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https://www.readbyqxmd.com/read/28445832/study-of-the-mechanism-of-protonated-histidine-induced-conformational-changes-in-the-zika-virus-dimeric-envelope-protein-using-accelerated-molecular-dynamic-simulations
#1
Jixue Sun, Yang Li, Pi Liu, Jianping Lin
The Zika virus has drawn worldwide attention because of the epidemic diseases it causes. It is a flavivirus that has an icosahedral protein shell constituted by an envelope glycoprotein (E-protein) and membrane protein (M-protein) in the mature virion. The multistep process of membrane fusion to infect the host cell is pH-induced. To understand the mechanism of the conformational changes in the (E-M)2 protein homodimer embedded in the membrane, two 200-ns accelerated dynamic simulations were performed under different pH conditions...
April 13, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28445648/electron-radiolysis-of-ammonium-perchlorate-a-reflectron-time-of-flight-mass-spectrometric-study
#2
Sándor Góbi, Alexandre Bergantini, Andrew M Turner, Ralf I Kaiser
Thin films of ammonium perchlorate (NH4ClO4) were exposed to energetic electrons at 5.5 K to explore the radiolytic decomposition mechanisms. The effects of radiolysis were monitored on line and in situ via Fourier-transform infrared spectroscopy (FTIR) in the condensed phase along with electron impact ionization quadrupole mass spectrometry (EI-QMS) and single-photon photoionization reflectron time-of-flight mass spectrometry (PI-ReTOF-MS) during the temperature programmed desorption (TPD) phase to probe the subliming molecules...
April 26, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28445397/radiation-and-thyroid-cancer
#3
REVIEW
Elisabetta Albi, Samuela Cataldi, Andrea Lazzarini, Michela Codini, Tommaso Beccari, Francesco Saverio Ambesi-Impiombato, Francesco Curcio
Radiation-induced damage is a complex network of interlinked signaling pathways, which may result in apoptosis, cell cycle arrest, DNA repair, and cancer. The development of thyroid cancer in response to radiation, from nuclear catastrophes to chemotherapy, has long been an object of study. A basic overview of the ionizing and non-ionizing radiation effects of the sensitivity of the thyroid gland on radiation and cancer development has been provided. In this review, we focus our attention on experiments in cell cultures exposed to ionizing radiation, ultraviolet light, and proton beams...
April 26, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28445288/association-between-proton-pump-inhibitors-and-hepatic-encephalopathy-a-meta-analysis
#4
Jin Bian, Anqiang Wang, Jianzhen Lin, Liangcai Wu, Hanchun Huang, Shanshan Wang, Xiaobo Yang, Xin Lu, Yiyao Xu, Haitao Zhao
BACKGROUND & AIMS: Several studies have shown that proton pump inhibitors (PPIs) use can increase the risk of developing hepatic encephalopathy (HE) in patients with liver dysfunction. However, no definite conclusion is drawn because of study design limitations. Therefore, we conducted a meta-analysis to explore the association between PPIs and HE. METHODS: We searched PubMed, EMBASE, and the Cochrane Library from inception until November 2016. Data from the identified studies were combined using a random effects model, and odds ratios (ORs) were calculated...
April 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28445189/proton-pump-inhibitor-responsive-esophageal-eosinophilia-still-a-valid-diagnosis
#5
Javier Molina-Infante, Pedro L Gonzalez-Cordero, Alfredo J Lucendo
PURPOSE OF REVIEW: To update rapidly evolving concepts regarding the controversial entity of 'proton pump inhibitor (PPI)-responsive esophageal eosinophilia,' referring to patients with clinical, endoscopic and histologic features of eosinophilic esophagitis (EoE) who achieve remission on PPI therapy. RECENT FINDINGS: Up to half of pediatric and adult patients with typical EoE symptoms and histology achieve clinico-pathologic remission on PPI therapy, irrespective of whether esophageal pH monitoring demonstrates abnormal acid reflux...
