NMR-based metabolomics of mammalian cell and tissue cultures.


:NMR spectroscopy was used to evaluate growth media and the cellular metabolome in two systems of interest to biomedical research. The first of these was a Chinese hamster ovary cell line engineered to express a recombinant protein. Here, NMR spectroscopy and a quantum mechanical total line shape analysis were utilized to quantify 30 metabolites such as amino acids, Krebs cycle intermediates, activated sugars, cofactors, and others in both media and cell extracts. The impact of bioreactor scale and addition of anti-apoptotic agents to the media on the extracellular and intracellular metabolome indicated changes in metabolic pathways of energy utilization. These results shed light into culture parameters that can be manipulated to optimize growth and protein production. Second, metabolomic analysis was performed on the superfusion media in a common model used for drug metabolism and toxicology studies, in vitro liver slices. In this study, it is demonstrated that two of the 48 standard media components, choline and histidine are depleted at a faster rate than many other nutrients. Augmenting the starting media with extra choline and histidine improves the long-term liver slice viability as measured by higher tissues levels of lactate dehydrogenase (LDH), glutathione and ATP, as well as lower LDH levels in the media at time points out to 94 h after initiation of incubation. In both models, media components and cellular metabolites are measured over time and correlated with currently accepted endpoint measures.


J Biomol NMR


Aranibar N,Borys M,Mackin NA,Ly V,Abu-Absi N,Abu-Absi S,Niemitz M,Schilling B,Li ZJ,Brock B,Russell RJ 2nd,Tymiak A,Reily MD




Has Abstract


2011-04-01 00:00:00












  • 1H NMR studies of deuterated ribonuclease HI selectively labeled with protonated amino acids.

    abstract::Two-dimensional (2D) 1H NMR experiments using deuterium labeling have been carried out to investigate the solution of ribonuclease HI (RNase HI) from Escherichia coli (E. coli), which consists of 155 amino acids. To simplify the 1H NMR spectra, two fully deuterated enzymes bearing several protonated amino acids were p...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Oda Y,Nakamura H,Yamazaki T,Nagayama K,Yoshida M,Kanaya S,Ikehara M

    更新日期:1992-03-01 00:00:00

  • Correlated motions of successive amide N-H bonds in proteins.

    abstract::New nuclear magnetic resonance (NMR) methods are described for the measurement of cross-correlation rates of zero- and double-quantum coherences involving two nitrogen nuclei belonging to successive amino acids in proteins and peptides. Rates due to the concerted fluctuations of two NH(N) dipole-dipole interactions an...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Pelupessy P,Ravindranathan S,Bodenhausen G

    更新日期:2003-04-01 00:00:00

  • Insight into human insulin aggregation revisited using NMR derived translational diffusion parameters.

    abstract::The NMR derived translational diffusion coefficients were performed on unlabeled and uniformly labeled 13C,15N human insulin in water, both in neat, with zinc ions only, and in pharmaceutical formulation, containing only m-cresol as phenolic ligand, glycerol and zinc ions. The results show the dominant role of the pH ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Sitkowski J,Bocian W,Bednarek E,Urbańczyk M,Koźmiński W,Borowicz P,Płucienniczak G,Łukasiewicz N,Sokołowska I,Kozerski L

    更新日期:2018-06-01 00:00:00

  • Optimization of 1H decoupling eliminates sideband artifacts in 3D TROSY-based triple resonance experiments.

    abstract::TROSY-based triple resonance experiments are essential for protein backbone assignment of large biomolecular systems by solution NMR spectroscopy. In a survey of the current Bruker pulse sequence library for TROSY-based experiments we found that several sequences were plagued by artifacts that affect spectral quality ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Xia Y,Rossi P,Tonelli M,Huang C,Kalodimos CG,Veglia G

    更新日期:2017-09-01 00:00:00

  • Backbone assignments and conformational dynamics in the S. typhimurium tryptophan synthase α-subunit from solution-state NMR.

