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https://www.readbyqxmd.com/read/28108663/determination-of-the-conformational-ensemble-of-the-tar-rna-by-x-ray-scattering-interferometry
#1
Xuesong Shi, Peter Walker, Pehr B Harbury, Daniel Herschlag
The conformational ensembles of structured RNA's are crucial for biological function, but they remain difficult to elucidate experimentally. We demonstrate with HIV-1 TAR RNA that X-ray scattering interferometry (XSI) can be used to determine RNA conformational ensembles. X-ray scattering interferometry (XSI) is based on site-specifically labeling RNA with pairs of heavy atom probes, and precisely measuring the distribution of inter-probe distances that arise from a heterogeneous mixture of RNA solution structures...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108628/metabolic-reprogramming-by-folate-restriction-leads-to-a-less-aggressive-cancer-phenotype
#2
Zahra Ashkavand, Ciara O'Flanagan, Mirko Hennig, Xiuxia Du, Stephen D Hursting, Sergey A Krupenko
: Folate coenzymes are involved in biochemical reactions of one-carbon transfer, and deficiency of this vitamin impairs cellular proliferation, migration, and survival in many cell types. Here, the effect of folate restriction on mammary cancer was evaluated using three distinct breast cancer subtypes differing in their aggressiveness and metastatic potential: noninvasive basal-like (E-Wnt), invasive but minimally metastatic claudin-low (M-Wnt), and highly metastatic claudin-low (metM-Wnt(liver)) cell lines, each derived from the same pool of MMTV-Wnt-1 transgenic mouse mammary tumors...
January 20, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28108411/production-and-characterization-of-medium-chain-length-polyhydroxyalkanoates-copolymer-from-arctic-psychrotrophic-bacterium-pseudomonas-sp-pamc-28620
#3
Ganesan Sathiyanarayanan, Shashi Kant Bhatia, Hun-Suk Song, Jong-Min Jeon, Jun-Young Kim, Yoo Kyung Lee, Yun-Gon Kim, Yung-Hun Yang
Arctic psychrotrophic bacterium Pseudomonas sp. PAMC 28620 was found to produce a distinctive medium-chain-length polyhydroxyalkanoates (MCL-PHAs) copolymer when grown on structurally unrelated carbon sources including glycerol. The maximum MCL-PHAs copolymer yield was obtained about 52.18±4.12% from 7.95±0.66g/L of biomass at 144h of fermentation when 3% glycerol was used as sole carbon and energy source during the laboratory-scale bioreactor process. Characterization of the copolymer was carried out using fourier transform infrared spectroscopy (FTIR), gas chromatography-mass spectrometry (GC-MS), proton ((1)H) and carbon ((13)C) nuclear magnetic resonance spectroscopy (NMR), gel permeation chromatography (GPC), differential scanning calorimeter (DSC) and thermo-gravimetric analysis (TGA)...
January 17, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28108382/new-xanthones-and-cytotoxic-constituents-from-garcinia-mangostana-fruit-hulls-against-human-hepatocellular-breast-and-colorectal-cancer-cell-lines
#4
Gamal A Mohamed, Ahmed M Al-Abd, Ali M El-Halawany, Hossam M Abdallah, Sabrin R M Ibrahim
ETHNOPHARMACOLOGICAL RELEVANCE: Cancer has proceeded to surpass one of the most chronic illnesses to be the major cause of mortality in both the developing and developed world. Garcinia mangostana L. (mangosteen, family Guttiferae) known as the queen of fruits, is one of the most popular tropical fruits. It is cultivated in Southeast Asian countries: Malaysia, Indonesia, Sri Lanka, Burma, Thailand, and Philippines. Traditionally, numerous parts of G. mangostana have been utilized to treat various ailments such as abdominal pain, haemorrhoids, food allergies, arthritis, leucorrhoea, gonorrhea, diarrhea, dysentery, wound infection, suppuration, and chronic ulcer...
January 17, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28108327/structurally-diverse-secondary-metabolites-from-a-deep-sea-derived-fungus-penicillium-chrysogenum-scsio-41001-and-their-biological-evaluation
#5
Shengtian Chen, Junfeng Wang, Zhen Wang, Xiuping Lin, Bingxin Zhao, Kumaravel Kaliaperumal, Xiaojian Liao, Zhengchao Tu, Jianlin Li, Shihai Xu, Yonghong Liu
Five new compounds, including a cytotoxic dimeric isocoumarin, bipenicilisorin (1), a merosesquiterpenoid, yaminterritrem C (2), a citrinin dimer, penicitrinone F (3), a alkaloid, terremide D (4), and a δ-valerolacton, (E)-4-(propen-1-yl)-5,6-dihydro-2H-pyran-2-one (5), along with ten known compounds (6-15) were isolated from a deep-sea-derived fungus Penicillium chrysogenum SCSIO 41001. Their structures and absolute configurations were elucidated by NMR spectra, MS, CD, optical rotation, X-ray crystallography, and compared with literature data...
