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https://www.readbyqxmd.com/read/28098184/infrared-laser-induced-gene-expression-for-tracking-development-and-function-of-single-c-elegans-embryonic-neurons
#1
Anupriya Singhal, Shai Shaham
Visualizing neural-circuit assembly in vivo requires tracking growth of optically resolvable neurites. The Caenorhabditis elegans embryonic nervous system, comprising 222 neurons and 56 glia, is attractive for comprehensive studies of development; however, embryonic reporters are broadly expressed, making single-neurite tracking/manipulation challenging. We present a method, using an infrared laser, for reproducible heat-dependent gene expression in small sublineages (one to four cells) without radiation damage...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28097280/freezing-induced-self-assembly-of-amphiphilic-molecules
#2
P A Albouy, S Deville, A Fulkar, K Hakouk, M Impéror-Clerc, M Klotz, Q Liu, M Marcellini, J Perez
The self-assembly of amphiphilic molecules usually takes place in a liquid phase, near room temperature. Here, using small angle X-ray scattering (SAXS) experiments performed in real time, we show that freezing of aqueous solutions of copolymer amphiphilic molecules can induce self-assembly below 0 °C.
January 18, 2017: Soft Matter
https://www.readbyqxmd.com/read/28093469/assembly-of-the%C3%A2-elongated-collagen-prolyl-4-hydroxylase-%C3%AE-2%C3%AE-2-heterotetramer%C3%A2-around-a-central-%C3%AE-2-dimer
#3
Kristian Koski, Jothi Anantharajan, Petri Kursula, Prathusha Dhavala, Abhinandan Venkatesha Murthy, Ulrich Bergmann, Johanna Myllyharju, Rik K Wierenga
COLLAGEN PROLYL 4-HYDROXYLASE C-P4H, AN Α2Β2 HETEROTETRAMER, IS A CRUCIAL ENZYME FOR COLLAGEN SYNTHESIS THE Α SUBUNIT CONSISTS OF AN N TERMINAL DIMERIZATION DOMAIN, A CENTRAL PEPTIDE-SUBSTRATE-BINDING PSB DOMAIN, AND A C TERMINAL CATALYTIC CAT DOMAIN THE Β SUBUNIT ALSO KNOWN AS PROTEIN DISULFIDE ISOMERASE PDI ACTS AS A CHAPERONE, STABILIZING THE FUNCTIONAL CONFORMATION OF C-P4H C-P4H HAS BEEN STUDIED FOR DECADES, BUT ITS STRUCTURE HAS REMAINED ELUSIVE HERE, WE PRESENT : A THREE-DIMENSIONAL SMALL-ANGLE X-RAY SCATTERING SAXS MODEL OF THE ENTIRE HUMAN C-P4H-I HETEROTETRAMER C-P4H IS AN ELONGATED, BILOBAL, SYMMETRIC MOLECULE WITH A LENGTH OF 290 Å THE DIMERIZATION DOMAINS FROM THE TWO A SUBUNITS FORM A PROTEIN-PROTEIN DIMER INTERFACE, ASSEMBLED AROUND THE CENTRAL ANTIPARALLEL COILED-COIL INTERFACE OF THEIR N TERMINAL Α HELICES THIS REGION FORMS A THIN WAIST IN THE BILOBAL TETRAMER THE TWO PSB/CAT UNITS, EACH COMPLEXED WITH A PDI/Β SUBUNIT, FORM TWO BULKY LOBES POINTING OUTWARD FROM THIS WAIST REGION, SUCH THAT THE PDI/Β SUBUNITS LOCATE AT THE FAR ENDS OF THE ΒΑΑΒ COMPLEX THE PDI/Β SUBUNIT INTERACTS EXTENSIVELY WITH THE CAT DOMAIN THE ASYMMETRIC SHAPE OF TWO TRUNCATED C-P4H-I VARIANTS, ALSO CHARACTERIZED IN THIS STUDY, AGREES WITH THIS ASSEMBLY FURTHERMORE, DATA FROM THESE TRUNCATED VARIANTS SHOW THAT DIMERIZATION BETWEEN THE A SUBUNITS HAS AN IMPORTANT ROLE IN ACHIEVING THE CORRECT PSB-CAT ASSEMBLY COMPETENT FOR CATALYTIC ACTIVITY KINETIC ASSAYS WITH VARIOUS PROLINE-RICH PEPTIDE SUBSTRATES AND INHIBITORS SUGGEST THAT IN THE COMPETENT ASSEMBLY, THE PSB DOMAIN BINDS TO THE PROCOLLAGEN SUBSTRATE DOWNSTREAM FROM THE CAT DOMAIN...
