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Conformity

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https://www.readbyqxmd.com/read/28108933/modelling-genome-wide-topological-associating-domains-in-mouse-embryonic-stem-cells
#1
REVIEW
Y Zhan, L Giorgetti, G Tiana
Chromosome conformation capture (3C)-based techniques such as chromosome conformation capture carbon copy (5C) and Hi-C revealed that the folding of mammalian chromosomes is highly hierarchical. A fundamental structural unit in the hierarchy is represented by topologically associating domains (TADs), sub-megabase regions of the genome within which the chromatin fibre preferentially interacts. 3C-based methods provide the mean contact probabilities between chromosomal loci, averaged over a large number of cells, and do not give immediate access to the single-cell conformations of the chromatin fibre...
January 20, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28108663/determination-of-the-conformational-ensemble-of-the-tar-rna-by-x-ray-scattering-interferometry
#2
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/28108662/coordination-between-the-polymerase-and-rnase-h-activity-of-hiv-1-reverse-transcriptase
#3
Małgorzata Figiel, Miroslav Krepl, Jarosław Poznański, Agnieszka Gołąb, Jiří Šponer, Marcin Nowotny
Replication of human immunodeficiency virus 1 (HIV-1) involves conversion of its single-stranded RNA genome to double-stranded DNA, which is integrated into the genome of the host. This conversion is catalyzed by reverse transcriptase (RT), which possesses DNA polymerase and RNase H domains. The available crystal structures suggest that at any given time the RNA/DNA substrate interacts with only one active site of the two domains of HIV-1 RT. Unknown is whether a simultaneous interaction of the substrate with polymerase and RNase H active sites is possible...
January 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28108412/deciphering-the-mechanistic-insight-into-the-stoichiometric-ratio-dependent-behavior-of-cu-ii-on-bsa-fibrillation
#4
Ajeet Singh, Poulami Datta, Lalit M Pandey
Various metal ions are recently implicated in protein aggregates and are associated with numerous neurodegenerative diseases. In the present work, we have scrutinized the effect of stoichiometric variation of Cu(II) on BSA fibrillation at physiological pH 7.4 through Thioflavin-T dye binding study, residual protein concentration, Fourier Transform Infrared spectroscopy (FTIR), Dynamic Light Scattering (DLS), Atomic Force Microscopy (AFM) and Isothermal Titration Calorimetry (ITC). Fibrillation kinetics was studied through ThT fluorescence, which illustrated dependency on stoichiometric ratio of Cu(II)...
January 17, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28108100/three-dimensional-quality-assurance-of-imrt-prostate-plans-using-gel-dosimetry
#5
M A Silveira, J F Pavoni, O Baffa
Intensity modulated radiotherapy (IMRT) is one of the most modern radiation therapy treatment techniques. Although IMRT can deliver high and complex conformational doses to the tumor volume, its implementation requires rigorous quality assurance (QA) procedures that include a dosimetric pre-treatment verification of individual patient planning. This verification usually involves measuring a small volume of absolute dose with an ionization chamber and checking bi-dimensional fluency with an array of detectors...
January 17, 2017: Physica Medica: PM
https://www.readbyqxmd.com/read/28107916/conformity-assessment-of-multicomponent-materials-or-objects-risk-of-false-decisions-due-to-measurement-uncertainty-a-case-study-of-denatured-alcohols
#6
Ilya Kuselman, Francesca Pennecchi, Ricardo J N B da Silva, D Brynn Hibbert
Risk of a false decision on conformity of a multicomponent material or object due to measurement uncertainty is discussed. Even if conformity assessment for each component of a material sample is successful, the total probability of a false decision (total consumer's risk or producer's risk) concerning the sample as a whole might still be significant. A model of the total probability of such false decisions is formulated based on the law (theorem) of total probability. It is shown that the total risk can be evaluated as a combination of the particular risks of conformity assessment of sample components...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107510/effect-of-the-crystal-environment-on-side-chain-conformational-dynamics-in-cyanovirin-n-investigated-through-crystal-and-solution-molecular-dynamics-simulations
#7
Logan S Ahlstrom, Ivan I Vorontsov, Jun Shi, Osamu Miyashita
Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure...
