Synthesis of (13)C-labeled gamma-hydroxybutyrates for EPR studies with 4-hydroxybutyryl-CoA dehydratase

4-Hydroxybutyryl-CoA dehydratase from Clostridium aminobutyricum catalyses the reversible dehydration of its substrate 4-hydroxybutyryl-CoA (4-HB-CoA) to crotonyl CoA. The enzyme contains one [4Fe-4S](2+) cluster and one flavin adenine dinucleotide (FAD) molecule per homotetramer. Incubation of the enzyme with its substrate under equilibrium conditions followed by freezing at 77K induced the EPR-spectrum of a neutral flavin semiquinone (g=2.005, linewidth 2.1 mT), while at 10K additional signals were detected. In an attempt to characterize these signals, 4-HB-CoA molecules specifically labeled with (13)C have been synthesized. This was achieved via (13)C-labeled gamma-butyrolactones, which were obtained from (13)C-labeled bromoacetic acids by efficient synthetic routes. Incubation of the (13)C-labeled 4-hydroxybutyrate-CoA molecules with 4-hydroxybutyryl-CoA dehydratase did not lead to marked broadening of the signals.     

Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards

A general method for the quantification of proteins in human serum was developed using mass spectrometry (MS) and stable isotope-labeled synthetic peptides as internal standards. Using this approach, C-reactive protein (CRP), a diagnostic marker of rheumatoid arthritis (RA), was detected in serum samples taken from patients with either erosive or nonerosive RA and compared to healthy individuals. Small volumes of serum samples were enriched for low-abundance proteins through the selective removal of human serum albumin (HSA), immunoglobulin G (IgG), and haptoglobin. After depletion of abundant proteins, the complexity of the protein mixture was further simplified using size exclusion chromatography (SEC) to fractionate denatured proteins into discrete molecular weight ranges. Fractions of interest containing CRP, M(r) = 25 000, were pooled, digested with trypsin, and then fixed quantities of the synthetic peptides were added to the mixture. The mixture of tryptic peptides was subsequently analyzed by nanoflow chromatography-tandem MS (nanoLC-MS/MS) using multiple-reaction monitoring (MRM) on a triple quadrupole mass spectrometer (TQ-MS). The ratio of transition ions derived from the endogenous and isotope-labeled peptides provided a quantitative measure of CRP in the original samples as assessed by independent measurement of CRP in the same patient samples using an immunoassay. The use of isotope-labeled synthetic peptides and MRM is a powerful analytical method for the prescreening of candidate protein biomarkers in human serum prior to antibody and immunoassay development.     

Synthesis of methyl 4'-O-methyl-13C12-beta-D-cellobioside from 13C6-D-glucose. Part 1: reaction optimization and synthesis

A high yielding synthetic route for methyl 4'-O-methyl-beta-D-cellobioside starting from d-glucose was established. The reaction conditions optimized with nonlabeled materials were used for the synthesis of methyl 4'-O-methyl-13C12-beta-D-cellobioside, a compound having more than 99% 13C enrichment at each of the twelve pyranose carbon atoms. The labeled compound is required to study the hydrogen bond network of cellodextrins and cellulose by CPMAS NMR experiments.     

Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards

A novel method was developed for the quantitative analysis of the microbial metabolome using a mixture of fully uniformly (U) (13)C-labeled metabolites as internal standard (IS) in the metabolite extraction procedure the subsequent liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis. This mixture of fully U (13)C-labeled metabolites was extracted from biomass of Saccharomyces cerevisiae cultivated in a fed-batch fermentation on fully U (13)C-labeled substrates. The obtained labeled cell extract contained, in principle, the whole yeast metabolome, allowing the quantification of any intracellular metabolite of interest in S. cerevisiae. We have applied the labeled cell extract as IS in the analysis of glycolytic and tricarboxylic acid (TCA) cycle intermediates in S. cerevisiae sampled in both steady-state and transient conditions following a glucose pulse. The use of labeled IS effectively reduced errors due to variations occurring in the analysis and sample processing. As a result, the linearity of calibration lines and the precision of measurements were significantly improved. Coextraction of the labeled cell extract with the samples also eliminates the need to perform elaborate recovery checks for each metabolite to be analyzed. In conclusion, the method presented leads to less workload, more robustness, and a higher precision in metabolome analysis.     

Synthesis of methyl 4'-O-methyl-beta-D-cellobioside-13C12 from D-glucose-13C6. Part 2: solid-state NMR studies

Double Quantum (DQ) NMR, which utilizes the magnetic dipole interaction between the (13)C atoms, was used for the complete assignment of the (13)C NMR resonances to the corresponding carbon ring positions for the monoclinic and triclinic allomorphs of methyl 4'-O-methyl-beta-D-cellobioside-(13)C(12)(1-(13)C(12)), a cellodextrin model compound of cellulose (13)C-perlabeled at the cellobiose core. The through-space interactions were used to identify the direct chemical bonds between adjacent carbon atoms in the rings. More importantly, the (13)C NMR signals of the carbon sites C1' and C4 involved in the glycosidic bond were identified. This allowed for the complete (13)C chemical shift assignment, that when combined with the X-ray crystallography data provides a complete characterization.     