January 16, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28088615/cloning-heterologous-expression-and-biochemical-characterization-of-a-non-specific-endoglucanase-family-12-from-aspergillus-terreus-nih2624
#4
Fernando Segato, Bruno Dias, Gabriela L Berto, Dyoni M de Oliveira, Flávio H M De Souza, Matheus Augusto R N da Silva, Ana Paula Citadini, Mario T Murakami, André R L Damásio, Fábio Márcio Squina, Igor Polikarpov
The cellulases from Glycoside Hydrolyses family 12 (GH12) play an important role in cellulose degradation and plant cell wall deconstruction being widely used in a number of bioindustrial processes. Aiming to contribute toward better comprehension of these class of the enzymes, here we describe a high-yield secretion of a endoglucanase GH12 from Aspegillus terreus (AtGH12), which was cloned and expressed in Aspergillus nidulans strain A773. The purified protein was used for complete biochemical and functional characterization...
January 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28088481/saxs-structural-studies-of-dps-from-deinococcus-radiodurans-highlights-the-conformation-of-the-mobile-n-terminal-extensions
#5
Sandra P Santos, Maxime G Cuypers, Adam Round, Stephanie Finet, Theyencheri Narayanan, Edward P Mitchell, Célia V Romão
The radiation resistant bacterium Deinococcus radiodurans contains two DNA binding proteins from starved cells (Dps): Dps1 (DR2263) and Dps2 (DRB0092). These are suggested to play a role in DNA interaction, manganese and iron storage. The proteins assemble as a conserved dodecameric structure with structurally uncharacterized N-terminal extensions. In the case of DrDps1 these extensions have been proposed to be involved in DNA interactions, while in DrDps2 their function has yet to be established. The reported data reveals the relative position of the N-terminal extensions to the dodecameric sphere in solution for both Dps...
January 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28080032/heteroprotein-complex-formation-of-bovine-lactoferrin-and-pea-protein-isolate-a-multiscale-structural-analysis
#6
Eda Adal, Amin Sadeghpour, Simon D A Connell, Michael Rappolt, Esra Ibanoglu, Anwesha Sarkar
Associative electrostatic interactions between two oppositely charged globular proteins, lactoferrin (LF) and pea protein isolate (PPI), the latter being a mixture of vicilin, legumin and convicilin, was studied with a specific PPI/ LF molar ratio at room temperature. Structural aspects of the electrostatic complexes probed at different length scales were investigated as a function of pH by means of different complementary techniques, namely with dynamic light scattering, small angle X-ray scattering (SAXS), turbidity measurements and atomic force microscopy (AFM)...
January 12, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28079879/the-cluspro-web-server-for-protein-protein-docking
#7
Dima Kozakov, David R Hall, Bing Xia, Kathryn A Porter, Dzmitry Padhorny, Christine Yueh, Dmitri Beglov, Sandor Vajda
The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28079203/complexation-of-short-ds-rna-dna-oligonucleotides-with-gemini-micelles-a-time-resolved-saxs-and-computational-study
#8
Sara Falsini, Emanuela Di Cola, Martin In, Maria Giordani, Stefano Borocci, Sandra Ristori
Gene therapy is based on nucleic acid delivery to pathogenic cells in order to modulate their gene expression. The most used non viral vectors are lipid-based nanoaggregates, which are safer than viral carriers and have been shown to assemble easily with both DNA and RNA. However, the transfection efficiency of non viral carriers still needs to be improved before intensive practise in clinical trials can be implemented. For this purpose, the in depth characterization of the complexes formed by nucleic acids and their transporters is of great relevance...
January 12, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28076957/collapse-precedes-folding-in-denaturant-dependent-assembly-of-ubiquitin
#9
Govardhan Reddy, Dave Thirumalai
The folding of small protein Ubiquitin (Ub), which plays an indispensable role in targeting proteins for degradation and DNA damage response is complex. A number of experiments on Ub folding have reached differing conclusions regarding the relation between collapse and folding, and whether intermediates are populated. In order to resolve these vexing issues, we elucidate the denaturant-dependent thermodynamics and kinetics of Ub folding at low and neutral pH as a function of Guanidinium chloride and Urea using coarse-grained molecular simulations...
January 11, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28075595/adsorption-of-small-cationic-nanoparticles-onto-large-anionic-particles-from-aqueous-solution-a-model-system-for-understanding-pigment-dispersion-and-the-problem-of-effective-particle-density
#10
Shannon M North, Elizabeth R Jones, Gregory N Smith, Oleksandr O Mykhaylyk, Tom Annable, Steven P Armes
This work focuses on the use of copolymer nanoparticles as a dispersant for a model pigment (silica). Reversible addition-fragmentation chain transfer (RAFT) alcoholic dispersion polymerization was used to synthesize sterically stabilized diblock copolymer nanoparticles. The steric stabilizer block was poly(2-dimethylamino)ethyl methacrylate) [PDMA] while the core-forming block was poly(benzyl methacrylate) [PBzMA]. The mean degrees of polymerization for the PDMA and PBzMA blocks were 71 and 100, respectively...
