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PubMed1976

NMR study of relative oxygen binding to the alpha and beta subunits of human adult hemoglobin.

NMR spectra of the downfield region of normal adult hemoglobin are reported as a function of oxygenation and temperature. Spectra were run in D2O at pD 7.4. A specially made NMR tube insert allowed precise measurement of the degree of oxygenation and of methemoglobin formation before and after taking the NMR spectrum. Plots of the estimated intensity of the most downfield prominent NMR peak, identified as arising from a deoxy-beta subunit by Davis et al. ((1971) J. Mol. Biol. 60, 101-111), versus the average degree of oxygenation y, measured optically, yield a nearly straight line within experimental error, for samples stripped of organic phosphates and for samples containing 2,3-diphosphoglycerate or inositol hexaphosphate. Intensities of peaks further upfield than this peak, previously attributed to deoxy-alpha subunits, are difficult to measure directly especially for samples containing inositol hexaphosphate. The latter samples show broadening in these alpha peaks as the degree of oxygenation increases. This extra broadening appears to increase with temperature. Linearity of the beta peak intensity with oxygenation is expected if there is no large oxygen affinity difference between alpha and beta subunits. However, the cooperativity of binding, and inaccuracy of the data, make it impossible to make accurate estimates of affinity differences.

Adult↗

PubMed2018

High-Throughput Metabolomics by 1D NMR.

Metabolomics deals with the whole ensemble of metabolites (the metabolome). As one of the -omic sciences, it relates to biology, physiology, pathology and medicine; but metabolites are chemical entities, small organic molecules or inorganic ions. Therefore, their proper identification and quantitation in complex biological matrices requires a solid chemical ground. With respect to for example, DNA, metabolites are much more prone to oxidation or enzymatic degradation: we can reconstruct large parts of a mammoth's genome from a small specimen, but we are unable to do the same with its metabolome, which was probably largely degraded a few hours after the animal's death. Thus, we need standard operating procedures, good chemical skills in sample preparation for storage and subsequent analysis, accurate analytical procedures, a broad knowledge of chemometrics and advanced statistical tools, and a good knowledge of at least one of the two metabolomic techniques, MS or NMR. All these skills are traditionally cultivated by chemists. Here we focus on metabolomics from the chemical standpoint and restrict ourselves to NMR. From the analytical point of view, NMR has pros and cons but does provide a peculiar holistic perspective that may speak for its future adoption as a population-wide health screening technique.

Animals↗

PubMed1978

NMR in cancer. X. A malignancy index to discriminate normal and cancerous tissue.

Proton nuclear magnetic resonance relaxation parameters (T1, T2, T1p) were measured on 84 normal and malignant samples of colon, lung and breast tissue at 22.5 MHz. The purpose of this study was to evaluate the ability of NMR measurements to discriminate between normal and malignant tissue. By combining T1 and T2 into a normalized NMR malignancy index, it was possible to discriminate malignant and normal tissue in all 36 colon samples, 22 out of 23 breast samples, and 26 out of 29 lung cases. Furthermore, histologically normal tissue adjacent to malignant colonic tissue was found to have an elevated NMR malignancy index comparable to that of malignant colon.

Breast↗

PubMed1976

GLC and NMR analysis of isomeric impurities in the new anti-inflammatory agent benoxaprofen.

GLC and NMR methods are described for the determination of four possible isomeric impurities in the novel anti-inflammatory agent benoxaprofen. The 2- and 3-chlorophenyl isomers were determined by GLC after alkaline hydrolysis and subsequent methylation. A rapid NMR procedure, using the lanthanide shift reagent tris- (1, 1, 1, 2, 2, 3, 3-heptafluoro- 7, 7-dimethyl- 4, 6-octanedionato)-europium, was developed for the 6- and 7- (alpha-methylacetic acid) isomers. Similar methodolology, with tris-(3-heptafluorobutyryl-d-camphorato)europium, enabled the determination of the enantiomer ratio for benoxaprofen. For the positional isomers, the limits of detection were 0.05% by GLC and 0.2% by NMR.

