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https://www.readbyqxmd.com/read/28211014/comprehensive-peptide-ion-structure-studies-using-ion-mobility-techniques-part-1-an-advanced-protocol-for-molecular-dynamics-simulations-and-collision-cross-section-calculation
#1
Samaneh Ghassabi Kondalaji, Mahdiar Khakinejad, Amirmahdi Tafreshian, Stephen J Valentine
Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics...
February 16, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28208655/experimental-evidence-and-in-silico-identification-of-tryptophan-decarboxylase-in-citrus-genus
#2
Luigi De Masi, Domenico Castaldo, Domenico Pignone, Luigi Servillo, Angelo Facchiano
Plant tryptophan decarboxylase (TDC) converts tryptophan into tryptamine, precursor of indolealkylamine alkaloids. The recent finding of tryptamine metabolites in Citrus plants leads to hypothesize the existence of TDC activity in this genus. Here, we report for the first time that, in Citrus x limon seedlings, deuterium labeled tryptophan is decarboxylated into tryptamine, from which successively deuterated N,N,N-trimethyltryptamine is formed. These results give an evidence of the occurrence of the TDC activity and the successive methylation pathway of the tryptamine produced from the tryptophan decarboxylation...
February 11, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28208418/mixing-with-applications-to-inertial-confinement-fusion-implosions
#3
V Rana, H Lim, J Melvin, J Glimm, B Cheng, D H Sharp
Approximate one-dimensional (1D) as well as 2D and 3D simulations are playing an important supporting role in the design and analysis of future experiments at National Ignition Facility. This paper is mainly concerned with 1D simulations, used extensively in design and optimization. We couple a 1D buoyancy-drag mix model for the mixing zone edges with a 1D inertial confinement fusion simulation code. This analysis predicts that National Ignition Campaign (NIC) designs are located close to a performance cliff, so modeling errors, design features (fill tube and tent) and additional, unmodeled instabilities could lead to significant levels of mix...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28205309/a-feasibility-study-of-a-deuterium-deuterium-neutron-generator-based-boron-neutron-capture-therapy-system-for-treatment-of-brain-tumors
#4
Mindy Hsieh, Yingzi Liu, Farshad Mostafaei, Jean M Poulson, Linda H Nie
PURPOSE: Boron neutron capture therapy (BNCT) is a binary treatment modality that uses high LET particles to achieve tumor cell killing. Deuterium-deuterium (DD) compact neutron generators have advantages over nuclear reactors and large accelerators as the BNCT neutron source, such as their compact size, low cost, and relatively easy installation. The purpose of this study is to design a beam shaping assembly (BSA) for a DD neutron generator and assess the potential of a DD-based BNCT system using Monte Carlo (MC) simulations...
February 2017: Medical Physics
https://www.readbyqxmd.com/read/28203656/iron-ii-catalyzed-sulfur-directed-c-sp-3-h-bond-amination-c-s-cross-coupling-reaction
#5
Fang-Fang Duan, Shi-Qian Song, Run-Sheng Xu
An efficient iron(ii)-catalyzed sulfur directed C(sp(3))-H bond amination/C-S cross coupling reaction has been developed. The reaction had high tolerance of functional groups under moderate conditions. The results of a deuterium labeling study and in situ ESI-MS experiments indicated that the reaction mechanism probably corresponds to a Fe(ii)/Fe(iii) catalytic cycle.
February 16, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28199104/cobalt-catalyzed-1-1-diboration-of-terminal-alkynes-scope-mechanism-and-synthetic-applications
#6
Simon Krautwald, Mate J Bezdek, Paul J Chirik
A cobalt-catalyzed method for the 1,1-diboration of terminal alkynes with bis(pinacolato)diboron (B2Pin2) is described. The reaction proceeds efficiently at 23 °C with excellent 1,1-selectivity and broad functional group tolerance. With the unsymmetrical diboron reagent PinB-BDan (Dan = naphthalene-1,8-diaminato), stereoselective 1,1-diboration provided products with two boron substituents that exhibit differential reactivity. One example prepared by diboration of 1-octyne was crystallized and its stereochemistry established by X-ray crystallography...
February 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28194737/regio-selective-intramolecular-hydrogen-deuterium-exchange-in-gas-phase-electron-transfer-dissociation
#7
Yoshitomo Hamuro
Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium...
