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https://www.readbyqxmd.com/read/28338127/phonon-bottleneck-and-long-lived-excited-states-in-%C3%AF-conjugated-pyrene-hoop
#1
Ricardo Franklin-Mergarejo, Tammie Nelson, Sergei Tretiak, Sebastian Fernandez-Alberti
In the last decade, recent synthetic advances have launched carbon-based π-conjugated hoops to the forefront of theoretical and experimental investigation not only for their potential use as bottom-up templates for carbon nanotube (CNT) growth, but also for the interesting excitonic effects arising from the cyclic geometry, unique π-system orientation, and unusual electronic interactions and couplings. In particular, cyclic materials based on pyrene, a common component in organic electronics, are popular candidates for the future design of π-conjugated nanorings for optoelectronic applications...
March 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28332833/uranyl-peroxide-clusters-incorporating-iron-trimers-and-bridging-by-bisphosphonate-and-carboxylate-containing-ligands
#2
Jie Qiu, Sining Dong, Jennifer E S Szymanowski, Malgorzata Dobrowolska, Peter C Burns
A hybrid uranium-iron cage nanocluster, [(UO2)24(FeOH)24(O2)24(PO4)8(CH(COO)(PO3)2)24](96-) (U24Fe24), was synthesized using bridging ligands containing bisphosphonate and carboxylate groups. U24Fe24 contains six tetramers of uranyl hexagonal bipyramids and eight iron trimers, each of which consists of three corner-sharing Fe(3+) octahedra and is stabilized by in situ formed phosphate and 2,2-bis(phosphonato)acetate (C2P2) groups. Tetramers and trimers are bridged by 24 C2P2 groups into a cage cluster. Crystals of U24Fe24 present a paramagnetic-like behavior...
March 23, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28332333/allo-hla-cross-reactivities-of-cmv-flu-and-vzv-specific-memory-t-cells-are-shared-by-different-individuals
#3
H van den Heuvel, K M Heutinck, E M W van der Meer-Prins, S L Yong, P P M C van Miert, J D H Anholts, M E I Franke-van Dijk, X Q Zhang, D L Roelen, R J M Ten Berge, F H J Claas
Virus-specific T cells can recognize allogeneic HLA (allo-HLA) through TCR cross-reactivity. The allospecificity often differs per individual ("private cross-reactivity"), but can also be shared by multiple individuals ("public cross-reactivity"). However, only a few examples of the latter have been described. Since these could facilitate alloreactivity prediction in transplantation, we aimed to identify novel public cross-reactivities of human virus-specific CD8+ T cells directed against allo-HLA by assessing their reactivity in mixed-lymphocyte reactions...
March 23, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28325841/an-inducible-amphipathic-helix-within-the-intrinsically-disordered-c-terminus-is-not-required-for-protein-biosynthesis-trafficking-or-garp2-interaction-but-can-participate-in-membrane-curvature-generation-by-peripherin-2-rds
#4
Michelle L Milstein, Victoria A Kimler, Chiranjib Ghatak, Alexey S Ladokhin, Andrew F X Goldberg
Peripherin-2/rds is required for biogenesis of vertebrate photoreceptor outer segment organelles. Its localization at the high curvature rim domains of outer segment disk membranes suggests that it may act to shape these structures; however, the molecular function of this protein is not yet resolved. Here, we apply biochemical, biophysical, and imaging techniques, to elucidate the role(s) played by the protein's intrinsically disordered C-terminal domain, and an incipient amphipathic α-helix contained within it...
March 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28321930/uncovering-allostery-and-regulation-in-samhd1-through-molecular-dynamics-simulations
#5
Kajwal Kumar Patra, Akash Bhattacharya, Swati Bhattacharya
The human sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a retroviral restriction factor in myeloid cells and non-cycling CD4+ T cells, a feature imputed to its phosphohydrolase activity - the enzyme depletes the cellular dNTP levels inhibiting reverse transcription. The functionally active form of SAMHD1 is an allosterically triggered tetramer which utilizes GTP-Mg(+2) -dNTP cross bridges to link and stabilize adjacent monomers. However, very little is known about how it assembles into a tetramer and how long the tetramer stays intact...
