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https://www.readbyqxmd.com/read/28339206/utilizing-electron-spin-echo-envelope-modulation-to-distinguish-between-the-local-secondary-structures-of-an-%C3%AE-helix-and-an-amphipathic-310-helical-peptide
#1
Lauren Bottorf, Sophia Rafferty, Indra Dev Sahu, Robert M McCarrick, Gary A Lorigan
Electron Spin Echo Envelope Modulation (ESEEM) spectroscopy was used to distinguish between the local secondary structures of an α-helix and a 310-helix. Previously, we have shown that ESEEM spectroscopy in combination with site-directed spin labeling (SDSL) and 2H-labeled amino acids (i) can probe the local secondary structure of α-helices, resulting in an obvious deuterium modulation pattern, where i+4 positions generally show larger 2H ESEEM peak intensities than i+3 positions. Here, we have hypothesized that due to the unique turn periodicities of an α-helix (3...
March 24, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28333463/determination-of-the-absolute-configuration-of-a-monoglyceride-antibolting-compound-and-isolation-of-related-compounds-from-radish-leaves-raphanus-sativus
#2
Tsuyoshi Ogihara, Naruki Amano, Yuki Mitsui, Kaien Fujino, Hiroyuki Ohta, Kosaku Takahashi, Hideyuki Matsuura
A monoglyceride (1) has been reported to possess an antibolting effect in radish (Raphanus sativus), but its absolute configuration at the C-2 position was not determined earlier. In this work, the absolute configuration of 1 was determined to be (2S), and it was also accompanied by one new (2) and two known monoglycerides (3 and 4). The chemical structure of 2 was determined as β-(7'Z,10'Z,13'Z)-hexadecatrienoic acid monoglyceride (β-16:3 monoglyceride). Qualitative and quantitative analytical methods for compounds 1-4 were developed, using two deuterium-labeled compounds (8 and 9) as internal standards...
March 23, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28328032/product-ion-tandem-mass-spectrometric-differentiation-of-regioisomeric-side-chain-groups-in-cathinone-derivatives
#3
Younis Abiedalla, Jack DeRuiter, C Randall Clark
RATIONALE: Precursor materials are available to prepare aminoketone drugs containing regioisomeric propyl and isopropyl side-chain groups related to the drug alpha-pyrrovalerone (Flakka) and MDPV (3,4-methylenedioxypyrrovalerone). These compounds yield equivalent regioisomeric iminium cation base peaks in electron ionization mass spectrometry (EI-MS). METHODS: The propyl and isopropyl side-chain groups related to alpha-pyrrovalerone and MDPV were prepared and evaluated in EI-MS and tandem mass spectrometry (MS/MS) product ion experiments...
July 30, 2016: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28325931/body-mass-index-adjustments-to-increase-the-validity-of-body-fatness-assessment-in-uk-black-african-and-south-asian-children
#4
M T Hudda, C M Nightingale, A S Donin, M S Fewtrell, D Haroun, S Lum, J E Williams, C G Owen, A R Rudnicka, J C K Wells, D G Cook, P H Whincup
BACKGROUND/OBJECTIVES: BMI (weight/height(2)) is the most widely used marker of childhood obesity and total body fatness (BF). However, its validity is limited, especially in children of South Asian and black African origins. We aimed to quantify BMI adjustments needed for UK children of black African and South Asian origins so that adjusted BMI related to BF in the same way as for white European children. METHODS: We used data from four recent UK studies which made deuterium dilution BF measurements in UK children of white European, South Asian and black African origins...
March 22, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/28323935/association-of-in-vivo-adipose-tissue-cellular-kinetics-with-markers-of-metabolic-health-in-humans
#5
Ursula A White, Mark D Fitch, Robbie A Beyl, Marc K Hellerstein, Eric Ravussin
Context: Adipose tissue expansion occurs by hypertrophy and hyperplasia. Impaired hyperplasia, or adipogenesis, has been associated with obesity-related diseases. The cellular mechanisms underlying in vivo adipose cell turnover are not elucidated. Objective: We previously reported differences in in vivo cellular kinetics between the subcutaneous abdominal (scABD) and femoral (scFEM) depots using an 8-week incorporation of deuterium in women with obesity. We have now examined how in vivo kinetics correlate with markers of metabolic health...
