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https://www.readbyqxmd.com/read/28731753/new-measurements-of-the-beam-normal-spin-asymmetries-at-large-backward-angles-with-hydrogen-and-deuterium-targets
#1
D Balaguer Ríos, K Aulenbacher, S Baunack, J Diefenbach, B Gläser, D von Harrach, Y Imai, E-M Kabuß, R Kothe, J H Lee, H Merkel, M C Mora Espí, U Müller, E Schilling, C Weinrich, L Capozza, F E Maas, J Arvieux, M A El-Yakoubi, R Frascaria, R Kunne, M Morlet, S Ong, J van de Wiele, S Kowalski, Y Prok
New measurements of the beam normal single spin asymmetry in the electron elastic and quasielastic scattering on the proton and deuteron, respectively, at large backward angles and at ⟨Q^{2}⟩=0.22  (GeV/c)^{2} and ⟨Q^{2}⟩=0.35  ( GeV/c)^{2} are reported. The experimentally observed asymmetries are compared with the theoretical calculation of Pasquini and Vanderhaeghen [Phys. Rev. C 70, 045206 (2004).PRVCAN0556-281310.1103/PhysRevC.70.045206]. The agreement of the measurements with the theoretical calculations shows a dominance of the inelastic intermediate excited states of the nucleon, πN and the Δ resonance...
July 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28727449/the-use-of-maldi-ms-combined-with-differential-hydrogen-deuterium-exchange-for-semi-automated-protein-global-conformational-screening
#2
Gregory F Pirrone, Heather Wang, Nicole Canfield, Alexander S Chin, Timothy A Rhodes, Alexey A Makarov
Matrix-assisted laser desorption/ionization (MALDI) coupled with a time-of-flight (TOF) mass-spectrometry (MS) detector is acknowledged to be very useful for analysis of biological molecules. At the same time, hydrogen-deuterium exchange (HDX) is a well-known technique for studying protein higher-order structure. However, coupling MALDI with HDX may be challenging due to undesired back-exchange reactions during analysis. In this report, we survey an approach that utilizes MALDI coupled with automated sample preparation to compare global conformational changes of proteins under different solution conditions using differential HDX...
July 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28727441/adsorption-induced-changes-of-human-hemoglobin-on-ferric-pyrophosphate-nanoparticle-surface-probed-by-isotope-exchange-mass-spectrometry-an-implication-on-structure-function-correlation
#3
Bindu Y Srinivasu, Beena Bose, Gopa Mitra, Anura V Kurpad, Amit Kumar Mandal
In general, proteins in the biological system interact with nanoparticles (NPs) via adsorption on the particle surface. Understanding the adsorption at molecular level is crucial to explore NP-protein interactions. The increasing concerns about the risk to human health on NP exposure have been explored through the discovery of a handful protein biomarkers and biochemical analysis. However, detailed information on structural perturbation and associated functional changes of proteins on interaction with NPs is limited...
July 20, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28727018/evaluation-of-electrical-broad-bandwidth-impedance-spectroscopy-as-a-tool-for-body-composition-measurement-in-cows-in-comparison-with-body-measurements-and-the-deuterium-oxide-dilution-method
#4
C T Schäff, U Pliquett, A Tuchscherer, R Pfuhl, S Görs, C C Metges, H M Hammon, C Kröger-Koch
Body fatness and degree of body fat mobilization in cows vary enormously during their reproduction cycle and influence energy partitioning and metabolic adaptation. The objective of the study was to test bioelectrical impedance spectroscopy (BIS) as a method for predicting fat depot mass (FDM), in living cows. The FDM is defined as the sum of subcutaneous, omental, mesenteric, retroperitoneal, and carcass fat mass. Bioelectrical impedance spectroscopy is compared with the prediction of FDM from the deuterium oxide (DO) dilution method and from body conformation measurements...
May 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28726423/radical-difluoromethylation-of-thiols-with-difluoromethyl-triphenylphosphonium-bromide
#5
Niklas B Heine, Armido Studer
A method for facile difluoromethylation of various thiols using (difluoromethyl)triphenylphosphonium bromide under mild reaction conditions is presented. The transformation proceeds in the absence of any transition metal using a bench-stable and readily accessible phosphonium salt. Deuterium labeling experiments and cyclic voltammetry measurements reveal that the difluoromethylation occurs via a SRN1-type mechanism. Substrate scope is broad, and various functional groups are tolerated (OH, NH2, amide, ester)...