February 13, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28193043/removal-of-n-linked-glycosylations-at-acidic-ph-by-pngase-a-facilitates-hydrogen-deuterium-exchange-mass-spectrometry-analysis-of-n-linked-glycoproteins
#8
Pernille Foged Jensen, Gerard Comamala, Morten Beck Trelle, Jeppe Buur Madsen, Thomas J D Jørgensen, Kasper D Rand
Protein glycosylation is the most frequent post-translational modification and is present on more than 50% of eukaryotic proteins. Glycosylation covers a wide subset of modifications involving many types of complex oligosaccharide structures, making structural analysis of glycoproteins and their glycans challenging for most analytical techniques. Hydrogen/deuterium exchange monitored by mass spectrometry is a sensitive technique for investigation of protein conformational dynamics of complex heterogeneous proteins in solution...
December 20, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/28193005/mapping-the-energetic-epitope-of-an-antibody-interleukin-23-interaction-with-hydrogen-deuterium-exchange-fast-photochemical-oxidation-of-proteins-mass-spectrometry-and-alanine-shave-mutagenesis
#9
Jing Li, Hui Wei, Stanley R Krystek, Derek Bond, Ty M Brender, Daniel Cohen, Jena Feiner, Nels Hamacher, Johanna Harshman, Richard Y-C Huang, Susan H Julien, Zheng Lin, Kristina Moore, Luciano Mueller, Claire Noriega, Preeti Sejwal, Paul Sheppard, Brenda Stevens, Guodong Chen, Adrienne A Tymiak, Michael L Gross, Lumelle A Schneeweis
Epitope mapping the specific residues of an antibody/antigen interaction can be used to support mechanistic interpretation, antibody optimization, and epitope novelty assessment. Thus, there is a strong need for mapping methods, particularly integrative ones. Here, we report the identification of an energetic epitope by determining the interfacial hot-spot that dominates the binding affinity for an anti-interleukin-23 (anti-IL-23) antibody by using the complementary approaches of hydrogen/deuterium exchange mass spectrometry (HDX-MS), fast photochemical oxidation of proteins (FPOP), alanine shave mutagenesis, and binding analytics...
February 9, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28186093/conformational-changes-in-intact-dengue-virus-reveal-serotype-specific-expansion
#10
Xin-Xiang Lim, Arun Chandramohan, Xin Ying Elisa Lim, Nirmalya Bag, Kamal Kant Sharma, Melissa Wirawan, Thorsten Wohland, Shee-Mei Lok, Ganesh S Anand
Dengue virus serotype 2 (DENV2) alone undergoes structural expansion at 37 °C (associated with host entry), despite high sequence and structural homology among the four known serotypes. The basis for this differential expansion across strains and serotypes is unknown and necessitates mapping of the dynamics of dengue whole viral particles to describe their coordinated motions and conformational changes when exposed to host-like environments. Here we capture the dynamics of intact viral particles of two serotypes, DENV1 and DENV2, by amide hydrogen/deuterium exchange mass spectrometry (HDXMS) and time resolved Förster Resonance Energy Transfer...
February 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28183147/synthesis-of-1%C3%AE-hydroxydeoxycholic-acid-in-h-2-and-unlabeled-forms
#11
Martin A Hayes, Ieuan Roberts, Gunnar Grönberg, Kexin Lv, Baorui Lin, Jonas Bergare, Charles S Elmore
1β-hydroxydeoxycholic acid in unlabeled and stable isotope labeled forms was required for use as a biomarker for Cytochrome P450 3A4/5. A lengthy synthesis was undertaken to deliver the unlabeled compound and in the process, to develop a route to the deuterium labeled compound. The synthesis of the unlabeled compound was completed, but in very low yield. Concurrent with the synthetic approach, a biosynthetic route was pursued and this approach proved to be much more rapid and afforded the compound in both unlabeled and deuterium labeled forms in a one-step oxidation from deoxycholic acid and [D4 ]deoxycholic acid respectively...
