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PubMed2006

Alternate-site isotopic labeling of ribonucleotides for NMR studies of ribose conformational dynamics in RNA.

Heteronuclear NMR spin relaxation studies of conformational dynamics are coming into increasing use to help understand the functions of ribozymes and other RNAs. Due to strong 13C-13C magnetic interactions within the ribose ring, however, these studies have thus far largely been limited to (13)C and (15)N resonances on the nucleotide base side chains. We report here the application of the alternate-site (13)C isotopic labeling scheme, pioneered by LeMaster for relaxation studies of amino acid side chains, to nucleic acid systems. We have used different strains of E. coli to prepare mononucleotides containing (13)C label in one of two patterns: Either C1' or C2' in addition to C4', termed (1'/2',4') labeling, or nearly complete labeling at the C2' and C4' sites only, termed (2',4') labeling. These patterns provide isolated 13C-1H spin systems on the labeled carbon atoms and thus allow spin relaxation studies without interference from 13C-13C scalar or dipolar coupling. Using relaxation studies of AMP dissolved in glycerol at varying temperature to produce systems with correlation times characteristic of different size RNAs, we demonstrate the removal of errors due to 13C-13C interaction in T (1) measurements of larger nucleic acids and in T (1rho) measurements in RNA molecules. By extending the applicability of spin relaxation measurements to backbone ribose groups, this technology should greatly improve the flexibility and completeness of NMR analyses of conformational dynamics in RNA.

Carbon Isotopes↗
PubMed2005

Quantification of acetylation at proximal lysine residues using isotopic labeling and tandem mass spectrometry.

With the emergence of the histone code as a key determinant in the regulation of gene expression, it has been important to develop tools that can not only identify the types and locations of myriad modifications, but also determine how the levels of these modifications change as a result of various processes in a cell. Mass spectrometry has become a method of choice for the investigation of post-translational modifications in histone proteins. Described in this article is a mass spectrometric method that is useful for direct quantification of levels of acetylation at lysines residues in close proximity to one another, as is the case for the amino terminal tail of histone H4. This method involves fragmentation of peptides into b and y ions that contain one or more sites of modification and isotopic labeling which ensures equivalent ionization and fragmentation.

Acetic Acid↗
PubMed2004

Microscale synthesis of isotopically labeled R-[6-xH]N5,N10-methylene-5,6,7,8-tetrahydrofolate as a cofactor for thymidylate synthase.

A one-pot synthesis of isotopically labeled R-[6-xH]N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2H4F) is presented, where x=1, 2, or 3 represents hydrogen, deuterium, or tritium, respectively. The current procedure offers high-yield, high-purity, and microscale-quantity synthesis. In this procedure, two enzymes were used simultaneously in the reaction mixture. The first was Thermoanaerobium brockii alcohol dehydrogenase, which stereospecifically catalyzed a hydride transfer from C-2-labeled isopropanol to the re face of oxidized nicotinamide adenine dinucleotide phosphate to form R-[4-xH]-labeled reduced nicotinamide adenine dinucleotide phosphate. The second enzyme, Escherichia coli dihydrofolate reductase, used the xH to reduce 7,8-dihydrofolate (H2F) to form S-[6-xH]5,6,7,8-tetrahydrofolate (S-[6-xH]H4F). The enzymatic reactions were followed by chemical trapping of S-[6-xH]H4F with formaldehyde to form the final product. Product purification was carried out in a single step by reverse phase high-pressure liquid chromatography separation followed by lyophilization. Two analytical methods were developed to follow the reaction progress. Finally, the utility of the labeled cofactor in mechanistic studies of thymidylate synthase is demonstrated by measuring the tritium kinetic isotope effect on the enzyme's second order rate constant.