March 2, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28322057/%C3%AE-dicationic-chelating-phosphines-synthesis-and-application-to-the-hydroarylation-of-dienes
#6
Lianghu Gu, Lawrence M Wolf, Adam Zieliński, Walter Thiel, Manuel Alcarazo
A series of new P^P-chelating ligands constituted by a dicationic -[P(H2Im)2](+2) unit (H2Im = 1,3-dimethyl-4,5-dihydroimidazol-2-ylidene) and a -PPh2 group connected through structurally different backbones have been synthesized. Evaluation of their reactivity toward different metal centers provides evidence that the dicationic fragment, otherwise reluctant to coordinate metals, readily participates in the formation of chelates when embedded into such a scaffold. Moreover, it significantly enhances the Lewis acidity of the metals to which it coordinates...
March 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28319116/quenched-hydrogen-deuterium-exchange-nmr-of-a-disease-relevant-a%C3%AE-1-42-amyloid-polymorph
#7
Marielle Aulikki Wälti, Julien Orts, Roland Riek
Alzheimer's disease is associated with the aggregation into amyloid fibrils of Aβ(1-42) and Aβ(1-40) peptides. Interestingly, these fibrils often do not obtain one single structure but rather show different morphologies, so-called polymorphs. Here, we compare quenched hydrogen-deuterium (H/D) exchange of a disease-relevant Aβ(1-42) fibril for which the 3D structure has been determined by solid-state NMR with H/D exchange previously determined on another structural polymorph. This comparison reveals secondary structural differences between the two polymorphs suggesting that the two polymorphisms can be classified as segmental polymorphs...
2017: PloS One
https://www.readbyqxmd.com/read/28318907/the-effects-of-mutating-tyr9-and-arg15-on-the-structure-stability-conformational-dynamics-and-mechanism-of-gsta3-3
#8
Gary J Robertson, Stoyan H Stoychev, Yasien Sayed, Ikechukwu Achilonu, Heini W Dirr
Glutathione S-transferase A3-3 is the most catalytically efficient steroid isomerase enzyme known in humans, transforming Δ(5)-androstene-3-17-dione into Δ(4)-androstene-3-17-dione. GSTA3-3 catalyzes this reaction with ten-fold greater efficiency than GSTA1-1, its closest competitor in the Alpha class of GSTs. In order to examine the differences between Alpha class GSTs and to better elucidate the mechanism of GSTA3-3 the roles of Tyr9 and Arg15 were examined. Tyr9 is the major catalytic residue of Alpha class GSTs and Arg15 is proposed to be catalytically important to GSTA3-3 but never before experimentally examined...
March 1, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28315390/quantifying-the-dynamic-density-driven-convection-in-high-permeability-packed-beds
#9
Ying Teng, Lanlan Jiang, Yingting Fan, Yu Liu, Dayong Wang, Abuliti Abudula, Yongchen Song
The density driven convection phenomenon is expected to have a significant and positive role in CO2 geological storage capacity and safety. The onset and development of density-driven convective on the core scale is critical to understand the mass transfer mechanism. In this paper, laboratory experiments were conducted to investigate the density-driven convective in a vertical tube. The deuterium oxide (D2O)/manganese chloride (MnCl2) water solution in water or brine were as an analog for CO2-rich brine in original brine...
March 14, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/28315238/comprehensive-gas-phase-peptide-ion-structure-studies-using-ion-mobility-techniques-part-2-gas-phase-hydrogen-deuterium-exchange-for-ion-population-estimation
#10
Mahdiar Khakinejad, Samaneh Ghassabi Kondalaji, Amirmahdi Tafreshian, Stephen J Valentine
Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data...