July 20, 2017: Organic Letters
https://www.readbyqxmd.com/read/28724631/the-axl-kinase-domain-in-complex-with-a-macrocyclic-inhibitor-offers-first-structural-insights-into-an-active-tam-receptor-kinase
#6
Ketan S Gajiwala, Neil Grodsky, Ben Bolaños, Junli Feng, RoseAnn Ferre, Sergei Timofeevski, Meirong Xu, Brion W Murray, Ted W Johnson, Al Stewart
The receptor tyrosine kinase (RTK) family consisting of Tyro3, Axl and Mer (TAM) is one of the most recently identified RTK families. TAM receptors are upregulated postnatally and maintained at high levels in adults. They all play an important role in immunity, but Axl has also been implicated in cancer and therefore is a target in the discovery and development of novel therapeutics. However, of the three members of the TAM family, the Axl kinase domain is the only one that has so far eluded structure determination...
July 19, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28719099/spontaneous-keto-enol-tautomerization-in-the-crystal-lattice-visualized-with-the-help-of-water-encapsulated-in-hydrophilic-reservoirs
#7
Marta K Dudek, Ewelina Wielgus, Piotr Paluch, Marek Potrzebowski
Keto-enol tautomerism in the solid phase is a process that is particularly difficult to follow. In this work we demonstrate how it can be done by introducing deuterium into the crystal lattice of organic compounds, which tend to form hydrates. In our studies we explored H-D exchange in the crystals stored in contact with deuterium oxide vapors. Employing barbituric acid (BA) and (+)-catechin (CAT) as model samples, by means of advanced solid-state NMR and mass spectrometry, we revealed that not only OH and NH protons of these chemicals undergo exchange to deuterium in a crystal lattice, but also usually immobile protons, i...
July 18, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28718923/using-homology-modeling-to-interrogate-binding-affinity-in-neutralization-of-ricin-toxin-by-a-family-of-single-domain-antibodies
#8
Andrea Bazzoli, David J Vance, Michael J Rudolph, Yinghui Rong, Siva Krishna Angalakurthi, Ronald T Toth, C Russell Middaugh, David B Volkin, David D Weis, John Karanicolas, Nicholas J Mantis
In this report we investigated, within a group of closely related single domain camelid antibodies (VH Hs), the relationship between binding affinity and neutralizing activity as it pertains to ricin, a fast-acting toxin and biothreat agent. The V1C7-like VH Hs (V1C7, V2B9, V2E8, and V5C1) are similar in amino acid sequence, but differ in their binding affinities and toxin-neutralizing activities. Using the X-ray crystal structure of V1C7 in complex with ricin's enzymatic subunit (RTA) as a template, Rosetta-based homology modeling coupled with energetic decomposition led us to predict that a single pairwise interaction between Arg29 on V5C1 and Glu67 on RTA was responsible for the difference in ricin toxin binding affinity between V1C7, a weak neutralizer, and V5C1, a moderate neutralizer...
July 18, 2017: Proteins
https://www.readbyqxmd.com/read/28712143/reliability-of-the-echomri-infants-system-for-water-and-fat-measurements-in-newborns
#9
Tatiana Toro-Ramos, Charles Paley, William W Wong, F Xavier Pi-Sunyer, Wen W Yu, John Thornton, Dympna Gallagher
OBJECTIVE: The precision and accuracy of a quantitative magnetic resonance (EchoMRI Infants) system in newborns were determined. METHODS: Canola oil and drinking water phantoms (increments of 10 g to 1.9 kg) were scanned four times. Instrument reproducibility was assessed from three scans (within 10 minutes) in 42 healthy term newborns (12-70 hours post birth). Instrument precision was determined from the coefficient of variation (CV) of repeated scans for total water, lean mass, and fat measures for newborns and the mean difference between weight and measurement for phantoms...
July 16, 2017: Obesity
https://www.readbyqxmd.com/read/28710791/origin-of-enhanced-vcd-in-amyloid-fibril-spectra-effect-of-deuteriation-and-ph
#10
Markéta Pazderková, Tomáš Pazderka, Maruda Shanmugasundaram, Rina K Dukor, Igor K Lednev, Laurence A Nafie
Supramolecular chirality of amyloid fibrils, protein aggregates related to many neurodegenerative diseases, is a remarkable property associated with fibril structure and polymorphism. Since its discovery almost 10 years ago there is still little understanding of this phenomenon, including the cause of the highly enhanced vibrational circular dichroism (VCD) intensity arising from fibril supramolecular chirality. In this study, VCD spectra, enhanced by filament supramolecular chirality, are presented for lysozyme and insulin fibrils above and below pH 2 and after deuterium exchange, above and below pD 2...