Chromatography, High Pressure Liquid↗
PubMed2006

Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.

miRNAs are small noncoding RNAs that regulate gene expression. We have used stable isotope labeling by amino acids in cell culture (SILAC) to investigate the effect of miRNA-1 on the HeLa cell proteome. Expression of 12 out of 504 investigated proteins was repressed by miRNA-1 transfection. This repressed set of genes significantly overlaps with miRNA-1 regulated genes that have been identified with DNA array technology and are predicted by computational methods. Moreover, we find that the 3'-untranslated region for the repressed set are enriched in miRNA-1 complementary sites. Our findings demonstrate that SILAC can be used for miRNA target identification and that one highly expressed miRNA can regulate the levels of many different proteins.

3' Untranslated Regions↗
PubMed1984

Syntheses with isotopically labelled carbon. Methyl iodide, formaldehyde and cyanide.

Many of the uniquely labelled synthetic precursors currently employed in the design of sophisticated radiolabelled compounds have their origins in the field of hot atom chemistry. Particularly, the development during the past few years of automated, on-line synthetic procedures which combine the nuclear reaction, hot atom and classical chemistry, and rapid purification methods has allowed the incorporation of useful radionuclides into suitable compounds of chemical and biochemical interest. The application of isotopically labelled methyl iodide, formaldehyde, and cyanide anion as synthetic intermediates in research involving human physiology and nuclear medicine, as well as their contributions to other scientific methodology, is reviewed.

Amines↗
PubMed2006

An isotopically labeled internal standard liquid chromatography-tandem mass spectrometry method for determination of ephedrine alkaloids and synephrine in dietary supplements.

We report a simplified analytical procedure for determination of ephedrine alkaloids and synephrine in dietary supplements. Cleanup by simple filtration, when combined with tandem mass spectrometry (MS/MS) detection, provided results comparable to our published method with solid phase extraction (SPE) cleanup and single-stage MS detection with in-source fragmentation. We also compared three mass spectrometric experimental configurations: electrospray (ESI) and atmospheric pressure chemical ionization (APCI) with MS/MS and APCI-MS with fragmentation provided by increasing cone voltage. Because these methods used one isotopically labeled internal standard to determine several different analytes, quantitation errors may arise from susceptibility to ionization suppression caused by the matrix. We therefore compared the results obtained by ESI and APCI ionization.

Alkaloids↗
PubMed2002

Impact of four (13)C-proline isotope labels on the infrared spectra of ribonuclease T1.

Ribonuclease T1 was biosynthesized, with all four prolines (13)C-labeled in the peptide C[double bond]O bond, using a proline auxotrophic yeast strain of Saccharomyces cerevisiae. The (13)C- and (12)C-proline isotopomers of ribonuclease T1 were investigated by infrared spectroscopy in the thermally unfolded and natively folded state at 80 and 20 degrees C, respectively. In the thermally unfolded state, both proteins established almost indistinguishable spectral features in the secondary structure sensitive amide I region. In contrast, the spectra measured at 20 degrees C revealed substantial qualitative and quantitative differences, though parallel analysis by circular dichroism suggested identical native folds for both isotopomers. Major spectral differences in the infrared spectra were detected at 1626 and 1679 cm(-1), which are diagnostic marker bands for antiparallel beta-sheets in ribonuclease T1 and at 1645 cm(-1), a region that is characteristic for the infrared absorption of irregular structures. Starting with the known three-dimensional structure of ribonuclease T1, the observed effects of the isotope labeling are discussed on the basis of transition dipole coupling between the (12)C[double bond]O and (13)C[double bond]O groups. The experimental results were confirmed by transition dipole coupling calculations of the amide I manifold of the labeled and unlabeled variant.

Aspergillus oryzae↗
PubMed1980

Study of theophylline metabolism in premature human newborns using stable isotope labelling.

A new metabolic pathway of theophylline has been investigated in premature human newborns using the ion cluster technique of stable isotope labelling combined with gas chromatography mass spectrometry. Labelled caffeine, paraxanthine and theobromine have been found in plasma and urine of two preterm newborns receiving [1,3-15N], [2-13C] theophylline for the treatment of primitive apneas. Theophylline is converted to caffeine by N-7 methylation. In adults, the inverse process exists wherein caffeine is demethylated to give theophylline.