March 21, 2017: Proteins
https://www.readbyqxmd.com/read/28321886/-inside-out-pegylation-of-bovine-%C3%AE-cross-linked-hemoglobin
#6
Kyle D Webster, Dana Dahhan, Abigail M Otto, Cheyanne L Frosti, William L Dean, Jonathan B Chaires, Kenneth W Olsen
The development of a blood substitute is urgent due to blood shortages and potential communicable diseases. A novel method, inside-out PEGylation, has been used here to conjugate a multiarm maleimide-PEG (Mal-PEG) to β-cross-linked (βXL-Hb) hemoglobin (Hb) tetramers through the Cys β93 residues. This method produces a polymer with a single PEG backbone that is surrounded by multiple proteins, rather than coating a single protein with multiple PEG chains. Electrophoresis under denaturing conditions showed a large molecular weight species...
March 20, 2017: Artificial Organs
https://www.readbyqxmd.com/read/28319659/improving-computational-predictions-of-single-stranded-rna-tetramers-with-revised-%C3%AE-%C3%AE-torsional-parameters-for-the-amber-force-field
#7
David J Wales, Ilyas Yildirim
With current advancements in RNA based therapeutics, it is becoming crucial to utilize theoretical and computational methods to describe properly the physical properties of RNA molecules. NMR and X-ray crystallography are two powerful techniques for investigating structural properties. However, if the RNA molecules are complex or dynamic, these methods might not be adequate. For computational approaches, the quality of the force field will determine accuracy of our predictions. In this contribution, we revise the α/γ torsional parameters of RNA for amber force field using a model system representing an RNA dimer backbone...
March 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28318259/ammonia-borane-clusters-energetics-of-dihydrogen-bonding-cooperativity-and-the-role-of-electrostatics
#8
Kunduchi P Vijayalakshmi, Cherumuttathu H Suresh
Cluster formation of ammonia borane (NH3BH3) driven by noncovalent H···H dihydrogen interaction is investigated at the M06L/6-311+G(d,p) level of density functional theory. For clusters containing up to six monomers, ladder, cyclic, stacked, cross-stacked, end-on, mixed and hexagonal configurations have been screened for their energetic stability. In the dimer, 7.94 kcal/mol stabilization energy per monomer (Em) is observed. Compared to ladder and cyclic configurations, a tetramer consisting of stacked dimer units is more stable by 3...
March 24, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28317744/molecular-study-of-mucin-procyanidin-interaction-by-fluorescence-quenching-and-saturation-transfer-difference-std-nmr
#9
Elsa Brandão, Mafalda Santos Silva, Ignacio García-Estévez, Nuno Mateus, Victor de Freitas, Susana Soares
Astringency is closely related to the interaction between procyanidins and salivary proteins (SP). The aim of this work was to study the interaction between mucin, a SP responsible for saliva lubricating properties, with different procyanidins (B4 dimer, tetramer (TT) and fractions of oligomeric procyanidins), and the influence of several conditions [pH, ionic strength, procyanidins' mean degree of polymerization (mDP) and different solvents (ethanol or dimethylsulfoxide)] on this interaction by fluorescence quenching and Saturation Transfer Difference (STD)-NMR...
August 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28316540/x-ray-crystallographic-analysis-epr-studies-and-computational-calculations-of-a-cu-ii-tetramic-acid-complex
#10
Dimitrios Matiadis, Dimitrios Tsironis, Valentina Stefanou, Olga Igglessi-Markopoulou, Vickie McKee, Yiannis Sanakis, Katerina N Lazarou, Athanassios Chrissanthopoulos, Spyros N Yannopoulos, John M Markopoulos
In this work we present a structural and spectroscopic analysis of a copper(II) N-acetyl-5-arylidene tetramic acid by using both experimental and computational techniques. The crystal structure of the Cu(II) complex was determined by single crystal X-ray diffraction and shows that the copper ion lies on a centre of symmetry, with each ligand ion coordinated to two copper ions, forming a 2D sheet. Moreover, the EPR spectroscopic properties of the Cu(II) tetramic acid complex were also explored and discussed...