Determination of a complete set of coupling constants in 13C-labeled oligonucleotides

Summary Three experiments are introduced to determine a complete set of coupling constants in RNA oligomers. In the HCCH-E.COSY experiment, the vicinal proton-proton coupling constants can be measured with high accuracy. In the P-FIDS-CT-HSQC experiment, vicinal proton-phosphorus and carbon-phosphorus couplings are measured that depend on the phosphodiester backbone torsion angles and . In the refocussed HMBC experiment, vicinal carbon-proton couplings are measured that depend on the glycosidic torsion angle .     

Convenient solid-phase synthesis of oligopeptides using pentacoordinated phosphoranes with amino acid residue as building blocks

The reactive intermediates of pentacoordinated phosphoranes with amino acids (P(5)-AA) as building blocks, which were obtained by the reaction of O-phenylene phosphorochloridate with N,O-bis(trimethylsilyl)amino acids, were linked to a solid-phase support containing a hydroxymethyl polystyrene functional group. The first amino acid residue was coupled to the solid-phase support after washing the resin with organic solvent. Repeating the procedure led to oligopeptides linked on the resin. A series of free oligopeptides including tetra-Gly, di-Val, tri-Val, di-Leu, di-Phe, and Phe-Leu were obtained after cleavage from solid-phase support. The structure of these oligopeptides were determined by IR, (1)H NMR, FAB-MS, and HPLC.     

Synthesis of substituted indazoles and their corresponding tris(indazolyl)borate tripodal ligands as key building blocks for molecular motors

The synthesis of functionalized indazoles at the 6-position of the indazole ring is developed. Such precursors give access to tris(indazolyl)borate ligands derived from the scorpionate ligands of Trofimenko. These tripodal ligands are truly bifunctional since they can coordinate a metal via the nitrogen centers of the indazolyl rings and be anchored on surfaces on the opposite side through their 6-functionalizations. Three pendant ester or thioether groups were selected to anchor metallic complexes onto, respectively, an oxide or a metallic surface in view of near-field microscopy experiments. These building blocks have been subsequently used as stator in a family of single molecular rotary motors. The architecture of such compounds is centered around half-sandwich complexes of the family of pentaphenylcyclopentadienyl hydrotris(indazolyl)borate ruthenium (II).     

Investigation of the synthetic route to pepstatin analogues by SPPS using O‐protected and O‐unprotected statine as building blocks

The synthetic route to pepstatin derivatives by a solid phase peptide synthesis using either O‐protected or O‐unprotected statine as a building block has been investigated. Statine was prepared according to a modified literature procedure, whereas protection of its 3‐hydroxyl moiety using tert‐butyldimethylsilylchloride (TBSCl) provided the novel O‐TBS‐protected statine building block. The O‐tert‐butyldimethylsilyl (TBS)‐protected statine approach provides an improved synthetic strategy for the preparation of statine‐containing peptides as demonstrated by the synthesis of the pepstatin analogue iva‐Val‐Leu‐Sta‐Ala‐Sta. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

Oxoperoxo molybdenum(VI)- and tungsten(VI) complexes with 1-(2′-hydroxyphenyl) ethanone oxime: Synthesis, structure and catalytic uses in the oxidation of olefins, alcohols, sulfides and amines using H2O2 as a terminal oxidant

High yield synthesis of two new oxodiperoxo-molybdate, PPh₄[MoO(O₂)₂(HPEOH)] (1), and -tungstate, PPh₄[WO(O₂)₂(HPEOH)] (2), complexes with 1-(2′-hydroxyphenyl) ethanone oxime (HPEOH₂) as organic ligand has been achieved by adding methanol solution of the ligand to the pale-yellow solution obtained by dissolving molybdic-/tungstic-acid (freshly prepared) in hydrogen peroxide and precipitating the complexes using tetraphenylphosphonium chloride. The orange-yellow complexes have been characterized by elemental analysis, IR, ¹H NMR, UV-Vis spectroscopy and finally by X-ray structure analysis. Both the complexes function as facile olefin epoxidation catalysts with hydrogen peroxide as terminal oxidant and bicarbonate as a co-catalyst at room temperature. Catalytic potentiality of 1 and 2 is also exhibited in the case of oxidation of alcohols, amines and sulfides. The catalysts are very much efficient especially in olefin epoxidation giving high yield, TON (turnover number) and TOF (turnover frequency). The method described is environmentally benign and cost-effective in all the cases.     

Selective backbone labeling of proteins using {1,2-<Superscript>13</Superscript>C<Subscript>2</Subscript>}-pyruvate as carbon source

A simple isotope labeling approach for selective ¹³C/¹⁵N backbone labeling of proteins is described. Using {1,2-¹³C₂}-pyruvate as the sole carbon source in bacterial growth media, selective incorporation of ¹³C^α-¹³CO spin-pairs into the backbones of protein molecules with medium-to-high levels of ¹³C-enrichment is possible for a subset of 12 amino acids. The isotope labeling scheme has been tested on a pair of proteins—a 7-kDa immunoglobulin binding domain B1 of streptococcal protein G and an 82-kDa enzyme malate synthase G. A number of protein NMR applications are expected to benefit from the {1,2-¹³C₂}-pyruvate based protein production.