April 25, 2017: Current Opinion in Gastroenterology
https://www.readbyqxmd.com/read/28445031/importance-of-loop-l1-dynamics-for-substrate-capture-and-catalysis-in-pseudomonas-aeruginosa-d-arginine-dehydrogenase
#6
Daniel Ouedraogo, Michael Souffrant, Sheena Vasquez, Donald Hamelberg, Giovanni Gadda
Mobile loops located at the active site entrance in enzymes often participate in conformational changes required to shield the reaction from bulk solvent, to control substrate access to the active site, and to position residues for substrate binding and catalysis. In D-arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) previous crystallographic data suggested that residues 45-47 in the FAD-binding domain and 50-56 in the substrate-binding domain in loop L1 could adopt two distinct conformations. In this study, we have used molecular dynamics, kinetics, and fluorescence spectroscopy on the S45A and A46G enzyme variants of PaDADH to investigate the impact of mutations of loop L1 on the catalytic function of the enzyme...
April 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28444914/dynamic-nuclear-polarization-studies-on-deuterated-nitroxyl-spin-probes
#7
David Jebaraj D, Hideo Utsumi, Milton Franklin Benial A
Detailed dynamic nuclear polarization and electron spin resonance studies were carried out for 3-carbamoyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl, 3-carboxy-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl,3-methoxycarbonyl-2,2,5,5-tetramethy pyrolidine-1-oxyl nitroxyl radicals and their corresponding deuterated nitroxyl radicals, used in Overhauser-enhanced magnetic resonance imaging for the first time. The dynamic nuclear polarization parameters such as DNP factor, longitudinal relaxivity, saturation parameter, leakage factor and coupling factor were estimated for deuterated nitroxyl radicals...
April 26, 2017: Magnetic Resonance in Chemistry: MRC
https://www.readbyqxmd.com/read/28444892/catalytic-mechanism-of-salicylate-dioxygenase-qm-mm-simulations-reveal-the-origin-of-unexpected-regiospecificity-of-the-ring-cleavage
#8
Subhendu Roy, Johannes Kästner
Salicylate 1,2-Dioxygenase (SDO) is the first enzyme discovered, in the family of iron dioxygenases, to catalyze the ring cleavage of a monohydroxylated aromatic compound, salicylate, without a proton donor. Salicylate is not electron-rich like the familiar dihydroxy or aromatic substrates with an electron donating group that are utilized in the well-known dioxygenases. We investigated the full catalytic mechanism of SDO by a combination of Quantum Mechanics and Molecular Mechanics (QM/MM) calculations. We unravel the basis for the unexpected 'intra' cleavage regioselectivity in SDO...
April 26, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28444840/topas-simulation-of-the-mevion-s250-compact-proton-therapy-unit
#9
Michael Prusator, Salahuddin Ahmad, Yong Chen
As proton therapy becomes increasingly popular, so does the need for Monte Carlo simulation studies involving accurate beam line modeling of proton treatment units. In this study, the 24 beam configurations of the Mevion S250 proton therapy system installed recently at our institution were modeled using the TOolkit for PArticle Simulation (TOPAS) code. Pristine Bragg peak, spread out Bragg peak (SOBP), and lateral beam profile dose distributions were simulated and matched to the measurements taken during commissioning of the unit...
April 26, 2017: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28444419/the-role-of-localized-acidity-generation-in-microbially-influenced-corrosion
#10
REVIEW
Yuriy Kryachko, Sean M Hemmingsen
Microbially influenced corrosion is of great industrial concern. Microbial coupling of metal oxidation to sulfate-, nitrate-, nitrite-, or CO2-reduction is proton-mediated, and some sulfate-reducing prokaryotes are capable of regulating extracellular pH. The analysis of the corrosive processes catalyzed by nitrate reducing bacteria and methanogenic archaea indicates that these microorganisms may be capable of regulating extracellular pH as well. It is proposed that nutrient limitation at metal-biofilm interfaces may induce activation of enzymatic proton-producing/proton-secreting functions in respiratory and methanogenic microorganisms to make them capable of using Fe(0) as the electron donor...