July 15, 2017: Chirality
https://www.readbyqxmd.com/read/28708326/loss-of-benzaldehyde-in-the-fragmentation-of-protonated-benzoylamines-benzoyl-cation-as-a-hydride-acceptor-in-the-gas-phase
#11
Yunfeng Chai, Yunlong Shao, Lu Wang, Lin Wang
In electrospray ionization tandem mass spectrometry of protonated 1-benzoylamines (1-benzoylpiperadine, 1-benzoylmorpholine, and 1-benzoyl-4-methylpiperazine), the dominant fragmentation pathway was amide bond cleavage to form benzoyl cation and neutral amine. Meanwhile, in their fragmentations, an interesting loss of benzaldehyde (106 Da) was observed and identified to derive from hydride transfer reaction between the benzoyl cation and amine. A stepwise mechanism for loss of 106 Da (benzene and CO) could be excluded with the aid of deuterium labeling experiment...
July 14, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28707339/neutron-structure-of-the-t26h-mutant-of-t4-phage-lysozyme-provides-insight-into-the-catalytic-activity-of-the-mutant-enzyme-and-how-it-differs-from-that-of-wild-type
#12
Takeshi Hiromoto, Flora Meilleur, Rumi Shimizu, Chie Shibazaki, Motoyasu Adachi, Taro Tamada, Ryota Kuroki
T4 phage lysozyme is an inverting glycoside hydrolase that degrades the murein of bacterial cell walls by cleaving the β-1,4-glycosidic bond. The substitution of the catalytic Thr26 residue to a histidine converts the wild type from an inverting to a retaining enzyme, which implies that the original general acid Glu11 can also act as an acid/base catalyst in the hydrolysis. Here, we have determined the neutron structure of the perdeuterated T26H mutant to clarify the protonation states of Glu11 and the substituted His26, which are key in the retaining reaction...
July 13, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28706470/structure-elucidation-of-metabolite-x17299-by-interpretation-of-mass-spectrometric-data
#13
Qibo Zhang, Lisa A Ford, Anne M Evans, Douglas R Toal
INTRODUCTION: A major bottleneck in metabolomic studies is metabolite identification from accurate mass spectrometric data. Metabolite x17299 was identified in plasma as an unknown in a metabolomic study using a compound-centric approach where the associated ion features of the compound were used to determine the true molecular mass. OBJECTIVES: The aim of this work is to elucidate the chemical structure of x17299, a new compound by de novo interpretation of mass spectrometric data...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/28702519/bottom-up-hydrogen-deuterium-exchange-mass-spectrometry-data-analysis-and-interpretation
#14
Kerene A Brown, Derek J Wilson
Hydrogen Deuterium Exchange (HDX) Mass Spectrometry (MS) is a sensitive analytical technique that provides information on protein conformation and dynamics in solution. It is commonly used in the study of protein-ligand and protein-protein interactions and more recently in the pharmaceutical industry for epitope mapping, screening drug candidates and in the comparison of biopharmaceuticals to biosimilars. HDX-MS monitors the exchange of protein backbone hydrogen atoms with deuterium in solution. Recent advancements in HDX automation and data analysis, have taken the emphasis off developing a fundamental understanding of HDX, which is still lacking...
July 13, 2017: Analyst
https://www.readbyqxmd.com/read/28700824/application-of-hdx-ms-to-biopharmaceutical-development-requirements-improved-sensitivity-to-detection-of-conformational-changes
#15
Lea Bonnington, Ingo Lindner, Ulrich Gilles, Tobias Kailich, Dietmar Reusch, Patrick Bulau
The usefulness of the higher-order structure information provided by hydrogen/deuterium exchange mass spectrometry (HDX-MS) in the protein therapeutic field is undisputed, however its applicability as a method for critical quality and comparability assessment has until now not been demonstrated. Here we present results demonstrating for the first time the applicability of the HDX-MS technique to monitor structural changes due to methionine oxidation at sensitivity levels realistic to the requirements of biopharmaceutical research and development...