January 17, 2017: Fitoterapia
https://www.readbyqxmd.com/read/28108278/comparison-of-the-redox-chemistry-of-sulfur-and-selenium-containing-analogs-of-uracil
#6
N Connor Payne, Andrew Geissler, Aileen Button, Alexandru R Sasuclark, Alayne L Schroll, Erik L Ruggles, Vadim N Gladyshev, Robert J Hondal
Selenium is present in proteins in the form of selenocysteine, where this amino acid serves catalytic oxidoreductase functions. The use of selenocysteine in nature is strongly associated with redox catalysis. However, selenium is also found in a 2-selenouridine moiety at the wobble position of tRNA(Glu), tRNA(Gln) and tRNA(Lys). It is thought that the modifications of the wobble position of the tRNA improves the selectivity of the codon-anticodon pair as a result of the physico-chemical changes that result from substitution of sulfur and selenium for oxygen...
January 17, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28108024/isolation-of-isoflavones-from-iris-kashmiriana-baker-as-potential-anti-proliferative-agents-targeting-nf-kappab
#7
Afroze Alam, Varun Jaiswal, Sohail Akhtar, B S Jayashree, K L Dhar
Cancer is possibly one of the most devastating and complex disease and therefore involves chemotherapy as one of the frontline strategies in its therapy. However, expected toxicity and resistance with chemotherapeutic agents encourage us to use the plant derived natural chemotherapeutic sources at the clinical stage of cancer therapy. In view of this strategy, herein new glycosides and isoflavonoids were isolated from Iris kashmiriana Baker and subjected to structure elucidation followed by their biological evaluation...
January 17, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28107934/tuning-sensitivity-of-a-simple-hydrazone-for-selective-fluorescent-turn-on-chemo-sensing-of-al-3-and-its-application-in-living-cells-imaging
#8
Faiz-Ur Rahman, Amjad Ali, Saira Khan Khalil, Rong Guo, Peng Zhang, Hui Wang, Zhan-Ting Li, Dan-Wei Zhang
Salicylaldehyde based hydrazones 2-((2-methyl-2-(pyridin-2-yl)hydrazono)methyl)phenol (SMPH), 4-methyl-2-((2-methyl-2-(pyridin-2-yl)hydrazono)methyl)phenol (MSMPH) and 4-fluoro-2-((2-methyl-2-(pyridin-2-yl)hydrazono)methyl)phenol (FSMPH) were prepared and structurally characterized. These hydrazones exhibited fluorescence "turn on" response toward Al(3+) in dimethyl formamide/water (DMF/H2O) (1: 1) mixture. SMPH showed enhanced emission (70 folds) as compared to MSMPH (46 folds) and FSMPH (28 folds) upon the addition of 3 equivalents of Al(3+)...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107695/antibacterial-activity-computational-analysis-and-host-toxicity-study-of-thymol-sulfonamide-conjugates
#9
Shasank S Swain, Sudhir K Paidesetty, Rabindra N Padhy
Methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus faecalis (VRE) are notorious pathogenic multidrug resistant (MDR) bacteria in both hospital and community sectors, and today the first antibacterial drug sulfamethoxazole is ineffective. The monoterpene phenol, thymol was conjugated with seven sulfa drug derivatives individually, adopting the dye-azo synthesis protocol, and conjugates were characterized using spectral analysis techniques such as, UV, FTIR, MS, HPLC, (1)H NMR, (13)C NMR and SEM...
January 17, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28107690/time-domain-nmr-as-a-new-process-monitoring-method-for-characterization-of-pharmaceutical-hydrates
#10
Stefanie Ulrike Schumacher, Benno Rothenhäusler, Alf Willmann, Jürgen Thun, Regina Moog, Martin Kuentz
Hydrates are of great pharmaceutical relevance and even though they have been characterized thoroughly by various analytical techniques, there is barely literature available on molecular mobility of the hydrate water studied by NMR relaxation in the time domain. The aim of this work was to examine the possibility of differentiating hydration states of drugs by (1)H time domain NMR (TD-NMR) regarding spin-spin and spin-lattice relaxation times (T2 and T1) using benchtop equipment. Caffeine and theophylline were selected as model compounds and binary mixtures of hydrate to anhydrate were analyzed for each drug using a spin echo and inversion recovery pulse sequence...
