Search

The cytochrome P450 family of monooxygenase enzymes have essential biological roles involving the selective oxidation of carbon-hydrogen bonds. They can also catalyze other important metabolic reactions including desaturation to form alkenes. Currently the factors that control the partition between P450 hydroxylation and desaturation pathways are poorly defined. The CYP199A4 enzyme from the bacterium Rhodopseudomonas palustris HaA2 catalyzes the oxidation of 4-ethyl- and 4-isopropyl- benzoic acids with hydroxylation and desaturation occurring in significant quantities. Here we demonstrate that 4-cyclopropylbenzoic acid is regioselectively hydroxylated by CYP199A4 at the benzylic carbon. In contrast, the oxidation of 4-n-propylbenzoic acid by CYP199A4 results in three major metabolites: an alkene from desaturation and two hydroxylation products at the benzylic (Cα) and Cβ carbons in similar quantities. Extending the length of the alkyl substituent resulted in 4-n-butylbenzoic acid being oxidized at the benzylic position (45%) and desaturated (55%). In contrast, 4-isobutylbenzoic generated very little alkene (5%) but was hydroxylated at the benzylic position (54%) and at the tertiary Cβ position (41%). The oxidation of 4-n-propylbenzoic acid by the F298 V mutant of CYP199A4 occurred with no hydroxylation at Cβ and a significant increase in metabolites arising from desaturation (73%). The X-ray crystal structures of CYP199A4 with each substrate revealed that they bind in the active site with the alkyl substituent positioned over the heme. However, the longer alkylbenzoic acids were bound in a different conformation as was 4-n-propylbenzoic acid in the F298 V mutant. Overall, the changes in metabolite distribution could be ascribed to bond strength differences and the position of the alkyl group relative to the heme.

There is intense interest in late‐stage catalytic CH bond functionalization as an integral part of synthesis. Effective catalysts must have a broad substrate range and tolerate diverse functional groups. Drug molecules provide a good test of these attributes of a catalyst. A library of P450BM3 mutants developed from four base mutants with high activity for hydrocarbon oxidation produced human metabolites of a panel of drugs that included neutral (chlorzoxazone, testosterone), cationic (amitriptyline, lidocaine) and anionic (diclofenac, naproxen) compounds. No single mutant was active for all the tested drugs but multiple variants in the library showed high activity with each compound. The high conversions enabled full product characterization that led to the discovery of the new P450 reaction type of oxidative decarboxylation of an α‐hydroxy carboxylic acid and the formation a protected imine from an amine, offering a novel route to α‐functionalization of amines. The substrate range and varied product profiles suggest that this library of enzymes is a good basis for developing late‐stage CH activation catalysts.

UNLABELLED Energy generation, synthesis of biomass and detoxification of synthetic compounds are driven by electron transfer in all living organisms. Soluble quinone oxidoreductases (QORs) catalyze transfer of electrons from NADPH to substrates. The open reading frame Rv1454c of Mycobacterium tuberculosis (Mtb) encodes a NADPH-dependent QOR that is known to catalyze one-electron reduction of quinones to produce semiquinones. Here, we report the crystal structures of the apo-enzyme of MtbQOR and its binary complex with NADPH determined at 1.80 and 1.85 A resolutions, respectively. The enzyme is bi-modular. Domain I binds the substrate, while domain II folds into a typical Rossmann fold for tethering NADPH. Binding of NADPH induces conformational changes. Among the known structures of QORs, MtbQOR exhibits the largest conformational change. Movement of Phe41 to stack against Ala244 results in partial closure of the active site. Comparison of the structure with homologs suggests a conserved topology. However, differences are observed in the region around the site of hydride transfer, highlighting differences in substrate specificities amongst the homologs. Unliganded as well as NADPH-bound MtbQOR crystallized as a dimer. Dimerization is mediated by homotypic intermolecular interactions involving main chain Cα as well as side-chain atoms of residues. The results of analytical ultracentrifugation analysis revealed that MtbQOR exists as a dimer in solution. Enzymatic assays indicate that MtbQOR prefers 9,10-phenanthrenequinone over 1,4-benzoquinone as a substrate. The ability to reduce quinones probably assists Mtb in detoxification of a range of harmful chemicals encountered in the host during invasion. DATABASE The coordinates and structure factors for apo- and NADPH-bound MtbQOR have been deposited in the Protein Data Bank under accession codes 4RVS and 4RVU, respectively.

This paper studies the problem of stabilization criteria for systems with two additive time-varying delays. First, the delay-dependent stability condition for the systems is established through computing the more general Lyapunov functional. The Lyapunov functional is constructed by making full use of the property and the information of the systems, and the condition has advantages over the existing ones in the skillful combination of the delay decomposition and the reciprocal convex approach. Second, considered to be more flexible for the controller design with the introduced positive scalar, a new controller method is presented. Finally, two examples are provided to demonstrate the advantage of the results in this paper.

