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Isotopic Labeling (isotopic + labeling)
Selected AbstractsInnentitelbild: Stereospecific Isotopic Labeling of Methyl Groups for NMR Spectroscopic Studies of High-Molecular-Weight Proteins (Angew. Chem.ANGEWANDTE CHEMIE, Issue 11 201011/2010) NMR-Spektroskopie großer Proteinsysteme gelingt nur nach gezielter Protonierung ausgewählter Positionen vor einem perdeuterierten Hintergrund. In der Zuschrift auf S.,2002,ff. von J. Boisbouvier et,al. wird eine Acetolactatvorstufe vorgestellt, um biosynthetisch 13C1H3 -Gruppen spezifisch in die pro- S -Methyl-Positionen von Leucin und Valin einzuführen. Dieses Markierungsverfahren verbessert die Spektrenqualität erheblich und schafft eine einfache und effiziente Grundlage für die Anwendung von Lösungs-NMR-Techniken auf komplexe Biomoleküle. [source] Stereospecific Isotopic Labeling of Methyl Groups for NMR Spectroscopic Studies of High-Molecular-Weight Proteins,ANGEWANDTE CHEMIE, Issue 11 2010Pierre Gans Dr. Manchmal ist weniger mehr: 13C1H3 -Methylisotopomere können biosynthetisch mithilfe einer Acetolactatvorstufe spezifisch als pro- S -Methylgruppen von Leucin- und Valinresten in ansonsten perdeuterierte Proteine eingefügt werden. Durch diese Markierungsstrategie wird die Qualität der NMR-Spektren großer Proteinassoziationen deutlich verbessert. [source] Isotopic labeling of 2-desoxoparaherquamide A (PNU-141962) with deuteriumJOURNAL OF LABELLED COMPOUNDS AND RADIOPHARMACEUTICALS, Issue 14 2002Byung H. Lee Abstract Modifications of marcfortine A and paraherquamide A led to the discovery of 2-desoxoparaherquamide A (PNU-141962, 3) which is as active as paraherquamide A and has an improved safety profile. In order to do preclinical studies, we wished to synthesize isotope-labeled PNU-141962. This account will describe the synthesis of [CD3]-2-desoxoparaherquamide A (4). The deuterium product was prepared in anticipation of using a similar synthesis for the preparation of the corresponding 14C- and 3H-labeled products. Copyright © 2002 John Wiley & Sons, Ltd. [source] Hyperpolarized 13C magnetic resonance detection of carboxypeptidase G2 activityMAGNETIC RESONANCE IN MEDICINE, Issue 5 2009Yann Jamin Abstract Carboxypeptidase G2 (CPG2) is a bacterial enzyme that is currently employed in a range of targeted cancer chemotherapy strategies such as gene-directed enzyme prodrug therapy (GDEPT). Employing dynamic nuclear polarization (DNP) and natural abundance 13C magnetic resonance spectroscopy (MRS), we observed the CPG2-mediated conversion of a novel hyperpolarized reporter probe 3,5-difluorobenzoyl-L-glutamic acid (3,5-DFBGlu) to 3,5-difluorobenzoic acid (3,5-DFBA) and L-glutamic acid (L-Glu) in vitro. Isotopic labeling of the relevant nuclei with 13C in 3,5-DFBGlu or related substrates will yield a further factor of 100 increase in the signal-to-noise. We discuss the feasibility of translating these experiments to generate metabolic images of CPG2 activity in vivo. Magn Reson Med, 2009. © 2009 Wiley-Liss, Inc. [source] Methionine gamma-lyase: The unique reaction mechanism, physiological roles, and therapeutic applications against infectious diseases and cancersIUBMB LIFE, Issue 11 2009Dan Sato Abstract Sulfur-containing amino acids (SAAs) are essential components in many biological processes and ubiquitously distributed to all organisms. Both biosynthetic and catabolic pathways of SAAs are heterogeneous among organisms and between developmental stages, and regulated by the environmental changes. Limited lineage of organisms ranging from archaea to plants, but not human, possess a unique enzyme methionine gamma-lyase (MGL, EC 4.4.1.11) to directly degrade SAA to ,-keto acids, ammonia, and volatile thiols. The reaction mechanisms and the physiological roles of this enzyme are partially demonstrated by the enzymological analyzes, structure determination, isotopic labeling of the intermediate metabolites, and functional analyzes of deficient mutants. MGL has been exploited as a drug target for the infectious diseases caused by parasitic protozoa and anaerobic periodontal bacteria. In addition, MGL has been utilized to develop therapeutic interventions of various cancers, by introducing recombinant proteins to deplete methionine essential for the growth of cancer cells. In this review, we discuss the current understanding of enzymological properties, putative physiological roles, and therapeutic applications of MGL. © 2009 IUBMB IUBMB Life, 61(11): 1019,1028, 2009 [source] PDK1 and PKB/Akt: Ideal Targets for Development of New Strategies to Structure-Based Drug DesignIUBMB LIFE, Issue 3 2003Thomas Harris Abstract Growth factor binding events