February 9, 2017: Journal of Labelled Compounds & Radiopharmaceuticals
https://www.readbyqxmd.com/read/28178031/effect-of-ugt2b10-ugt2b17-fmo3-and-oct2-genetic-variation-on-nicotine-and-cotinine-pharmacokinetics-and-smoking-in-african-americans
#12
Taraneh Taghavi, Gideon St Helen, Neal L Benowitz, Rachel F Tyndale
OBJECTIVES: Nicotine metabolism rates differ considerably among individuals, even after controlling for variation in the major nicotine-metabolizing enzyme, CYP2A6. In this study, the impact of genetic variation in alternative metabolic enzymes and transporters on nicotine and cotinine (COT) pharmacokinetics and smoking was investigated. METHODS: We examined the impact of UGT2B10, UGT2B17, FMO3, NAT1, and OCT2 variation on pharmacokinetics and smoking (total nicotine equivalents and topography) before and after stratifying by CYP2A6 genotype in 60 African American (AA) smokers who received a simultaneous intravenous infusion of deuterium-labeled nicotine and COT...
February 7, 2017: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/28171682/unusual-electrospray-ionization-induced-fragmentation-structural-elucidation-of-an-in-process-synthetic-intermediate-of-doravirine-mk-1439-using-lc-hrms-ms-and-2d-nmr
#13
Huaming Sheng, Katrina W Lexa, Li-Kang Zhang, Rong-Sheng Yang, Timothy J Wright, Benjamin D Sherry, Roy Helmy, Gary E Martin
RATIONALE: During the development of a novel synthetic route to doravirine; (1), a human immunodeficiency type 1 virus (HIV-1) nonnucleoside reverse transcriptase inhibitor (NNRTI), an unanticipated reaction intermediate, methyl (Z)-2-(3-chloro-5-cyanophenoxy)-5-(3-(3-chloro-5-cyanophenoxy)-2-oxo-4-(trifluoromethyl)pyridin-1(2H)-yl)-5-ethoxy-3-(trifluoromethyl)pent-2-enoate (2), was isolated. Moreover, the unusual ESI induced fragmentation was observed for 2. Hence, efforts were made towards the understanding of the structure of 2, which was crucial for the understanding of the reaction mechanism...
February 7, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28170222/nitric-oxide-induced-conformational-changes-govern-h-nox-and-histidine-kinase-interaction-and-regulation-in-shewanella-oneidensis
#14
Minxi Rao, Mark A Herzik, Anthony T Iavarone, Michael A Marletta
Nitric oxide (NO) is implicated in biofilm regulation in several bacterial families via heme-nitric oxide/oxygen binding (H-NOX) protein signaling. The Shewanella oneidensis H-NOX (So H-NOX) is associated with a histidine kinase (So HK) encoded on the same operon, and together form a multi-component signaling network whereby the NO-bound state of So H-NOX inhibits So HK autophosphorylation activity. Although the conformational changes of So H-NOX upon NO binding have been structurally characterized, the mechanism of HK inhibition by NO-bound So H-NOX remains unclear...
February 7, 2017: Biochemistry
https://www.readbyqxmd.com/read/28168880/increased-%C3%AE-sheet-dynamics-and-d-e-loop-repositioning-are-necessary-for-cu-ii-induced-amyloid-formation-by-%C3%AE-2-microglobulin
#15
Nicholas B Borotto, Zhe Zhang, Jia Dong, Brittney Burant, Richard W Vachet
β-2-microglobulin (β2m) forms amyloid fibrils in the joints of patients undergoing dialysis treatment as a result of kidney failure. One of the ways in which β2m can be induced to form amyloid fibrils in vitro is via incubation with stoichiometric amounts of Cu(II). To better understand the structural changes caused by Cu(II) binding that allow β2m to form amyloid fibrils, we compared the effect of Ni(II) and Zn(II) binding, which are two similarly-sized divalent metal ions that do not induce β2m amyloid formation...
February 7, 2017: Biochemistry
https://www.readbyqxmd.com/read/28167786/functional-importance-of-stripping-in-nf%C3%AE%C2%BAb-signaling-revealed-by-a-stripping-impaired-i%C3%AE%C2%BAb%C3%AE-mutant
#16
Holly E Dembinski, Kevin Wismer, Jesse D Vargas, Gajendra W Suryawanshi, Nadja Kern, Gerard Kroon, H Jane Dyson, Alexander Hoffmann, Elizabeth A Komives
Stress-response transcription factors such as NFκB turn on hundreds of genes and must have a mechanism for rapid cessation of transcriptional activation. We recently showed that the inhibitor of NFκB signaling, IκBα, dramatically accelerates the dissociation of NFκB from transcription sites, a process we have called "stripping." To test the role of the IκBα C-terminal PEST (rich in proline, glutamic acid, serine, and threonine residues) sequence in NFκB stripping, a mutant IκBα was generated in which five acidic PEST residues were mutated to their neutral analogs...