    abstract::Backbone assignments for the isolated α-subunit of Salmonella typhimurium tryptophan synthase (TS) are reported based on triple resonance solution-state NMR experiments on a uniformly 2H,13C,15N-labeled sample. From the backbone chemical shifts, secondary structure and random coil index order parameters (RCI-S2) are p...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Sakhrani VV,Hilario E,Caulkins BG,Hatcher-Skeers ME,Fan L,Dunn MF,Mueller LJ

    更新日期:2020-07-01 00:00:00

  • Interaction of the tail with the catalytic region of a class II E2 conjugating enzyme.

    abstract::Ubiquitination plays an important role in many biological processes, including DNA repair, cell cycle regulation, and protein degradation. In the latter pathway the ubiquitin-conjugating enzymes or E2 enzymes are important proteins forming a key E2-ubiquitin thiolester prior to substrate labelling. While the structure...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Merkley N,Shaw GS

    更新日期:2003-06-01 00:00:00

  • Determination of molecular alignment tensors without backbone resonance assignment: Aid to rapid analysis of protein-protein interactions.

    abstract::Based on high-resolution structures of the free molecules accurate determination of structures of protein complexes by NMR spectroscopy is possible using residual dipolar couplings. In order, however, to be able to apply these methods, protein backbone resonances have to be assigned first. This NMR assignment process ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Zweckstetter M

    更新日期:2003-09-01 00:00:00

  • Trans-hydrogen bond deuterium isotope effects of A:T base pairs in DNA.

    abstract::The chemical shifts of (13)C2 of adenosine residues of DNA were observed to experience a through-space or trans-hydrogen bond isotope effect as a result of deuterium substitution at the imino hydrogen site of base-paired thymidine residues. NMR measurements of several self-complementary DNA duplexes at natural abundan...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Vakonakis I,LiWang AC

    更新日期:2004-05-01 00:00:00

  • NMR structure determination of proteins supplemented by quantum chemical calculations: detailed structure of the Ca2+ sites in the EGF34 fragment of protein S.

    abstract::We present and test two methods to use quantum chemical calculations to improve standard protein structure refinement by molecular dynamics simulations restrained to experimental NMR data. In the first, we replace the molecular mechanics force field (employed in standard refinement to supplement experimental data) for...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Hsiao YW,Drakenberg T,Ryde U

    更新日期:2005-02-01 00:00:00

  • Pulse EPR-enabled interpretation of scarce pseudocontact shifts induced by lanthanide binding tags.

    abstract::Pseudocontact shifts (PCS) induced by tags loaded with paramagnetic lanthanide ions provide powerful long-range structure information, provided the location of the metal ion relative to the target protein is known. Usually, the metal position is determined by fitting the magnetic susceptibility anisotropy (Δχ) tensor ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Abdelkader EH,Yao X,Feintuch A,Adams LA,Aurelio L,Graham B,Goldfarb D,Otting G

    更新日期:2016-01-01 00:00:00

  • Specific binding of a naturally occurring amyloidogenic fragment of Streptococcus mutans adhesin P1 to intact P1 on the cell surface characterized by solid state NMR spectroscopy.

    abstract::The P1 adhesin (aka Antigen I/II or PAc) of the cariogenic bacterium Streptococcus mutans is a cell surface-localized protein involved in sucrose-independent adhesion and colonization of the tooth surface. The immunoreactive and adhesive properties of S. mutans suggest an unusual functional quaternary ultrastructure c...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Tang W,Bhatt A,Smith AN,Crowley PJ,Brady LJ,Long JR

    更新日期:2016-02-01 00:00:00

  • Measurement of 15N-13C J couplings in staphylococcal nuclease.

    abstract::15N-C alpha and 15N-C' J couplings were measured for the backbone of staphylococcal nuclease, uniformly enriched with 15N and 13C. It is found that the 1JC'N coupling is similar for beta-sheet, J = 14.8 +/- 0.5 and for alpha-helix, J = 14.8 +/- 0.4 but tends to be larger for the unstructured N- and C-terminal ends of ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Delaglio F,Torchia DA,Bax A

    更新日期:1991-11-01 00:00:00

  • NMRlib: user-friendly pulse sequence tools for Bruker NMR spectrometers.

