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Molecules (Basel, Switzerland) Apr 2013An extremely strong H/D isotope effect observed in hydrogen bonded A-H…B systems is connected with a reach diversity of the potential shape for the proton/deuteron... (Review)
Review
An extremely strong H/D isotope effect observed in hydrogen bonded A-H…B systems is connected with a reach diversity of the potential shape for the proton/deuteron motion. It is connected with the anharmonicity of the proton/deuteron vibrations and of the tunneling effect, particularly in cases of short bridges with low barrier for protonic and deuteronic jumping. Six extreme shapes of the proton motion are presented starting from the state without possibility of the proton transfer up to the state with a full ionization. The manifestations of the H/D isotope effect are best reflected in the infra-red absorption spectra. A most characteristic is the run of the relationship between the isotopic ratio nH/nD and position of the absorption band shown by using the example of NHN hydrogen bonds. One can distinguish a critical range of correlation when the isotopic ratio reaches the value of ca. 1 and then increases up to unusual values higher than . The critical range of the isotope effect is also visible in NQR and NMR spectra. In the critical region one observes a stepwise change of the NQR frequency reaching 1.1 MHz. In the case of NMR, the maximal isotope effect is reflected on the curve presenting the dependence of Δd (¹H,²H) on d (¹H). This effect corresponds to the range of maximum on the correlation curve between dH and ΔpKa that is observed in various systems. There is a lack in the literature of quantitative information about the influence of isotopic substitution on the dielectric properties of hydrogen bond except the isotope effect on the ferroelectric phase transition in some hydrogen bonded crystals.
Topics: Deuterium; Hydrogen Bonding; Isotopes; Magnetic Resonance Spectroscopy; Models, Chemical; Protons; Vibration
PubMed: 23591926
DOI: 10.3390/molecules18044467 -
Scientific Reports Apr 2022The doubly labelled water (DLW) method is widely used to determine energy expenditure. In this work, we demonstrate the addition of the third stable isotope, O, to turn...
The doubly labelled water (DLW) method is widely used to determine energy expenditure. In this work, we demonstrate the addition of the third stable isotope, O, to turn it into triply labelled water (TLW), using the three isotopes measurement of optical spectrometry. We performed TLW (H, O andO) measurements for the analysis of the CO production (r) of mice on different diets for the first time. Triply highly enriched water was injected into mice, and the isotope enrichments of the distilled blood samples of one initial and two finals were measured by an off-axis integrated cavity output spectroscopy instrument. We evaluated the impact of different calculation protocols and the values of evaporative water loss fraction. We found that the dilution space and turnover rates of O and O were equal for the same mice group, and that values of r calculated based on O-H, or on O-H agreed very well. This increases the reliability and redundancy of the measurements and it lowers the uncertainty in the calculated r to 3% when taking the average of two DLW methods. However, the TLW method overestimated the r compared to the indirect calorimetry measurements that we also performed, much more for the mice on a high-fat diet than for low-fat. We hypothesize an extra loss or exchange mechanism with a high fractionation for H to explain this difference.
Topics: Animals; Carbon Dioxide; Deuterium; Energy Metabolism; Mice; Oxygen Isotopes; Reproducibility of Results; Water
PubMed: 35428795
DOI: 10.1038/s41598-022-10377-8 -
Biophysical Journal Apr 2019Hydrogen/deuterium exchange monitored by mass spectrometry is a promising technique for rapidly fingerprinting structural and dynamical properties of proteins. The...
Hydrogen/deuterium exchange monitored by mass spectrometry is a promising technique for rapidly fingerprinting structural and dynamical properties of proteins. The time-dependent change in the mass of any fragment of the polypeptide chain depends uniquely on the rate of exchange of its amide hydrogens, but determining the latter from the former is generally not possible. Here, we show that, if time-resolved measurements are available for a number of overlapping peptides that cover the whole sequence, rate constants for each amide hydrogen exchange (or equivalently, their protection factors) may be extracted and the uniqueness of the solutions obtained depending on the degree of peptide overlap. However, in most cases, the solution is not unique, and multiple alternatives must be considered. We provide a statistical method that clusters the solutions to further reduce their number. Such analysis always provides meaningful constraints on protection factors and can be used in situations in which obtaining more refined experimental data is impractical. It also provides a systematic way to improve data collection strategies to obtain unambiguous information at single-residue level (e.g., for assessing protein structure predictions at atomistic level).
Topics: Amides; Complement C3; Deuterium; Hydrogen Bonding; Mass Spectrometry; Peptides
PubMed: 30885379
DOI: 10.1016/j.bpj.2019.02.024 -
Chemical & Pharmaceutical Bulletin Dec 2010The synthesis of D- and L-selenomethionine labeled with ⁸²Se and three deuteriums at Se-methyl group (D- and L-[²H₃, ⁸²Se]selenomethionine) was described. D-...