Anti-Inflammatory Agents↗

PubMed1977

Application of 13C-NMR spectroscopy to in vitro analysis of enzyme kinetics.

The conversion of D,L-alpha-13C-histidine to similarly labeled alpha-13C histamine by bacterial and mammalian histidine decarboxylase was studied by 13C-NMR spectroscopy and GLC-mass spectrometry. The results obtained with the partially purified bacterial enzyme were in essentially perfect agreement with results obtained simultaneously with a standard radioisotopic method using carboxyl-labeled-14C-L-histidine. For a crude tissue preparation of the mammalian enzyme, the radioisotopic method indicated an activity three times that based on 13C-NMR measurement of alpha-13C-histamine. The difference in results was accountable in terms of additional 13C-NMR signals attributable to products other than histamine due in part to enzymatic degradation of the latter.

Animals↗

PubMed1979

NMR of fd coat protein.

The conformations of the major coat protein of a filamentous bacteriophage can be described by nuclear magnetic resonance spectroscopy of the protein and the virus. The NMR experiments involve detection of the 13C and 1H nuclei of the coat protein. Both the 13C and 1H nuclear magnetic resonance (NMR) spectra show that regions of the polypeptide chain have substantially more motion than a typical globular protein. The fd coat protein was purified by gel chromatography of the SDA solubilized virus. Natural abundance 13C NMR spectra at 38 MHz resolve all of the nonprotonated aromatic carbons from the three phenylalanines, two tyrosines, and one tryptophan of the coat protein. The alpha carbons of the coat protein show at least two different classes of relaxation behavior, indicative of substantial variation in the motion of the backbone carbons in contrast to the rigidity of the alpha carbons of globular proteins. The 1H spectrum at 360 MHz shows all of the aromatic carbons and many of the amide protons. Titration of a 1H spectra gives the pKas for the tyrosines.

Amino Acid Sequence↗

PubMed1978

Evidence for isotropic motion of phospholipids in liver microsomal membranes. A 31P NMR study.

1. The motional properties of phospholipids in bovine and rat liver microsomes and aqueous dispersions of the extracted lipids have been investigated employing 31 P NMR techniques. 2. The 31P NMR spectra obtained from the microsomes indicate that a considerable portion of the constituent phospholipids experience isotropic motion on the NMR timescale (10(-5) s). This is in strong contrast to the spectra obtained from aqueous dispersions of the extracted lipids, which display the characteristic lineshape associated with liquid crystalline phospholipids in (large) bilayer structures, which experience restricted anisotropic motion. 3. Evidence is presented which strongly suggests that the isotropic motion of microsomal phospholipids does not arise from tumbling of the microsomal vesicles or from lateral diffusion of phospholipids around these vesicles. 4. These results are discussed in terms of possible transitory formation of intramembrane non-bilayer lipid configurations, with which the bulk (bilayer) phospholipids are in rapid exchange.

Animals↗

PubMed1975

19-F NMR studies of the binding of a fluorine-labeled phosphonate ion to E. coli alkaline phosphatase.

The interaction of a fluorinated phosphonate with Zn-2+-and Mn-2+-alkaline phosphatase as studied by 19-F NMR revealed a stoichiometry of 1:1 for the binding of the phosphonate anion to the enzyme. In the presence of two metal ions, one fluorinated phosphonate ion was found to interact strongly with the enzyme, while a different interaction was observed when the number of metal ions per enzyme exceeded two. Phosphate replaced enzyme bound phosphonate, as is shown by the 19-F NMR spectra. No direct interaction between the fluorinated phosphonate and the metal ion responsible for enzyme activity was indicated by the 19-F NMR data. This observation supports the idea of a considerable distance between metal ion and substrate binding site in Escherichia coli alkaline phosphatase.