January 9, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28107633/binding-and-proton-blockage-by-amantadine-variants-of-the-influenza-m2wt-and-m2s31n-explained
#11
Christina Tzitzoglaki, Anna K Wright, Kathrin-Maria Freudenberger, Anja Hoffmann, Ian Tietjen, Ioannis Stylianakis, Felix Kolarov, David Fedida, Michaela Schmidtke, Guenter Gauglitz, Timothy A Cross, Antonios Kolocouris
While aminoadamantanes are well-established inhibitors of the influenza A M2 proton channel, the mechanisms by which they are rendered ineffective against M2S31N are unclear. Solid state NMR, isothermal titration calorimetry, electrophysiology, anti-viral assays and molecular dynamics simulations suggest stronger binding interactions for aminoadamantanes to M2WT compared to negligible or weak binding to M2S31N. This is due to reshaping of the M2pore when N31 is present, which in contrast to WT, leads: A) to the loss of the V27 pocket for the adamantyl cage and to a predominant orientation of the ligand's ammonium group toward the N-terminus and, B) to the lack of a helical kink upon ligand binding...
January 20, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28107624/tocilizumab-alendronate-conjugate-for-treatment-of-rheumatoid-arthritis
#12
Hwiwon Lee, Suk Ho Bhang, Jeong Ho Lee, Hyemin Kim, Sei Kwang Hahn
An autoimmune disease of rheumatoid arthritis (RA) causes severe inflammation on the synovial membrane, which results in the destruction of articular cartilage and bone. Here, Tocilizumab (TCZ) - Alendronate (ALD) conjugate is synthesized for the early intervention of RA. A humanized monoclonal antibody of TCZ shows an immunosuppressive effect, targeting interleukin-6 (IL-6) receptor in the RA pathogenesis. ALD is an anti-inflammatory bisphosphonate drug which can bind to the exposed bone surface. ALD is conjugated selectively to N-glycan on Fc region of TCZ using a chemical linker of 3-(2-pyridyldithio) propionyl hydrazide (PDPH) - poly(ethylene glycol) - N-hydroxysuccinimide (PDPH-PEG-NHS)...
January 20, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28107435/peptide-targeted-by-human-antibodies-associated-with-hiv-vaccine-associated-protection-assumes-a-dynamic-%C3%AE-helical-structure
#13
Mohammed S Aiyegbo, Evgeny Shmelkov, Lorenzo Dominguez, Michael Goger, Shibani Battacharya, Allan C deCamp, Peter B Gilbert, Phillip W Berman, Timothy Cardozo
The only evidence of vaccine-induced protection from HIV acquisition in humans was obtained in the RV144 HIV vaccine clinical trial. One immune correlate of risk in RV144 was observed to be higher titers of vaccine-induced antibodies (Abs) reacting with a 23-mer non-glycosylated peptide with the same amino acid sequence as a segment in the second variable (V2) loop of the MN strain of HIV. We used NMR to analyze the dynamic 3D structure of this peptide. Distance restraints between spatially proximate inter-residue protons were calculated from NOE cross peak intensities and used to constrain a thorough search of all possible conformations of the peptide...
2017: PloS One
https://www.readbyqxmd.com/read/28107017/cooperative-binding-in-a-phosphine-oxide-based-halogen-bonded-dimer-drives-supramolecular-oligomerization
#14
Leonardo Maugeri, Tomas Lebl, David B Cordes, Alexandra M Z Slawin, Douglas Philp
Triphenylphosphine oxide forms halogen-bonded (XB) complexes with pentafluoroiodobenzene and a 1,4-diaryl-5-iodotriazole. The stability of these complexes is assessed computationally and by 31P NMR spectroscopy in d8-toluene solution, where they are both complexes are weakly associated. This knowledge is applied to the design and synthesis of two self-complementary phosphine oxide-iodotriazole hybrids that incorporate a phosphine oxide XB acceptor and a 1,4-diphenyl-5-iodotriazole XB donor within the same molecule...