2017: PloS One
https://www.readbyqxmd.com/read/28107481/bet-inhibitors-disrupt-rad21-dependent-conformational-control-of-kshv-latency
#8
Horng-Shen Chen, Alessandra De Leo, Zhuo Wang, Andrew Kerekovic, Robert Hills, Paul M Lieberman
Kaposi's Sarcoma-associated Herpesvirus (KSHV) establishes stable latent infection in B-lymphocytes and pleural effusion lymphomas (PELs). During latency, the viral genome persists as an epigenetically constrained episome with restricted gene expression programs. To identify epigenetic regulators of KSHV latency, we screened a focused small molecule library containing known inhibitors of epigenetic factors. We identified JQ1, a Bromodomain and Extended Terminal (BET) protein inhibitor, as a potent activator of KSHV lytic reactivation from B-cells carrying episomal KSHV...
January 20, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28107435/peptide-targeted-by-human-antibodies-associated-with-hiv-vaccine-associated-protection-assumes-a-dynamic-%C3%AE-helical-structure
#9
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/28107022/substituted-pyrrololactams-via-ring-expansion-of-spiro-2h-pyrroles-from-intermolecular-alkyne-isocyanide-click-reactions
#10
Jimil George, Hun Young Kim, Kyungsoo Oh
The facile synthesis of 6- to 8-membered pyrrololactams has been developed using a ring expansion of spiro-2H-pyrroles, the products of intermolecular alkyne-isocyanide click reactions. The key to successful ring expansion of spiro-2H-pyrroles to pyrrololactams is the enforced orbital overlap between the internal alkene and the amide carbonyl group through the conformationally locked bicyclic structures. The newly disclosed α-isocyano lactams, substrates for click reactions, should find their utility in the synthesis of pharmaceutically important heterocyclic compounds...
January 20, 2017: Organic Letters
https://www.readbyqxmd.com/read/28107009/nmr-and-computation-reveal-a-pressure-sensitive-folded-conformation-of-trp-cage
#11
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/28106929/conformational-analysis-of-an-antibacterial-cyclodepsipeptide-active-against-m-tuberculosis-by-a-combined-roe-and-rdc-analysis
#12
Maic Fredersdorf, Michael Kurz, Armin Bauer, Marc-Olivier Ebert, Carla Rigling, Laurie Lannes, Christina Thiele
Griselimycin (GM) and methylgriselimycin (MGM), naturally produced by microorganisms of the genus Streptomyces, are cyclic depsipeptides composed of ten amino acids. They exhibit antibacterial activity against mycobacterium species by inhibiting the sliding clamp of prokaryotic DNA polymerase III and are therefore considered as potential anti-tuberculosis drugs. The difference between both peptides is the presence of L -(R)-4-methylproline in MGM instead of L -proline in GM at position 8 of the amino acid sequence...
January 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28106780/integrins-and-cell-metabolism-an-intimate-relationship-impacting-cancer
#13
REVIEW
Rehman Ata, Costin N Antonescu
Integrins are important regulators of cell survival, proliferation, adhesion and migration. Once activated, integrins establish a regulated link between the extracellular matrix and the cytoskeleton. Integrins have well-established functions in cancer, such as in controlling cell survival by engagement of many specific intracellular signaling pathways and in facilitating metastasis. Integrins and associated proteins are regulated by control of transcription, membrane traffic, and degradation, as well as by a number of post-translational modifications including glycosylation, allowing integrin function to be modulated to conform to various cellular needs and environmental conditions...
January 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28106755/the-performance-of-several-docking-programs-at-reproducing-protein-macrolide-like-crystal-structures
#14
Alejandro Castro-Alvarez, Anna M Costa, Jaume Vilarrasa
The accuracy of five docking programs at reproducing crystallographic structures of complexes of 8 macrolides and 12 related macrocyclic structures, all with their corresponding receptors, was evaluated. Self-docking calculations indicated excellent performance in all cases (mean RMSD values ≤ 1.0) and confirmed the speed of AutoDock Vina. Afterwards, the lowest-energy conformer of each molecule and all the conformers lying 0-10 kcal/mol above it (as given by Macrocycle, from MacroModel 10.0) were subjected to standard docking calculations...