The synthesis of D- and L-selenomethionine labeled with ⁸²Se and three deuteriums at Se-methyl group (D- and L-[²H₃, ⁸²Se]selenomethionine) was described. D- And L-[²H₃, ⁸²Se]selenomethionine were prepared by condensation of (R)- and (S)-2-amino-4-bromobutylic acid with lithium [²H₃, ⁸²Se]methaneselenolate, which was prepared from metal (82)Se and [²H₃]methyl iodide. The optical purities of D- and L-[²H₃, ⁸²Se]selenomethionine were determined by HPLC with a chiral stationary phase column and were found more than 99% ee. The chemical ionization mass spectra showed that the molecular related ion for N-isobutyloxycarbonyl ethyl ester derivatives of [²H₃, ⁸²Se]selenomethionine did not overlap with the m/z values known from that of non-labeled selenomethionine.
Topics: Chromatography, High Pressure Liquid; Deuterium; Isotope Labeling; Isotopes; Selenium; Selenomethionine; Stereoisomerism
PubMed: 21139275
DOI: 10.1248/cpb.58.1658 -
NeuroImage Dec 2021To present first highly spatially resolved deuterium metabolic imaging (DMI) measurements of the human brain acquired with a dedicated coil design and a fast chemical...
PURPOSE
To present first highly spatially resolved deuterium metabolic imaging (DMI) measurements of the human brain acquired with a dedicated coil design and a fast chemical shift imaging (CSI) sequence at an ultrahigh field strength of B = 9.4 T. H metabolic measurements with a temporal resolution of 10 min enabled the investigation of the glucose metabolism in healthy human subjects.
METHODS
The study was performed with a double-tuned coil with 10 TxRx channels for H and 8TxRx/2Rx channels for H and an Ernst angle 3D CSI sequence with a nominal spatial resolution of 2.97 ml and a temporal resolution of 10 min.
RESULTS
The metabolism of [6,6'-H]-labeled glucose due to the TCA cycle could be made visible in high resolution metabolite images of deuterated water, glucose and Glx over the entire human brain.
CONCLUSION
X-nuclei MRSI as DMI can highly benefit from ultrahigh field strength enabling higher temporal and spatial resolutions.
Topics: Brain; Deuterium; Glucose; Gray Matter; Humans; Magnetic Resonance Imaging
PubMed: 34637905
DOI: 10.1016/j.neuroimage.2021.118639 -
Plant, Cell & Environment Jun 2017How water moves through leaves, and where the phase change from liquid to vapour occurs within leaves, remain largely mysterious. Some time ago, we suggested that the... (Review)
Review
How water moves through leaves, and where the phase change from liquid to vapour occurs within leaves, remain largely mysterious. Some time ago, we suggested that the stable isotope composition of leaf water may contain information on transport pathways beyond the xylem, through differences in the development of gradients in enrichment within the various pathways. Subsequent testing of this suggestion provided ambiguous results and even questioned the existence of gradients in enrichment within the mesophyll. In this review, we bring together recent theoretical developments in understanding leaf water transport pathways and stable isotope theory to map a path for future work into understanding pathways of water transport and leaf water stable isotope composition. We emphasize the need for a spatially, anatomically and isotopically explicit model of leaf water transport.
Topics: Biological Transport; Deuterium; Models, Biological; Oxygen Isotopes; Plant Leaves; Water; Xylem
PubMed: 27739589
DOI: 10.1111/pce.12845 -
Briefings in Bioinformatics Mar 2022Protein turnover is vital for cellular functioning and is often associated with the pathophysiology of a variety of diseases. Metabolic labeling with heavy water...
Protein turnover is vital for cellular functioning and is often associated with the pathophysiology of a variety of diseases. Metabolic labeling with heavy water followed by liquid chromatography coupled to mass spectrometry is a powerful tool to study in vivo protein turnover in high throughput and large scale. Heavy water is a cost-effective and easy to use labeling agent. It labels all nonessential amino acids. Due to its toxicity in high concentrations (20% or higher), small enrichments (8% or smaller) of heavy water are used with most organisms. The low concentration results in incomplete labeling of peptides/proteins. Therefore, the data processing is more challenging and requires accurate quantification of labeled and unlabeled forms of a peptide from overlapping mass isotopomer distributions. The work describes the bioinformatics aspects of the analysis of heavy water labeled mass spectral data, available software tools and current challenges and opportunities.
Topics: Chromatography, Liquid; Deuterium Oxide; Isotope Labeling; Peptides; Proteolysis; Tandem Mass Spectrometry
PubMed: 35062023
DOI: 10.1093/bib/bbab598 -
The Journal of Biological Chemistry Sep 2022The analysis of hydrogen deuterium exchange by mass spectrometry as a function of temperature and mutation has emerged as a generic and efficient tool for the spatial...