    abstract::We present NMRlib, a suite of jython-based tools designed for Bruker spectrometers (TopSpin versions 3.2-4.0) that allow easy setup, management, and exchange of NMR experiments. A NMR experiment can be set up and executed in a few clicks by navigating through the NMRlib GUI tree structure, without any further paramete...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Favier A,Brutscher B

    更新日期:2019-05-01 00:00:00

  • Resolving complex mixtures: trilinear diffusion data.

    abstract::Complex mixtures are at the heart of biology, and biomacromolecules almost always exhibit their function in a mixture, e.g., the mode of action for a spider venom is typically dependent on a cocktail of compounds, not just the protein. Information about diseases is encoded in body fluids such as urine and plasma in th...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Björnerås J,Botana A,Morris GA,Nilsson M

    更新日期:2014-04-01 00:00:00

  • Automated 1H and 13C chemical shift prediction using the BioMagResBank.

    abstract::A computer program has been developed to accurately and automatically predict the 1H and 13C chemical shifts of unassigned proteins on the basis of sequence homology. The program (called SHIFTY) uses standard sequence alignment techniques to compare the sequence of an unassigned protein against the BioMagResBank--a pu...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Wishart DS,Watson MS,Boyko RF,Sykes BD

    更新日期:1997-12-01 00:00:00

  • Feasibility of trifluoromethyl TROSY NMR at high magnetic fields.

    abstract::Insights into the structure and dynamics of large biological systems has been greatly improved by two concurrent NMR approaches: the application of transverse relaxation-optimized spectroscopy (TROSY) techniques in multi-dimensional NMR, especially the methyl-TROSY, and the resurgence of 19F NMR using trifluoromethyl ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Klein BA,Sykes BD

    更新日期:2019-11-01 00:00:00

  • Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm.

    abstract::We present a computational method for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional strategies. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273-6279 (1982)), types of amino acids are labeled with (1...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Hefke F,Bagaria A,Reckel S,Ullrich SJ,Dötsch V,Glaubitz C,Güntert P

    更新日期:2011-02-01 00:00:00

  • Efficient DNP NMR of membrane proteins: sample preparation protocols, sensitivity, and radical location.

    abstract::Although dynamic nuclear polarization (DNP) has dramatically enhanced solid-state NMR spectral sensitivities of many synthetic materials and some biological macromolecules, recent studies of membrane-protein DNP using exogenously doped paramagnetic radicals as polarizing agents have reported varied and sometimes surpr...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Liao SY,Lee M,Wang T,Sergeyev IV,Hong M

    更新日期:2016-03-01 00:00:00

  • The secondary structure of a pyrimidine-guanine sequence-specific ribonuclease possessing cytotoxic activity from the oocytes of Rana catesbeiana.

    abstract::RC-RNase is a pyrimidine-guanine sequence-specific ribonuclease and a sialic-acid-binding lectin purified from Rana catesbeiana (bullfrog) oocytes. This 111-amino acid protein exhibits cytotoxicity toward several tumor cell lines. In this paper we report the assignments of proton NMR resonances and the identification ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Chen C,Hom K,Huang RF,Chou PJ,Liao YD,Huang T

    更新日期:1996-10-01 00:00:00

  • Perspective: revisiting the field dependence of TROSY sensitivity.

    abstract::The discovery of the TROSY effect (Pervushin et al. in Proc Natl Acad Sci USA 94:12366-12371, 1997) for reducing transverse relaxation and line sharpening through selecting pathways in which dipole-dipole and CSA Hamiltonians partially cancel each other had a tremendous impact on solution NMR studies of macromolecules...

    journal_title:Journal of biomolecular NMR

    pub_type: 信件


    authors: Takeuchi K,Arthanari H,Wagner G

    更新日期:2016-12-01 00:00:00

  • A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers.

    abstract::We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly (15)N,(13)C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Hu KN,Qiang W,Tycko R

    更新日期:2011-07-01 00:00:00

  • Validation of a new restraint docking method for solution structure determinations of protein-ligand complexes.

    abstract::A new method is proposed for docking ligands into proteins in cases where an NMR-determined solution structure of a related complex is available. The method uses a set of experimentally determined values for protein-ligand, ligand-ligand, and protein-protein restraints for residues in or near to the binding site, comb...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Polshakov VI,Morgan WD,Birdsall B,Feeney J