January 17, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28106397/kinetics-of-detergent-induced-activation-and-inhibition-of-a-minimal-lipase
#15
Daniel Kuebler, Anna Bergmann, Lukas Weger, Kim Nadine Ingenbosch, Kerstin Hoffmann-Jacobsen
Detergents are commonly applied in lipase assays to solubilize the sparingly soluble model substrates. However, detergents affect lipases as well as substrates in multiple ways. The effect of detergents on lipase activity is commonly attributed to conformational changes in the lid region. This study deals with the effect of the non-ionic detergent, polyethylene glycol dodecyl ether, on a lipase that does not contain a lid sequence, lipase A from Bacillus subtilis (BSLA). We show that BSLA activity depends strongly on detergent concentration and the dependency profile changes with pH...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28106319/palladium-catalyzed-ring-forming-aminoalkenylation-of-alkenes-with-aldehydes-initiated-by-intramolecular-aminopalladation
#16
Yue Hu, Yinjun Xie, Zhiqiang Shen, Hanmin Huang
A palladium-catalyzed aminopalladation reaction followed by nucleophilic addition with aldehydes and dehydration is described. This direct and operationally simple procedure provides a rapid and reliable approach to a wide range of functionalized tetrahydroisoquinolines with high selectivity. Mechanistic studies disclosed that the nucleophilic addition, performed via a highly ordered transition-state, is the turnover-limiting step in which the inherent β-hydride elimination of the key Csp(3) -Pd species was controlled by the confined conformation and the nucleophilicity of the Csp(3) -Pd bond was enhanced by the strong electron-donating effect of the nitrogen atom...
January 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28106315/peptide-n-amination-supports-%C3%AE-sheet-conformations
#17
Matthew P Sarnowski, Chang Won Kang, Yassin M Elbatrawi, Lukasz Wojtas, Juan R Del Valle
The conformational heterogeneity of backbone N-substituted peptides limits their ability to adopt stable secondary structures. Herein, we describe a practical synthesis of backbone aminated peptides that readily adopt β-sheet folds. Data derived from model N-amino peptides suggest that extended conformations are stabilized through cooperative steric, electrostatic, and hydrogen-bonding interactions.
January 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28106310/mechanism-of-type-iii-protein-secretion-regulation-of-flha-conformation-by-a-functionally-critical-charged-residue-cluster
#18
Marc Erhardt, Paige Wheatley, Eun A Kim, Takanori Hirano, Yang Zhang, Mayukh K Sarkar, Kelly T Hughes, David F Blair
The bacterial flagellum contains a specialized secretion apparatus in its base that pumps certain protein subunits through the growing structure to their sites of installation beyond the membrane. A related apparatus functions in the injectisomes of gram-negative pathogens to export virulence factors into host cells. This mode of protein export is termed type-III secretion (T3S). Details of the T3S mechanism are unclear. It is energized by the proton gradient; here, a mutational approach was used to identify proton-binding groups that might function in transport...
January 20, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28106305/diversity-oriented-peptide-stapling-a-third-generation-cuaac-stapling-and-functionalisation-strategy
#19
Thu Tran Phuong, Christian Ørnbøl Larsen, Tobias Røndbjerg, Martina De Foresta, Micha Ben Achim Kunze, Ales Marek, Jacob Hartvig Løper, Lotte-Emilie Boyhus, Astrid Knuhtsen, Kresten Lindorff-Larsen, Daniel Sejer Pedersen
The introduction of macrocyclic constraints in peptides (peptide stapling) is an important tool within peptide medicinal chemistry for stabilising and pre-organising peptides in a desired conformation. In recent years, the copper-catalysed azide-alkyne cycloaddition (CuAAC) has emerged as a powerful method for peptide stapling. However, to date CuAAC stapling has not provided a simple method for obtaining peptides that are easily diversified further. In the present study, we report a new diversity-oriented peptide stapling (DOPS) methodology based on CuAAC chemistry...
January 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28106178/exploring-the-relevance-of-gas-phase-structures-to-biology-cold-ion-spectroscopy-of-the-decapeptide-neurokinin-a
#20
A Y Pereverzev, O V Boyarkin
Linking the intrinsic tertiary structures of biomolecules to their native geometries is a central prerequisite for making gas-phase studies directly relevant to biology. The isolation of molecules in the gas phase eliminates hydrophilic interactions with solvents, to some extent mimicking a hydrophobic environment. Intrinsic structures therefore may resemble native ones for peptides that in vivo reside in a hydrophobic environment (e.g., binding pockets of receptors). In this study, we investigate doubly protonated neurokinin A (NKA) using IR-UV double resonance cold ion spectroscopy and find only five conformers of this decapeptide in the gas phase...
January 20, 2017: Physical Chemistry Chemical Physics: PCCP
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