cofactor formation depends on a different metal (iron, copper, molybdenum) and also the enzymes finally harbouring the molybdenum cofactor need additional metal-containing groups to function (iron sulfur-clusters, heme-iron).     

Polymeric Catalysts

The present-day position in the field of polymeric catalysts is outlined. The following selected groups of polymeric catalysts are discussed: synthetic hydrolases, immobilized enzymes, phase-transfer catalysts, nucleophilically active bases, polymers with conjugated π-systems, photosensitizers, polymers as carriers for catalytically active metals or ions, and immobilized homogeneous catalysts. Polymeric catalysts have the following valuable properties: insoluble polymeric catalysts are readily separable from reaction solutions and can often be re-used without loss of activity; a hydrophobic matrix protects the organometallic active center from deactivation by oxygen and water; by fixation of finely divided metals on an ion exchanger, multistage reactions may be effected successively in one reactor. Polymeric carriers may influence the catalytic properties; for example, in the case of immobilized enzymes on polyionic carriers the pH of the activity maximum may be shifted.     

The biotin enzyme family: conserved structural motifs and domain rearrangements

The biotin carboxylase family is comprised of a group of enzymes that utilize a covalently bound prosthetic group, biotin, as a cofactor. These enzymes, which include acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranoyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase, are found in diverse biosynthetic pathways in both pro-karyotes and eukaryotes. The reactions catalyzed by most members of this group of enzymes share two common features: (1) carboxylation of biotin, apparently via the formation of a carboxyphosphate intermediate, followed by (2) transcarboxylation of CO(2) from biotin to specific acceptor molecules to yield different products. Structural determinations by NMR and X-ray crystallography, complemented by mutagenesis studies, have identified some motifs that are structurally or catalytically important. Analysis of the amino acid sequences of a number of biotin carboxylases not only shows remarkable similarities within certain domains but also that there appears to have been domain rearrangements between groups of carboxylases. Acyl-coenzyme A derivatives, which bind either as substrates or as allosteric regulators of the biotin carboxylases, do not appear to share any of the CoA binding motifs that have been identified in other CoA-SH/acyl-CoA binding proteins. Further comparisons of biotin-dependent carboxylases with other groups of enzymes in the protein data bank reveal that this family of biotin enzymes has strong similarities in specific domains to a number of ATP-utilizing enzymes and to the lipoyl-containing enzymes. These structural homologies are so extensive as to be highly suggestive of evolutionary relationships between biotin carboxylases and these other enzymes.     

Novel small-molecule inhibitors of arylamine N-acetyltransferases: drug discovery by high-throughput screening

Arylamine N-acetyltransferases (NATs) are a family of enzymes found in eukaryotes and prokaryotes. While the precise endogenous function of NAT remains unknown for most organisms, recent evidence has shown that the expression of human NAT1 is up-regulated in estrogen receptor positive breast cancer. Additionally, NAT in mycobacteria is required for mycobacterial cell wall biosynthesis and survival of the organisms within macrophage. It is therefore important to develop small molecule inhibitors of NATs as molecular tools to study the function of NATs in various organisms. Such inhibitors may also prove useful in future drug design, for example in the development of anti tubercular agents. We describe a high-throughput screen of a proprietary library of 5016 drug-like compounds against three prokaryotic NAT enzymes and two eukaryotic NAT enzymes.     

Synthesis of bridged cobaloximes

Chloro-pyridino-bis (glyoximato)-cobalt(III) complexes (cobaloximes) have been synthesized in which two corners are connected by a bridge consisting of 10 or 12 methylene groups. These compounds are designed to mimic some important features of the active site of coenzyme B₁₂ dependent enzymes.     

Biochemical Reactions and Their Biological Contributions in Honey

Honey is known for its content of biomolecules, such as enzymes. The enzymes of honey originate from bees, plant nectars, secretions or excretions of plant-sucking insects, or from microorganisms such as yeasts. Honey can be characterized by enzyme-catalyzed and non-enzymatic reactions. Notable examples of enzyme-catalyzed reactions are the production of hydrogen peroxide through glucose oxidase activity and the conversion of hydrogen peroxide to water and oxygen by catalase enzymes. Production of hydroxymethylfurfural (HMF) from glucose or fructose is an example of non-enzymatic reactions in honey.     

Cytochromes P450 as useful biocatalysts: addressing the limitations

Cytochrome P450 monooxygenases (P450s or CYPs) are a unique family of enzymes which are capable of catalysing the regio- and stereospecific oxidation of non-functionalised hydrocarbons. Despite the enormous synthetic potential of P450s, these enzymes have yet to be extensively employed for research purposes or in industry. Lack of stability, low activity, narrow substrate specificity, expensive cofactor requirements, limited solvent tolerance and electron supply are some of the main reasons why the academic and industrial implementation of these important biocatalysts remains a challenge. Considering the significance of P450s, many research groups have focused on improving their properties in an effort to make more robust catalysts with broad synthetic applications. This article focuses on some of the factors that have limited the exploitation of P450s and explores some of the significant steps that have been taken towards addressing these limitations.     