to receptor tyrosine kinases result in activation of phosphatidylinositol 3-kinase (PI3K), and activated PI3K generates the membrane-bound second messengers phosphatidylinositol 3,4-diphosphate [PI(3,4)P2] and PI(3,4,5)P3, which mediate membrane translocation of the phosphoinositide-dependent kinase-1 (PDK1) and protein kinase B (PKB, also known as Akt). In addition to the kinase domain, PDK1 and PKB contain a pleckstrin homology (PH) domain that binds to the second messenger, resulting in the phosphorylation and activation of PKB by PDK1. Recent evidence indicates that constitutive activation of PKB contributes to cancer progression by promoting proliferation and increased cell survival. The indicating of PDK1 and PKB as primary targets for discovery of anticancer drugs, together with the observations that both PDK1 and PKB contain small-molecule regulatory binding sites that may be in proximity to the kinase active site, make PDK1 and PKB ideal targets for the development of new strategies to structure-based drug design. While X-ray structures have been reported for the kinase domains of PDK1 and PKB, no suitable crystals have been obtained for either PDK1 or PKB with their PH domains intact. In this regard, a novel structure-based strategy is proposed, which utilizes segmental isotopic labeling of the PH domain in combination with site-directed spin labeling of the kinase active site. Then, long-range distance restraints between the 15N-labeled backbone amide groups of the PH domain and the unpaired electron of the active site spin label can be determined from magnetic resonance studies of the enhancement effect that the paramagnetic spin label has on the nuclear relaxation rates of the amide protons. The determination of the structure and position of the PH domain with respect to the known X-ray structure of the kinase active site could be useful in the rational design of potent and selective inhibitors of PDK1 and PKB by 'linking' the free energies of binding of substrate (ATP) analogs with analogs of the inositol polar head group of the phospholipid second messenger. The combined use of X-ray crystallography, segmental isotopic and spin labeling, and magnetic resonance studies can be further extended to the study of other dynamic multidomain proteins and targets for structure-based drug design. IUBMB Life, 55: 117-126, 2003 [source] Synthesis of 15N-, 13C-, and 2H-labeled methanandamide analogsJOURNAL OF LABELLED COMPOUNDS AND RADIOPHARMACEUTICALS, Issue 2 2003Fen-Mei Yao Abstract Four isotopically labeled, metabolically stable analogs of arachidony-lethanolamide (anandamide), an endogenous cannabinoid ligand, were synthesized via a five-step reaction sequence starting from arachidonic acid. These stable methanandamide derivatives will serve as probes for studying the conformational properties of anandamide in model membrane systems using solid-state NMR spectroscopy. The synthetic methods described can be applied to the preparations of other anandamide analogs with isotopic labeling in different positions of the molecule, which could be utilized in biochemical and pharmacological experiments. Copyright © 2002 John Wiley & Sons, Ltd. [source] Assignments and hydrogen bond sensitivities of UV resonance Raman bands of the C8-deuterated guanine ringJOURNAL OF RAMAN SPECTROSCOPY, Issue 9 2002Akira Toyama Isotope-edited Raman spectroscopy, a combination of site-selective isotopic labeling and Raman difference spectroscopy, is a useful method for studying the structure and interaction of individual nucleic acid residues in oligonucleotides. To obtain basic data for applying isotope-edited Raman spectroscopy to guanine residues, we studied the vibrational modes of UV resonance Raman bands of the C8-deuterated guanine ring by examining the wavenumber shifts upon seven isotopic substitutions (2- 13C, 2- 15N, 6- 18O, 7- 15N, 8- 13C, 9- 15N and 1,- 13C). The hydrogen bond sensitivities of the Raman bands were also investigated by comparing the Raman spectra recorded in several solvents of different hydrogen bonding properties. Some of the Raman bands were found to be markers of hydrogen bonding at specific donor or acceptor sites on the guanine ring. The Raman bands, which shift on C8-deuteration, remain in the difference spectrum between the unlabeled and C8-deuterated guanine rings. Among them, a negative peak around 1525 cm,1 and a strong positive/negative peak pair around 1485/1465 cm,1 serve as markers of hydrogen bonding at N7 and C6O, respectively. Another weak positive/negative peak pair around 1025/1040 cm,1 is sensitive to hydrogen bonding at the proton donor sites (N1,H and N2,H2). The applicability of the hydrogen bond