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Biochemical Society Transactions Oct 2020The use of neutrons as a scattering probe to investigate biological membranes has steadily grown in the past three decades, shedding light on the structure and behaviour... (Review)
Review
The use of neutrons as a scattering probe to investigate biological membranes has steadily grown in the past three decades, shedding light on the structure and behaviour of this ubiquitous and fundamental biological barrier. Meanwhile, the rise of antibiotic resistance has catalysed a renewed interest in understanding the mechanisms underlying the dynamics of antibiotics interaction with the bacterial cell envelope. It is widely recognised that the key reason behind the remarkable success of Gram-negative pathogens in developing antibiotic resistance lies in the effectiveness of their outer membrane (OM) in defending the cell from antibacterial compounds. Critical to its function, the highly asymmetric lipid distribution between the inner and outer bilayer leaflets of the OM, adds an extra level of complexity to the study of this crucial defence barrier. Here we review the opportunities offered by neutron scattering techniques, in particular reflectometry, to provide structural information on the interactions of antimicrobials with in vitro models of the OM. The differential sensitivity of neutrons towards hydrogen and deuterium makes them a unique probe to study the structure and behaviour of asymmetric membranes. Molecular-level understanding of the interactions between antimicrobials and the Gram-negative OM provides valuable insights that can aid drug development and broaden our knowledge of this critically important biological barrier.
Topics: Anti-Bacterial Agents; Bacteria; Bacterial Outer Membrane Proteins; Biophysics; Cell Membrane; Deuterium; Gram-Negative Bacteria; Hydrogen; Lipid Bilayers; Lipopolysaccharides; Neutrons; Scattering, Radiation
PubMed: 33005925
DOI: 10.1042/BST20200320 -
Journal of the American Chemical Society Feb 2022Analyzing the δH values in individual amino acids of proteins extracted from vertebrates, we unexpectedly found in some samples, notably bone collagen from seals, more...
Analyzing the δH values in individual amino acids of proteins extracted from vertebrates, we unexpectedly found in some samples, notably bone collagen from seals, more than twice as much deuterium in proline and hydroxyproline residues than in seawater. This corresponds to at least 4 times higher δH than in any previously reported biogenic sample. We ruled out diet as a plausible mechanism for such anomalous enrichment. This finding puts into question the old adage that "you are what you eat".
Topics: Animals; Anseriformes; Bone and Bones; Collagen; Deuterium; Fibroblasts; Humans; Hydroxyproline; Mice; Proline; Seals, Earless; Ursidae
PubMed: 35107291
DOI: 10.1021/jacs.1c12512 -
European Journal of Nutrition Jun 2023Choline deficiency leads to pathologies particularly of the liver, brain and lung. Adequate supply is important for preterm infants and patients with cystic fibrosis. We... (Randomized Controlled Trial)
Randomized Controlled Trial
BACKGROUND
Choline deficiency leads to pathologies particularly of the liver, brain and lung. Adequate supply is important for preterm infants and patients with cystic fibrosis. We analysed the assimilation of four different enterally administered deuterium-labelled (D9-) choline supplements in adults.
METHODS
Prospective randomised cross-over study (11/2020-1/2022) in six healthy men, receiving four single doses of 2.7 mg/kg D9-choline equivalent each in the form of D9-choline chloride, D9-phosphorylcholine, D9-alpha-glycerophosphocholine (D9-GPC) or D9-1-palmitoyl-2-oleoyl-glycero-3-phosphoryl-choline (D9-POPC), in randomised order 6 weeks apart. Plasma was obtained at baseline (t = - 0.1 h) and at 0.5 h to 7d after intake. Concentrations of D9-choline and its D9-labelled metabolites were analysed by tandem mass spectrometry. Results are shown as median and interquartile range.
RESULTS
Maximum D9-choline and D9-betaine concentrations were reached latest after D9-POPC administration versus other components. D9-POPC and D9-phosphorylcholine resulted in lower D9-trimethylamine (D9-TMAO) formation. The AUCs (0-7d) of plasma D9-PC concentration showed highest values after administration of D9-POPC. D9-POPC appeared in plasma after fatty acid remodelling, predominantly as D9-1-palmitoyl-2-linoleyl-PC (D9-PLPC), confirming cleavage to 1-palmitoyl-lyso-D9-PC and re-acylation with linoleic acid as the most prominent alimentary unsaturated fatty acid.
CONCLUSION
There was a delayed increase in plasma D9-choline and D9-betaine after D9-POPC administration, with no differences in AUC over time. D9-POPC resulted in a higher AUC of D9-PC and virtually absent D9-TMAO levels. D9-POPC is remodelled according to enterocytic fatty acid availability. D9-POPC seems best suited as choline supplement to increase plasma PC concentrations, with PC as a carrier of choline and targeted fatty acid supply as required by organs. This study was registered at Deutsches Register Klinischer Studien (DRKS) (German Register for Clinical Studies), DRKS00020498, 22.01.2020.
STUDY REGISTRATION
This study was registered at Deutsches Register Klinischer Studien (DRKS) (German Register for Clinical Studies), DRKS00020498.
