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https://read.qxmd.com/read/30785747/cofactor-analogues-as-active-site-probes-in-lysine-acetyltransferases
#1
Roman P Simon, Tobias Rumpf, Vaida Linkuvienė, Daumantas Matulis, Asifa Akhtar, Manfred Jung
Lysine acetyltransferases (KATs, also termed histone acetyltransferases, HATs) catalyze the acetylation of substrate lysine residues by employing the cofactor acetyl-coenzyme A (AcCoA), thereby providing a dynamic control mechanism of protein function. Because of their major involvement in cell development and homeostasis, small molecule modulators of KAT activity are urgently needed to assess their therapeutic potential and for probing their underlying biology. Recent advances in the field suggest that targeting the cofactor binding site represents a promising strategy for identifying potent and selective ligands...
February 20, 2019: Journal of Medicinal Chemistry
https://read.qxmd.com/read/30785435/equilibrium-structures-of-the-tetramezine-diastereomers-and-their-ratio-joint-analysis-of-gas-phase-electron-diffraction-quantum-chemistry-and-spectroscopic-data
#2
Leonid S Khaikin, Igor V Kochikov, Anatoliy N Rykov, Olga E Grikina, Georgiy G Ageev, Igor F Shishkov, Vladimir V Kuznetsov, Nina N Makhova
For the first time, we applied a gas-phase electron diffraction (GED) method together with vibrational spectroscopy and quantum chemical calculations to investigate the equilibrium geometries of achiral meso and enantiomeric diastereomers of tetramezine [1,2-bis-(3,3-dimethyldiaziridin-1-yl)ethane] and their ratio in the mixture. In the joint structural analysis of these data, a new approach based on PES parameters is used in the framework of a static molecular model (small amplitude motion approximation). The agreement between the theoretical and experimental molecular intensities is characterized by a divergence factor Rf of 5...
February 20, 2019: Physical Chemistry Chemical Physics: PCCP
https://read.qxmd.com/read/30785287/thermodynamically-consistent-force-field-for-coarse-grained-modeling-of-aqueous-electrolyte-solution
#3
Carlos Nieto-Draghi, Bernard Rousseau
We propose a thermodynamically consistent methodology to parameterize interactions between charged particles inside the dissipative particle dynamics (DPD) formalism. We used osmotic pressure experimental data as a function of the salinity in order to optimize interaction parameters. Results for NaCl aqueous solution show that both mean osmotic and activity coefficient of individual ions allow to determine the Na+-water, Cl--water and Na+-Cl- DPD repulsion parameters. A simple linear relationship between the hydration free energies of ions and the ion-water repulsion parameters that allows the parameterization of the complete series of halide and alkaline ions is proposed...
February 20, 2019: Journal of Physical Chemistry. B
https://read.qxmd.com/read/30785162/ni-ii-doped-anionic-metal-organic-framework-nanowire-arrays-for-enhancing-the-oxygen-evolution-reaction
#4
Zhi-Qiang Jiang, Yu-Feng Li, Xue-Jun Zhu, Jin Lu, Tian Wen, Lei Zhang
Herein, an anionic metal-organic framework nanowire array not only directly grew on Cu foam, but also captured Ni(ii) ions at an ultra-small particle level. The hybrid material exhibited high activity with low overpotential (310 mV at 20 mA cm-2 in 1.0 M KOH solution) toward the oxygen evolution reaction (OER) (1 M KOH), with performance comparable to that of the precious metal benchmark. These findings may expand the field of MOFs for scaled-up water electrolysis.
February 20, 2019: Chemical Communications: Chem Comm
https://read.qxmd.com/read/30784738/distribution-and-release-of-phosphorus-fractions-associated-with-soil-aggregate-structure-in-restored-wetlands
#5
Hu Cui, Yang Ou, Lixia Wang, Haitao Wu, Baixing Yan, Yingxin Li
Phosphorus, a dominating element responsible for eutrophication, is a potential limiting nutrient in wetland ecosystem. In this study, the release risk of phosphorus was evaluated by investigating the distribution of phosphorus fractions in different grain-sizes of soil aggregates in wetlands with restoration durations of 1, 2, 3, 5, 13 or 19 years. The results showed that the soil aggregate structure tended to be stable when paddy fields were changed into wetland, though aggregate structure first condensed fine-aggregates (<0...