Biotransformation↗
PubMedDate not supplied

Identification of some human urinary metabolites of orally administered potassium canrenoate by stable isotope-labeling techniques.

A single oral dose (200 mg) of an equimolar mixture of potassium canrenoate and its 20,20,21,21-tetradeutero analogue was administered to three healthy men. The steroids in urine collected for 24 hr after dosage were isolated on XAD-2 resin, and purified and fractionated into groups by lipophilic gel chromatography before and after hydrolysis of conjugates. GC/MS analysis of these fractions allowed the detection and identification of canrenone, canrenoic acid and its ester glucuronide, 3 beta-hydroxy-3-deoxocanrenone, 3beta-hydroxy-4,5alpha-dihydro-3-deoxocanrenone and a 3epsilon-hydroxy-4,5,6,7-tetrahydro-3-deoxocanrenone. In addition a number of di- and trihydroxy compounds formed by reduction and hydroxylation were partially identified from their E1 and C1 mass spectra. The results provide information on the metabolism of oral potassium canrenoate in man, and demonstrate the utility of combining stable isotope labeling, lipophilic gel chromatography, and GC/MS in studies of steroidal spirolactones.

Administration, Oral↗
PubMed2005

Expression clustering reveals detailed co-expression patterns of functionally related proteins during B cell differentiation: a proteomic study using a combination of one-dimensional gel electrophoresis, LC-MS/MS, and stable isotope labeling by amino acids in cell culture (SILAC).

B cells play an essential role in the immune response. Upon activation they may differentiate into plasma cells that secrete specific antibodies against potentially pathogenic non-self antigens. To identify the cellular proteins that are important for efficient production of these antibodies we set out to study the B cell differentiation process at the proteome level. We performed an in-depth proteomic study to quantify dynamic relative protein expression patterns of several hundreds of proteins at five consecutive time points after lipopolysaccharide-induced activation of B lymphocytes. The proteome analysis was performed using a combination of stable isotope labeling using [13C6]leucine added to the murine B cell cultures, one-dimensional gel electrophoresis, and LC-MS/MS. In this study we identified 1,001 B cell proteins. We were able to quantify the expression levels of a quarter of all identified proteins (i.e. 234) at each of the five different time points. Nearly all proteins revealed changes in expression patterns. The quantitative dataset was further analyzed using an unbiased clustering method. Based on their expression profiles, we grouped the entire set of 234 quantified proteins into a limited number of 12 distinct clusters. Functionally related proteins showed a strong correlation in their temporal expression profiles. The quality of the quantitative data allowed us to even identify subclusters within functionally related classes of proteins such as in the endoplasmic reticulum proteins that are involved in antibody production.

Amino Acids↗
PubMed2004

Efficient production of isotopically labeled proteins by cell-free synthesis: a practical protocol.

We provide detailed descriptions of our refined protocols for the cell-free production of labeled protein samples for NMR spectroscopy. These methods are efficient and overcome two critical problems associated with the use of conventional Escherichia coli extract systems. Endogenous amino acids normally present in E. coli S30 extracts dilute the added labeled amino acids and degrade the quality of NMR spectra of the target protein. This problem was solved by altering the protocol used in preparing the S30 extract so as to minimize the content of endogenous amino acids. The second problem encountered in conventional E. coli cell-free protein production is non-uniformity in the N-terminus of the target protein, which can complicate the NMR spectra. This problem was solved by adding a DNA sequence to the construct that codes for a cleavable N-terminal peptide tag. Addition of the tag serves to increase the yield of the protein as well as to ensure a homogeneous protein product following tag cleavage. We illustrate the method by describing its stepwise application to the production of calmodulin samples with different stable isotope labeling patterns for NMR analysis.