Integration of Layered Redox Proteins and Conductive Supports for Bioelectronic Applications

Integration of redox enzymes with an electrode support and formation of an electrical contact between the biocatalysts and the electrode is the fundamental subject of bioelectronics and optobioelectronics. This review addresses the recent advances and the scientific progress in electrically contacted, layered enzyme electrodes, and discusses the future applications of the systems in various bioelectronic devices, for example, amperometric biosensors, sensoric arrays, logic gates, and optical memories. This review presents the methods for the immobilization of redox enzymes on electrodes and discusses the covalent linkage of proteins, the use of supramolecular affinity complexes, and the reconstitution of apo-redox enzymes for the nanoengineering of electrodes with protein monolayers of electrodes with protein monolayers and multilayers. Electrical contact in the layered enzyme electrode is achieved by the application of diffusional electron mediators, such as ferrocene derivatives, ferricyanide, quinones, and bipyridinium salts. Covalent tethering of electron relay units to layered enzyme electrodes, the cross-linking of affinity complexes formed between redox proteins and electrodes functionalized with relay-cofactor units, or surface reconstitution of apo-enzymes on relay-cofactor-functionalized electrodes yield bioelectrocatalytic electrodes. The application of the functionalized electrodes as biosensor devices is addressed and further application of electrically "wired" enzymes as catalytic interfaces in biofuel cells is discussed. The organization of sensor arrays, self-calibrated biosensors, or gated bioelectronic devices requires the microstructuring of biomaterials on solid supports in the form of ordered micro-patterns. For example, light-sensitive layers composed of azides, benzophenone, or diazine derivatives associated with solid supports can be irradiated through masks to enable the patterned covalent linkage of biomaterials to surfaces. Alternatively, patterning of biomaterials can be accomplished by noncovalent interactions (such as in affinity complexes between avidin and a photolabeled biotin, or between an antibody and a photoisomerizable antigen layer) to provide a means of organizing protein microstructures on surfaces. The organization of patterned hydrophilic/hydrophobic domains on surfaces, by using photolithography, stamping, or micromachining methods, allows the selective patterning of surfaces by hydrophobic, noncovalent interactions. Photoactivated layered enzyme electrodes act as light-switchable optobioelectronic systems for the amperometric transduction of recorded photonic information. These systems can act as optical memories, biomolecular amplifiers, or logic gates. The photoswitchable enzyme electrodes are generated by the tethering of photoisomerizable groups to the protein, the reconstitution of apo-enzymes with semisynthetic photoisomerizable cofactor units, or the coupling of photoisomerizable electron relay units.     

Bifunctional inhibitors of mevalonate kinase and mevalonate 5-diphosphate decarboxylase

[structure: see text] A bifunctional inhibitor of mevalonate kinase and mevalonate 5-diphosphate decarboxylase was synthesized. Both enzymes are in the cholesterol biosynthetic pathway and play an important role in regulating cholesterol biosynthesis. The molecule may become a useful lead compound for further development for treating cardiovascular disease and cancer. This study provides a novel example of a single inhibitor blocking two sequential steps simultaneously in the cholesterol biosynthetic pathway.     

Properties and Synthetic Applications of Enzymes in Organic Solvents

Biotransformations already represent an effective and sometimes preferable alternative to chemical synthesis for the production of fine chemicals and optically active compounds. To further widen the versatility of the biological approach, the so-called "nonaqueous enzymology", which now represents an important area of research and biotechnological development, has emerged in the last ten years or so. This new methodology is especially suitable for the modification of precursors of pharmaceutical compounds and fine chemicals, which, in most cases, are insoluble or poorly soluble in water. Even though the idea of carrying out an enzymatic process in organic solvent was initially considered with scepticism, biocatalysis in such media is now investigated and exploited in numerous academic and industrial laboratories. One of the reasons that makes enzymatic catalysis in nonaqueous media so appealing, is the important new properties that enzymes exhibit in organic solvents. For example, they are often more stable and can catalyze reactions that are impossible or difficult in water. Furthermore, enzyme selectivity can also differ from that in water and can change, or even reverse, from one solvent to another. This phenomenon, which can be called "medium engineering", can be exploited as a valid alternative to protein engineering. The first part of this review examines the thermodynamic, kinetic, spectroscopic, and physical approaches that have been adopted to investigate the factors that affect activity, stability, structure, and selectivity of enzymes in organic solvents. These combined studies have brought the understanding of enzyme catalysis in organic solvents to a level almost comparable to that reached for biocatalysis in aqueous media. The second part surveys a number of the synthetic applications of enzymes in organic media, which span from the preparation of milligrams of specifically labeled compounds to the modification of fats on multiton scale and from the preparation of complex key intermediates for the pharmaceutical industry to the synthesis of polymers.     

