Mass Spectrometric Analysis of Cucurbitacins and Dihydrocucurbitacins from the Tuber of .

The vast pool of structurally and functionally distinct secondary metabolites (i.e., natural products (NPs)) is constantly being expanded, a process also driven by the rapid progress in the development of analytical techniques.

Integrated Metabolomic and Transcriptomic Analysis of Modified Nucleosides for Biomarker Discovery in Clear Cell Renal Cell Carcinoma.

Clear cell renal cell carcinoma (ccRCC) accounts for ~75% of kidney cancers. The biallelic inactivation of the von Hippel-Lindau tumor suppressor gene () is the truncal driver mutation of most cases of ccRCC. Cancer cells are metabolically reprogrammed and excrete modified nucleosides in larger amounts due to their increased RNA turnover.

Mitochondrial Metabolomics of Sym1-Depleted Yeast Cells Revealed Them to Be Lysine Auxotroph.

Metabolomics has expanded from cellular to subcellular level to elucidate subcellular compartmentalization. By applying isolated mitochondria to metabolome analysis, the hallmark of mitochondrial metabolites has been unraveled, showing compartment-specific distribution and regulation of metabolites. This method was employed in this work to study a mitochondrial inner membrane protein Sym1, whose human ortholog MPV17 is related to mitochondria DNA depletion syndrome.

Metabolic and Lipidomic Assessment of Kidney Cells Exposed to Nephrotoxic Vancomycin Dosages.

Vancomycin is a glycopeptide antibiotic used against multi-drug resistant gram-positive bacteria such as (MRSA). Although invaluable against resistant bacteria, vancomycin harbors adverse drug reactions including cytopenia, ototoxicity, as well as nephrotoxicity. Since nephrotoxicity is a rarely occurring side effect, its mechanism is incompletely understood.

A comparative structural analysis of the surface properties of asco-laccases.

Laccases of different biological origins have been widely investigated and these studies have elucidated fundamentals of the generic catalytic mechanism. However, other features such as surface properties and residues located away from the catalytic centres may also have impact on enzyme function. Here we present the crystal structure of laccase from Myceliophthora thermophila (MtL) to a resolution of 1.

Thermodynamic Integration Networks and Their Application to Charge Transfer Reactions within the AauDyPI Fungal Peroxidase.

We present a computer simulation study of the thermodynamics and kinetics of charge transfer reactions within the fungal peroxidase AauDyPI from Auricularia auriculae-judae. Driving forces and reorganization energies are obtained from a thermodynamic integration scheme based upon molecular dynamics simulations. To enhance the numerical accuracy, the free energies are analyzed within a least-squares scheme of a closely knit thermodynamic network.

Oxidation and nitration of mononitrophenols by a DyP-type peroxidase.

Substantial conversion of nitrophenols, typical high-redox potential phenolic substrates, by heme peroxidases has only been reported for lignin peroxidase (LiP) so far. But also a dye-decolorizing peroxidase of Auricularia auricula-judae (AauDyP) was found to be capable of acting on (i) ortho-nitrophenol (oNP), (ii) meta-nitrophenol (mNP) and (iii) para-nitrophenol (pNP). The pH dependency for pNP oxidation showed an optimum at pH 4.

The toolbox of Auricularia auricula-judae dye-decolorizing peroxidase - Identification of three new potential substrate-interaction sites.

Dye-decolorizing peroxidases (DyPs) such as AauDyPI from the fungus Auricularia auricula-judae are able to oxidize substrates of different kinds and sizes. A crystal structure of an AauDyPI-imidazole complex gives insight into the binding patterns of organic molecules within the heme cavity of a DyP. Several small N-containing heterocyclic aromatics are shown to bind in the AauDyPI heme cavity, hinting to susceptibility of DyPs to azole-based inhibitors similar to cytochromes P450.

Mechanistic investigations of the rhodium catalyzed propargylic CH activation.

Previously we reported the redox-neutral atom economic rhodium catalyzed coupling of terminal alkynes with carboxylic acids using the DPEphos ligand. We herein present a thorough mechanistic investigation applying various spectroscopic and spectrometric methods (NMR, in situ-IR, ESI-MS) in combination with DFT calculations. Our findings show that in contrast to the originally proposed mechanism, the catalytic cycle involves an intramolecular protonation and not an oxidative insertion of rhodium in the OH bond of the carboxylic acid.