April 26, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28444374/measurement-of-neutron-ambient-dose-equivalent-in-proton-radiotherapy-with-line-scanning-and-wobbling-mode-treatment-system
#11
Sangmin Lee, Chaeyeong Lee, Eun Hyuk Shin, Sungkoo Cho, Dae-Hyun Kim, Youngyih Han, Doo Ho Choi, Sung-Joon Ye, Jin Sung Kim
The primary objective of this study was to measure secondary neutron dose during proton therapy using a detector that covers the entire neutron energy range produced in proton therapy. We analyzed and compared the neutron dose during proton treatment with passive scattering and line scanning. The neutron ambient dose equivalents were measured with a 190 MeV wobbling and line-scanning proton beam. The center of a plastic water phantom (30 × 30 × 60 cm3) was placed at the isocenter. A Wide-Energy Neutron Detection Instrument (WENDI-2) was located 1m from the isocenter at four different angles (0°, 45°, 90° and 135°)...
April 24, 2017: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/28443910/spin-state-variability-in-fe-2-complexes-of-substituted-2-pyridin-2-yl-1-10-phenanthroline-ligands-as-versatile-terpyridine-analogues
#12
Holm Petzold, Paul Djomgoue, Gerald Hörner, Silvio Heider, Charles Lochenie, Birgit Weber, Tobias Rüffer, Dieter Schaarschmidt
Fe(2+) spin crossover complexes [Fe(L)2](2+) (L = 2-(6-R(1)-pyridin-2-yl)-1,10-phenanthroline with R(1) = H, methoxy, bromo, -(1H-pyrazol-1-yl) or L = 2-(3-methoxy-pyridin-2-yl)-1,10-phenanthroline) were prepared. These air stable and durable complexes show SCO behaviour with very different transition temperatures T1/2 ranging from 130 K to 600 K depending on the substitution pattern. The use of (1)H NMR spectroscopy to elucidate the thermodynamics and kinetics of SCO in a solution of this series is described in detail...
April 26, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28443892/near-infrared-fluorescent-dyes-with-large-stokes-shifts-light-generation-in-bodipys-undergoing-excited-state-intramolecular-proton-transfer
#13
Qiang Fei, Xianfeng Gu, Yajing Liu, Ben Shi, Hengyan Liu, Ge Xu, Chunbao Li, Ping Shi, Chunchang Zhao
Novel BODIPYs undergoing excited state intramolecular proton transfer are reported. The molecules afford NIR emission with a large Stokes shift and possess a free hydroxyl unit that is easy to functionalize, allowing the dyes to be exploited as a valuable scaffold in probe design.
April 26, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28443663/host-guest-interactions-accompanying-the-encapsulation-of-1-4-diazabicyclo-2-2-2-octane-within-endo-functionalized-macrocycles
#14
Dipali N Lande, Maneesha N Shewale, Shridhar P Gejji
Binding of novel endo-functionalized bis-urea/thiourea molecular receptors toward neutral 1,4-diazabicyclo[2.2.2]octane (DABCO) demonstrating stronger binding of the bis-thiourea macrocycles than their urea analogues by employing M06-2X/6-31+G(d,p) based density functional theory. The formation of such inclusion complexes is spontaneous, thermodynamically favorable and facilitated via the bifurcated N-H•••N•••H-N hydrogen bonding, C-H•••π, dipole-dipole and other non-covalent interactions, which reflect in the 'frequency shift' of their characteristic N-H vibrations in the calculated vibrational spectra of these complexes...
April 26, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28443626/nanodiamond-enhanced-mri-via-in-situ-hyperpolarization
#15
David E J Waddington, Mathieu Sarracanie, Huiliang Zhang, Najat Salameh, David R Glenn, Ewa Rej, Torsten Gaebel, Thomas Boele, Ronald L Walsworth, David J Reilly, Matthew S Rosen
Nanodiamonds are of interest as nontoxic substrates for targeted drug delivery and as highly biostable fluorescent markers for cellular tracking. Beyond optical techniques, however, options for noninvasive imaging of nanodiamonds in vivo are severely limited. Here, we demonstrate that the Overhauser effect, a proton-electron polarization transfer technique, can enable high-contrast magnetic resonance imaging (MRI) of nanodiamonds in water at room temperature and ultra-low magnetic field. The technique transfers spin polarization from paramagnetic impurities at nanodiamond surfaces to (1)H spins in the surrounding water solution, creating MRI contrast on-demand...