Alkaline Phosphatase↗

PubMed1978

Structural interpretation of lanthanide binding to the basic pancreatic trypsin inhibitor by 1H NMR at 360 MHz.

The weak binding of lanthanides to the five carboxyl groups of the basic pancreatic trypsin inhibitor (hereafter termed "the inhibitor"), has been investigated in detail using high resolution 1H NMR at 360 MHz. Lanthanides bind to the C-terminus with an apparent binding constant of 30 M-1, and thus competitively inhibit the formation of a salt-bridge between the C-terminus and the N-terminus, Lanthanides bind also to the side chain carboxyl groups of Asp 3, Glu 7, Glu 49 and Asp 50, with binding constants of 10--30 M-1. With the use of lanthanides individual resonance assignments for Phe 4 and Phe 45 were obtained in the 1H NMR spectrum of the inhibitor, and for several spin systems previous identifications were independently confirmed. The present experiments also provide a nice illustration for the use of shift reagents to improve the resolution in 1H NMR spectra of proteins. The exchange broadening for Tyr 35 and Phe 45 over the temperature range 4--72 degrees C could thus be observed for almost all the components of these aromatic spin systems and new details on the dynamic properties were obtained also for other aromatic residues.

Amino Acid Sequence↗

PubMed1979

Cross-peptide bond 13C--15N coupling constants by 13C and J cross-polarization 15N NMR.

Comparative 13C--15N coupling constants are reported for the linear dipeptide tBoc-L-[U-13C]Ala-[15N]GlyOMe and the corresponding cyclic diketopiperazine, both in dimethylsulfoxide (DMSO) and, upon removal of the tBoc group, in water solutions. Spectra were obtained by 13C NMR and by the first application of J cross-polarization (JCP) 15N NMR, which greatly reduces the time required to accumulate 15N NMR spectra. In DMSO there was evidence for the formation of complexed species which were not present in water. The values obtained for the cross-peptide bond coupling constant 2J13C alpha--15N were consistently less (by 2.2 Hz in DMSO, 4.3 Hz in water) for the cyclic than for the linear peptide, which may be related to the cross-peptide bond conformation. The 15N resonance for the cyclic peptide was shifted only 2 ppm downfield from the linear peptide chemical shift value in both solvents.

Alanine↗

PubMed1976

A high-resolution NMR study (1H, 13C, 31P) of the interaction of paramagnetic ions with phospholipids in aqueous dispersions.

1H-, 13C- and 31P-NMR spectra of egg-yolk phosphatidylcholine (PC), phosphatidylserine (PS) and phosphatidic acid (PA) and cosonicated mixtures of these phospholipids were obtained from ultrasonicated dispersions containing Pr3+, Eu3+, Gd3+ and Mn2+ ions. The differences in chemical shift values, deltaN, between the "inner" and "outer" resonance signals for the different nuclei of the polar head group of egg-yolk phosphatidyl choline provide information about the average distances of the paramagnetic ion within the polar groups of the phospholipid molecules. In the Pr(2H2O)3+n/egg-yolk phosphatidylcholine system the ions are nearest to the phosphate and -CH2CH2 group, respectively but relatively far from the N(CH3)3 group of the polar head group of the lipid. The integral analysis of the 1H-NMR spectra obtained from dispersions containing Pr3+ and Mn2+ ions enables us to calculate the number of the polar groups in both sides of the egg-yolk phosphatidylcholine bilayer, the size of lipid vesicle and to give some features of the arrangement of the phospholipid molecules in cosonicated egg-yolk phosphatidylcholine/phosphatidylserine vesicles. At p2H 8.3 in PC/PS mixtures an extreme asymmetry is observed with PS preferentially in the outer side of the membrane. This side contains approximately three times more PS than PC molecules. Some comments are made concerning the quantitative integral analysis of proton-noise decoupled 31P-NMR spectra as obtained from similar phospholipid mixtures by Michaelson et al. and Berden et al.

