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PubMed2001

Synthesis of isotopically labeled D-[1'-13C]ribonucleoside phosphoramidites.

The preparation of fully protected labeled diisopropylamino-beta-cyanoethyl-[1'-13C]ribonucleoside phosphoramidites with regioisomeric purity is described. We demonstrated in this paper that a regioselective 2'-O-silylation, through a 3',5'-O-di-tert-butylsilanediyl protection, has been applied for the synthesis of [1'-13C]ribonucleoside phosphoramidite units. This method allowed us to obtain only the desired 2'-O-silyl-3'-O-phosphoramidites avoiding the undesired 3'-O-silyl-2'-O-phosphoramidite nucleosides isolated by standard procedures. This is a suitable procedure to RNA precursors with respect to the isotope-containing precursors.

Carbon Isotopes↗
PubMed1987

[ATP-phosphocreatine metabolism catalyzed by creatine kinase. Comparison of saturation transfer (NMR) and isotope labeling technics].

Unidirectional fluxes from ATP to phosphocreatine (PCr) catalyzed by MM-isoenzyme of creatine kinase (CK) were measured by using 31P-NMR saturation transfer technique and by means of radioactively labeled [gamma-32P]ATP. At 30-37 degrees C and pH 7.4 in a wide range of [PCr]/[creatine] ([PCr]/[Cr]) ratios (0.2 to 3.0) both of these methods gave similar results, thus showing that magnetization (saturation) transfer allows to determine fluxes close to real ones under "physiological" conditions. However, at [PCr]/[Cr] ratio higher than 5 ([ADP] less than 30 microM) or at decreased temperatures (7-15 degrees C, [PCr]/[Cr] approximately 1) fluxes determined by saturation transfer substantially exceeded those measured with the radioactive label. These data imply that under "physiological" conditions phosphoryl group transfer is actually rate-determining step of the CK reaction. On the contrary, at high [PCr]/[Cr] values or at low temperature the control step could be shifted from the phosphoryl group transfer or distributed among other steps of the reaction.

Adenosine Triphosphate↗
PubMed1976

Comparison of isotope labeling patterns of purines in three specific transfer RNAs.

Purine C-8 tritium-labeling rates have been measured at specific sites in Escherichia coli tRNAIle and tRNA2Tyr. The results are compared with those obtained for yeast tRNAPhe (preceding paper(Gamble et al., 1976)). The tRNAIle and tRNAPhe fall into the same general class of tRNA structures, while tRNA2Tyr is in a differint class; in particular, the latter is characterized by a large extra loop. In each of the three tRNAs the 3'-terminal A has the same labeling rate and, on a relative basis, appears to be the most rapidly labeled site. Bases in cloverleaf helical sections have markedly retarded labeling rates that collectively fall within an approximately threefold range of time constants. At some of the common purines, believed to be essential for the construction of a general system of tertiary interactions, exchange rates for yeast tRNAPhe are significantly different than those for the two Escherichia coli tRNAs. these differences may arise from variations among the tRNAs in the relative stabilities of specific tertiary interactions, or from other factors as well. In the case of tRNA2Tyr, labeling rates for bases in the large variable region are sufficiently retarded to suggest some structural organization for this part of the molecule. In addition, since exchange rates are similar for some of the bases common to Escherichia coli tRNAIle and tRNA2Tyr, it is likely that the large variable loop of tRNA2Tyr does not interact with or perturb these common sites. Finally, for all three tRNAs, structure formation (e.g., base pairing, base stacking) invariably decreases the labeling rate, even though the variety of base environments in the three-dimensional structures of these tRNAs might be expected to affect the acidity of C-8 and other chemical properties in diverse ways. Although these chemical effects no doubt bear influence, in these studies the dominant influence on exchange may be the effect of structure on the accessibility of solvent molecules, i.e. water.

Base Sequence↗
PubMed1999

Assignment of the L30-mRNA complex using selective isotopic labeling and RNA mutants.