markers has been tested by using a 22-mer oligonucleotide duplex containing eight guanine residues and its analog in which a single guanine residue is C8-deuterated. The difference spectrum shows that the hydrogen bonding state of the guanine residue at the labeled position is consistent with the Watson,Crick base pair structure of DNA. Isotope-edited Raman spectroscopy is a useful tool for studying the hydrogen bonding state of selected guanine residues in oligonucleotides. Copyright © 2002 John Wiley & Sons, Ltd. [source] Profiling human gut bacterial metabolism and its kinetics using [U- 13C]glucose and NMRNMR IN BIOMEDICINE, Issue 1 2010Albert A. de Graaf Abstract This study introduces a stable-isotope metabolic approach employing [U- 13C]glucose that, as a novelty, allows selective profiling of the human intestinal microbial metabolic products of carbohydrate food components, as well as the measurement of the kinetics of their formation pathways, in a single experiment. A well-established, validated in vitro model of human intestinal fermentation was inoculated with standardized gastrointestinal microbiota from volunteers. After culture stabilization, [U- 13C]glucose was added as an isotopically labeled metabolic precursor. System lumen and dialysate samples were taken at regular intervals. Metabolite concentrations and isotopic labeling were determined by NMR, GC, and enzymatic methods. The main microbial metabolites were lactate, acetate, butyrate, formate, ethanol, and glycerol. They together accounted for a 13C recovery rate as high as 91.2%. Using an NMR chemical shift prediction approach, several minor products that showed 13C incorporation were identified as organic acids, amino acids, and various alcohols. Using computer modeling of the 12C contents and 13C labeling kinetics, the metabolic fluxes in the gut microbial pathways for synthesis of lactate, formate, acetate, and butyrate were determined separately for glucose and unlabeled background substrates. This novel approach enables the study of the modulation of human intestinal function by single nutrients, providing a new rational basis for achieving control of the short-chain fatty acids profile by manipulating substrate and microbiota composition in a purposeful manner. Copyright © 2009 John Wiley & Sons, Ltd. [source] Hypophosphorylation of the architectural chromatin protein DEK in death-receptor-induced apoptosis revealed by the isotope coded protein label proteomic platformPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 21 2006Anja Tabbert Abstract During apoptosis nuclear morphology changes dramatically due to alterations of chromatin architecture and cleavage of structural nuclear proteins. To characterize early events in apoptotic nuclear dismantling we have performed a proteomic study of apoptotic nuclei. To this end we have combined a cell-free apoptosis system with a proteomic platform based on the differential isotopic labeling of primary amines with N -nicotinoyloxy-succinimide. We exploited the ability of this system to produce nuclei arrested at different stages of apoptosis to analyze proteome alterations which occur prior to or at a low level of caspase activation. We show that the majority of proteins affected at the onset of apoptosis are involved in chromatin architecture and RNA metabolism. Among them is DEK, an architectural chromatin protein which is linked to autoimmune disorders. The proteomic analysis points to the occurrence of multiple PTMs in early apoptotic nuclei. This is confirmed by showing that the level of phosphorylation of DEK is decreased following apoptosis induction. These results suggest the unexpected existence of an early crosstalk between cytoplasm and nucleus during apoptosis. They further establish a previously unrecognized link between DEK and cell death, which will prove useful in the elucidation of the physiological function of this protein. [source] Quantitative proteomic approaches for biomarker discoveryPROTEOMICS - CLINICAL APPLICATIONS, Issue 9 2007Zhiyuan Hu Abstract The rapid advances in proteomic technologies have made possible systematic analysis of hundreds to thousands of proteins in clinical samples with the promise of uncovering novel protein biomarkers for various disease conditions. We will discuss in this review article current MS and protein chip-based quantitative proteomic approaches and their application in biomarker discovery. The emphasis will be placed on new quantification strategies employing stable isotopic labeling coupled with MS/MS, and antibody-based protein chips and nanodevices. The strength and weakness of each technology are briefly highlighted. [source] | ||||||||||||||||