April 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28443330/mechanisms-by-which-salt-concentration-moderates-the-dynamics-of-human-serum-transferrin
#16
Haleh Abdizadeh, Ali Rana Atilgan, Canan Atilgan
The dynamical and thermodynamic behavior of human transferrin (hTf) protein in saline aqueous solution of various concentrations is studied. hTf is an essential transport protein circulating iron in the blood and delivering it to tissues. It displays highly pH dependent cooperativity between the two lobes each carrying an iron, and forms a tight complex with the receptor during endocytosis, eventually recycled to the serum after iron release. Molecular dynamics simulations are used to investigate the effects of the amount of salt on protein conformation and dynamics to analyze the structure-function relationship in free hTf at serum pH...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28443327/acidity-triggered-tumor-retention-internalization-of-chimeric-peptide-for-enhanced-photodynamic-therapy-and-real-time-monitoring-of-therapeutic-effects
#17
Kai Han, Wei-Yun Zhang, Zhao-Yu Ma, Shi-Bo Wang, Lu-Ming Xu, Jia Liu, Xianzheng Zhang, Heyou Han
Photodynamic therapy (PDT) holds great promise in tumor treatment. Nevertheless, it remains highly desirable to develop easy-to-fabricated PDT systems with improved tumor accumulation/internalization and timely therapeutic feedback. Here, we report a tumor acidity responsive chimeric peptide for enhanced PDT and noninvasively real-time apoptosis imaging. Both in vitro and in vivo studies revealed that tumor mildly acidic microenvironment could trigger rapid protonation of carboxylate anion in chimeric peptide, which led to increased zeta potential, improved hydrophobicity, controlled size enlargement and precise morphology switch from sphere to spherocylinder shape of chimeric peptide...
April 26, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28443028/improved-model-of-proton-pump-crystal-structure-obtained-by-interactive-molecular-dynamics-flexible-fitting-expands-the-mechanistic-model-for-proton-translocation-in-p-type-atpases
#18
Dorota Focht, Tristan I Croll, Bjorn P Pedersen, Poul Nissen
The plasma membrane H(+)-ATPase is a proton pump of the P-type ATPase family and essential in plants and fungi. It extrudes protons to regulate pH and maintains a strong proton-motive force that energizes e.g., secondary uptake of nutrients. The only crystal structure of a H(+)-ATPase (AHA2 from Arabidopsis thaliana) was reported in 2007. Here, we present an improved atomic model of AHA2, obtained by a combination of model rebuilding through interactive molecular dynamics flexible fitting (iMDFF) and structural refinement based on the original data, but using up-to-date refinement methods...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28442805/proton-pump-inhibitors-are-associated-with-a-reduced-likelihood-for-sexually-transmitted-diseases-in-women-in-the-emergency-department
#19
Johnathan Michael Sheele, Nathan Morris, Donald Byars, Frank Counselman
BACKGROUND: Proton pump inhibitors (PPIs) have been shown in cell culture to kill Trichomonas vaginalis (TV) at lower half maximal inhibitory concentration values than metronidazole (Flagyl), the most common medication used to treat the infection. However, there have been no previous clinical investigations to determine if PPIs are associated with reduced risk for TV. MATERIALS AND METHODS: We examined the records of female patients who received testing in the emergency department for TV, Neisseria gonorrhoea (GC), and Chlamydia trachomatis (CT) between 2010 and 2014 at two academic medical centers to determine if PPI and histamine type 2 receptor antagonist (H2RA) drugs were associated with TV and GC/CT infections...
January 2017: Indian Journal of Sexually Transmitted Diseases
https://www.readbyqxmd.com/read/28442567/perfect-chemomechanical-coupling-of-fof1-atp-synthase
#20
Naoki Soga, Kazuya Kimura, Kazuhiko Kinosita, Masasuke Yoshida, Toshiharu Suzuki
FoF1-ATP synthase (FoF1) couples H(+) flow in Fo domain and ATP synthesis/hydrolysis in F1 domain through rotation of the central rotor shaft, and the H(+)/ATP ratio is crucial to understand the coupling mechanism and energy yield in cells. Although H(+)/ATP ratio of the perfectly coupling enzyme can be predicted from the copy number of catalytic β subunits and that of H(+) binding c subunits as c/β, the actual H(+)/ATP ratio can vary depending on coupling efficiency. Here, we report actual H(+)/ATP ratio of thermophilic Bacillus FoF1, whose c/β is 10/3...
April 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
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