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https://www.readbyqxmd.com/read/28635268/isotope-controlled-selectivity-by-quantum-tunneling-hydrogen-migration-versus-ring-expansion-in-cyclopropylmethylcarbenes
#1
Ashim Nandi, Dennis Gerbig, Peter R Schreiner, Weston Thatcher Borden, Sebastian Kozuch
Using the tunneling-controlled reactivity of cyclopropylmethylcar-bene, we demonstrate the viability of isotope-controlled selectivity (ICS), a novel non-classical control element of chemical reactivity where a molecular system with two conceivable products of tunneling exclusively produces one or the other, depending only on isotopic composition. Our multidimensional small-curvature tunneling (SCT) computations indicate that under cryogenic conditions, 1-methoxycyclopropylmethylcarbene shows rapid H-migration to 1-methoxy-1-vinylcyclopropane, whereas deuterium-substituted 1-methoxycyclopropyl-d3-methylcarbene undergoes ring expansion to 1-d3-methylcyclobutene...
June 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28634405/shedding-new-light-on-an-old-molecule-quinophthalone-displays-uncommon-n-to-o-excited-state-intramolecular-proton-transfer-esipt-between-photobases
#2
Gi Rim Han, Doyk Hwang, Seunghoon Lee, Jong Woo Lee, Eunhak Lim, Jiyoung Heo, Seong Keun Kim
Excited state dynamics of common yellow dye quinophthalone (QPH) was probed by femtosecond transient absorption spectroscopy. Multi-exponential decay of the excited state and significant change of rate constants upon deuterium substitution indicate that uncommon nitrogen-to-oxygen excited state intramolecular proton transfer (ESIPT) occurs. By performing density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations, we found that adiabatic surface crossing between the S1 and S2 states takes place in the photoreaction...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634122/mapping-the-binding-interface-in-a-non-covalent-size-variant-of-a-monoclonal-antibody-using-native-mass-spectrometry-hydrogen-deuterium-exchange-mass-spectrometry-and-computational-analysis
#3
Yuetian Yan, Hui Wei, Sutjano Jusuf, Stanley R Krystek, Jie Chen, Guodong Chen, Richard T Ludwig, Li Tao, Tapan K Das
Variants of monoclonal antibody containing an extra light chain has been reported in protein products(1-3). Due to potential impact on potency and immunogenicity, it is important to understand the formation mechanism of such variants so that appropriate control strategies can be implemented to assure product quality. In a model monoclonal antibody, we observed a size variant with an extra light chain non-covalently associated with the monomer (later named as "1.2mer"). The interaction between monomer and the extra light chain was characterized by native spray and hydrogen/deuterium exchange mass spectrometry (HDX MS) techniques...
June 17, 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28631209/allelopathic-effects-of-exogenous-phenylalanine-a-comparison-of-four-monocot-species
#4
Barbara R Evans, Garima Bali, Art Ragauskas, Riddhi Shah, Hugh O'Neill, Cory Howard, Fayola Lavenhouse, Dawn Ramirez, Kelly Weston, Kelly Ramey, Valerie Cangemi, Brian Kinney, Claudia Partee, Teresa Ware, Brian Davison
Exogenous phenylalanine stunted annual ryegrass but not switchgrass or winter grain rye, with deuterium incorporation up to 3% from phenyalanine-d 8 . Toxicity to duckweed varied with illumination intensity and glucose uptake. Isotopic labeling of biomolecules through biosynthesis from deuterated precursors has successfully been employed for both structural studies and metabolic analysis. Phenylalanine is the precursor of many products synthesized by plants, including the monolignols used for synthesis of lignin...