E factors, green chemistry and catalysis: an odyssey

The development of green chemistry is traced from the introduction of the concepts of atom economy (atom utilisation) and E factors in the early 1990s. The important role of catalysis in reducing or eliminating waste is emphasised and illustrated with examples from heterogeneous catalytic oxidations with hydrogen peroxide, homogeneous catalytic oxidations and carbonylations and organocatalytic oxidations with stable N-oxy radicals. Catalytic reactions in non-conventional media, e.g. aqueous biphasic, supercritical carbon dioxide and ionic liquids, are presented. Biotransformations involving non-natural reactions of enzymes, e.g. ester ammoniolysis, and the rational design of semi-synthetic enzymes, such as vanadate phytase, are discussed. The optimisation of enzyme properties using in vitro evolution and improvement of their operational stability by immobilisation as cross-linked enzyme aggregates (CLEA) are presented. The ultimate in green chemistry is the integration of catalytic steps into a one-pot, catalytic cascade process. An example of a chemoenzymatic synthesis of an enantiomerically pure amino acid in water and a trienzymatic cascade process using a triple-decker oxynitrilase/nitrilase/amidase CLEA are discussed. Finally, catalytic conversions of renewable raw materials are examined and the biocatalytic aerobic oxidation of starch to carboxy starch is presented as an example of green chemistry in optima forma i.e. a biocompatible product from a renewable raw material using a biocatalytic air oxidation.     

Enantiocomplementary enzymes: classification, molecular basis for their enantiopreference, and prospects for mirror-image biotransformations

One often-cited weakness of biocatalysis is the lack of mirror-image enzymes for the formation of either enantiomer of a product in asymmetric synthesis. Enantiocomplementary enzymes exist as the solution to this problem in nature. These enzyme pairs, which catalyze the same reaction but favor opposite enantiomers, are not mirror-image molecules; however, they contain active sites that are functionally mirror images of one another. To create mirror-image active sites, nature can change the location of the binding site and/or the location of key catalytic groups. In this Minireview, X-ray crystal structures of enantiocomplementary enzymes are surveyed and classified into four groups according to how the mirror-image active sites are formed.     

Recent trends in enzyme engineering aiming to improve bioelectrocatalysis proceeding with direct electron transfer

Among the known types of electrochemical biosensors, the third generation based on the ability of some enzymes to direct electron transfer (DET) is the most promising one. The enzyme property to DET is depending on its capability to electron transfer from enzymatically reduced built-in native cofactor (flavin mononucleotide, flavin adenine dinucleotide, pyrroloquinoline quinone, or heme) to a conductive surface directly for single cofactor enzymes or through a native structural electron acceptor (heme or copper-containing prosthetic groups) for multicofactor enzymes. Thus, there are two possibilities to use such type enzymes: to find a natural source of the enzyme with these properties; or to construct the recombinant chimeric analogs using the gene-engineering techniques. The modern molecular genetics opens the possibility to be independent of million-year natural evolution and engineer the specific enzymes for scientific and technological needs. This brief review is focused mostly on the recent publications on application of DET-capable engineered enzymes for the third-generation electrochemical biosensors.     

Aminoacyl-tRNA Synthetases: The Division into Two Classes Predicted by the Chemistry of Substrates and Enzymes

In biological systems, almost all chemical reactions are catalyzed by enzymes. In order to understand the mode of action of these biocatalysts, we need to know precise details of their structures, their active sites, and their functional groups. Most important are those parts of the protein molecule that are responsible for precise recognition of the substrates, for the specific interaction between the enzymes and their reactants. Decades can pass between the isolation of an enzyme and the determination of its exact structure by X-ray analysis. For the chemist, however, means are known by which initial information may be gathered relatively quickly: the synthesis of modified substrates and affinity labeling. During the last twenty five years these two methods have been put to the test on aminoacyl-tRNA synthetases. Today, we know enough about the structures of these enzymes to evaluate the success of this “chemistry on macromolecules,” or their substrates. Chemists have had some successes, which provided the structural analysts with valuable preliminary results.     

Systemic approach in the physical and structural chemistry of enzyme catalysis: From primary structure to elementary event

The state of the art in enzyme catalysis is considered in terms of physical and structural chemistry. The main chemical kinetic and structural approaches are presented that can provide detailed information concerning the elementary processes making up the multistep catalytic cycle of molecular conversion at the active site of an enzyme. It is demonstrated that knowledge of the sequence of amino acids in a protein is sufficient to reconstruct the tertiary structure of this protein, to identify the catalytic groups, and to elucidate the molecular mechanism of catalysis. This approach is based on highly efficient information and computational technologies. The architecture of the active sites of enzymes is analyzed, including geometric invariants and the characteristic bond distances and angles of catalytic groups. The template method for identifying catalytic sites in the protein 4D structure is considered. The potential of molecular mechanics in the study of active sites is illustrated by the example of computer-simulated mutagenesis. Quantum chemical calculations applied to elementary events of the catalytic cycle are considered as a physical basis for understanding the catalytic mechanism and the origin of the efficiency and specificity of enzymes.