Structural basis of substrate conversion in a new aromatic peroxygenase: cytochrome P450 functionality with benefits.

Aromatic peroxygenases (APOs) represent a unique oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity and were thus recently assigned a distinct EC classification (EC 1.11.2.

Radical formation on a conserved tyrosine residue is crucial for DyP activity.

Dye-decolorizing peroxidases (DyPs) are able to cleave bulky anthraquinone dyes. The recently published crystal structure of AauDyPI reveals that a direct oxidation in the distal heme cavity can be excluded for most DyP substrates. It is shown that a surface-exposed tyrosine residue acts as a substrate interaction site for bulky substrates.

First crystal structure of a fungal high-redox potential dye-decolorizing peroxidase: substrate interaction sites and long-range electron transfer.

Dye-decolorizing peroxidases (DyPs) belong to the large group of heme peroxidases. They utilize hydrogen peroxide to catalyze oxidations of various organic compounds. AauDyPI from Auricularia auricula-judae (fungi) was crystallized, and its crystal structure was determined at 2.

Oxidative cleavage of α-aryl aldehydes using iodosylbenzene.

We found that α-aryl aldehydes can be cleaved to chain-shortened carbonyl compounds and formaldehyde by various iodosylbenzene complexes. A mechanistic scheme is presented that accounts for the loss of one carbon atom. Formaldehyde is further oxidized to CO and CO(2) under the reaction conditions.

[P9]+ [Al(OR(F))4)]-, the salt of a homopolyatomic phosphorus cation.

Positive at last: The first condensed-phase homopolyatomic phosphorus cation [P(9)](+) was prepared using a combination of the oxidant [NO](+) and weakly coordinating anion, [Al{OC(CF(3))(3)}(4)](-). [P(9)](+) consists of two P(5) cages linked by a phosphonium atom to give a D(2d)-symmetric Zintl cluster. NMR (see picture), Raman, and IR spectroscopy, mass spectrometry, and quantum-chemical calculations confirmed the structure.

Crystallization of a 45 kDa peroxygenase/peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron.

Some litter-decaying fungi secrete haem-thiolate peroxygenases that oxidize numerous organic compounds and therefore have a high potential for applications such as the detoxification of recalcitrant organic waste and chemical synthesis. Like P450 enzymes, they transfer oxygen functionalities to aromatic and aliphatic substrates. However, in contrast to this class of enzymes, they only require H(2)O(2) for activity.

Online ESI-MS analysis of reactions under high pressure.

A new approach for real-time mass spectrometric analysis and identification of intermediates in confined, pressurized vessels is presented. The high-pressure reaction media is depressurized, mixed with a solvent, and fed directly to the atmospheric pressure electrospray ionization source of a tandem mass spectrometer. The method was applied to track product evolution for the dehydration of hydroxenin monoacetate, a commercially, important vitamin A precursor, and for the hydrogenation of 5-norbornene-2-carbonitrile with Pd/CaCO(3) as catalyst.

Defect-induced acceleration of a solid-state chemical reaction in zinc alkoxide single crystals.

A family of dinuclear (salicylaldimato)zinc(micro(2)-alkoxide) complexes show unusual behavior, decomposing to olefins and the corresponding micro(2)-hydroxide complexes under very mild conditions in the solid state. The reaction in homogeneous solution is, on the other hand, not observable, even at elevated temperatures over extended periods of time. The reaction in the solid state occurs preferentially on one crystallographic face and displays kinetics characteristic of polymorphic transformations in single crystals.

Rate Enhancement and Enantioselectivity of the Jacobsen-Katsuki Epoxidation: The Significance of the Sixth Coordination Site.

New light on the origin of the high enantioselectivities achieved in the Jacobsen-Katsuki epoxidation is shed by the results of density functional calculations. Axial ligation to the metal center not only enhances the epoxidation rate, but in addition leads to highly nonplanar, bent conformations of the active catalyst.