February 11, 2019: Chemosphere
https://read.qxmd.com/read/30784602/whole-organ-genomic-characterization-of-mucosal-field-effects-initiating-bladder-carcinogenesis
#6
Tadeusz Majewski, Hui Yao, Jolanta Bondaruk, Woonbok Chung, Sangkyou Lee, June Goo Lee, Shizhen Zhang, David Cogdell, Guoliang Yang, Woonyoung Choi, Colin Dinney, H Barton Grossman, Christopher Logothetis, Steven E Scherer, Charles C Guo, Li Zhang, Peng Wei, John N Weinstein, Jean-Pierre Issa, Keith Baggerly, David J McConkey, Bogdan Czerniak
We used whole-organ mapping to study the locoregional molecular changes in a human bladder containing multifocal cancer. Widespread DNA methylation changes were identified in the entire mucosa, representing the initial field effect. The field effect was associated with subclonal low-allele frequency mutations and a small number of DNA copy alterations. A founder mutation in the RNA splicing gene, ACIN1, was identified in normal mucosa and expanded clonally with an additional 21 mutations in progression to carcinoma...
February 19, 2019: Cell Reports
https://read.qxmd.com/read/30784488/a-winter-energetics-model-for-bobcats-in-a-deep-snow-environment
#7
Roberta K Newbury, Karen E Hodges
Understanding basic energetic requirements of wildlife species is critical to evaluate how individuals persist in their current environments as well as to forecast responses to changed climates or habitats. Indeed, northern range limits are often thought to reflect harsh abiotic conditions that exceed the capacity of individuals to stay in energetic balance. Bobcats (Lynx rufus) occur across much of North America; at northern latitudes, they face winter challenges such as deep snows, cold temperatures, and possible food scarcity...
February 2019: Journal of Thermal Biology
https://read.qxmd.com/read/30784411/combinatorial-biosynthesis-of-small-molecules-in-plants-engineering-strategies-and-tools
#8
Iryna Gerasymenko, Yuriy Sheludko, Sabine Fräbel, Agata Staniek, Heribert Warzecha
Biosynthetic capacity of plants, rooted in a near inexhaustible supply of photosynthetic energy and founded upon an intricate matrix of metabolic networks, makes them versatile chemists producing myriad specialized compounds. Along with tremendous success in elucidation of several plant biosynthetic routes, their reestablishment in heterologous hosts has been a hallmark of recent bioengineering endeavors. However, current efforts in the field are, in the main, aimed at grafting the pathways to fermentable recipient organisms, like bacteria or yeast...
2019: Methods in Enzymology
https://read.qxmd.com/read/30783720/development-of-a-biosensing-platform-based-on-a-laccase-hydrophobin-chimera
#9
Ilaria Sorrentino, Paola Giardina, Alessandra Piscitelli
A simple and stable immobilization of a laccase from Pleurotus ostreatus was obtained through genetic fusion with a self-assembling and adhesive class I hydrophobin. The chimera protein was expressed in Pichia pastoris and secreted into the culture medium. The crude culture supernatant was directly used for coatings of polystyrene multi-well plates without additional treatments, a procedure that resulted in a less time-consuming and chemicals reduction. Furthermore, the gene fusion yielded a positive effect with respect to the wild-type recombinant enzyme in terms of both immobilization and stability...
February 19, 2019: Applied Microbiology and Biotechnology
https://read.qxmd.com/read/30783500/cytosine-based-tet-enzyme-inhibitors
#10
Gabriella N L Chua, Kelly L Wassarman, Haoyu Sun, Joseph A Alp, Emma I Jarczyk, Nathanael J Kuzio, Michael J Bennett, Beth G Malachowsky, Martin Kruse, Andrew J Kennedy
DNA methylation is known as the prima donna epigenetic mark for its critical role in regulating local gene transcription. Changes in the landscape of DNA methylation across the genome occur during cellular transition, such as differentiation and altered neuronal plasticity, and become dysregulated in disease states such as cancer. The TET family of enzymes is known to be responsible for catalyzing the reverse process that is DNA demethylation by recognizing 5-methylcytosine and oxidizing the methyl group via an Fe(II)/alpha-ketoglutarate-dependent mechanism...
