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Jonathan Negrel, Francine Javelle, Dominique Morandi, Géraldine Lucchi
A Gram-negative bacterium able to grow using chlorogenic acid (5-caffeoylquinic acid) as sole carbon source has been isolated from the roots of tomato plants inoculated with the arbuscular mycorrhizal fungus Rhizophagus irregularis. An intracellular esterase exhibiting very high affinity (Km = 2 μM) for chlorogenic acid has been extracted and purified by FPLC from the chlorogenate-grown cultures of this bacterium. The molecular mass of the purified esterase determined by SDS-PAGE was 61 kDa and its isoelectric point determined by chromatofocusing was 7...
October 17, 2016: Plant Physiology and Biochemistry: PPB
Ju Hui Jeong, Yong Jin Oh, Yunmee Lho, Sun You Park, Kwang-Hyeon Liu, Eunyoung Ha, Young Ho Seo
The molecular chaperone Hsp90 plays an important role in cancer cell survival and proliferation by regulating the maturation and stabilization of numerous oncogenic proteins. Due to its potential to simultaneously disable multiple signaling pathways, Hsp90 has emerged as an attractive therapeutic target for cancer treatment. In this study, the design, synthesis, and biological evaluation of a series of Hsp90 inhibitors are described. Among the synthetic compounds, 6,7-dihydrothieno [3,2-c]pyridin-5(4H)-yl amide 19 exhibits a remarkable binding affinity to the N-terminus of Hsp90 in a fluorescence polarization (FP) binding assay (IC50 = 50...
October 18, 2016: European Journal of Medicinal Chemistry
Tomasz Molcan, Sylwia Swigonska, Karina Orlowska, Kamil Myszczynski, Anna Nynca, Agnieszka Sadowska, Monika Ruszkowska, Jan Pawel Jastrzebski, Renata E Ciereszko
Polychlorinated dibenzo-p-dioxins (PCDDs) are widespread by-products of human industrial activity. They accumulate in tissues of animals and humans, exerting numerous adverse effects on different systems. In living organisms, dioxins are metabolized by enzymes of the cytochrome P450 family, including CYP1A1. Particular dioxin congeners differ in their toxicity level and ability to undergo biodegradation. Since the molecular mechanisms underlying dioxin susceptibility or resistance to biodegradation are unknown, in the present study the molecular interactions between five selected dioxins and porcine CYP1A1 protein were investigated...
October 23, 2016: Chemosphere
Michael A White, Jamie C Kwasnieski, Connie A Myers, Susan Q Shen, Joseph C Corbo, Barak A Cohen
Transcription factors often activate and repress different target genes in the same cell. How activation and repression are encoded by different arrangements of transcription factor binding sites in cis-regulatory elements is poorly understood. We investigated how sites for the transcription factor CRX encode both activation and repression in photoreceptors by assaying thousands of genomic and synthetic cis-regulatory elements in wild-type and Crx(-/-) retinas. We found that sequences with high affinity for CRX repress transcription, whereas sequences with lower affinity activate...
October 25, 2016: Cell Reports
F Pelin Kinik, Cigdem Altintas, Volkan Balci, Burak Koyuturk, Alper Uzun, Seda Keskin
Experiments were combined with atomically-detailed simulations and density functional theory (DFT) calculations to understand the effect of incorporation of an ionic liquid (IL), 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]), into a metal organic framework (MOF with a zeolitic imidazolate framework), ZIF-8, on the CO2 separation performance. The interactions between [BMIM][PF6] and ZIF-8 were examined in deep detail and their consequences on CO2/CH4, CO2/N2, and CH4/N2 separation have been elucidated by using experimental measurements complemented by DFT calculations and atomically-detailed simulations...
October 26, 2016: ACS Applied Materials & Interfaces
T J Mai, R Ma, Z Li, S C Bi
Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) is a negative regulator of T cell activation, which competes with CD28 for B7.1/B7.2 binding, and which has a greater affinity. Fusion of specific antigens to extracellular domain of CTLA4 represents a promising approach to increase the immunogenicity of DNA vaccines. In this study, we evaluated this interesting approach for CTLA4 enhancement on prostate stem cell antigen (PSCA)-specific immune responses and its anti-tumor effects in a prostate cancer mouse model...