The analysis of hydrogen deuterium exchange by mass spectrometry as a function of temperature and mutation has emerged as a generic and efficient tool for the spatial resolution of protein networks that are proposed to function in the thermal activation of catalysis. In this work, we extend temperature-dependent hydrogen deuterium exchange from apo-enzyme structures to protein-ligand complexes. Using adenosine deaminase as a prototype, we compared the impacts of a substrate analog (1-deaza-adenosine) and a very tight-binding inhibitor/transition state analog (pentostatin) at single and multiple temperatures. At a single temperature, we observed different hydrogen deuterium exchange-mass spectrometry properties for the two ligands, as expected from their 10-fold differences in strength of binding. By contrast, analogous patterns for temperature-dependent hydrogen deuterium exchange mass spectrometry emerge in the presence of both 1-deaza-adenosine and pentostatin, indicating similar impacts of either ligand on the enthalpic barriers for local protein unfolding. We extended temperature-dependent hydrogen deuterium exchange to a function-altering mutant of adenosine deaminase in the presence of pentostatin and revealed a protein thermal network that is highly similar to that previously reported for the apo-enzyme (Gao et al., 2020, JACS 142, 19936-19949). Finally, we discuss the differential impacts of pentostatin binding on overall protein flexibility versus site-specific thermal transfer pathways in the context of models for substrate-induced changes to a distributed protein conformational landscape that act in synergy with embedded protein thermal networks to achieve efficient catalysis.
Topics: Adenosine; Adenosine Deaminase; Deuterium; Deuterium Exchange Measurement; Ligands; Pentostatin; Protein Conformation; Proteins; Temperature
PubMed: 35933011
DOI: 10.1016/j.jbc.2022.102350 -
Microbial Biotechnology Mar 2020Human intestinal microbiota is important to host health and is associated with various diseases. It is a challenge to identify the functions and metabolic activity of...
Human intestinal microbiota is important to host health and is associated with various diseases. It is a challenge to identify the functions and metabolic activity of microorganisms at the single-cell level in gut microbial community. In this study, we applied Raman microspectroscopy and deuterium isotope probing (Raman-DIP) to quantitatively measure the metabolic activities of intestinal bacteria from two individuals and analysed lipids and phenylalanine metabolic pathways of functional microorganisms in situ. After anaerobically incubating the human faeces with heavy water (D O), D O with specific substrates (glucose, tyrosine, tryptophan and oleic acid) and deuterated glucose, the C-D band in single-cell Raman spectra appeared in some bacteria in faeces, due to the Raman shift from the C-H band. Such Raman shift was used to indicate the general metabolic activity and the activities in response to the specific substrates. In the two individuals' intestinal microbiota, the structures of the microbial communities were different and the general metabolic activities were 76 ± 1.0% and 30 ± 2.0%. We found that glucose, but not tyrosine, tryptophan and oleic acid, significantly stimulated metabolic activity of the intestinal bacteria. We also demonstrated that the bacteria within microbiota preferably used glucose to synthesize fatty acids in faeces environment, whilst they used glucose to synthesize phenylalanine in laboratory growth environment (e.g. LB medium). Our work provides a useful approach for investigating the metabolic activity in situ and revealing different pathways of human intestinal microbiota at the single-cell level.
Topics: Bacteria; Deuterium; Deuterium Oxide; Gastrointestinal Microbiome; Humans; Spectrum Analysis, Raman
PubMed: 31821744
DOI: 10.1111/1751-7915.13519 -
Scientific Reports Feb 2021Radiation doses from organically bound tritium (OBT) in foods have been a major concern near nuclear facilities. The current dose coefficient for OBT is calculated using...
Radiation doses from organically bound tritium (OBT) in foods have been a major concern near nuclear facilities. The current dose coefficient for OBT is calculated using a standard model from the International Commission on Radiological Protection, in which some biokinetic values are not based on human metabolic data. Here, the biokinetics of ingested OBT, and radiation doses from them, were estimated by administering labelled compounds and foods to volunteers, using a deuterium (D) tracer as a substitute for tritium. After the administration of D-labelled glucose, alanine, palmitic acid, or soybean, the D/H ratios in urine were measured for up to 119 days, and the biokinetic parameter values were determined for OBT metabolism. The slow degradation rates of OBT could not be obtained, in many volunteers administered glucose and alanine. The estimated committed effective dose for 1 Bq of tritium in palmitic acid varied from 3.2 × 10 to 3.5 × 10 Sv Bq among volunteers and, for those administered soybean, it varied from 1.9 × 10 to 1.8 × 10 Sv Bq. These results suggest that OBT, present in some ingested ingredients, gives higher doses than the current dose coefficient value of 4.2 × 10 Sv Bq.
Topics: Adult; Deuterium; Female; Food; Food Contamination, Radioactive; Humans; Male; Radiation Dosage; Tritium; Young Adult
PubMed: 33531641
DOI: 10.1038/s41598-021-82460-5