2017: Bioinorganic Chemistry and Applications
https://www.readbyqxmd.com/read/28315525/insights-into-the-molecular-architecture-and-histone-h3-h4-deposition-mechanism-of-yeast-chromatin-assembly-factor-1
#11
Paul Victor Sauer, Jennifer Timm, Danni Liu, David Sitbon, Elisabetta Boeri-Erba, Christophe Velours, Norbert Mücke, Jörg Langowski, Françoise Ochsenbein, Geneviève Almouzni, Daniel Panne
How the very first step in nucleosome assembly, deposition of histone H3-H4 as tetramers or dimers on DNA, is accomplished remains largely unclear. Here we report that yeast chromatin assembly factor 1 (CAF1), a conserved histone chaperone complex that deposits H3-H4 during DNA replication, binds a single H3-H4 heterodimer in solution. We identify a new DNA binding domain in the large Cac1 subunit of CAF1, which is required for high-affinity DNA binding by the CAF1 three-subunit complex, and which is distinct from the previously described C-terminal winged-helix domain...
March 18, 2017: ELife
https://www.readbyqxmd.com/read/28315523/dna-mediated-association-of-two-histone-bound-caf-1-complexes-drives-tetrasome-assembly-in-the-wake-of-dna-replication
#12
Francesca Mattiroli, Yajie Gu, Tejas Yadav, Jeremy L Balsbaugh, Michael R Harris, Eileen S Findlay, Yang Liu, Catherine A Radebaugh, Laurie A Stargell, Natalie G Ahn, Iestyn Whitehouse, Karolin Luger
Nucleosome assembly in the wake of DNA replication is a key process that regulates cell identity and survival. Chromatin assembly factor 1 (CAF-1) is a H3-H4 histone chaperone that associates with the replisome and orchestrates chromatin assembly following DNA synthesis. Little is known about the mechanism and structure of this key complex. Here we investigate the CAF-1•H3-H4 binding mode and the mechanism of nucleosome assembly. We show that CAF-1 binding to a H3-H4 dimer activates the Cac1 winged helix domain interaction with DNA...
March 18, 2017: ELife
https://www.readbyqxmd.com/read/28315222/tetramer-guided-epitope-mapping-a-rapid-approach-to-identify-hla-restricted-t-cell-epitopes-from-composite-allergens
#13
Luis L Diego Archila, William W Kwok
Tetramer-guided epitope mapping (TGEM) is a technique in immunology that permits the rapid identification of allergenic epitopes through peptide screening procedures utilizing human lymphocyte antigen (HLA) class II tetramers as staining reagents for detection. The identification of allergenic epitopes is a prerequisite for the accurate characterization of allergen-specific CD4(+) T cells without in vitro stimulation. Additionally, these MHC-II/peptide complexes that interact with T-cell receptors (TCR) of pathogenic CD4(+) T cells are compatible with a different number of assays like Intracelullar Cytokine Staining (ICS), and Carboxyfluorescein succinimidyl ester (CFSE) making it a robust technology to study the functionality of allergen-specific CD4(+) T cells...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28314858/identification-and-characterization-of-a-20%C3%AE-hydroxysteroid-dehydrogenase-from-the-anaerobic-gut-bacterium-butyricicoccus-desmolans-atcc-43058
#14
Saravanan Devendran, Celia Méndez-Garcia, Jason M Ridlon
Members of the gastrointestinal microbiota are known to convert glucocorticoids to androstanes, which can be subsequently converted to potent androgens by other members of the gut microbiota or host tissues. Butyricicoccus desmolans and Clostridium cadaveris has previously been reported for steroid-17,20-desmolase and 20β-hydroxysteroid dehydrogenase (20β-HSDH) activities that were responsible for androstane formation from cortisol, however the gene encoding these enzymes has yet to be reported. In this work, we identified and located a gene encoding 20β-HSDH in both B...
March 17, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28304166/twisted-macrocycles-with-folded-ortho-phenylene-subunits
#15
Zacharias J Kinney, C Scott Hartley
Many foldamers, oligomers that adopt well-defined secondary structures, are now known, including many exhibiting functional behavior. However, examples of foldamer subunits within larger architectures remain rare, despite the importance of higher-order structure in biomacromolecules. Here, we investigate the dynamic covalent assembly of short o-phenylenes, a simple class of aromatic foldamers, into twisted macrocycles. o-Phenylene tetramers have been combined with rod-shaped p-phenylene-, tolane-, and diphenylbutadiyene-based linkers using imine formation...