June 19, 2017: Planta
https://www.readbyqxmd.com/read/28630467/computational-method-allowing-hydrogen-deuterium-exchange-mass-spectrometry-at-single-amide-resolution
#5
Chris Gessner, Wieland Steinchen, Sabrina Bédard, John J Skinner, Virgil L Woods, Thomas J Walsh, Gert Bange, Dionysios P Pantazatos
Hydrogen-deuterium exchange (HDX) coupled with mass spectrometry (HDXMS) is a rapid and effective method for localizing and determining protein stability and dynamics. Localization is routinely limited to a peptide resolution of 5 to 20 amino acid residues. HDXMS data can contain information beyond that needed for defining protein stability at single amide resolution. Here we present a method for extracting this information from an HDX dataset to generate a HDXMS protein stability fingerprint. High resolution (HR)-HDXMS was applied to the analysis of a model protein of a spectrin tandem repeat that exemplified an intuitive stability profile based on the linkage of two triple helical repeats connected by a helical linker...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28629860/hydrogen-deuterium-exchange-kinetics-in-%C3%AE-lactoglobulin-epicatechin-complexes-studied-by-ftir-spectroscopy
#6
Francesca Caporaletti, Marina Carbonaro, Paola Maselli, Alessandro Nucara
Hydrogen-Deuterium exchange kinetics of of β-lactoglobulin and β-lactoglobulin (-)-epicatechin solutions has been investigated through the analysis of the amide I absorption band at 1650cm(-1) in the FTIR spectrum. H-D substitution in NH amides and residues of the protein results in a slight red-shift and in intensity changes of the amide I components: either these effects have been inspected in the framework of the Principal Components Analysis methods. The present analysis allowed to unveil three H-D kinetics at the timescale of the oligomeric fluctuations of the protein...
June 16, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28628739/predictive-validity-of-body-fat-percentage-by-bioimpedance-compared-with-deuterium-oxide-dilution-in-costa-rican-schoolchildren
#7
Juan Diego Zamora Salas, Adriana Laclé-Murray
OBJECTIVE: The purpose of this study was to verify the validity of body fat percentage (BF%) by bioelectrical impedance analysis (BIA) in a sample of Costa Rican schoolchildren. METHODS: The sample consisted of 52 male (mean age 8.1 ± 0.9 years) and 49 female (mean age 7.5 ± 1.0 years) schoolchildren. Deuterium oxide dilution was the reference method used as the "gold standard" to determine the fat mass (FM) expressed as BF%. Linear regression analyses and paired sample t-tests were used to test the association and mean differences between BIA and deuterium oxide dilution BF%...
June 19, 2017: American Journal of Human Biology: the Official Journal of the Human Biology Council
https://www.readbyqxmd.com/read/28628309/dissecting-orthosteric-contacts-for-a-reverse-fragment-based-ligand-design
#8
Arun Chandramohan, Nikhil Kumar Tulsian, Ganesh Srinivasan Anand
Orthosteric sites on proteins are formed typically from non-contiguous interacting sites in three dimensional space where the composite binding interaction of a biological ligand is mediated by multiple synergistic interactions of its constituent functional groups. Through these multiple interactions, ligands stabilize both the ligand binding site and the protein fold. However, relative energetic contributions of the individual contacts in these protein-ligand interactions are difficult to resolve. Deconvolution of the contributions of these various functional groups in natural inhibitors/ligand would greatly aid in iterative fragment-based drug discovery (FBDD)...
June 19, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28627884/hdx-ms-reveals-calcium-binding-properties-and-allosteric-regulation-of-downstream-regulatory-element-antagonist-modulator-dream
#9
Jun Zhang, Jing Li, Theodore A Craig, Rajiv Kumar, Michael L Gross
Downstream regulatory element antagonist modulator (DREAM) is an EF-hand Ca2+-binding protein that also binds to specific DNA sequence, downstream regulatory elements (DRE), and thereby regulates transcription in a calcium-dependent fashion. DREAM binds to DRE in the absence of Ca2+, but detaches from DRE under Ca2+ stimulation, allowing gene expression. The Ca2+-binding properties of DREAM and the consequences of the binding on protein structure are key to understanding the function of DREAM. Here we describe the application of hydrogen deuterium exchange mass spectrometry (HDX-MS) and site-directed mutagenesis to investigate the Ca2+ binding properties and the subsequent conformational changes of full length DREAM...
June 19, 2017: Biochemistry
https://www.readbyqxmd.com/read/28627053/recovery-of-insulin-sensitivity-and-optimal-body-composition-after-rapid-weight-loss-in-obese-dogs-fed-a-high-protein-medium-carbohydrate-diet
#10
A André, I Leriche, G Chaix, C Thorin, M Burger, P Nguyen
This study investigated the effects of an experimental high-protein medium-carbohydrate diet (protein level, 46% metabolizable energy, ME). First, postprandial plasma glucose and insulin kinetics were determined in steady-state overweight/obese Beagle dogs (28%-41% excess body weight) for an experimental high-protein medium-carbohydrate diet (protein level, 46% ME) and a commercial high-carbohydrate medium-protein diet (protein level, 24%ME) in obese dogs. Secondly, all the dogs were included in a weight loss programme...