February 14, 2019: ACS Medicinal Chemistry Letters
https://read.qxmd.com/read/30783496/evolution-of-small-molecule-kinase-drugs
#11
Helen L Lightfoot, Frederick W Goldberg, Joerg Sedelmeier
The development of small molecule kinase drugs is a rapidly evolving field and represents one of the most important research areas within oncology. This innovation letter provides an overview and analysis of approved kinase drugs according to their WHO registration (INN) dates, primary biological targets, and selectivity and structural similarities, which are also depicted in an associated poster. It also discusses new trends in kinase drug discovery programs such as new kinase targets, novel mechanisms of action, and diverse indications...
February 14, 2019: ACS Medicinal Chemistry Letters
https://read.qxmd.com/read/30782970/structure-of-sph-self-incompatibility-protein-homologue-proteins-a-widespread-family-of-small-highly-stable-secreted-proteins
#12
Karthik Rajasekar, Shuangxi Ji, Rachael J Coulthard, Jon P Ride, Gillian L Reynolds, Peter J Winn, Michael P Wheeler, Eva I Hyde, Lorna J Smith
SPH proteins are a large family of small, disulphide-bonded, secreted proteins, initially found in the self-incompatibility response in the field poppy (Papaver rhoeas) , but now known to be widely distributed in plants, many containing multiple members of this protein family. Using the Origami strain of E. coli , we expressed one member of this family, SPH15 from Arabidopsis thaliana , as a folded thioredoxin-fusion protein and purified it from the cytosol. The fusion protein was cleaved and characterised by analytical ultracentrifugation, circular dichroism, and NMR spectroscopy...
February 19, 2019: Biochemical Journal
https://read.qxmd.com/read/30782029/an-update-on-extracellular-vesicles-in-multiple-myeloma-a-focus-on-their-role-in-cell-to-cell-cross-talk-and-as-potential-liquid-biopsy-biomarkers
#13
Luciana De Luca, Ilaria Laurenzana, Stefania Trino, Daniela Lamorte, Antonella Caivano, Pellegrino Musto
Multiple myeloma (MM) is characterized by a clonal proliferation of neoplastic plasma cells (PCs) in bone marrow (BM) and the interplay between MM PCs and the BM microenvironment, which plays a relevant role in its pathogenesis. In this important cross-talk, extracellular vesicles (EVs) are active. EVs, including small and medium/large EVs, are lipid bi-layer particles released in circulation by normal and neoplastic cells. A selected cargo of lipids, proteins, and nucleic acids is loaded into EVs, and delivered locally and to distant sites, thus influencing the physiology of recipient cells...
February 20, 2019: Expert Review of Molecular Diagnostics
https://read.qxmd.com/read/30781676/ex-vivo-expansion-of-hematopoietic-stem-cells-for-therapeutic-purposes-lessons-from-development-and-the-niche
#14
REVIEW
Parisa Tajer, Karin Pike-Overzet, Sagrario Arias, Menzo Havenga, Frank J T Staal
Expansion of hematopoietic stem cells (HSCs) for therapeutic purposes has been a "holy grail" in the field for many years. Ex vivo expansion of HSCs can help to overcome material shortage for transplantation purposes and genetic modification protocols. In this review, we summarize improved understanding in blood development, the effect of niche and conservative signaling pathways on HSCs in mice and humans, and also advances in ex vivo culturing protocols of human HSCs with cytokines or small molecule compounds...
February 18, 2019: Cells
https://read.qxmd.com/read/30781585/nanoemulsions-for-nose-to-brain-drug-delivery
#15
REVIEW
Maria Cristina Bonferoni, Silvia Rossi, Giuseppina Sandri, Franca Ferrari, Elisabetta Gavini, Giovanna Rassu, Paolo Giunchedi
The blood⁻brain barrier (BBB) plays a fundamental role in protecting the brain from toxic substances and therefore also controls and restricts the entry of therapeutic agents. The nasal administration of drugs using the nose-to-brain pathway allows direct drug targeting into the brain, avoiding the first-pass effect and bypassing the BBB. Through the nasal route, the drug can access the brain directly along the trigeminal and olfactory nerves, which are located in the upper part of the nasal cavity. Nanoemulsions are formulations belonging to the field of nanomedicine...