October 24, 2016: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
Matilda Baptist, Candace Panagabko, Shamshad Cockcroft, Jeffrey Atkinson
Phosphatidylinositol transfer proteins (PITPs) are believed to be lipid transfer proteins because of their ability to transfer either phosphatidylinositol (PI) or phosphatidylcholine (PC) between membrane compartments, in vitro. However, the detailed mechanism of this transfer process is not fully established. To further understand the transfer mechanism of PITPs we examined the interaction of PITPs with membranes using dual polarization interferometry (DPI), which measures protein binding affinity on a flat immobilized lipid surface...
April 18, 2016: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
Debodyuti Dutta, Sabyashachi Mishra
In the fight against bacterial infections and antibiotic resistance, the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) is a potentially safe target enzyme. The role of Glu134, His67, and His349 residues in the binding and hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP) are investigated by employing MD simulation and hybrid QM/MM calculations of E134D, H67A, and H349A mutants of DapE. The free energy of substrate binding obtained from MM-PBSA approach correctly reproduced the experimentally observed ordering of substrate affinity, i...
October 26, 2016: Journal of Physical Chemistry. B
Yao Liu, Volodimyr V Duzhko, Zachariah A Page, Todd Emrick, Thomas P Russell
Conjugated polymer zwitterions (CPZs) are neutral, hydrophilic, polymer semiconductors. The pendent zwitterions, viewed as side chain dipoles, impart solubility in polar solvents for solution processing, and open opportunities as interfacial components of optoelectronic devices, for example, between metal electrodes and organic semiconductor active layers. Such interlayers are crucial for defining the performance of organic electronic devices, e.g., field-effect transistors (OFETs), light-emitting diodes (OLEDs), and photovoltaics (OPVs), all of which consist of multilayer structures...
October 26, 2016: Accounts of Chemical Research
Svenja Winzen, James Ciro Schwabacher, Julius Mueller, Katharina Landfester, Kristin Mohr
Surfactants, even in miniscule amounts, are often used for the synthesis and especially the stabilization of nanomaterials, which is essential for in vivo applications. In this study, we show that the interaction between nanoparticles and proteins strongly depends on the type of stabilizing surfactants and their (small) concentration changes. The reaction between human serum albumin (HSA) and polystyrene nanoparticles (PS-NPs) stabilized by an ionic or nonionic surfactant - sodium dodecyl sulfate (SDS) or Lutensol AT50, respectively - was monitored using isothermal titration calorimetry (ITC)...
October 26, 2016: Biomacromolecules
Anders Lundgren, Björn Agnarsson, Ronald Zirbs, Vladimir P Zhdanov, Erik Reimhult, Fredrik Höök
Emerging biomedical applications such as molecular imaging and drug delivery often require directed binding of nanoparticles to cell-membrane receptors. The specific apparent affinity of such ligand-functionalized particles is size-dependent, an observation so far solely attributed to multivalent receptor-ligand interaction. We question the universality of this explanation by demonstrating that the binding kinetics also depends on weak, attractive colloidal-type interaction between nanoparticles and a lipid membrane...
October 26, 2016: ACS Nano
Juan Liu, Guang Hong, Yu-Han Wu, Kosei Endo, Jian-Min Han, Hiroyuki Kumamoto, Takeshi Wada, Hidemi Kato, Ping Gao, Keiichi Sasaki
The aim of this study was to investigate and compare the surface characteristics and initial bioactivity of ceria-stabilized zirconia/alumina nanocomposite (NANOZR) with those of yttria-stabilized zirconia (3Y-TZP) and pure titanium (CpTi) following the use of three surface modification methods; polishing, sandblasting/acid-etching (SB-E) and electrochemical deoxidation (ECD). Physical properties including surface morphology, chemical composition, X-ray diffraction, surface wettability, surface roughness, and hardness were measured...
October 26, 2016: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
Lisa Sandersjöö, Andreas Jonsson, John Löfblom
Proteases are involved in fundamental biological processes and are important tools in both biotechnological and biomedical research. An important property of proteases is to discriminate among potential substrates. Here, we present a new method for substrate profiling of proteases. The substrates are displayed between two anti-idiotypic affinity domains on the Gram-positive bacterium Staphylococcus carnosus. The first domain functions as a reporter tag and has affinity for a labeled reporter protein, whereas the second domain blocks the reporter tag from interacting with the reporter protein...