    更新日期:1999-06-01 00:00:00

  • Conformational analysis of alpha-D-Fuc-(1-->4)-beta-D-GlcNAc-OMe. One-dimensional transient NOE experiments and Metropolis Monte Carlo simulations.

    abstract::One-dimensional transient NOE build-up curves were measured for the synthetic disaccharide alpha-D-Fuc-(1-->4)-beta-D-GlcNAc 1 utilizing Gaussian shaped pulses. Simulated build-up curves from Metropolis Monte Carlo simulations were compared to the experimental data. Disaccharide 1 is structurally related to methyl bet...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Weimar T,Meyer B,Peters T

    更新日期:1993-07-01 00:00:00

  • Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins.

    abstract::It has been demonstrated that protein folds can be determined using appropriate computational protocols with NMR chemical shifts as the sole source of experimental restraints. While such approaches are very promising they still suffer from low convergence resulting in long computation times to achieve accurate results...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Rasia RM,Lescop E,Palatnik JF,Boisbouvier J,Brutscher B

    更新日期:2011-11-01 00:00:00

  • A chemical approach for site-specific identification of NMR signals from protein side-chain NH₃⁺ groups forming intermolecular ion pairs in protein-nucleic acid complexes.

    abstract::Protein-nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein-DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH3 (+) g...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Anderson KM,Nguyen D,Esadze A,Zandrashvili L,Gorenstein DG,Iwahara J

    更新日期:2015-05-01 00:00:00

  • Improved NMR spectra of a protein-DNA complex through rational mutagenesis and the application of a sensitivity optimized isotope-filtered NOESY experiment.

    abstract::The NMR spectra of the complex between the DNA-binding domain of the Dead ringer protein (DRI-DBD, Gly262-Gly398) and its DNA binding site (DRI-DBD:DNA, 26 kDa) have been optimized by biochemical and spectroscopic means. First, we demonstrate the utility of a modified 2D [F1,F2] 13C-filtered NOESY experiment that empl...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Iwahara J,Wojciak JM,Clubb RT

    更新日期:2001-03-01 00:00:00

  • Nucleotide-type chemical shift assignment of the encapsulated 40 kbp dsDNA in intact bacteriophage T7 by MAS solid-state NMR.

    abstract::The icosahedral bacteriophage T7 is a 50 MDa double-stranded DNA (dsDNA) virus that infects Escherichia coli. Although there is substantial information on the physical and morphological properties of T7, structural information, based mostly on Raman spectroscopy and cryo-electron microscopy, is limited. Here, we apply...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Abramov G,Goldbourt A

    更新日期:2014-08-01 00:00:00

  • 1H and 13C NMR assignments for the glycans in glycoproteins by using 2H/13C-labeled glucose as a metabolic precursor.

    abstract::In order to understand the role of the glycans in glycoproteins in solution, structural information obtained by NMR spectroscopy is obviously required. However, the assignment of the NMR signals from the glycans in larger glycoproteins is still difficult, mainly due to the lack of appropriate methods for the assignmen...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Yamaguchi Y,Takizawa T,Kato K,Arata Y,Shimada I

    更新日期:2000-12-01 00:00:00

  • A solubility-enhancement tag (SET) for NMR studies of poorly behaving proteins.

    abstract::Protein-fusion constructs have been used with great success for enhancing expression of soluble recombinant protein and as tags for affinity purification. Unfortunately the most popular tags, such as GST and MBP, are large, which hinders direct NMR studies of the fusion proteins. Cleavage of the fusion proteins often ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Zhou P,Lugovskoy AA,Wagner G

    更新日期:2001-05-01 00:00:00

  • Improved three-dimensional 1H-13C-1H correlation spectroscopy of a 13C-labeled protein using constant-time evolution.

    abstract::An improved version of the three-dimensional HCCH-COSY NMR experiment is described that correlates the resonances of geminal and vicinal proton pairs with the chemical shift of the 13C nucleus attached to one of the protons. The experiment uses constant-time evolution of transverse 13C magnetization which optimizes tr...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章


    authors: Ikura M,Kay LE,Bax A

    更新日期:1991-09-01 00:00:00