Binding Sites↗

PubMed2025

Hyperpolarized NMR Reveals Low-Populated Folding Intermediates in DNA.

Nuclear magnetic resonance (NMR) spectroscopy is the only biophysical technique capable of characterizing nucleic acid structures at atomic resolution under near-physiological liquid-state conditions. Still, it is fundamentally limited by intrinsically low sensitivity, particularly when analyzing high-molecular-weight, low-abundance, or polymorphic targets, such as DNAs (DNA). In this study, we demonstrate that hyperpolarized aqueous buffers generated via dissolution dynamic nuclear polarization (dDNP) significantly enhance the 1H NMR signals of multiple DNA motifs. The resonances of labile imino and amino protons of DNAs dissolved in hyperpolarized buffers are enhanced up to ∼200-fold and ∼370-fold, respectively. These intense signals serve a 2-fold purpose: (i) as structural fingerprints of DNA folding topologies and (ii) they enable the direct observation of low-populated folding intermediates in DNA polymorphs, such as G-quadruplexes (G4) and i-motifs (iM), which remain undetectable by standard methods. Thus, our findings establish hyperpolarized NMR as a high-sensitivity method for probing DNA structures and folding intermediates across a wide range of motifs, opening possible avenues in liquid biopsy applications and cell-free DNA.

DNA↗

PubMed1979

Changes in NMR relaxation times of adjacent muscle after implantation of malignant and normal tissue.

In separate experiments, normal foreign tissue and malignant tumour were implanted s.c. into the rat thigh. NMR T1 values of the adjacent normal muscle, resulting from local inflammatory reactions or from malignant invasion, were measured. Elevations in T1 of the underlying muscle occurred within 24 h in both experiments, and it is believed these were caused by rapid inflammatory and immunological reactions to the implants. However the T1 values of muscle samples adjacent to the non-malignant implants decreased during the 11 days after implantation, dropping to values within the normal range. In the second experiment there was progressive malignant invasion into the normal adjacent tissue and the elevated T1 values were maintained throughout the 12-day period. The effects of the implantation on tissue water content are discussed in relation to NMR T1 relaxation times, and the relevance to whole-body NMR imaging of elevated T1 values due to nonmalignant pathological states is considered.

Animals↗

PubMed1979

13C NMR quantitation of polymer in deoxyhemoglobin S gels.

13C/1H magnetic double-resonance spectroscopy has been used to quantitate the amount of polymerized hemoglobin S in deoxygenated gels at 30 degrees C, for samples whose hemoglobin concentration range from 21 to 32 g/dl. Scalar- and dipolar-decoupled spectra and a 13C proton-enhanced dipolar-decoupled spectrum were recorded for each sample as was a scalar-decoupled spectrum for a matching oxyhemoglobin S control. The difference between the oxyhemoglobin S and deoxyhemoglobin S scalar-decoupled spectra was used to determine the polymer fraction, and this value was compared with the polymer fraction determined by using ultracentrifugation sedimentation on the same sample (assuming a two-phase model). The polymer fraction value determined by uncorrected sedimentation averaged 0.15 more than the value obtained from NMR. The discrepancy between the two techniques was largely removed when the analysis of the sedimentation data included a correction for depletion of hemoglobin in the supernatant or sol phase due to sedimentation of free molecules. The best fit to both the sedimentation and NMR data was obtained by using a solubility of deoxyhemoglobin S at 30 degrees C of 17.3 +/- 1 g/dl. These results indicate that the NMR techniques, which do not require separation of the sample into a sol phase and a pellet phase, provide quantitative information about the deoxyhemoglobin S polymer and will be useful for studies of sickle erythrocytes.

Erythrocytes↗

PubMed1978

The use of 13C-nmr spectroscopy for the detection and identification of metabolites of carbon-13 labelled amitriptyline.