This study describes the enrichment ability of ZnO-modified methacrylic acid-co-ethylene dimethacrylate polymer monoliths as stationary phases for the simultaneous determination of antibiotics (ofloxacin, ciprofloxacin, enoxacin, and pefloxacin) combined with high-performance liquid chromatography. The prepared monolith was characterized by scanning electron microscopy, X-ray photoelectron spectroscopy, Fourier-transformed infrared spectroscopy, and thermogravimetric analysis. The polymer monolith microextraction method has been applied to the enrichment of fluoroquinolone antibiotics and satisfactory results were obtained in the analysis of water samples. Compared with the conventional methacrylic acid based monolith, the developed monolith exhibited a higher enrichment capacity because of the introduction of zinc oxide into the preparation process.

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is one of the most devastating human diseases, and is responsible for ~ 2 million deaths worldwide each year. The nutritional requirements for the growth of mycobacteria have been extensively studied since the discovery of M. tuberculosis, but the essential nutrients for M. tuberculosis inside the human host and the identity of the corresponding transporters remain unknown. The UgpABCE transporter of M. tuberculosis is one of five putative permeases for carbohydrate uptake, and is genetically predicted to be an sn-glycerol 3-phosphate importer. We have determined the 1.5-A crystal structure of M. tuberculosis UgpB, which has been reported to be a promising vaccine candidate against TB. M. tuberculosis UgpB showed no detectable binding activity for sn-glycerol 3-phosphate by isothermal titration calorimetry, but instead showed a preference for glycerophosphocholine (GPC). M. tuberculosis UgpB largely resembles its Escherichia coli homolog, but with the critical Trp169 in the substrate-binding site of E. coli UgpB replaced by Leu205. Mutation of Leu205 abolishes GPC binding, suggesting that Leu205 is a determinant of GPC binding. The work reported here not only contributes to our understanding of the carbon and phosphate sources utilized by M. tuberculosis inside the human host, but will also promote improvements in TB chemotherapy. Database Structural data are available in the Protein Data Bank database under the accession number PDB 4MFI.

The recent crystal structures of CYP101D2, a cytochrome P450 protein from the oligotrophic bacterium Novosphingobium aromaticivorans DSM12444 revealed that both the native (substrate-free) and camphor-soaked forms have open conformations. Furthermore, two other potential camphor-binding sites were also identified from electron densities in the camphor-soaked structure, one being located in the access channel and the other in a cavity on the surface near the F-helix side of the F-G loop termed the substrate recognition site. These latter sites may be key intermediate positions on the pathway for substrate access to or product egress from the active site. Here, we show via the use of unbiased atomistic molecular dynamics simulations that despite the open conformation of the native and camphor-bound crystal structures, the underlying dynamics of CYP101D2 appear to be very similar to other CYP proteins. Simulations of the native structure demonstrated that the protein is capable of sampling many different conformational substates. At the same time, simulations with the camphor positioned at various locations within the access channel or recognition site show that movement towards the active site or towards bulk solvent can readily occur on a short timescale, thus confirming many previously reported in silico studies using steered molecular dynamics. The simulations also demonstrate how the fluctuations of an aromatic gate appear to control access to the active site. Finally, comparison of camphor-bound simulations with the native simulations suggests that the fluctuations can be of similar level and thus are more representative of the conformational selection model rather than induced fit.

In this study, a novel method for the determination of nitroanilines in hair dye samples has been developed based on poly(methacrylic acid-co-ethylene glycol dimethacrylate) monolith microextraction (PMME) and high-performance liquid chromatography (HPLC) analysis. Four nitroanilines, p-nitroaniline (PNAL), m-nitroaniline (MNAL), o-nitroaniline (ONAL), and 2,4-dinitroaniline (DNAL), are studied as representatives. To obtain optimum extraction efficiency, several experimental parameters including sample flow rate, sample volume, sample pH, and eluent flow rate have been investigated. Under the optimal experimental conditions, the linear regression coefficients of the standard curves are greater than 0.9990. The limits of detection for p-nitroaniline, m-nitroaniline, o-nitroaniline, and 2,4-dinitroaniline are 0.012, 0.008, 0.018, and 0.005 μg/mL, respectively. The intraday and interday relative standard deviations are less than 3.1 and 5.4%, respectively. The proposed method is simple, rapid, sensitive, and competent when used for the determination of nitroanilines in hair dye samples and the accuracy is assessed through recovery experiments.