June 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/28621749/surface-acoustic-wave-sensors-for-hydrogen-and-deuterium-detection
#11
Aurelian Marcu, Cristian Viespe
A delay-line-type surface acoustic wave (SAW) sensor based on a zinc oxide (ZnO) sensitive layer was developed. Two types of sensitive layers were obtained: ZnO nanowires and ZnO thin films, both deposited using laser methods (VLS-PLD and PLD, respectively) onto quartz substrates. The responses of sensors with two different nanowire lengths (300 and 600 nm) were compared with those of sensors with thin films of different thicknesses (ca. 100 and 200 nm) to different concentrations of hydrogen and deuterium...
June 16, 2017: Sensors
https://www.readbyqxmd.com/read/28621541/expanding-the-scope-of-electrophiles-capable-of-targeting-k-ras-oncogenes
#12
Lynn M McGregor, Meredith L Jenkins, Caitlin Kerwin, John E Burke, Kevan M Shokat
There is growing interest in reversible and irreversible covalent inhibitors that target noncatalytic amino acids in target proteins. With a goal of targeting oncogenic K-Ras variants (e.g., G12D) by expanding the types of amino acids that can be targeted by covalent inhibitors, we survey a set of electrophiles for their ability to label carboxylates. We functionalized an optimized ligand for the K-Ras switch II pocket with a set of electrophiles previously reported to react with carboxylates and characterized the ability of these compounds to react with model nucleophiles and oncogenic K-Ras proteins...
June 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28621526/orthogonal-mass-spectrometry-based-footprinting-for-epitope-mapping-and-structural-characterization-the-il-6-receptor-upon-binding-of-protein-therapeutics
#13
Ke Sherry Li, Guodong Chen, Jingjie Mo, Richard Y-C Huang, Ekaterina G Deyanova, Brett R Beno, Steve O'Neil, Adrienne A Tymiak, Michael L Gross
Higher order structure (HOS) is a crucial determinant for the biological functions and quality attributes of protein therapeutics. Mass spectrometry (MS)-based protein footprinting approaches play an important role in elucidating the relationship between protein biophysical properties and structure. Here, we describe the use of a combined method including hydrogen-deuterium exchange (HDX), fast photochemical oxidation of proteins (FPOP) and site-specific carboxyl group footprinting to investigate the HOS of protein and protein complexes...
June 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28615457/deconvoluting-amp-dependent-kinase-ampk-adenine-nucleotide-binding-and-sensing
#14
Xin Gu, Yan Yan, Scott J Novick, Amanda Kovich, Devrishi Goswami, Jiyuan Ke, M H Eileen Tan, Lili Wang, Xiaodan Li, Parker de Waal, Martin R Webb, Patrick R Griffin, H Eric Xu, Karsten Melcher
AMP-activated protein kinase (AMPK) is a central cellular energy sensor that adapts metabolism and growth to the energy state of the cell. AMPK senses the ratio of adenine nucleotides (adenylate energy charge) by competitive binding of AMP, ADP, and ATP to three sites (CBS1, CBS3, and CBS4) in its γ-subunit. Since these three binding sites are functionally interconnected, it remains unclear how nucleotides bind to individual sites, which nucleotides occupy each site under physiological conditions, and how binding to one site affects binding to the other sites...
June 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28614804/in-vivo-kinetics-and-nonradioactive-imaging-of-rapidly-proliferating-cells-in-graft-versus-host-disease
#15
Nataliya P Buxbaum, Donald E Farthing, Natella Maglakelidze, Martin Lizak, Hellmut Merkle, Andrea C Carpenter, Brittany U Oliver, Veena Kapoor, Ehydel Castro, Gregory A Swan, Liliane M Dos Santos, Nicolas J Bouladoux, Catherine V Bare, Francis A Flomerfelt, Michael A Eckhaus, William G Telford, Yasmine Belkaid, Remy J Bosselut, Ronald E Gress
Hematopoietic stem cell transplantation (HSCT) offers a cure for cancers that are refractory to chemotherapy and radiation. Most HSCT recipients develop chronic graft-versus-host disease (cGVHD), a systemic alloimmune attack on host organs. Diagnosis is based on clinical signs and symptoms, as biopsies are risky. T cells are central to the biology of cGVHD. We found that a low Treg/CD4+ T effector memory (Tem) ratio in circulation, lymphoid, and target organs identified early and established mouse cGVHD. Using deuterated water labeling to measure multicompartment in vivo kinetics of these subsets, we show robust Tem and Treg proliferation in lymphoid and target organs, while Tregs undergo apoptosis in target organs...
