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https://www.readbyqxmd.com/read/27933420/comparative-simulation-study-of-chemical-synthesis-of-functional-dadne-material
#1
Min Hsien Liu, Chuan Wen Liu
Amorphous molecular simulation to model the reaction species in the synthesis of chemically inert and energetic 1,1-diamino-2,2-dinitroethene (DADNE) explosive material was performed in this work. Nitromethane was selected as the starting reactant to undergo halogenation, nitration, deprotonation, intermolecular condensation, and dehydration to produce the target DADNE product. The Materials Studio (MS) forcite program allowed fast energy calculations and reliable geometric optimization of all aqueous molecular reaction systems (0...
January 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/27933298/non-targeted-plasma-metabolome-of-early-and-late-lactation-gilts
#2
Lea A Rempel, Jeremy R Miles, William T Oliver, Corey D Broeckling
Female pigs nursing their first litter (first-parity gilts) have increased energy requirements not only to support their piglets, but they themselves are still maturing. Non-targeted plasma metabolomics were used to investigate the differences between (1) post-farrowing and weaning (early or late lactation), (2) degree of body condition loss after lactation (extreme or minimal), and (3) interactions; to potentially identify compounds or pathways that could aide in alleviating energetic demands of lactation in gilts...
2016: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/27932572/a-mechanism-for-acetylcholine-receptor-gating-based-on-structure-coupling-phi-and-flip
#3
Shaweta Gupta, Srirupa Chakraborty, Ridhima Vij, Anthony Auerbach
Nicotinic acetylcholine receptors are allosteric proteins that generate membrane currents by isomerizing ("gating") between resting and active conformations under the influence of neurotransmitters. Here, to explore the mechanisms that link the transmitter-binding sites (TBSs) with the distant gate, we use mutant cycle analyses to measure coupling between residue pairs, phi value analyses to sequence domain rearrangements, and current simulations to reproduce a microsecond shut component ("flip") apparent in single-channel recordings...
December 8, 2016: Journal of General Physiology
https://www.readbyqxmd.com/read/27932294/large-scale-structure-based-prediction-and-identification-of-novel-protease-substrates-using-computational-protein-design
#4
Manasi A Pethe, Aliza B Rubenstein, Sagar D Khare
Characterizing the substrate specificity of protease enzymes is critical for illuminating the molecular basis of their diverse and complex roles in a wide array of biological processes. Rapid and accurate prediction of their extended substrate specificity would also aid in the design of custom proteases capable of selectively and controllably cleaving biotechnologically or therapeutically relevant targets. However, current in silico approaches for protease specificity prediction, rely on, and are therefore limited by, machine learning of sequence patterns in known experimental data...
December 5, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27931000/thorium-impact-on-tobacco-root-transcriptome
#5
Kateřina Mazari, Přemysl Landa, Sylva Přerostová, Karel Müller, Radomíra Vaňková, Petr Soudek, Tomáš Vaněk
Thorium is natural actinide metal with potential use in nuclear energetics. Contamination by thorium, originated from mining activities or spills, represents environmental risk due to its radioactivity and chemical toxicity. A promising approach for cleaning of contaminated areas is phytoremediation, which need to be based, however, on detail understanding of the thorium effects on plants. In this study we investigated transcriptomic response of tobacco roots exposed to 200μM thorium for one week. Thorium application resulted in up-regulation of 152 and down-regulation of 100 genes (p-value <0...
November 30, 2016: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/27930299/imaging-the-he2-quantum-halo-state-using-a-free-electron-laser
#6
Stefan Zeller, Maksim Kunitski, Jörg Voigtsberger, Anton Kalinin, Alexander Schottelius, Carl Schober, Markus Waitz, Hendrik Sann, Alexander Hartung, Tobias Bauer, Martin Pitzer, Florian Trinter, Christoph Goihl, Christian Janke, Martin Richter, Gregor Kastirke, Miriam Weller, Achim Czasch, Markus Kitzler, Markus Braune, Robert E Grisenti, Wieland Schöllkopf, Lothar Ph H Schmidt, Markus S Schöffler, Joshua B Williams, Till Jahnke, Reinhard Dörner
Quantum tunneling is a ubiquitous phenomenon in nature and crucial for many technological applications. It allows quantum particles to reach regions in space which are energetically not accessible according to classical mechanics. In this "tunneling region," the particle density is known to decay exponentially. This behavior is universal across all energy scales from nuclear physics to chemistry and solid state systems. Although typically only a small fraction of a particle wavefunction extends into the tunneling region, we present here an extreme quantum system: a gigantic molecule consisting of two helium atoms, with an 80% probability that its two nuclei will be found in this classical forbidden region...