BACKGROUND: 2-ethylhexylphosphonic acid mono-(2-ethylhexyl) ester (HEHEHP, H(2)A(2)) has been applied extensively to the extraction of rare earths. However, there are some limitations to its further utilization and the synergistic extraction of rare earths with mixtures of HEHEHP and another extractant has attracted much attention. Organic carboxylic acids are also a type of extractant employed for the extraction of rare earths, e.g. naphthenic acid has been widely used to separate yttrium from rare earths. Compared with naphthenic acid, sec-nonylphenoxy acetic acid (CA100, H2B2) has many advantages such as stable composition, low solubility, and strong acidity in the aqueous phase. In the present study, the extraction of rare earths with mixtures of HEHEHP and CA100 has been investigated. The separation of the rare earth elements is also studied.

BACKGROUND: Di-(2-ethylhexyl)phosphoric acid (D2EHPA, H2A2) has been used extensively in hydrometallurgy for the extraction of rare earths, but it has some limitations. Synergistic extraction has attracted much attention because of its enhanced extractabilities and selectivities. In the present study, sec-octylphenoxyacetic acid (CA12, H2B2) was added into D2EHPA systems for the extraction and separation of rare earths. The extraction mechanism of lanthanum with the mixtures and the separation of lanthanoids and yttrium were investigated. RESULTS: The synergistic enhancement coefficient for La3+ extracted with D2EHPA + CA12 was calculated as 3.63. La3+ was extracted as La(NO3)2H2A2B with the mixture. The logarithm of the equilibrium constant was determined as 0.80. The thermodynamic functions, ΔH, ΔG, and ΔS were calculated to be 4.03 kJ mol−1, − 1.96 kJ mol−1, and 20.46 J mol−1 K−1, respectively. The mixtures have synergistic effects on Ce3+, Nd3+, and Y3+, with an especially strong synergistic effect on Y3+. Neither synergistic nor antagonistic effects on Dy3+ and weak antagonistic effects on Lu3+ were found. CONCLUSION: Mixtures of D2EHPA and CA12 exhibit evident synergistic effects when used to extract La3+ from nitric solution. The stoichiometries of the extracted complexes have been determined by graphical and numerical methods to be La(NO3)2H2A2B with the mixture. The extraction is an endothermic process. The mixture exhibits different extraction effects on rare earths, which provides possibilities for the separation of Y3+ from Ln3+ at a proper ratio of D2EHPA and CA12. Copyright © 2008 Society of Chemical Industry

A novel [Ru(bpy)(2)(dcbpy)NHS] labeling/aptamer-based biosensor combined with gold nanoparticle amplification for the determination of lysozyme with an electrochemiluminescence (ECL) method is presented. In this work, an aptamer, an ECL probe, gold nanoparticle amplification, and competition assay are the main protocols employed in ECL detection. With all the protocols used, an original biosensor coupled with an aptamer and [Ru(bpy)(2)(dcbpy)NHS] has been prepared. Its high selectivity and sensitivity are the main advantages over other traditional [Ru(bpy)(3)](2+) biosensors. The electrochemical impedance spectroscopy (EIS) and atomic force microscopy (AFM) characterization illustrate that this biosensor is fabricated successfully. Finally, the biosensor was applied to a displacement assay in different concentrations of lysozyme solution, and an ultrasensitive ECL signal was obtained. The ECL intensity decreased proportionally to the lysozyme concentration over the range 1.0x10(-13)-1.0x10(-8) mol L(-1) with a detection limit of 1.0x10(-13) mol L(-1). This strategy for the aptasensor opens a rapid, selective, and sensitive route for the detection of lysozyme and potentially other proteins.

We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE. Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links.

We developed an electrochemical detector on a hybrid chip for the determination of glucose in human plasma. The microchip system described in this paper consists of a poly(dimethylsiloxane) (PDMS) layer containing separation and injection channels and an electrode plate. The copper microelectrode is fabricated by selective electroless deposition. The fabrication of the decoupler is performed by platinum electrochemical deposition on the metal film formed by electroless deposition. Factors influencing the performance, including detection potential, separation field strength, and buffer concentration, were studied. The electrodes exhibited good stability and durability in the analytical procedures. Under optimized detection conditions, glucose responded linearly from 10 microM to 1 mM. Finally, glucose in human plasma from three healthy individuals and two diabetics was successfully determined, giving a good prospect for a new clinical diagnostic instrument.

Complex polysaccharide mixtures were analyzed directly without derivatization by capillary zone electrophoresis in strongly alkaline solutions and electrochemical detection at a Cu electrode. The positively charged surfactant cetyltrimethylammonium bromide was included in the electrophoresis medium in order to reverse the electroosmotic flow and permit elution to be in order of increasing polysaccharide size. Carbohydrate samples analyzed by this approach included linear maltoses, enzymatically hydrolyzed starch, and commercially available dextrans of up to an average molecular weight of 18,300. Detection by constant-potential oxidation at a Cu electrode was very sensitive, with detection limits for individual carbohydrates generally below the femtomole level.

The reaction is applied to a wide range of substituted indoles under moderate hydrogen pressure.