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https://www.readbyqxmd.com/read/28821744/exploring-the-sequence-based-prediction-of-folding-initiation-sites-in-proteins
#1
Daniele Raimondi, Gabriele Orlando, Rita Pancsa, Taushif Khan, Wim F Vranken
Protein folding is a complex process that can lead to disease when it fails. Especially poorly understood are the very early stages of protein folding, which are likely defined by intrinsic local interactions between amino acids close to each other in the protein sequence. We here present EFoldMine, a method that predicts, from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events. The method is based on early folding data from hydrogen deuterium exchange (HDX) data from NMR pulsed labelling experiments, and uses backbone and sidechain dynamics as well as secondary structure propensities as features...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28820192/comparison-of-classical-reaction-paths-and-tunneling-paths-studied-with-the-semiclassical-instanton-theory
#2
Jan Meisner, Max N Markmeyer, Matthias U Bohner, Johannes Kästner
Atom tunneling in the hydrogen atom transfer reaction of the 2,4,6-tri-tert-butylphenyl radical to 3,5-di-tert-butylneophyl, which has a short but strongly curved reaction path, was investigated using instanton theory. We found the tunneling path to deviate qualitatively from the classical intrinsic reaction coordinate, the steepest-descent path in mass-weighted Cartesian coordinates. To perform that comparison, we implemented a new variant of the predictor-corrector algorithm for the calculation of the intrinsic reaction coordinate...
August 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28818652/adsorption-desorption-mediated-separation-of-low-concentrated-d2o-from-water-with-hydrophobic-activated-carbon-fiber
#3
Yuji Ono, Ryusuke Futamura, Yoshiyuki Hattori, Toshio Sakai, Katsumi Kaneko
The adsorption and desorption of D2O on hydrophobic activated carbon fiber (ACF) occurs at a smaller pressure than the adsorption and desorption of H2O. The behavior of the critical desorption pressure difference between D2O and H2O in the pressure range of 1.25-1.80kPa is applied to separate low concentrated D2O from water using the hydrophobic ACF, because the desorption branches of D2O and H2O drop almost vertically. The deuterium concentration of all desorbed water in the above pressure range is lower than that of water without adsorption-treatment on ACF...
August 9, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28813004/lactose-binding-induces-opposing-dynamics-changes-in-human-galectins-revealed-by-nmr-based-hydrogen-deuterium-exchange
#4
Chih-Ta Henry Chien, Meng-Ru Ho, Chung-Hung Lin, Shang-Te Danny Hsu
Galectins are β-galactoside-binding proteins implicated in a myriad of biological functions. Despite their highly conserved carbohydrate binding motifs with essentially identical structures, their affinities for lactose, a common galectin inhibitor, vary significantly. Here, we aimed to examine the molecular basis of differential lactose affinities amongst galectins using solution-based techniques. Consistent dissociation constants of lactose binding were derived from nuclear magnetic resonance (NMR) spectroscopy, intrinsic tryptophan fluorescence, isothermal titration calorimetry and bio-layer interferometry for human galectin-1 (hGal1), galectin-7 (hGal7), and the N-terminal and C-terminal domains of galectin-8 (hGal8(NTD) and hGal8(CTD), respectively)...
August 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28810782/first-principles-molecular-dynamics-study-of-deuterium-diffusion-in-liquid-tin
#5
Xiaohui Liu, Daye Zheng, Xinguo Ren, Lixin He, Mohan Chen
Understanding the retention of hydrogen isotopes in liquid metals, such as lithium and tin, is of great importance in designing a liquid plasma-facing component in fusion reactors. However, experimental diffusivity data of hydrogen isotopes in liquid metals are still limited or controversial. We employ first-principles molecular dynamics simulations to predict diffusion coefficients of deuterium in liquid tin at temperatures ranging from 573 to 1673 K. Our simulations indicate faster diffusion of deuterium in liquid tin than the self-diffusivity of tin...