Topics: Adult; Humans; Infant; Infant, Newborn; Male; Betaine; Choline; Cross-Over Studies; Deuterium; Fatty Acids; Infant, Premature; Phosphatidylcholines; Phosphorylcholine; Prospective Studies
PubMed: 36840817
DOI: 10.1007/s00394-023-03121-z -
Journal of Labelled Compounds &... Mar 2023Selective deuterium installation into small molecules is becoming increasingly desirable not only for the elucidation of mechanistic pathways and studying biological...
Selective deuterium installation into small molecules is becoming increasingly desirable not only for the elucidation of mechanistic pathways and studying biological processes but also because of deuterium's ability to favorably adjust the pharmacokinetic parameters of bioactive molecules. Fused bicyclic moieties, especially those containing heteroatoms, are prevalent in drug discovery and pharmaceuticals. Herein, we report a copper-catalyzed transfer hydrodeuteration of cyclic and heterocyclic alkenes, which enables the synthesis of chromans, quinolinones, and tetrahydronaphthalenes that are precisely deuterated at the benzylic position. We also demonstrate the ability to place one deuterium atom at the homobenzylic site of these scaffolds with high regioselectivity by swapping transfer reagents for their isotopic analogs. Furthermore, examples of chemoselective transfer hydrogenation and transfer deuteration are disclosed, allowing for the simultaneous incorporation of two vicinal hydrogen or deuterium atoms into a double bond.
Topics: Deuterium; Cycloparaffins; Hydrogen; Copper; Catalysis; Alkenes
PubMed: 36772856
DOI: 10.1002/jlcr.4015 -
Cancer Control : Journal of the Moffitt... 2021The effects of deuterium-depleted water (DDW) containing deuterium (D) at a concentration of 25 parts per million (ppm), 50 ppm, 105 ppm and the control at 150 ppm were...
The effects of deuterium-depleted water (DDW) containing deuterium (D) at a concentration of 25 parts per million (ppm), 50 ppm, 105 ppm and the control at 150 ppm were monitored in MIA-PaCa-2 pancreatic cancer cells by the real-time cell impedance detection xCELLigence method. The data revealed that lower deuterium concentrations corresponded to lower MiA PaCa-2 growth rate. Nuclear membrane turnover and nucleic acid synthesis rate at different D-concentrations were determined by targeted [1,2-C]-D-glucose fate associations. The data showed severely decreased oxidative pentose cycling, RNA ribose C labeling from [1,2-C]-D-glucose and nuclear membrane lignoceric (C24:0) acid turnover. Here, we treated advanced pancreatic cancer patients with DDW as an extra-mitochondrial deuterium-depleting strategy and evaluated overall patient survival. Eighty-six (36 male and 50 female) pancreatic adenocarcinoma patients were treated with conventional chemotherapy and natural water (control, 30 patients) or 85 ppm DDW (56 patients), which was gradually decreased to preparations with 65 ppm and 45 ppm deuterium content for each 1 to 3 months treatment period. Patient survival curves were calculated by the Kaplan-Meier method and Pearson correlation was taken between medial survival time (MST) and DDW treatment in pancreatic cancer patients. The MST for patients consuming DDW treatment (n = 56) was 19.6 months in comparison with the 6.36 months' MST achieved with chemotherapy alone (n = 30). There was a strong, statistically significant Pearson correlation (r = 0.504, p < 0.001) between survival time and length and frequency of DDW treatment.
Topics: Cell Proliferation; Deuterium; Female; Humans; Male; Nuclear Envelope; Pancreatic Neoplasms; RNA
PubMed: 33760674
DOI: 10.1177/1073274821999655 -
Molecules (Basel, Switzerland) Sep 2022The structure and function of biological macromolecules change due to intermolecular deuterium bond formation or deuterium substitution with environmental DO. In this...
The structure and function of biological macromolecules change due to intermolecular deuterium bond formation or deuterium substitution with environmental DO. In this study, surface-enhanced Raman spectroscopy (SERS) was used to detect interaction sites between DO and ssDNA and their action mechanisms. SERS peaks of ssDNA changed with increasing DO proportions, and the site of action mainly involved A and G bases, whose number strengthened the interaction between sequences and DO and hence the SERS peak intensities. Fixing the number of A and G bases prevented changes in their positions from significantly altering the map. We also identified the interaction between ssDNA sequences that easily formed a G-quadruplex structure and DO. The amplitude of the SERS peak intensity change reflected the ssDNA structural stability and number of active sites. These findings are highly significant for exploring genetic exchanges and mutations and could be used to determine the stability and structural changes of biological macromolecules.