July 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28700220/mechanistic-characterization-of-escherichia-coli-l-aspartate-oxidase-from-kinetic-isotope-effects
#16
Carmen Chow, Subray S Hegde, John S Blanchard
L-Aspartate oxidase, encoded by the nadB gene, is the first enzyme in the de novo synthesis of NAD+ in bacteria. This FAD-dependent enzyme catalyzes the oxidation of L-aspartate to generate iminoaspartate and reduced flavin. Distinct from most amino acid oxidases, it can use either molecular oxygen or fumarate to reoxidize the reduced enzyme. Primary sSequence alignments and the three-dimensional crystal structure have revealed that the overall fold and catalytic residues of NadB closely resemble those of the succinate dehydrogenase/fumarate reductase family rather than the prototypical D-amino acid oxidases...
July 12, 2017: Biochemistry
https://www.readbyqxmd.com/read/28698930/proliposome-powders-for-the-generation-of-liposomes-the-influence-of-carbohydrate-carrier-and-separation-conditions-on-crystallinity-and-entrapment-of-a-model-antiasthma-steroid
#17
Iftikhar Khan, Sakib Yousaf, Sneha Subramanian, Mohamed Albed Alhnan, Waqar Ahmed, Abdelbary Elhissi
Formulation effects on the entrapment of beclometasone dipropionate (BDP) in liposomes generated by hydration of proliposomes were studied, using the high-density dispersion medium deuterium oxide in comparison to deionized water (DW). Proliposomes incorporating BDP (2 mol% of the lipid phase consisting of soya phosphatidylcholine (SPC) and cholesterol; 1:1) were manufactured, using lactose monohydrate (LMH), sorbitol or D-mannitol as carbohydrate carriers (1:5 w/w lipid to carrier). Following hydration of proliposomes, separation of BDP-entrapped liposomes from the unentrapped (free) BDP at an optimized centrifugation duration of 90 min and a centrifugation force of 15,500g were identified...
July 11, 2017: AAPS PharmSciTech
https://www.readbyqxmd.com/read/28698492/the-application-of-redor-nmr-to-understand-the-conformation-of-epothilone-b
#18
Jae-Ho Lee, Moon-Su Kim, Hyo Won Lee, Ihl-Young C Lee, Hyun Kyoung Kim, Nam Doo Kim, SangGap Lee, Hwajeong Seo, Younkee Paik
The structural information of small therapeutic compounds complexed in biological matrices is important for drug developments. However, structural studies on ligands bound to such a large and dynamic system as microtubules are still challenging. This article reports an application of the solid-state NMR technique to investigating the bioactive conformation of epothilone B, a microtubule stabilizing agent, whose analog ixabepilone was approved by the U.S. Food and Drug Administration (FDA) as an anticancer drug...
July 9, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28698283/long-term-rates-of-mitochondrial-protein-synthesis-are-increased-in-mouse-skeletal-muscle-with-high-fat-feeding-regardless-of-insulin-sensitizing-treatment
#19
Sean A Newsom, Benjamin F Miller, Karyn L Hamilton, Sarah E Ehrlicher, Harrison D Stierwalt, Matthew M Robinson
Skeletal muscle mitochondrial protein synthesis is regulated in part by insulin. The development of insulin resistance with diet-induced obesity may therefore contribute to impairments to protein synthesis and decreased mitochondrial respiration. Yet, the impact of diet-induced obesity and insulin resistance on mitochondrial energetics is controversial with reports varying from decreases to increases in mitochondrial respiration. We investigated the impact of changes in insulin sensitivity on long-term rates of mitochondrial protein synthesis as a mechanism for changes to mitochondrial respiration in skeletal muscle...
July 11, 2017: American Journal of Physiology. Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28696098/enhanced-binding-affinity-via-destabilization-of-the-unbound-state-a-millisecond-hydrogen-deuterium-exchange-study-of-the-interaction-between-p53-and-a-pleckstrin-homology-domain
#20
Shaolong Zhu, Rahima Khatun, Cristina Lento, Yi Sheng, Derek J Wilson
The incorporation of intrinsically disordered domains enables proteins to engage a wide variety of targets, with phosphorylation often modulating target specificity and affinity. Although phosphorylation can clearly act as a chemical driver of complexation in structured proteins, e.g., by abrogating or permitting new charge-charge interactions, the basis for enhancement of the hydrophobically driven interactions that are typical of disordered protein-target complexation is less clear. To determine how phosphorylation can positively impact target recruitment in disordered domains, we have examined the interaction between the disordered N-terminal transactivation domain (TAD) of p53 and the pleckstrin homology (PH) domain of p62...
July 19, 2017: Biochemistry
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