August 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28809482/structural-dynamics-of-15-lipoxygenase-2-via-hydrogen-deuterium-exchange
#6
Kristin Diane Droege, Mary E Keithly, Charles R Sanders, Richard N Armstrong, Matthew K Thompson
Eicosanoids are inflammatory signaling lipids that are biosynthesized in response to cellular injury or threat. They were originally thought to be pro-inflammatory molecules, but at least one sub-class, the lipoxins, are able to resolve inflammation. The first step in lipoxin synthesis is the oxygenation of arachidonic acid by 15-Lipoxygenase (15-LOX). 15-LOX contains two domains: a Ca2+ binding PLAT domain and a catalytic domain. 15-LOX is a soluble cytosolic protein until Ca2+ binding to the PLAT domain promotes translocation to the membrane surface...
August 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28808005/conformational-dynamics-of-1-deoxy-d-xylulose-5-phosphate-synthase-on-ligand-binding-revealed-by-h-d-exchange-ms
#7
Jieyu Zhou, Luying Yang, Alicia DeColli, Caren Freel Meyers, Natalia S Nemeria, Frank Jordan
The enzyme 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) is a key enzyme in the methylerythritol 4-phosphate pathway and is a target for the development of antibiotics, herbicides, and antimalarial drugs. DXPS catalyzes the formation of 1-deoxy-d-xylulose 5-phosphate (DXP), a branch point metabolite in isoprenoid biosynthesis, and is also used in the biosynthesis of thiamin (vitamin B1) and pyridoxal (vitamin B6). Previously, we found that DXPS is unique among the superfamily of thiamin diphosphate (ThDP)-dependent enzymes in stabilizing the predecarboxylation intermediate, C2-alpha-lactyl-thiamin diphosphate (LThDP), which has subsequent decarboxylation that is triggered by d-glyceraldehyde 3-phosphate (GAP)...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28807886/mechanistic-insights-into-f420-dependent-glucose-6-phosphate-dehydrogenase-using-isotope-effects-and-substrate-inhibition-studies
#8
Mercy A Oyugi, Ghader Bashiri, Edward N Baker, Kayunta Johnson-Winters
F420-dependent glucose-6-phosphate dehydrogenase (FGD) is involved in the committed step of the pentose phosphate pathway within mycobacteria, where it catalyzes the reaction between glucose-6-phosphate (G6P) and the F420 cofactor to yield 6-phosphogluconolactone and the reduced cofactor, F420H2. Here, we aim to probe the FGD reaction mechanism using dead-end inhibition experiments, as well as solvent and substrate deuterium isotope effects studies. The dead-end inhibition studies performed using citrate as the inhibitor revealed competitive and uncompetitive inhibition patterns for G6P and F420 respectively, thus suggesting a mechanism of ordered addition of substrates in which the F420 cofactor must first bind to FGD before G6P binding...
August 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28805994/monitoring-photosynthetic-activity-in-microalgal-cells-by-raman-spectroscopy-with-deuterium-oxide-as-a-tracking-probe
#9
Yusuke Yonamine, Yuta Suzuki, Takuro Ito, Yoshiko Miura, Keisuke Goda, Yasuyuki Ozeki, Yu Hoshino
Microalgae offer great potential for biofuel production, but high photosynthetic activity is demanded for practical realization of microalgal biofuels. To this end, it is essential to evaluate the photosynthetic activity of single microalgal cells in a heterogeneous population. In this study, we present a method for monitoring photosynthetic activity of microalgae (in particular Euglena gracilis, a microalgal species of unicellular, photosynthetic, flagellate protists as our model organism) at single-cell resolution by Raman spectroscopy with deuterium from deuterium oxide (D2O) as a tracking probe...
August 14, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28803776/mechanism-of-enzyme-repair-by-the-aaa-chaperone-rubisco-activase
#10
Javaid Y Bhat, Goran Miličić, Gabriel Thieulin-Pardo, Andreas Bracher, Andrew Maxwell, Susanne Ciniawsky, Oliver Mueller-Cajar, John R Engen, F Ulrich Hartl, Petra Wendler, Manajit Hayer-Hartl
How AAA+ chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA+ protein Rubisco activase (Rca) in metabolic repair of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits containing eight catalytic sites. Rubisco is prone to inhibition by tight-binding sugar phosphates, whose removal is catalyzed by Rca. We engineered a stable Rca hexamer ring and analyzed its functional interaction with Rubisco...