December 6, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27929420/tumor-microenvironment-metabolism-a-new-checkpoint-for-anti-tumor-immunity
#7
REVIEW
Nicole E Scharping, Greg M Delgoffe
When a T cell infiltrates a tumor, it is subjected to a variety of immunosuppressive and regulatory signals in the microenvironment. However, it is becoming increasingly clear that due to the proliferative and energetically-deregulated nature of tumor cells, T cells also operate at a metabolic disadvantage. The nutrient dearth of the tumor microenvironment (TME) creates "metabolic checkpoints" upon infiltrating T cells, impacting their ability to survive, proliferate and function effectively. In this review, we summarize the basics of tumor cell and T cell metabolism and discuss recent advances elucidating the individual metabolic checkpoints exerted on T cells that drive their dysfunction in the TME...
December 6, 2016: Vaccines
https://www.readbyqxmd.com/read/27929163/on-the-role-of-charge-transfer-in-halogen-bonding
#8
Jan Řezáč, Aurélien de la Lande
The role of charge transfer in halogen bonding is the subject of an ongoing debate and controversy. It is clear from experimental data that charge transfer occurs in halogen bonds, but its contribution to the energetics of the interaction can be evaluated only computationally. Since the charge transfer is not a physically well-defined property, there are multiple computational approaches, which could yield very different results. In this work, we investigate this topic using our recently developed method based on constrained DFT, which allows the quantification of net charge transfer and the associated interaction energy component [Řezáč et al...
December 8, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27929146/reactivity-of-the-nitrogen-centered-tryptophanyl-radical-in-the-catalysis-by-the-radical-sam-enzyme-nosl
#9
Haocheng Qianzhu, Wenjuan Ji, Xinjian Ji, Leixia Chu, Chuchu Guo, Wei Lu, Wei Ding, Jiangtao Gao, Qi Zhang
The radical SAM tryptophan (Trp) lyase NosL involved in nosiheptide biosynthesis catalyzes two parallel reactions, converting l-Trp to 3-methyl-2-indolic acid (MIA) and to dehydroglycine and 3-methylindole, respectively. The two parallel reactions diverge from a nitrogen-centered tryptophanyl radical intermediate. Here we report an investigation on the intrinsic reactivity of the tryptophanyl radical using a chemical model study and DFT calculations. The kinetics of the formation and fragmentation of this nitrogen-centered radical in NosL catalysis were also studied in detail...
December 8, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27928960/research-advances-in-molecular-modeling-in-cyclodextrins
#10
Qianqian Zhao, Weixiang Zhang, Runmiao Wang, Yitao Wang, Defang Ouyang
BACKGROUND: Cyclodextrins (CDs), as one type of the novel pharmaceutical excipients, have been widely used in drug delivery and pharmaceutical industry. Over the past decades, a large amount of molecular modeling studies in CDs were reported for profound understanding of structural, dynamic and energetic features of CDs systems. Thus, this review is focused on qualitative and quantitative analysis of research outputs on molecular modeling in CDs. METHODS: The original data were collected from Web of Science and analyzed by scientific knowledge mapping tools, including Citespace, Science of Science, VOSviewer, GPSvisualizer and Gephi software...