Animals↗
PubMedDate not supplied

Site-directed isotope labeling and FTIR spectroscopy: assignment of tyrosine bands in the bR-->M difference spectrum of bacteriorhodopsin.

Fourier transform infrared difference spectroscopy has been used extensively to probe structural changes in bacteriorthodopsin and other retinal proteins. However, the absence of a general method to assign bands to individual chemical groups in a protein has limited the application of this technique. While site-directed mutagenesis has been successful in special cases for such assignments, in general, this approach induces perturbations in the structure and function of the protein, thereby preventing unambiguous band assignments. A new approach has recently been reported (Sonar et al., Nature Struct. Biol. 1 (1994) 512-517) which involves cell-free expression of bacteriorhodopsin and site-directed isotope labeling (SDIL). We have now used this method to re-examine bands assigned in the bR-->M difference spectrum to tyrosine residues. Our results show that out of 11 tyrosines in bR, only Tyr 185 is structurally active. This work further demonstrates the power of SDIL and FTIR to probe conformational changes at the level of individual amino acid residues in proteins.

Amino Acid Sequence↗
PubMed1998

Ion trap mass spectrometry for kinetic studies of stable isotope labeled vitamin A at low enrichments.

The role of beta-carotene in chemoprevention of cancers and other chronic diseases generated controversy when subpopulations taking beta-carotene supplements showed increased mortality in clinical trials. Determination of the dynamics of beta-carotene in individual human subjects has emerged as a high priority. Stable isotope labeled beta-carotene tracers can be employed to determine rates of conversion to retinol (vitamin A), but tracer doses must be small to minimize perturbation of endogenous retinoid and carotenoid pools. In such cases, ratios of labeled tracer/endogenous retinol are often low, and quantitative analysis at enrichments of < 1 mol% are unreliable owing to ion-molecule reactions that generate ions at the same mass as the labeled tracer even when no tracer is present. The current study demonstrates improved gas chromatography/mass spectrometry quantification of retinol-d4 and unlabeled retinol, as their tert-butyldimethylsilyl ethers, at low enrichments using an ion trap mass spectrometer operated in selected ion storage mode. Electron ionization of analyte takes place in the ion trap using conditions that eject ions outside the range m/z 390-420, and molecular ions at m/z 400 and 404 from retinol and retinol-d4 are quantified. Using this approach, unlabeled retinol yields a signal close to values calculated from natural isotopic abundances (approximately 0.13%), whereas several quadrupole instruments operated using selected ion monitoring yielded 2-5 times greater signal when no labeled retinol was present.

Adult↗
PubMed2004

High-throughput construction method for expression vector of peptides for NMR study suited for isotopic labeling.

Fusion protein constructs for labeled peptides were generated with the 114 amino acid thioredoxin (TRX), coupled with the incorporation of a histidine tag for affinity purification. Two tandem AhdI sites were designed in the multiple cloning site of the fusion vector according to our novel unidirectional TA cloning methodology named PRESAT-vector, allowing one-step background-free cloning of DNA fragments. Constructs were designed to incorporate the four residue sequence Ile-Asp-Gly-Arg to generate pure peptides following Factor Xa cleavage of the fusion protein. The system is efficient and cost-effective for isotopic labeling of peptides for heteronuclear NMR studies. Seven peptides of varying length, including pituitary adenylate cyclase activating polypeptide (PACAP), vasoactive intestinal peptide (VIP) and ubiquitin interacting motif (UIM), were expressed using this TRX fusion system to give soluble fusion protein constructs in all cases. Three alternative methods for the preparation of DNA fragments were applied depending on the length of the peptides, such as polymerase chain reaction, chemical synthesis or a 'semi-synthetic method', which is a combination of chemical synthesis and enzymatic extension. The ability easily to construct, express and purify recombinant peptides in a high-throughput manner will be of enormous benefit in areas of biomedical research and drug discovery.