July 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28801550/active-neutron-and-gamma-ray-imaging-of-highly-enriched-uranium-for-treaty-verification
#11
Michael C Hamel, J Kyle Polack, Marc L Ruch, Matthew J Marcath, Shaun D Clarke, Sara A Pozzi
The detection and characterization of highly enriched uranium (HEU) presents a large challenge in the non-proliferation field. HEU has a low neutron emission rate and most gamma rays are low energy and easily shielded. To address this challenge, an instrument known as the dual-particle imager (DPI) was used with a portable deuterium-tritium (DT) neutron generator to detect neutrons and gamma rays from induced fission in HEU. We evaluated system response using a 13.7-kg HEU sphere in several configurations with no moderation, high-density polyethylene (HDPE) moderation, and tungsten moderation...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28798232/conformational-characterization-of-nerve-growth-factor-%C3%AE-reveals-that-its-regulatory-pro-part-domain-stabilizes-three-loop-regions-in-its-mature-part
#12
Esben Trabjerg, Fredrik Kartberg, Søren Christensen, Kasper D Rand
Nerve growth factor-β (NGF) is essential for correct development of the nervous system. NGF exists both in a mature and a pro-form (proNGF). The two forms have opposing effects on neurons, in which NGF induces proliferation, while proNGF induces apoptosis via binding to a receptor complex of the common neurotrophine receptor (p75NTR) and Sortilin. Overexpression of both proNGF and Sortilin has been associated with several neurodegenerative diseases. Insights into the conformational differences between proNGF and NGF are central to a better understanding of the opposing mechanisms of action of NGF and proNGF on neurons...
August 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28797100/mapping-the-contact-surfaces-in-the-lamin-a-aimp3-complex-by-hydrogen-deuterium-exchange-ft-icr-mass-spectrometry
#13
Yeqing Tao, Pengfei Fang, Sunghoon Kim, Min Guo, Nicolas L Young, Alan G Marshall
Aminoacyl-tRNA synthetases-interacting multifunctional protein3 (AIMP3/p18) is involved in the macromolecular tRNA synthetase complex via its interaction with several aminoacyl-tRNA synthetases. Recent reports reveal a novel function of AIMP3 as a tumor suppressor by accelerating cellular senescence and causing defects in nuclear morphology. AIMP3 specifically mediates degradation of mature Lamin A (LmnA), a major component of the nuclear envelope matrix; however, the mechanism of how AIMP3 interacts with LmnA is unclear...
2017: PloS One
https://www.readbyqxmd.com/read/28792473/taxol-%C3%A2-the-first-microtubule-stabilizing-agent
#14
REVIEW
Chia-Ping Huang Yang, Susan Band Horwitz
Taxol(®), an antitumor drug with significant activity, is the first microtubule stabilizing agent described in the literature. This short review of the mechanism of action of Taxol(®) emphasizes the research done in the Horwitz' laboratory. It discusses the contribution of photoaffinity labeled analogues of Taxol(®) toward our understanding of the binding site of the drug on the microtubule. The importance of hydrogen/deuterium exchange experiments to further our insights into the stabilization of microtubules by Taxol(®) is addressed...
August 9, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28781083/kras-g12c-drug-development-discrimination-between-switch-ii-pocket-configurations-using-hydrogen-deuterium-exchange-mass-spectrometry
#15
Jia Lu, Rane A Harrison, Lianbo Li, Mei Zeng, Sudershan Gondi, David Scott, Nathanael S Gray, John R Engen, Kenneth D Westover
KRAS G12C, the most common RAS mutation found in non-small-cell lung cancer, has been the subject of multiple recent covalent small-molecule inhibitor campaigns including efforts directed at the guanine nucleotide pocket and separate work focused on an inducible pocket adjacent to the switch motifs. Multiple conformations of switch II have been observed, suggesting that switch II pocket (SIIP) binders may be capable of engaging a range of KRAS conformations. Here we report the use of hydrogen/deuterium-exchange mass spectrometry (HDX MS) to discriminate between conformations of switch II induced by two chemical classes of SIIP binders...