The helix-loop-helix structure formed in the pre-mRNA and the mRNA of L30, a ribosomal protein from the yeast Saccharomyces cerevisiae, serves as an auto-regulatory binding site for the protein to suppress the L30 synthesis upon overproduction. Using a 33-nucleotide model RNA, the structures of the L30 binding site RNA in the presence and absence of the protein were investigated using nuclear magnetic resonance (NMR) spectroscopy. Homonuclear and(13)C/(15)N-based resonance assignments and spectral comparisons indicated that the purine-rich internal loop is dynamic in the free RNA but becomes ordered in the presence of L30 protein. Although the resonances in the loop region are sharper and more disperse in the bound RNA, their assignment was extremely challenging, due to spectral complexity and broadened resonances caused by local dynamics. Two strategies, namely selective(13)C/(15)N-labeling and NMR analyses of five complexes with RNA mutants, were used to overcome these difficulties. Only using these approaches could assignment of the internal loop resonances and identification of the unusual NOEs and nucleotide conformations within the internal loop be made. In the case of structural determination of the L30-mRNA complex, it was critical to be able to take advantage of the available biochemical information in order to complete the structure determination.

Base Sequence↗
PubMed2006

High resolution 1H detected 1H,13C correlation spectra in MAS solid-state NMR using deuterated proteins with selective 1H,2H isotopic labeling of methyl groups.

MAS solid-state NMR experiments applied to biological solids are still hampered by low sensitivity and resolution. In this work, we employ a deuteration scheme in which individual methyl groups are selectively protonated. This labeling scheme allows the acquisition of proton carbon correlation spectra with a resolution comparable to that in solution-state NMR experiments. We observe an increase in resolution by a factor of 10-15 compared to standard heteronuclear correlation experiments using PMLG for 1H,1H dipolar decoupling in the indirect dimension. At the same time, the full sensitivity of the proton-based experiment is retained. In comparison to the heteronuclear detected version of the experiment, a gain in sensitivity of a factor of approximately 4.7 is achieved.

Animals↗
PubMed1977

Isotope-labelled alpha-amino-isobutyric acid as an indicator in cytotoxicity tests.

The effect of rabbit antisera on the uptake and release of alpha-amino-isobutyric acid (AIBA) in LS- and P-388 cells was investigated. In the presence of homologous antiserum and complement, the uptake of AIBA was inhibited. In the absence of complement, no effect of antiserum was seen. Using prelabelled cells, the efflux of AIBA was greatly accelerated in the presence of antiserum and complement. The AIBA-uptake method was compared with the trypan blue exclusion test and the 51Cr release technique. The AIBA-uptake method was more sensitive in quantitative cytotoxic studies.

Aminoisobutyric Acids↗
PubMed1995

Application of a double isotopic labeling method to a study of the interaction of mitochondrially bound rat brain hexokinase with intramitochondrial compartments of ATP generated by oxidative phosphorylation.

gamma-Labeled ATP was produced by rat brain mitochondria utilizing [32P]Pi as substrate for oxidative phosphorylation. The 32P/14C ratio of Glc-6-P produced by the endogenous mitochondrially bound hexokinase (ATP:D-hexose 6-phosphotransferase, EC 2.7.1.1) using [U-14C]Glc as substrate was determined as a function of time after initiation of oxidative phosphorylation. This same ratio was determined for Glc-6-P formed by added yeast hexokinase using extramitochondrial ATP as substrate. The specific activity of ATP formed by oxidative phosphorylation was manipulated either by initiating the reaction with labeled Pi and subsequently adding excess unlabeled Pi or by initiating the reaction with unlabeled Pi and introducing the labeled substrate at a later time. The 32P/14C ratio of Glc-6-P formed by yeast hexokinase, reflecting the specific activity of ATP in the extramitochondrial space, was rapidly responsive to such manipulations, but the corresponding changes in the 32P/14C ratio of Glc-6-P produced by the endogenous hexokinase were markedly different. The results are consistent with the view that mitochondrially bound hexokinase does not utilize extramitochondrial ATP as substrate but rather is functionally coupled to a discrete intramitochondrial compartment of ATP produced by oxidative phosphorylation.

Adenosine Triphosphate↗
PubMed1989

Beta-lactamase-catalyzed aminolysis of depsipeptides: proof of the nonexistence of a specific D-phenylalanine/enzyme complex by double-label isotope trapping.