June 15, 2017: JCI Insight
https://www.readbyqxmd.com/read/28611361/discovery-of-a-novel-conformational-equilibrium-in-urokinase-type-plasminogen-activator
#16
Tobias Kromann-Hansen, Eva Louise Lange, Hans Peter Sørensen, Gholamreza Hassanzadeh-Ghassabeh, Mingdong Huang, Jan K Jensen, Serge Muyldermans, Paul J Declerck, Elizabeth A Komives, Peter A Andreasen
Although trypsin-like serine proteases have flexible surface-exposed loops and are known to adopt higher and lower activity conformations, structural determinants for the different conformations have remained largely obscure. The trypsin-like serine protease, urokinase-type plasminogen activator (uPA), is central in tissue remodeling processes and also strongly implicated in tumor metastasis. We solved five X-ray crystal structures of murine uPA (muPA) in the absence and presence of allosteric molecules and/or substrate-like molecules...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28611092/altering-metabolic-profiles-of-drugs-by-precision-deuteration-2-discovery-of-a-deuterated-analog-of-ivacaftor-with-differentiated-pharmacokinetics-for-clinical-development
#17
Scott L Harbeson, Adam J Morgan, Julie F Liu, Ara M Aslanian, Sophia Nguyen, Gary W Bridson, Christopher L Brummel, Lijun Wu, Roger D Tung, Lana Pilja, Virginia Braman, Vinita Uttamsingh
Ivacaftor is currently used for the treatment of cystic fibrosis as both monotherapy (Kalydeco®) and combination therapy with lumacaftor (Orkambi®). Each therapy targets specific patient populations: Kalydeco treats patients carrying one of nine gating mutations in the cystic fibrosis transmembrane conductance regulator protein (CFTR), while Orkambi treats patients homozygous for the F508del CFTR mutation. In this study, we explored the pharmacological and metabolic effects of precision deuteration chemistry on ivacaftor by synthesizing two novel deuterated ivacaftor analogs, CTP-656 (d9-ivacaftor) and d18-ivacaftor...
June 13, 2017: Journal of Pharmacology and Experimental Therapeutics
https://www.readbyqxmd.com/read/28607395/on-the-phonon-dissipation-contribution-to-nanoscale-friction-by-direct-contact
#18
S R Sales de Mello, M E H Maia da Costa, C M Menezes, C D Boeira, F L Freire, F Alvarez, C A Figueroa
The friction phenomenon is a ubiquitous manifestation of nature. Models considering phononic, electronic, magnetic, and electrostatic interactions are invoked to explain the fundamental forces involved in the friction phenomenon. In order to establish the incidence of the phonon prompting at the nanoscale friction by direct contact, we study a diamond spherical dome sliding on carbon thin films containing different amount of deuterium and hydrogen. The friction coefficient decreases by substituting hydrogen by deuterium atoms...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28607185/isotopic-tracing-of-hydrogen-transport-and-trapping-in-nuclear-materials
#19
Jacques Chêne, Frantz Martin
Some illustrations of the use of deuterium or tritium for isotopic tracing of hydrogen absorption, transport and trapping in nuclear materials are presented. Isotopic tracing of hydrogen has been shown to be successful for the determination of the boundaries conditions for hydrogen desorption or absorption in a material exposed to a hydrogen source. Also, the unique capabilities of isotopic tracing and related techniques to characterize H interactions with point defects and dislocations acting as moving traps has been demonstrated...
July 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28606987/the-fate-and-lifespan-of-human-monocyte-subsets-in-steady-state-and-systemic-inflammation
#20
Amit A Patel, Yan Zhang, James N Fullerton, Lies Boelen, Anthony Rongvaux, Alexander A Maini, Venetia Bigley, Richard A Flavell, Derek W Gilroy, Becca Asquith, Derek Macallan, Simon Yona
In humans, the monocyte pool comprises three subsets (classical, intermediate, and nonclassical) that circulate in dynamic equilibrium. The kinetics underlying their generation, differentiation, and disappearance are critical to understanding both steady-state homeostasis and inflammatory responses. Here, using human in vivo deuterium labeling, we demonstrate that classical monocytes emerge first from marrow, after a postmitotic interval of 1.6 d, and circulate for a day. Subsequent labeling of intermediate and nonclassical monocytes is consistent with a model of sequential transition...
June 12, 2017: Journal of Experimental Medicine
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