October 26, 2016: Biotechnology Journal
Song Cai, Chuwen Ling, Jun Lu, Songwei Duan, Yingzhao Wang, Huining Zhu, Ruibang Lin, Liang Chen, Xingchang Pan, Muyi Cai, Huaiyu Gu
A primary pathogeny of epilepsy is excessive activation of α-amino-3-hydroxy-5-methyl-4-isoxazole propionate receptors (AMPARs). To find potential molecules to inhibit AMPARs, high-throughput screening was performed in a library of tetrapeptides in silico. Computational results suggest that some tetrapeptides bind stably to the AMPAR. We aligned these sequences of tetrapeptide candidates with those from in vitro digestion of the trout skin protein. Among salmon-derived products, Glu-Gly-Ala-Arg (EGAR) showed a high biological affinity toward AMPAR when tested in silico...
October 25, 2016: Neurotherapeutics: the Journal of the American Society for Experimental NeuroTherapeutics
Ximena Corso-Díaz, Charles N de Leeuw, Vivian Alonso, Diana Melchers, Bibiana K Y Wong, René Houtman, Elizabeth M Simpson
BACKGROUND: NR2E1 (Tlx) is an orphan nuclear receptor that regulates the maintenance and self-renewal of neural stem cells, and promotes tumourigenesis. Nr2e1-null mice exhibit reduced cortical and limbic structures and pronounced retinal dystrophy. NR2E1 functions mainly as a repressor of gene transcription in association with the co-repressors atrophin-1, LSD1, HDAC and BCL11A. Recent evidence suggests that NR2E1 also acts as an activator of gene transcription. However, co-activator complexes that interact with NR2E1 have not yet been identified...
October 26, 2016: BMC Genomics
Chuan Zhou, Heang-Ping Chan, Lubomir M Hadjiiski, Aamer Chughtai, Jun Wei, Ella A Kazerooni
PURPOSE: The authors are developing an automated method to identify the best-quality coronary arterial segment from multiple-phase coronary CT angiography (cCTA) acquisitions, which may be used by either interpreting physicians or computer-aided detection systems to optimally and efficiently utilize the diagnostic information available in multiple-phase cCTA for the detection of coronary artery disease. METHODS: After initialization with a manually identified seed point, each coronary artery tree is automatically extracted from multiple cCTA phases using our multiscale coronary artery response enhancement and 3D rolling balloon region growing vessel segmentation and tracking method...
October 2016: Medical Physics
Allan M Oliveira, Julia H Lehman, Anne B McCoy, W Carl Lineberger
We report the negative ion photoelectron spectroscopy of the hydroxymethoxide anion, H2C(OH)O(-). The photoelectron spectra show that 3.49 eV photodetachment produces two distinct electronic states of the neutral hydroxymethoxy radical (H2C(OH)O(⋅)). The H2C(OH)O(⋅) ground state (X̃ (2)A) photoelectron spectrum exhibits a vibrational progression consisting primarily of the OCO symmetric and asymmetric stretches, the OCO bend, as well as combination bands involving these modes with other, lower frequency modes...
September 28, 2016: Journal of Chemical Physics
Vaibhav Jain, Prabal K Maiti, Prasad V Bharatam
Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details...
September 28, 2016: Journal of Chemical Physics
Szymon Śmiga, Odile Franck, Bastien Mussard, Adam Buksztel, Ireneusz Grabowski, Eleonora Luppi, Julien Toulouse
We introduce an orbital-optimized double-hybrid (DH) scheme using the optimized-effective-potential (OEP) method. The orbitals are optimized using a local potential corresponding to the complete exchange-correlation energy expression including the second-order Møller-Plesset correlation contribution. We have implemented a one-parameter version of this OEP-based self-consistent DH scheme using the BLYP density-functional approximation and compared it to the corresponding non-self-consistent DH scheme for calculations on a few closed-shell atoms and molecules...
October 14, 2016: Journal of Chemical Physics
Jared O Kafader, Josey E Topolski, Caroline Chick Jarrold
The anion photoelectron (PE) spectra of Ce2Oy(-) (y = 1, 2), Ce3Oy(-) (y = 0-4), Ce4Oy(-) (y = 0-2), and Ce5Oy(-) (y = 1, 2) are reported and analyzed with supporting results from density functional theory calculations. The PE spectra all exhibit an intense electronic transition to the neutral ground state, all falling in the range of 0.7 to 1.1 eV electron binding energy, with polarization dependence consistent with detachment from diffuse Ce 6s-based molecular orbitals. There is no monotonic increase in electron affinity with increasing oxidation...
October 21, 2016: Journal of Chemical Physics
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