February 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28167755/conformational-disruption-of-pi3k%C3%AE-regulation-by-immunodeficiency-mutations-in-pik3cd-and-pik3r1
#17
Gillian L Dornan, Braden D Siempelkamp, Meredith L Jenkins, Oscar Vadas, Carrie L Lucas, John E Burke
Activated PI3K Delta Syndrome (APDS) is a primary immunodeficiency disease caused by activating mutations in either the leukocyte-restricted p110δ catalytic (PIK3CD) subunit or the ubiquitously expressed p85α regulatory (PIK3R1) subunit of class IA phosphoinositide 3-kinases (PI3Ks). There are two classes of APDS: APDS1 that arises from p110δ mutations that are analogous to oncogenic mutations found in the broadly expressed p110α subunit and APDS2 that occurs from a splice mutation resulting in p85α with a central deletion (Δ434-475)...
February 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28167534/detection-of-lipid-induced-structural-changes-of-the-marburg-virus-matrix-protein-vp40-using-hydrogen-deuterium-exchange-mass-spectrometry
#18
Kaveesha J Wijesinghe, Sarah Urata, Nisha Bhattarai, Edgar E Kooijman, Bernard S Gerstman, Prem P Chapagain, Sheng Li, Robert V Stahelin
Marburg virus (MARV) is a lipid-enveloped virus from the Filoviridae family containing a negative sense RNA genome. One of the seven MARV genes encodes the matrix protein VP40, which forms a matrix layer beneath the plasma membrane inner leaflet to facilitate budding from the host cell. MARV VP40 (mVP40) has been shown to be a dimeric peripheral protein with a broad and flat basic surface that can associate with anionic phospholipids such as phosphatidylserine. While a number of mVP40 cationic residues have been shown to facilitate binding to membranes containing anionic lipids, much less is known on how mVP40 assembles to form the matrix layer following membrane binding...
February 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28165769/applications-of-deuterium-oxide-in-human-health
#19
Wendell Costa Bila, Reysla Maria da Silveira Mariano, Valmin Ramos Silva, Maria Emília Soares Martins Dos Santos, Joel Alves Lamounier, Eduardo Ferriolli, Alexsandro Sobreira Galdino
The main aim goal of this review was to gather information about recent publications related to deuterium oxide (D2O), and its use as a scientific tool related to human health. Searches were made in electronic databases Pubmed, Scielo, Lilacs, Medline and Cochrane. Moreover, the following patent databases were consulted: EPO (Espacenet patent search), USPTO (United States Patent and Trademark Office) and Google Patents, which cover researches worldwide related to innovations using D2O.
February 6, 2017: Isotopes in Environmental and Health Studies
https://www.readbyqxmd.com/read/28165752/mechanism-of-me-re-bond-addition-to-platinum-ii-and-dioxygen-activation-by-the-resulting-pt-re-bimetallic-center
#20
Kothanda Rama Pichaandi, Lara Kabalan, Hashem Amini, Guanghui Zhang, Hanyu Zhu, Hilkka I Kenttämaa, Phillip E Fanwick, Jeffrey T Miller, Sabre Kais, S Masoud Nabavizadeh, Mehdi Rashdi, Mahdi M Abu-Omar
Unusual cis-oxidative addition of methyltrioxorhenium (MTO) to [PtMe2(bpy)], (bpy = 2,2'-bipyridine) (1) is described. Addition of MTO to 1 first gives the Lewis acid-base adduct [(bpy)Me2Pt-Re(Me)(O)3] (2) and subsequently affords the oxidative addition product [(bpy)Me3PtReO3] (3). All complexes 1, MTO, 2, and 3 are in equilibrium in solution. The structure of 2 was confirmed by X-ray crystallography, and its dissociation constant in solution is 0.87 M. The structure of 3 was confirmed by extended X-ray absorption fine structure and X-ray absorption near-edge structure in tandem with one- and two-dimensional NMR spectroscopy augmented by deuterium and (13)C isotope-labeling studies...
February 20, 2017: Inorganic Chemistry
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