December 8, 2016: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/27928570/photochemical-and-computational-studies-of-inclusion-complexes-between-%C3%AE-cyclodextrin-and-1-2-dihydroxyanthraquinones
#11
Sonaimuthu Mohandoss, Thambusamy Stalin
The formation of an inclusion complex between 1,2-dihydroxyanthraquinones (1,2-DHAQ) and β-cyclodextrin (β-CD) has been studied by UV-visible, fluorescence spectroscopy and electrochemical methods. The stoichiometric ratio of the inclusion complex was found to be 1 : 1 and the binding constant was evaluated using the Benesi-Hildebrand equation. The peak currents (Ipa and Ipc) change drastically with increasing β-CD concentration and the peak potentials (Epa and Epc) shifted. A mechanism is proposed to explain the inclusion process...
December 8, 2016: Photochemical & Photobiological Sciences
https://www.readbyqxmd.com/read/27926841/broken-tales-transcription-activator-like-effectors-populate-partly-folded-states
#12
Kathryn Geiger-Schuller, Doug Barrick
Transcription activator-like effector proteins (TALEs) contain large numbers of repeats that bind double-stranded DNA, wrapping around DNA to form a continuous superhelix. Since unbound TALEs retain superhelical structure, it seems likely that DNA binding requires a significant structural distortion or partial unfolding. In this study, we use nearest-neighbor "Ising" analysis of consensus TALE (cTALE) repeat unfolding to quantify intrinsic folding free energies, coupling energies between repeats, and the free energy distribution of partly unfolded states, and to determine how those energies depend on the sequence that determines DNA-specificity (called the "RVD")...
December 6, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27926838/high-resolution-mapping-of-a-repeat-protein-folding-free-energy-landscape
#13
Martin J Fossat, Thuy P Dao, Kelly Jenkins, Mariano Dellarole, Yinshan Yang, Scott A McCallum, Angel E Garcia, Doug Barrick, Christian Roumestand, Catherine A Royer
A complete description of the pathways and mechanisms of protein folding requires a detailed structural and energetic characterization of the conformational ensemble along the entire folding reaction coordinate. Simulations can provide this level of insight for small proteins. In contrast, with the exception of hydrogen exchange, which does not monitor folding directly, experimental studies of protein folding have not yielded such structural and energetic detail. NMR can provide residue specific atomic level structural information, but its implementation in protein folding studies using chemical or temperature perturbation is problematic...
December 6, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27925682/influence-of-morphology-and-pbi%C3%A2-on-the-intrinsic-trap-state-distribution-in-perovskite-film-determined-by-temperature-dependent-fluorescence-spectroscopy
#14
Yi Wang, Hao-Yi Wang, Man Yu, Li-Min Fu, Yujun Qin, Jian-Ping Zhang, Xi-Cheng Ai
Perovskite films with different particle sizes and PbI₂ contents are prepared by controlled single- or sequential-method. By means of temperature dependent fluorescence spectroscopy, the energetic distribution of intrinsic intra-gap trap states in perovskite is quantitatively determined, and the radiative charge recombinations through band edge and via trap states are respectively studied. Furthermore, a series of thermodynamics parameters, such as the demarcation energy between radiative and non-radiative recombination regions, detrapping activation energy and characteristic temperature, are extracted out, based on which, the possible radiative and non-radiative recombination mechanisms are proposed...
December 7, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/27925207/acetate-metabolism-does-not-reflect-astrocytic-activity-contributes-directly-to-gaba-synthesis-and-is-increased-by-silent-information-regulator-1-activation
#15
Benjamin D Rowlands, Matthias Klugmann, Caroline D Rae
[(13) C]acetate is known to label metabolites preferentially in astrocytes rather than neurons and it has consequently been used as a marker for astrocytic activity. Recent discoveries suggest that control of acetate metabolism and its contributions to the synthesis of metabolites in brain is not as simple as first thought. Here, using a Guinea pig brain cortical tissue slice model metabolizing [1-(13) C]D-glucose and [1,2-(13) C]acetate, we investigated control of acetate metabolism and the degree to which it reflects astrocytic activity...