Amino Acid Sequence↗
PubMed1998

Overexpression, isotopic labeling, and spectral characterization of Enterobacter cloacae nitroreductase.

Bacterial nitroreductases have generated much interest recently due to their central roles in both nitroaromatic bioremediation and nitroaromatic toxicity, mutagenicity, and carcinogenicity. Enterobacter cloacae nitroreductase (NR) has been subcloned into the pET overexpression system and purified to homogeneity via a four-step procedure resulting in a final yield of 65.7 mg per liter. Overexpression in minimal media containing 15NH4Cl as the sole source of nitrogen yielded 37.6 mg per liter of homogenous NR containing > 99 atom % 15N. A series of melting curves generated under a variety of solvent conditions established the optimal conditions for NR stability as pH 7.5, low ionic strength phosphate buffer. A two-dimensional 1H-15N heteronuclear single quantum coherence nuclear magnetic resonance spectrum demonstrates this enzyme to be amenable to study by high-resolution multidimensional NMR in combination with amino-acid-specific isotopic labeling. Optical spectra of the purified enzyme suggest that the noncovalently bound flavin mononucleotide cofactor binds in a hydrophobic environment and is in the neutral and anionic protonation states in the oxidized and two-electron reduced oxidation states, respectively. NR exhibits a novel visible region circular dichroism spectrum which has a small distinct negative band at 366 nm and a large positive ellipticity at 454 nm with a shoulder centered at 480 nm.

Base Sequence↗
PubMed2003

Location of structural transitions in an isotopically labeled lung surfactant SP-B peptide by IRRAS.

Pulmonary surfactant, a lipid/protein complex that lines the air/water interface in the mammalian lung, functions to reduce the work of breathing. Surfactant protein B (SP-B) is a small, hydrophobic protein that is an essential component of this mixture. Structure-function relationships of SP-B are currently under investigation as the protein and its peptide analogs are being incorporated into surfactant replacement therapies. Knowledge of the structure of SP-B and its related peptides in bulk and monolayer phases will facilitate the design of later generation therapeutic agents. Prior infrared reflection-absorption spectroscopic studies reported notable, reversible surface pressure-induced antiparallel beta-sheet formation in a synthetic peptide derived from human SP-B, residues 9-36 (SP-B(9-36)). In the current work, infrared reflection-absorption spectroscopy is applied in conjunction with isotopic labeling to detect the site and pressure dependence of the conformational change. SP-B(9-36), synthesized with (13)C=O-labeled Ala residues in positions 26, 28, 30, and 32, shifted the beta-sheet marker band to approximately 1600 cm(-1) and thus immediately identified this structural element within the labeled region. Surface pressure-induced alterations in the relative intensities of Amide I band constituents are interpreted using a semiempirical transition dipole coupling model. In addition, electron micrographs reveal the formation of tubular myelin structures from in vitro preparations using SP-B(9-36) in place of porcine SP-B indicating that the peptide has the potential to mimic this property of the native protein.

Amino Acid Sequence↗
PubMed1976

Carbohydrate moieties of procollagen: incorporation of isotopically labeled mannose and glucosamine into propeptides of procollagen secreted by matrix-free chick embryo tendon cells.

Cells obtained from chick embryo tendons incorporate isotopically labeled glucosamine and mannose into the pro-alpha1 and pro-alpha2 chains of procollagen as judged by sodium dodecyl sulfate-gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The label was further localized to the propeptides of pro-alpha1 and pro-alpha2 by its chromatographic behavior after digestion with bacterial collagenase or alpha-chymotrypsin. Carbohydrate analysis of isolated pro-alpha chains showed the presence of labeled galactosamine in addition to mannose and glucosamine. Resistance to mild alkaline hydrolysis suggested that greater than 90% of the oligosaccharide units are not linked to the propeptide backbone by either serine or threonine.

Animals↗