February 17, 2019: Pharmaceutics
https://read.qxmd.com/read/30781541/rapid-green-synthesis-and-characterization-of-silver-nanoparticles-arbitrated-by-curcumin-in-an-alkaline-medium
#16
Muhammad Jamshed Khan, Kamyar Shameli, Awis Qurni Sazili, Jinap Selamat, Suriya Kumari
Green synthesis of silver nanoparticles is desirable practice. It is not only the required technique for industrial and biomedical purposes but also a promising research area. The aim of this study was to synthesize green curcumin silver nanoparticles (C-Ag NPs). The synthesis of C-Ag NPs was achieved by reduction of the silver nitrate (AgNO₃) in an alkaline medium. The characterizations of the prepared samples were conducted by ultraviolet visible (UV-vis) spectroscopy, powder X-ray diffraction (PXRD), field emission scanning electron microscopy (FESEM), high-resolution transmission electron microscopy (HRTEM), selected area electron diffraction (SAED) and zeta potential (ZP) analyses...
February 16, 2019: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://read.qxmd.com/read/30780332/ab-initio-computational-analysis-of-spectral-properties-of-dielectric-spheroidal-resonators-interacting-with-a-subwavelength-nanoparticle
#17
Vladimir Shuvayev, Lev Deych
An efficient numerical method for determining the spectral characteristics and spatial distribution of the field of a spheroidal whispering-gallery-mode (WGM) resonator interacting with a dielectric nanoparticle is presented. The developed approach is based on a combination of T-matrix formalism applied to a single resonator with a dipole approximation for the field of the nanoparticle. The method is illustrated by computation of the scattered field of the resonator-particle system illuminated by an incident field in the form of a single WGM mode of TE or TM polarization mimicking the excitation of the resonances by a tapered fiber...
January 2019: Physical Review. E
https://read.qxmd.com/read/30780316/robustness-of-heat-transfer-in-confined-inclined-convection-at-high-prandtl-number
#18
Linfeng Jiang, Chao Sun, Enrico Calzavarini
We investigate the dependency of the magnitude of heat transfer in a convection cell as a function of its inclination by means of experiments and simulations. The study is performed with a working fluid of large Prandtl number, Pr≃480, and at Rayleigh numbers Ra≃10^{8} and Ra≃5×10^{8} in a quasi-two-dimensional rectangular cell with unit aspect ratio. By changing the inclination angle (β) of the convection cell, the character of the flow can be changed from moderately turbulent, for β=0^{∘}, to laminar and steady at β=90^{∘}...
January 2019: Physical Review. E
https://read.qxmd.com/read/30780305/optimized-brute-force-algorithms-for-the-bifurcation-analysis-of-a-binary-neural-network-model
#19
Diego Fasoli, Stefano Panzeri
Bifurcation theory is a powerful tool for studying how the dynamics of a neural network model depends on its underlying neurophysiological parameters. However, bifurcation theory of neural networks has been developed mostly for mean-field limits of infinite-size spin-glass models, for finite-size dynamical systems whose units have a graded, continuous output, and for models with discrete-output neurons that evolve in continuous time. To allow progress on understanding the dynamics of some widely used classes of neural network models with discrete units and finite size, which could not be studied thoroughly with the previous methodology, here we introduced algorithms that perform a semianalytical bifurcation analysis of a finite-size firing-rate neural network model with binary firing rates and discrete-time evolution...
January 2019: Physical Review. E
https://read.qxmd.com/read/30780223/ground-state-properties-of-the-one-dimensional-transverse-ising-model-in-a-longitudinal-magnetic-field
#20
O F de Alcantara Bonfim, B Boechat, J Florencio
The critical properties of the one-dimensional spin-1/2 transverse Ising model in the presence of a longitudinal magnetic field were studied by the quantum fidelity method. We used exact diagonalization to obtain the ground-state energies and corresponding eigenvectors for lattice sizes up to 24 spins. The maximum of the fidelity susceptibility was used to locate the various phase boundaries present in the system. The type of dominant spin ordering for each phase was identified by examining the corresponding ground-state eigenvector...
January 2019: Physical Review. E
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