December 7, 2016: Journal of Neurochemistry
https://www.readbyqxmd.com/read/27924857/electrohydrodynamic-assisted-assembly-of-hierarchically-structured-3d-crumpled-nanostructures-for-efficient-solar-conversions
#16
Hidetaka Ishihara, Yen-Chang Chen, Nicholas De Marco, Oliver Lin, Chih-Meng Huang, Vipawee Limsakoune, Yi-Chia Chou, Yang Yang, Vincent Tung
The tantalizing prospect of harnessing the unique properties of graphene crumpled nanostructures continues to fuel tremendous interest in energy storage and harvesting applications. However, the paper ball-like, hard texture, and closed-sphere morphology of current 3D graphitic nanostructure production not only constricts the conductive pathways but also limits the accessible surface area. Here, we report new insights into electrohydrodynamically-generated droplets as colloidal nanoreactors in that the stimuli-responsive nature of reduced graphene oxide can lead to the formation of crumpled nanostructures with a combination of open structures and doubly curved, saddle-shaped edges...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924328/cycloreversion-of-the-co2-trimer-a-paradigmatic-pseudopericyclic-2-2-2-cycloaddition-reaction
#17
Roberto Villar López, Olalla Nieto Faza, Eduard Matito, Carlos Silva López
Very recently, the CO2 trimer has been experimentally synthesized, isolated and characterized. This process opens new ways for the withdrawal and storage of this greenhouse gas. The trimer is reported to be stable up to -40 °C, with a lifetime of about 40 min at this temperature. At these or under harsher thermal conditions it reverts to the three monomers. The mechanism of this reaction has been theoretically studied and the electronic character of the associated transition state has been analyzed from a variety of perspectives (energetic, magnetic, electron localization and delocalization functions) which indicate that it has paradigmatic pseudopericyclic character...
December 7, 2016: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/27924259/cation-limited-kinetic-model-for-microbial-extracellular-electron-transport-via-an-outer-membrane-cytochrome-c-complex
#18
REVIEW
Akihiro Okamoto, Yoshihide Tokunou, Junki Saito
Outer-membrane c-type cytochrome (OM c-Cyt) complexes in several genera of iron-reducing bacteria, such as Shewanella and Geobacter, are capable of transporting electrons from the cell interior to extracellular solids as a terminal step of anaerobic respiration. The kinetics of this electron transport has implications for controlling the rate of microbial electron transport during bioenergy or biochemical production, iron corrosion, and natural mineral cycling. Herein, we review the findings from in-vivo and in-vitro studies examining electron transport kinetics through single OM c-Cyt complexes in Shewanella oneidensis MR-1...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27923210/study-on-the-interactional-behaviour-of-transition-metal-ions-with-myoglobin-a-detailed-calorimetric-spectroscopic-and-light-scattering-analysis
#19
Amandeep Kaur, Parampaul K Banipal, Tarlok S Banipal
The energetics and the impact on the conformation of heme containing protein myoglobin (Mb) due to the binding of three transition metal ions (Zn(2+), Ni(2+), and Mn(2+)) have been investigated using isothermal titration calorimetry (ITC), dynamic light scattering (DLS), UV-vis, and circular dichroism (CD) spectroscopy under physiological conditions. The binding affinity of the order of 10(4)M(-1) has been observed for all metal ions from calorimetry as well as from absorption spectroscopy. The binding of these metal ions with Mb is a spontaneous process that exposes the hydrophobic groups away from the protein core as exhibited by the negative Gibbs free energy change (ΔG) and positive heat capacity change (ΔCp) values...
November 27, 2016: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/27922186/characterization-of-the-pro-inflammatory-cytokine-il-1%C3%AE-on-butyrate-oxidation-in-colorectal-cancer-cells
#20
Megan Johnstone, Natalie Bennett, Cynthia Standifer, Alexis Smith, Anna Han, Ahmed Bettaieb, Jay Whelan, Dallas R Donohoe
Cancer, in part, is driven, by alterations in cellular metabolism that promote cell survival and cell proliferation. Identifying factors that influence this shift in cellular metabolism in cancer cells is important. Interleukin-1β (IL-1β) is a pro-inflammatory cytokine that has been reported to be elevated in colorectal cancer patients. While much is known towards the effect of dietary nutrients on regulating inflammation and the inflammatory response, which includes cytokines such as IL-1β, far less is understood how cytokines impact nutrient fate to alter cancer cell metabolism...
December 6, 2016: Journal of Cellular Biochemistry
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