January 20, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28107012/anion-caffeine-interactions-studied-by-13-c-and-1-h-nmr-and-atr-ftir-spectroscopy
#15
Nicolas O Johnson, Taylor Patrick Light, Gina MacDonald, Yanjie Zhang
This work investigates the interactions of a series of 11 anions with caffeine by utilizing (13)C and (1)H NMR and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. The aim of this study is to elucidate the molecular mechanisms of ion interactions with caffeine and to study how these interactions affect caffeine aggregation in aqueous solution. The chemical shift changes of caffeine (13)C and (1)H in the presence of salts provide a measure for anions' salting-out/salting-in abilities on individual carbon and hydrogen atoms in caffeine...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28107009/nmr-and-computation-reveal-a-pressure-sensitive-folded-conformation-of-trp-cage
#16
Soichiro Kitazawa, Martin J Fossat, Scott A McCallum, Angel E Garcia, Catherine Ann Royer
Beyond defining the structure and stability of folded states of proteins, primary amino acid sequences determine all of the features of their conformational landscapes. Characterizing how sequence modulates the population of protein excited states or folding pathways requires atomic level detailed structural and energetic information. Such insight is essential for improving protein design strategies, as well as for interpreting protein evolution. Here, high pressure NMR and molecular dynamics simulations were combined to probe the conformational landscape of a small model protein, the tryptophan cage variant, Tc5b...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28107003/fast-initiating-ruthenium-based-catalysts-for-improved-activity-in-highly-e-selective-cross-metathesis
#17
Tonia S Ahmed, Robert H Grubbs
Ruthenium-based olefin metathesis catalysts bearing dithiolate ligands have been recently employed to generate olefins with high E-selectivity (>99% E) but have been limited by low to moderate yields. In this report, (1)H NMR studies reveal that a major contributing factor to this low activity is the extremely low initiation rates of these catalysts with trans olefins. Introducing a 2-isopropoxy-3-phenylbenzylidene ligand in place of the conventional 2-isopropoxybenzylidene ligand resulted in catalysts that initiate rapidly under reaction conditions...
January 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28106998/identification-of-cyclic-depsipeptides-and-their-dedicated-synthetase-from-hapsidospora-irregularis
#18
Shuwei Zhang, Yixing Qiu, Thomas B Kakule, Zhenyu Lu, Fuchao Xu, John G Lamb, Christopher A Reilly, Yong Zheng, Shing Wo Simon Sham, Wei Wang, Lijiang Xuan, Eric W Schmidt, Jixun Zhan
Seven cyclic depsipeptides were isolated from Hapsidospora irregularis and structurally characterized as the calcium channel blocker leualacin and six new analogues based on the NMR and HRESIMS data. These new compounds were named leualacins B-G. The absolute configurations of the amino acids and 2-hydroxyisocaproic acids were determined by recording the optical rotation values. Biological studies showed that calcium influx elicited by leualacin F in primary human lobar bronchial epithelial cells involves the TRPA1 channel...
January 20, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28106844/phenolic-compounds-from-the-leaves-of-castanopsis-fargesii
#19
Yong-Lin Huang, Ya-Feng Wang, Jin-Lei Liu, Lei Wang, Takashi Tanaka, Yue-Yuan Chen, Feng-Lai Lu, Dian-Peng Li
In the course of a phytochemical and chemotaxonomical investigation of Castanopsis species (Fagaceae), three new phenolic compounds, (3R,1'S)-[1'-(6″-O-galloyl-β-d-gluco-pyranosyl)oxyethyl]-3-hydroxy-dihydrofuran-2(3H)-one (1), (2R,3S)-2-[2'-(galloyl)oxyethyl]-dihydroxybutanoic acid (2), and (3S,4S)-3-hydroxymethyl-3,4-dihydro-5,6,7-trihydroxy-4-(4'-hydroxy-3'-methoxyphenyl)-1H-[2]-benzopyran-1-one (3) were isolated from the fresh leaves of Castanopsis fargesii. In addition, a known phenolic glycoside, gentisic acid 5-O-α-l-rhamnopyranosyl-(1→2)-β-d-glucopyranoside (4) was also isolated and identified...
January 19, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28106757/new-enzyme-inhibitory-triterpenoid-from-marine-macro-brown-alga-padina-boergesenii-allender-kraft
#20
Liaqat Ali, Abdul Latif Khan, Muhammad Al-Broumi, Rashid Al-Harrasi, Lubna Al-Kharusi, Javid Hussain, Ahmed Al-Harrasi
In continuation to our study of the chemical and biological potential of the secondary metabolites isolated from Omani seaweeds, we investigated a marine brown alga, Padina boergesenii. The phytochemical investigation resulted in the isolation of a new secondary metabolite, padinolic acid (1), along with some other semi-pure fractions and sub-fractions. The planar structure was confirmed through MS and NMR (1D and 2D) spectral data. The NOESY experiments coupled with the biogenetic consideration were helpful in assigning the stereochemistry in the molecule...
January 18, 2017: Marine Drugs
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