Topics: DNA, Single-Stranded; Deuterium; Deuterium Oxide; G-Quadruplexes; Spectrum Analysis, Raman
PubMed: 36144761
DOI: 10.3390/molecules27186023 -
Solid State Nuclear Magnetic Resonance Feb 2021Slow timescale dynamics in proteins are essential for a variety of biological functions spanning ligand binding, enzymatic catalysis, protein folding and misfolding... (Review)
Review
Slow timescale dynamics in proteins are essential for a variety of biological functions spanning ligand binding, enzymatic catalysis, protein folding and misfolding regulations, as well as protein-protein and protein-nucleic acid interactions. In this review, we focus on the experimental and theoretical developments of H static NMR methods applicable for studies of microsecond to millisecond motional modes in proteins, particularly rotating frame relaxation dispersion (R), quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) relaxation dispersion, and quadrupolar chemical exchange saturation transfer NMR experiments (Q-CEST). With applications chosen from amyloid-β fibrils, we show the complementarity of these approaches for elucidating the complexities of conformational ensembles in disordered domains in the non-crystalline solid state, with the employment of selective deuterium labels. Combined with recent advances in relaxation dispersion backbone measurements for N/C/H nuclei, these techniques provide powerful tools for studies of biologically relevant timescale dynamics in disordered domains in the solid state.
Topics: Amyloid; Amyloid beta-Peptides; Deuterium; Magnetic Resonance Spectroscopy; Nuclear Magnetic Resonance, Biomolecular; Protein Conformation; Protein Folding
PubMed: 33450712
DOI: 10.1016/j.ssnmr.2020.101710 -
International Journal of Molecular... Mar 2022Much of the work probing antimicrobial peptide (AMP) mechanisms has focussed on how these molecules permeabilize lipid bilayers. However, AMPs must also traverse a... (Review)
Review
Much of the work probing antimicrobial peptide (AMP) mechanisms has focussed on how these molecules permeabilize lipid bilayers. However, AMPs must also traverse a variety of non-lipid cell envelope components before they reach the lipid bilayer. Additionally, there is a growing list of AMPs with non-lipid targets inside the cell. It is thus useful to extend the biophysical methods that have been traditionally applied to study AMP mechanisms in liposomes to the full bacteria, where the lipids are present along with the full complexity of the rest of the bacterium. This review focusses on what can be learned about AMP mechanisms from solid-state NMR of AMP-treated intact bacteria. It also touches on flow cytometry as a complementary method for measuring permeabilization of bacterial lipid membranes in whole bacteria.
Topics: Antimicrobial Cationic Peptides; Antimicrobial Peptides; Bacteria; Cell Membrane; Deuterium; Lipid Bilayers
PubMed: 35269882
DOI: 10.3390/ijms23052740 -
Polymers Mar 2024The peculiarities of crystal growth on a Nafion polymeric substrate from supersaturated aqueous solutions of initial substances were studied. The solutions were prepared...
The peculiarities of crystal growth on a Nafion polymeric substrate from supersaturated aqueous solutions of initial substances were studied. The solutions were prepared based on deionized natural water and deuterium-depleted water. As was found earlier, in natural water (deuterium content 157 ± 1 ppm) polymer fibers are capable of unwinding towards the bulk of the liquid, while in deuterium-depleted water (deuterium content ≤ 3 ppm) there is no such effect. Since the distance between the unwound fibers falls in a nanometer range (which is close to the size of the unit cell of the crystal lattice), and these fibers are directed normally to the polymeric substrate, the unwinding can affect crystal growth on the polymer substrate. As was obtained in experiments with X-ray diffractometry, the unwound polymer fibers predetermine syngony of crystals, for which the unit cell is either a rectangular parallelepiped (monoclinic system) or an oblique parallelepiped (triclinic system). A quantitative theoretical model that describes the local interaction of the polymer substrate with the crystalline complexes is presented. Within this model, the polymer substrate can be considered as a flexible matrix for growing crystals.
PubMed: 38543350
DOI: 10.3390/polym16060744 -
Journal of Chromatography. A Jan 2023Reversed-phase peptide separation in hydrogen deuterium exchange (HDX) mass spectrometry (MS) must be done with conditions where the back exchange is the slowest...
Reversed-phase peptide separation in hydrogen deuterium exchange (HDX) mass spectrometry (MS) must be done with conditions where the back exchange is the slowest possible, the so-called quench conditions of low pH and low temperature. To retain maximum deuterium, separation must also be done as quickly as possible. The low temperature (0 °C) of quench conditions complicates the separation and leads primarily to a reduction in separation quality and an increase in chromatographic backpressure. To improve the separation in HDX MS, one could use a longer gradient, smaller particles, a different separation mechanism (for example, capillary electrophoresis), or multi-dimensional separations such as combining ion mobility separation with reversed-phase separation. Another way to improve separations under HDX MS quench conditions is to use a higher flow rate where separation efficiency at 0 °C is more ideal. Higher flow rates, however, require chromatographic systems (both pumps and fittings) with higher backpressure limits. We tested what improvements could be realized with a commercial UPLC/UHPLC system capable of ∼20,000 psi backpressure. We found that a maximum flow rate of 225 µL/min (using a 1 × 50 mm column packed with 1.8 µm particles) was possible and that higher flow rate clearly led to higher peak capacity. HDX MS analysis of both simple and particularly complex samples improved, permitting both shorter separation time, if desired, and providing more deuterium recovery.
Topics: Hydrogen Deuterium Exchange-Mass Spectrometry; Deuterium; Deuterium Exchange Measurement; Mass Spectrometry; Peptides; Hydrogen
PubMed: 36586285
DOI: 10.1016/j.chroma.2022.463742