March 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28306316/first-measurements-of-deuterium-tritium-and-deuterium-deuterium-fusion-reaction-yields-in-ignition-scalable-direct-drive-implosions
#11
C J Forrest, P B Radha, J P Knauer, V Yu Glebov, V N Goncharov, S P Regan, M J Rosenberg, T C Sangster, W T Shmayda, C Stoeckl, M Gatu Johnson
The deuterium-tritium (D-T) and deuterium-deuterium neutron yield ratio in cryogenic inertial confinement fusion (ICF) experiments is used to examine multifluid effects, traditionally not included in ICF modeling. This ratio has been measured for ignition-scalable direct-drive cryogenic DT implosions at the Omega Laser Facility [T. R. Boehly et al., Opt. Commun. 133, 495 (1997)OPCOB80030-401810.1016/S0030-4018(96)00325-2] using a high-dynamic-range neutron time-of-flight spectrometer. The experimentally inferred yield ratio is consistent with both the calculated values of the nuclear reaction rates and the measured preshot target-fuel composition...
March 3, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28306261/asymmetric-synthesis-of-the-major-metabolite-of-a-cgrp-receptor-antagonist-and-mechanism-of-epoxide-hydrogenolysis
#12
Guanglin Luo, Ling Chen, Charles M Conway, Walter Kostich, Benjamin M Johnson, Alicia Ng, John E Macor, Gene M Dubowchik
An asymmetric synthesis of the major metabolite of the CGRP recepotor antagonist BMS-846372 is presented. The variously substituted cyclohepta[b]pyridine ring system represents an under-explored ring system, and showed some unexpected chemistry. Reactivities of epoxide and ketone functional groups on cycloheptane ring were greatly controlled by a remote bulky TIPS group. The rate difference of the hydrogenolysis between two diastereomeric epoxide intermediates shed some light on the mechanism of epoxide hydrogenolysis, and further deuterium labeling studies unravelled more mechanistic details on this well known chemical transformation for the first time...
March 17, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28304155/gas-phase-hydrogen-deuterium-exchange-for-distinguishing-isomeric-carbohydrate-ions
#13
Sanjit S Uppal, Sarah E Beasley, Michele Scian, Miklos Guttman
The structural diversity of carbohydrates presents a major challenge for glycobiology and the analysis of glycoconjugates. Mass spectrometry has become a primary tool for glycan analysis thanks to its speed and sensitivity, but the information content regarding the glycan structure of protonated glycoconjugates is hindered by the inability to differentiate linkage and stereoisomers. Here we examine a variety of protonated carbohydrate structures by gas-phase hydrogen/deuterium exchange (HDX) to discover that the exchange rates are distinct for isomeric carbohydrates with even subtle structural differences...
March 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28302855/direct-observation-of-individual-hydrogen-atoms-at-trapping-sites-in-a-ferritic-steel
#14
Y-S Chen, D Haley, S S A Gerstl, A J London, F Sweeney, R A Wepf, W M Rainforth, P A J Bagot, M P Moody
The design of atomic-scale microstructural traps to limit the diffusion of hydrogen is one key strategy in the development of hydrogen-embrittlement-resistant materials. In the case of bearing steels, an effective trapping mechanism may be the incorporation of finely dispersed V-Mo-Nb carbides in a ferrite matrix. First, we charged a ferritic steel with deuterium by means of electrolytic loading to achieve a high hydrogen concentration. We then immobilized it in the microstructure with a cryogenic transfer protocol before atom probe tomography (APT) analysis...
March 17, 2017: Science
https://www.readbyqxmd.com/read/28297841/molecular-dynamics-simulation-of-strong-shock-waves-propagating-in-dense-deuterium-taking-into-consideration-effects-of-excited-electrons
#15
Hao Liu, Yin Zhang, Wei Kang, Ping Zhang, Huiling Duan, X T He
We present a molecular dynamics simulation of shock waves propagating in dense deuterium with the electron force field method [J. T. Su and W. A. Goddard, Phys. Rev. Lett. 99, 185003 (2007)PRLTAO0031-900710.1103/PhysRevLett.99.185003], which explicitly takes the excitation of electrons into consideration. Nonequilibrium features associated with the excitation of electrons are systematically investigated. We show that chemical bonds in D_{2} molecules lead to a more complicated shock wave structure near the shock front, compared with the results of classical molecular dynamics simulation...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28291519/structural-studies-of-neurospora-crassa-lpmo9d-and-redox-partner-cdhiia-using-neutron-crystallography-and-small-angle-scattering
#16
Annette M Bodenheimer, William B O'Dell, Christopher B Stanley, Flora Meilleur
Sensitivity to hydrogen/deuterium and lack of observable radiation damage makes cold neutrons an ideal probe the structural studies of proteins with highly photosensitive groups such as the copper center of lytic polysaccharide monooxygenases (LPMOs) and flavin adenine dinucleotide (FAD) and heme redox cofactors of cellobiose dehydrogenases (CDHs). Here, neutron crystallography and small-angle neutron scattering are used to investigate Neurospora crassa LPMO9D (NcLPMO9D) and CDHIIA (NcCDHIIA), respectively...