The steady-state kinetics of the Enterobacter cloacae P99 beta-lactamase-catalyzed aminolysis of the depsipeptide m-[[(phenylacetyl)glycyl]oxy]benzoic acid by D-phenylalanine were consistent with an ordered sequential mechanism with D-phenylalanine binding first [Pazhanisamy, S., Govardhan, C. P., & Pratt, R. F. (1989) Biochemistry (first of three papers in this issue)]. In terms of this mechanism, the kinetics data required that in 20 mM MOPS buffer, pH 7.5, the dissociation constant of the initially formed enzyme/D-phenylalanine complex be around 1.3 mM; at pH 9.0 in 0.1 M carbonate buffer, the complex should be somewhat more stable. Attempts to detect this complex in a binary mixture by spectroscopic methods (fluorescence, circular dichroic, and nuclear magnetic resonance spectra) failed. Kinetic methods were also unsuccessful--the presence of 20 mM D-phenylalanine did not appear to affect beta-lactamase activity nor inhibition of the enzyme by phenylmethanesulfonyl fluoride, phenylboronic acid, or (3-dansylamidophenyl)boronic acid. Equilibrium dialysis experiments appeared to indicate that the dissociation constant of any binary enzyme/D-phenylalanine complex must be somewhat higher than the kinetics allowed (greater than 2 mM). Since the kinetics also required that, at high depsipeptide concentrations, and again with the assumption of the ordered sequential mechanism, the reaction of the enzyme/D-phenylalanine complex to aminolysis products be faster than its reversion to enzyme and D-phenylalanine, a double-label isotope-trapping experiment was performed.(ABSTRACT TRUNCATED AT 250 WORDS)

Circular Dichroism↗
PubMed1997

A resonance Raman study of the C=C stretch modes in bovine and octopus visual pigments with isotopically labeled retinal chromophores.

Previous resonance Raman spectroscopic studies of bovine and octopus rhodopsin and bathorhodopsin in the C-C stretch fingerprint region have shown drastically different spectral patterns, which suggest different chromophore-protein interactions. We have extended our resonance Raman studies of bovine and octopus pigments to the C=C stretch region in order to reveal a more detailed picture about the difference in retinal-protein interactions between these two pigments. The C=C stretch motions of the protonated retinal Schiff base are strongly coupled to form highly delocalized ethylenic modes located in the 1500 to 1650 cm-1 spectral region. In order to decouple these vibrations, a series of 11,12-D2-labeled retinals, with additional 13C labeling at C8, C10, C11 and C14, respectively, are used to determine the difference of specific C=C stretch modes between bovine and octopus pigments. Our results show that the C9=C10 and C13=C14 stretch mode are about 20 cm-1 lower in the Raman spectrum of octopus bathorhodopsin than in bovine bathorhodopsin, while the other C=C stretch modes in these two bathorhodopsins are similar. In contrast, only the C9=C10 stretch mode in octopus rhodopsin is about 10 cm-1 lower than in bovine rhodopsin, while other C=C stretches are similar.

Animals↗
PubMed1987

Preparation and storage of isotopically labeled reduced nicotinamide adenine dinucleotide.

A method for obtaining highly purified NADH in a dry, solid, and stable form is described. The method involves improvements of the ion-exchange and reversed-phase chromatographic procedures of C. J. Newton and S. M. Faynor, and D. B. Northrop (Anal. Biochem., 1983, 132, 50-53). The necessary time to prepare pure NADH has been reduced to a few hours. The final product, obtained by drying the nucleotide from absolute ethanol, shows no detectable decomposition either during the drying procedure or during storage under nitrogen gas at -20 degrees C for several months. Using dry product prepared from fixed volumes of ethanolic solution, standardized solutions of known amounts of the highly purified and stored NADH can be obtained in a few seconds.

Chromatography, High Pressure Liquid↗
PubMedDate not supplied

Selected ion monitoring assay for the antidepressant mianserin in human plasma with stable isotope labeled analog as internal standard.

A quantitative gas chromatographic/mass spectrometric (GC/MS) assay was developed for the determination of Mianserin in human plasma. The assay utilizes selected ion monitoring in a GLC effluent, the molecular ion of Mianserin generated by electron impact ionization. Mianserin-d3, site specific, was synthesized and used as an internal standard. The assay can measure 5 ng/mL of drug with about 5% precision. The curve relating the amounts of drug added to control plasma versus the ion intensity ratio at m/e 264-267 is a straight line with a slope of 0.99 + 0.02 and zero intercept. The method was used for the analysis of drug in plasma of patients maintained on Mianserin therapy. Assay specificity was confirmed by complete identity of the mass spectrum of Mianserin in the biological extract with that of the authentic material.

Deuterium↗
PubMed2005

Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling.