The antidepressant drug amitriptyline and two of its metabolites, nortriptyline and desmethylnortriptyline, each containing two 13C atoms, have been used to determine the sensitivity and selectivity of 13C-nmr spectroscopy for the detection of unchanged amitriptyline and N-desmethyl metabolites in the urine of animals dosed orally with the labelled drug. The resonance signals from the 13C atoms detected in the 13C-nmr spectrum of entire extract from a control 12 h rat urine sample to which 1 mg of each labelled compound had been added were easily detected, using an instrument accumulation time of 1 h. The 13C-nmr spectrum of an extract of hydrolysed urine from a dog that had received an oral dose of [13C2]amitriptyline (30mg) exhibited signals that could be assigned to metabolites resulting from N-dealkylation and N-oxidation, as well as those bearing the intact amitriptyline side-chain. These assignments were confirmed by analysis of the same extract by g.c.--ms and h.p.l.c.

Amitriptyline↗

PubMed1977

Spectral differences in the 31P NMR of normal and malignant tissue.

High-resolution 31P NMR spectra of normal and malignant muscle tissue from mice were obtained at 100 MHz. The spectrum of normal muscle was found to resemble that obtained by Hoult et al. for normal rat skeletal muscle. But the spectrum of malignant muscle tumor (rhabdomyosarcoma) was found to comprise only the inorganic phosphate and sugar phosphate peaks, which indicates potential usefulness of this NMR method for diagnosis. Moreover, the inorganic phosphate peak was observed to be shifted downfield 70 Hz from the location seen in normal muscle. This identification of an NMR absorption frequency different in cancer tissue than in normal, singles out what may be the first of many absorption frequencies that could be utilized as target frequencies for delivery of cancer-destructive radiation.

Adenosine Diphosphate↗

PubMedDate not supplied

[Selective broadening of NMR lines as a criterion in studying the interaction of Mn(II) with amino acids and peptides in D20].

A proton NMR study was carried out on complexes of Mn(II) with amino acids and peptides in aqueous solution. The theory, based on the Solomon-Bloembergen equations, was summarized and discussed. Different types of equilibria involving the anionic and zwittrionic forms of the amino acids were taken into account, together with the presence of outer- and inner-sphere species. The related correlation times were evaluated. Sarcosine, beta-alanine, threonine, tyrosine, valine, beta-alanine, proline, histidine and cystein complexes with Mn(II) were investigated on the basis of the NMR spectra. Moreover, diglycine and triglycine were studied in the presence of manganous ion at different pH value. The findings were discussed in terms of selective broadening of the NMR peaks and compared with data in the literature.

Amino Acids↗

PubMed2026

Hyperpolarized NMR study of the impact of alzheimer's disease on diabetes using a novel rat model.

Most researchers have long focused on linkage between type 2 diabetes (T2D) and the increased risk of Alzheimer's disease (AD) but have often overlooked whether AD modulates T2D. Investigating the reciprocal interaction between two complex diseases provides perspectives on the mechanistic linkage. The endeavor, however, confronts challenges without a robust rodent model that develops T2D and AD as the animal ages. Cross breeding a T2D rat with a hemizygous TgF344AD +/- rat that contains the mutant human amyloid precursor protein (APPsw) and the presenilin 1 (PS1ΔE9) genes has produced a new T2D-AD +/- rat model. The T2D-AD +/- rat expresses both the T2D and AD phenotypes as the animal ages. As AD progresses, the time to T2D onset decreases, and the diabetes severity increases. Hyperpolarized NMR experiments using dynamic nuclear polarization (DNP) show that T2D and T2D-AD rats share a common metabolic impairment in the brain pyruvate dehydrogenase (PDH) activity as reflected in the NMR determined decline in the bicarbonate/lactate (bic/lac) ratio. The bic/lac ratio decreases in both T2D and T2D-AD brain. AD exacerbates the decline of the bic/lac ratio.

Animals↗