July 25, 2017: Structure
https://www.readbyqxmd.com/read/28776923/observation-and-identification-of-an-atomic-oxygen-structure-on-catalytic-gold-nanoparticles
#16
Kai Liu, Tao Chen, Shuyue He, Jason P Robbins, Simon G Podkolzin, Fei Tian
Interactions between oxygen and gold surfaces are fundamentally important in diverse areas of science and technology. Here, an oxygen dimer structure was identified on gold nanoparticles in catalytic decomposition of hydrogen peroxide to oxygen and water. This structure, different from isolated atomic or molecular oxygen structures, was observed with in situ surface-enhanced Raman spectroscopic measurements and identified with density functional theory calculations. The measurements were performed using monodisperse gold particles supported on silica with liquid-phase hydrogen and deuterium peroxides...
August 3, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28772661/novel-pefc-application-for-deuterium-isotope-separation
#17
Hisayoshi Matsushima, Ryota Ogawa, Shota Shibuya, Mikito Ueda
The use of a polymer electrolyte fuel cell (PEFC) with a Nafion membrane for isotopic separation of deuterium (D) was investigated. Mass analysis at the cathode side indicated that D diffused through the membrane and participated in an isotope exchange reaction. The exchange of D with protium (H) in H₂O was facilitated by a Pt catalyst. The anodic data showed that the separation efficiency was dependent on the D concentration in the source gas, whereby the water produced during the operation of the PEFC was more enriched in D as the D concentration of the source gas was increased...
March 16, 2017: Materials
https://www.readbyqxmd.com/read/28770632/an-overview-of-hydrogen-deuterium-exchange-mass-spectrometry-hdx-ms-in-drug-discovery
#18
Glenn R Masson, Meredith L Jenkins, John E Burke
Introduction- Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful methodology to study protein dynamics, protein folding, protein-protein interactions, and protein small molecule interactions. The development of novel methodologies and technical advancements in mass spectrometers has greatly expanded the accessibility and acceptance of this technique within both academia and industry. Areas covered- This review examines the theoretical basis of how amide exchange occurs, how different mass spectrometer approaches can be used for HDX-MS experiments, as well as the use of HDX-MS in drug development, specifically focusing on how HDX-MS is used to characterize bio-therapeutics, and its use in examining protein-protein and protein small molecule interactions...
August 3, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28770577/sec-saxs-and-hdx-ms-a-powerful-combination-the-case-of-the-calcium-binding-domain-of-a-bacterial-toxin
#19
REVIEW
Darragh P O'Brien, Sébastien Brier, Daniel Ladant, Dominique Durand, Alexandre Chenal, Patrice Vachette
Small-angle X-ray Scattering (SAXS) is a relatively simple experimental technique that provides information on the global conformation of macromolecules in solution, be they fully structured, partially, or extensively unfolded. Size Exclusion chromatography in line with a SAXS measuring cell considerably improves the mono-dispersity and ideality of solutions, the two main requirements of a "good" SAXS sample. Hydrogen/Deuterium eXchange monitored by Mass Spectrometry (HDX-MS) offers a wealth of information regarding the solvent accessibility at the local (peptide) level...
August 2, 2017: Biotechnology and Applied Biochemistry
https://www.readbyqxmd.com/read/28765527/calcium-ion-induced-structural-changes-promote-dimerization-of-secretagogin-which-is-required-for-its-insulin-secretory-function
#20
Jae-Jin Lee, Seo-Yun Yang, Jimin Park, James E Ferrell, Dong-Hae Shin, Kong-Joo Lee
Secretagogin (SCGN), a hexa EF-hand calcium binding protein, plays key roles in insulin secretion in pancreatic β-cells. It is not yet understood how the binding of Ca(2+) to human SCGN (hSCGN) promotes secretion. Here we have addressed this question, using mass spectrometry combined with a disulfide searching algorithm DBond. We found that the binding of Ca(2+) to hSCGN promotes the dimerization of hSCGN via the formation of a Cys193-Cys193 disulfide bond. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics studies revealed that Ca(2+) binding to the EF-hands of hSCGN induces significant structural changes that affect the solvent exposure of N-terminal region, and hence the redox sensitivity of the Cys193 residue...
August 1, 2017: Scientific Reports
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