In this study, S. cerevisiae crude membrane fractions were prepared using the acid-labile detergent RapiGest from cells grown under rich and minimal media conditions using 14N and 15N ammonium sulfate as the sole nitrogen source. Four independent MudPIT analyses of 1:1 mixtures of sample were prepared and analyzed via quantitative multidimensional protein identification technology on a two-dimensional ion trap mass spectrometer. Using the method described in this study, low-abundance integral membrane proteins with up to 14 transmembrane domains were identified and their protein expression determined when sufficient spectrum counting and ion chromatogram information was generated. We demonstrate that spectrum counting and mass spectrometry derived ion chromatograms strongly correlate for determining quantitative changes in protein expression. Spectrum counting proved more reproducible and has a wider dynamic range contributing to the deviation of the two quantitative approaches from a perfect positive correlation.

Amino Acid Sequence↗
PubMedDate not supplied

Formation of 1,N2- and N2,3-ethenoguanine from 2-halooxiranes: isotopic labeling studies and isolation of a hemiaminal derivative of N2-(2-oxoethyl)guanine.

Vinyl halides are oxidized to 2-halooxiranes, which rapidly rearrange to 2-haloacetaldehydes. Both of these species can react with DNA to generate a variety of adducts, including the potentially mutagenic etheno (epsilon) products. Evidence was provided through kinetic studies that the epsilon-Gua adducts are formed primarily from 2-haloxiranes; consistent with this view, epoxide hydrolase inhibited the formation of N2,3-epsilon-Gua from vinyl chloride but alcohol dehydrogenase did not. Assignments of the NMR shifts of the etheno protons of 1,N2- and N2,3-epsilon-Gua were made with the use of 15N labeling and nuclear Overhauser effects, in revision of the literature. The H-5 proton of N2,3-epsilon-Gua showed facile exchange in acid or base; the H-7 proton of 1,N2-epsilon-Gua was exchanged at neutral or basic pH but not in acid. Reaction of Br2CHCH2OH (labeled at C1 with 2H or 13C) with Guo yielded 1,N2-epsilon-Gua and N2,3-epsilon-Gua, presumably through the intermediacy of 2-bromooxirane. 1H NMR analysis indicated that the labeled carbon was attached to the original Guo N2 atom in both cases. When N2-(2-oxoethyl)Gua was generated from a diethyl acetal or from a glycol, the major product was the cyclic derivative 5,6,7,9-tetrahydro-7-hydroxy-9-oxoimidazo[1,2-alpha]purine. This compound was also formed in considerable yield from the reaction of 2-chlorooxirane with Guo, dGuo 5'-phosphate, or DNA and is relatively stable in the presence of acid or mild base. It does not appear to be readily dehydrated to yield the etheno adducts but may be of significance as a DNA adducts in its own right.

Alcohol Dehydrogenase↗
PubMed2002

Expression, purification, and isotope labeling of a gp120 V3 peptide and production of a Fab from a HIV-1 neutralizing antibody for NMR studies.

Most human immunodeficiency virus type 1 (HIV-1) neutralizing antibodies in infected individuals and in immunized animals are directed against the third variable loop (V3) of the envelope glycoprotein (gp120) of the virus. This loop plays a crucial role in phenotypic determination, cytopathicity (syncytium induction), and coreceptor usage of HIV-1. The human monoclonal antibody 447-52D was found to neutralize a broad spectrum of HIV-1 strains. In order to solve the solution structure of the V3MN peptide bound to the 447-52D Fab fragment by NMR, large quantities of labeled peptide and a protocol for the purification of the Fab fragment were needed. An expression plasmid coding for the 23-residue V3 peptide of the HIV-1MN strain (V3MN peptide, YNKRKRIHIGPGRAFYTTKNIIG) linked to a derivative of the RNA-binding domain of hnRNCP1 was constructed. The fusion protein attached to the V3 peptide prevents its degradation. Using this system, U-15N, U-13C,15N, and U-13C,15N, 50% 2H labeled fusion protein molecules were expressed in Escherichia coli grown on rich Celtone medium with yields of about 240 mg/liter. The V3MN peptide was released by CNBr cleavage and purified by RP-HPLC, giving final yields of 6-13 mg/liter. This expression system is generally applicable for biosynthesis of V3-related peptides and was also used to prepare the V3JR-FL. The 447-52D Fab fragment was obtained by a short enzymatic papain cleavage of the whole antibody. Preliminary NMR spectra demonstrate that full structural analysis of the V3MN complexed to the 447-52D Fab is feasible. This system enables studies of the same epitope bound to different HIV-1 neutralizing antibodies.