March 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28303107/localization-and-ordering-of-lipids-around-aquaporin-0-protein-and-lipid-mobility-effects
#16
Rodolfo Briones, Camilo Aponte-Santamaría, Bert L de Groot
Hydrophobic matching, lipid sorting, and protein oligomerization are key principles by which lipids and proteins organize in biological membranes. The Aquaporin-0 channel (AQP0), solved by electron crystallography (EC) at cryogenic temperatures, is one of the few protein-lipid complexes of which the structure is available in atomic detail. EC and room-temperature molecular dynamics (MD) of dimyristoylglycerophosphocholine (DMPC) annular lipids around AQP0 show similarities, however, crystal-packing and temperature might affect the protein surface or the lipids distribution...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28301164/effect-of-meso-vs-macro-size-of-hierarchical-porous-silica-on-the-adsorption-and-activity-of-immobilized-%C3%AE-galactosidase
#17
Ileana-Alexandra Pavel, Sofia F Prazeres, Gemma Montalvo, Carmen Garcia-Ruiz, Vincent Nicolas, Alain Celzard, Francois Dehez, Laetitia Canabady-Rochelle, Nadia Canilho, Andreea Pasc
β-galactosidase (β-Gal) is one of the most important enzymes used in milk processing for improving their nutritional quality and digestibility. Herein, β-Gal has been entrapped into a meso-macroporous material (average pore size 9 and 200 nm, respectively) prepared by a sol-gel method from a silica precursor and a dispersion of solid lipid nanoparticles in a micelle phase. The physisorption of the enzyme depends on the concentration of the feed solution and on the pore size of the support. The enzyme is preferentially adsorbed either in mesopores or in macropores, depending on its initial concentration...
March 16, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28298647/inhibition-of-the-mechano-enzymatic-amyloidogenesis-of-transthyretin-role-of-ligand-affinity-binding-cooperativity-and-occupancy-of-the-inner-channel
#18
Guglielmo Verona, P Patrizia Mangione, Sara Raimondi, Sofia Giorgetti, Giulia Faravelli, Riccardo Porcari, Alessandra Corazza, Julian D Gillmore, Philip N Hawkins, Mark B Pepys, Graham W Taylor, Vittorio Bellotti
Dissociation of the native transthyretin (TTR) tetramer is widely accepted as the critical step in TTR amyloid fibrillogenesis. It is modelled by exposure of the protein to non-physiological low pH in vitro and is inhibited by small molecule compounds, such as the drug tafamidis. We have recently identified a new mechano-enzymatic pathway of TTR fibrillogenesis in vitro, catalysed by selective proteolytic cleavage, which produces a high yield of genuine amyloid fibrils. This pathway is efficiently inhibited only by ligands that occupy both binding sites in TTR...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28298179/preparation-of-peptide-mhc-and-t-cell-receptor-dextramers-by-biotinylated-dextran-doping
#19
Michael T Bethune, Begoña Comin-Anduix, Yu-Hsien Hwang Fu, Antoni Ribas, David Baltimore
Peptide-major histocompatibility complex (pMHC) multimers enable the detection, characterization, and isolation of antigen-specific T-cell subsets at the single-cell level via flow cytometry and fluorescence microscopy. These labeling reagents exploit a multivalent scaffold to increase the avidity of individually weak T-cell receptor (TCR)-pMHC interactions. Dextramers are an improvement over the original streptavidin-based tetramer technology because they are more multivalent, improving sensitivity for rare, low-avidity T cells, including self/tumor-reactive clones...
March 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28295019/m2e-tetramer-specific-memory-cd4-t-cells-are-broadly-protective-against-influenza-infection
#20
D G Eliasson, A Omokanye, K Schön, U A Wenzel, V Bernasconi, M Bemark, A Kolpe, K El Bakkouri, T Ysenbaert, L Deng, W Fiers, X Saelens, N Lycke
Matrix protein 2 ectodomain (M2e) is considered an attractive component of a broadly protective, universal influenza A vaccine. Here we challenge the canonical view that antibodies against M2e are the prime effectors of protection. Intranasal immunizations of Balb/c mice with CTA1-3M2e-DD-generated M2e-specific memory CD4 T cells that were I-A(d) restricted and critically protected against infection, even in the complete absence of antibodies, as observed in JhD mice. Whereas some M2e-tetramer-specific memory CD4 T cells resided in spleen and lymph nodes, the majority were lung-resident Th17 cells, that rapidly expanded upon a viral challenge infection...
March 15, 2017: Mucosal Immunology
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