March 4, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/28289959/quantum-isotope-effects-on-the-h-li2-reaction
#17
Thiago Ferreira da Cunha, Henrique Vieira Rivera Vila, Wiliam Ferreira da Cunha, Luiz Guilherme M de Macedo, Ricardo Gargano
This work presents a detailed study concerning the quantum isotope effects on the H+Li[Formula: see text] reaction, when the hydrogen is replaced by muonium, deuterium, and tritium. To verify such effects on these isotope reactions, it was applied an accurate time-independent quantum scattering approach to determine the dynamic properties, such as state-to-state probabilities as a function of the total energy, the product energetic distribution, and the contribution of the ro-vibrational excitation on the reaction probabilities...
April 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28289188/ligand-induced-allostery-in-the-interaction-of-the-pseudomonas-aeruginosa-heme-binding-protein-with-heme-oxygenase
#18
Daniel J Deredge, Weiliang Huang, Colleen Hui, Hirotoshi Matsumura, Zhi Yue, Pierre Moënne-Loccoz, Jana Shen, Patrick L Wintrode, Angela Wilks
A heme-dependent conformational rearrangement of the C-terminal domain of heme binding protein (PhuS) is required for interaction with the iron-regulated heme oxygenase (HemO). Herein, we further investigate the underlying mechanism of this conformational rearrangement and its implications for heme transfer via site-directed mutagenesis, resonance Raman (RR), hydrogen-deuterium exchange MS (HDX-MS) methods, and molecular dynamics (MD). HDX-MS revealed that the apo-PhuS C-terminal α6/α7/α8-helices are largely unstructured, whereas the apo-PhuS H212R variant showed an increase in structure within these regions...
March 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28288347/exploration-of-the-metal-coordination-region-of-concanavalin-a-for-its-interaction-with-human-norovirus
#19
Duwoon Kim, Hee-Min Lee, Kyung-Seo Oh, Ah Young Ki, Rachael A Protzman, Dongkyun Kim, Jong-Soon Choi, Min Ji Kim, Sung Hyun Kim, Bipin Vaidya, Seung Jae Lee, Joseph Kwon
Rapid methods for the detection and clinical treatment of human norovirus (HuNoV) are needed to control foodborne disease outbreaks, but reliable techniques that are fast and sensitive enough to detect small amounts of HuNoV in food and aquatic environments are not yet available. We explore the interactions between HuNoV and concanavalin A (Con A), which could facilitate the development of a sensitive detection tool for HuNoV. Biophysical studies including hydrogen/deuterium exchange (HDX) mass spectrometry and surface plasmon resonance (SPR) revealed that when the metal coordinated region of Con A, which spans Asp16 to His24, is converted to nine alanine residues (mCon A(MCR)), the affinity for HuNoV (GII...
March 6, 2017: Biomaterials
https://www.readbyqxmd.com/read/28286729/a-novel-cytochrome-p450-cyp3201b1-is-involved-in-r-mandelonitrile-biosynthesis-in-a-cyanogenic-millipede
#20
Takuya Yamaguchi, Yasumasa Kuwahara, Yasuhisa Asano
Specialized arthropods and more than 2500 plant species biosynthesize hydroxynitriles and release hydrogen cyanide as a defensive mechanism. The millipede Chamberlinius hualienensis accumulates (R)-mandelonitrile as a cyanide precursor. Although biosynthesis of hydroxynitriles in cyanogenic plants and in an insect are extensively studied, (R)-mandelonitrile biosynthesis in cyanogenic millipedes has remained unclear. In this study, we identified the biosynthetic precursors of (R)-mandelonitrile and an enzyme involved in (R)-mandelonitrile biosynthesis...
March 2017: FEBS Open Bio
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