Amino Acid Sequence↗
PubMed2004

Differential and quantitative molecular analysis of ischemia complexity reduction by isotopic labeling of proteins using a neural embryonic stem cell model.

The analysis of rapid changes of protein expression in living systems in response to insults requires rigorous methods of complexity reduction. To control dynamic pattern of hundreds or even thousands of protein isoforms, we applied a novel method of differential molecular analysis to a cellular model which is suited to study ischemia. Neural derivatives of murine embryonic stem cells were exposed to chemical ischemia. The model was used to obtain starting material for a quantitative differential proteomics analysis. Fractionation of phosphoproteins from these samples and subsequent identification by mass spectrometry of differential proteins provide proof of principle of how novel molecular analytical tools provide new insight into the network of neuroprotective molecular events during specific situations of neuronal stress and related pharmaceutical intervention. Our results indicate a particular role of an isoform of the acidic calcium-independent phospholipase A2 in this type of insult.

Alkylation↗
PubMed1977

Quantification of lidocaine and several metabolites utilizing chemical-ionization mass spectrometry and stable isotope labeling.

Quantification of the suspected metabolites of lidocaine in humans was carried out using the direct insertion probe and chemicalionization mass spectrometry. Deuterated analogs of the metabolites of lidocaine were added to serial human plasma and urine samples and were used as internal standards following oral administration of 250 mg of lidocaine hydrochloride monohydrate to two male subjects and 202 mg of lidocaine free base to one male subject. The average results after analysis of the 0-24 hr urine samples, before beta-glucuronidase-sulfatase treatment, indicated the presence of seven of the possible metabolites in the following amounts (percent of administered dose based on the free base): lidocaine, 1.95; omega-ethylamino-2,6-dimethylacetanilide, 4.90; omega-amino-2,6-dimethylacetanilide, 0.88; m- and/or p-hydroxylidocaine, 0.73; m- and/or p-hydroxy-omega-ethylamino-2,6-dimethylacetanilide, 0.56; 2,6-dimethylaniline, 0.97; and 4-hydroxy-2,6-dimethylaniline, 63.5. Both N-ethyl- and N,N-diethylglycine were detected in human and Rhesus monkey urine, although quantification was not achieved.

Acetanilides↗
PubMed1978

Mass fragmentographic determination of methadyl acetate in urine using stable isotope labeled analog as internal standard.

A quantitative GLC-mass spectrometric assay was developed for the determination of methadyl acetate in urine. The assay utilized selective ion focusing to monitor, in a GLC effluent, the M--15 ion generated by electron-impact ionization of methadyl acetate. Methadyl acetate-d4 was used as an internal standard. The assay can measure 10 ng of drug/ml with about 6% precision. The curve relating the amounts of drug added to control urine versus the amounts experimentally found over a large concentration range is a straight line with a slope of 0.98 +/- 0.02 and a nearly zero intercept. Assay specificity was confirmed by complete identity of the mass spectrum of methadyl acetate in the biological extract with that of the authentic material. The method was used for the urinary analysis of methadyl acetate in a rabbit given a single intravenous dose. The animal excreted less than 1% of the intact drug with a half-life of approximately 15 hr. Consequently, the long-acting characteristic of methadyl acetate must be attributed to its metabolism into active metabolites.

Animals↗
PubMed1994

Quantitation of urinary 7-methyladenine by gas chromatography-mass spectrometry using isotopically labeled internal standards.

We have developed a procedure for isolating and quantifying 7-methyladenine from rat urine following the administration to the rat of methylating agents, such as dimethylnitrosamine. Urinary 7-methyladenine and its trideutero isomer, added as an internal standard, were precipitated with silver nitrate, the precipitate was extracted with HCl, and the extract was further purified by C18-Sep-Pak chromatography. The recovered 7-methyladenine was then derivatized with pentafluorobenzyl bromide at alkaline pH for analysis by gas chromatography-mass spectrometry, indicating a bis(pentafluorobenzyl) conjugate, m/z 509. The mass spectrum of this derivative shows a major fragmentation ion at m/z 328 (and 331 for the trideutero derivative) resulting from the loss of one pentafluorobenzyl group. Levels of urinary 7-methyladenine above 150 pg could be detected from the ratio of the gas chromatography peak areas for these ions, using selective-ion monitoring. The method was selective for the 7-methyl isomer. The procedures developed for the syntheses of deuterated and tritiated 7-methyladenine, which were required for these studies, are also described.

Adenine↗