January 11, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28074899/mof-derived-multifractal-porous-carbon-with-ultrahigh-lithium-ion-storage-performance
#11
Ang Li, Yan Tong, Bin Cao, Huaihe Song, Zhihong Li, Xiaohong Chen, Jisheng Zhou, Gen Chen, Hongmei Luo
Porous carbon is one of the most promising alternatives to traditional graphite materials in lithium-ion batteries. This is not only attributed to its advantages of good safety, stability and electrical conductivity, which are held by all the carbon-based electrodes, but also especially ascribed to its relatively high capacity and excellent cycle stability. Here we report the design and synthesis of a highly porous pure carbon material with multifractal structures. This material is prepared by the vacuum carbonization of a zinc-based metal-organic framework, which demonstrates an ultrahigh lithium storage capacity of 2458 mAh g(-1) and a favorable high-rate performance...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28074868/nucleoplasmin-like-domain-of-fkbp39-from-drosophila-melanogaster-forms-a-tetramer-with-partly-disordered-tentacle-like-c-terminal-segments
#12
Małgorzata Kozłowska, Aneta Tarczewska, Michał Jakób, Dominika Bystranowska, Michał Taube, Maciej Kozak, Mariusz Czarnocki-Cieciura, Andrzej Dziembowski, Marek Orłowski, Katarzyna Tkocz, Andrzej Ożyhar
Nucleoplasmins are a nuclear chaperone family defined by the presence of a highly conserved N-terminal core domain. X-ray crystallographic studies of isolated nucleoplasmin core domains revealed a β-propeller structure consisting of a set of five monomers that together form a stable pentamer. Recent studies on isolated N-terminal domains from Drosophila 39-kDa FK506-binding protein (FKBP39) and from other chromatin-associated proteins showed analogous, nucleoplasmin-like (NPL) pentameric structures. Here, we report that the NPL domain of the full-length FKBP39 does not form pentameric complexes...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28074088/accurate-optimization-of-amino-acid-form-factors-for-computing-small-angle-x-ray-scattering-intensity-of-atomistic-protein-structures
#13
Dudu Tong, Sichun Yang, Lanyuan Lu
Structure modelling via small-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures...
August 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28073257/protein-containing-lipid-bilayers-intercalated-with-size-matched-mesoporous-silica-thin-films
#14
Simon Isaksson, Erik B Watkins, Kathryn L Browning, Tania Kjellerup Lind, Marité Cárdenas, Kristina Hedfalk, Fredrik Höök, Martin Andersson
Proteins are key components in a multitude of biological processes, of which the functions carried out by transmembrane (membrane-spanning) proteins are especially demanding for investigations. This is because this class of protein needs to be incorporated into a lipid bilayer representing its native environment, and in addition, many experimental conditions also require a solid support for stabilization and analytical purposes. The solid support substrate may, however, limit the protein functionality due to protein-material interactions and a lack of physical space...
January 11, 2017: Nano Letters
https://www.readbyqxmd.com/read/28072399/organization-of-high-level-visual-cortex-in-human-infants
#15
Ben Deen, Hilary Richardson, Daniel D Dilks, Atsushi Takahashi, Boris Keil, Lawrence L Wald, Nancy Kanwisher, Rebecca Saxe
How much of the structure of the human mind and brain is already specified at birth, and how much arises from experience? In this article, we consider the test case of extrastriate visual cortex, where a highly systematic functional organization is present in virtually every normal adult, including regions preferring behaviourally significant stimulus categories, such as faces, bodies, and scenes. Novel methods were developed to scan awake infants with fMRI, while they viewed multiple categories of visual stimuli...
January 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28071844/a-vesicle-to-worm-transition-provides-a-new-high-temperature-oil-thickening-mechanism
#16
Matthew J Derry, Oleksandr O Mykhaylyk, Steven P Armes
Diblock copolymer vesicles are prepared via RAFT dispersion polymerization directly in mineral oil. Such vesicles undergo a vesicle-to-worm transition on heating to 150 °C, as judged by TEM and SAXS. Variable-temperature (1) H NMR spectroscopy indicates that this transition is the result of surface plasticization of the membrane-forming block by hot solvent, effectively increasing the volume fraction of the stabilizer block and so reducing the packing parameter for the copolymer chains. The rheological behavior of a 10 % w/w copolymer dispersion in mineral oil is strongly temperature-dependent: the storage modulus increases by five orders of magnitude on heating above the critical gelation temperature of 135 °C, as the non-interacting vesicles are converted into weakly interacting worms...
January 10, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28071810/deer-leather-analysis-of-the-microstructure-affecting-pebble
#17
Hannah C Wells, Katie Sizeland, Sue M Cooper, Nigel Kirby, Adrian Hawley, Stephen Mudie, Richard G Haverkamp
BACKGROUND: Deer leather has a characteristic pattern, referred to as "pebble", that is accorded such importance that a lack of it renders a leather defective. Synchrotron-based small angle X-ray scattering (SAXS), ultrasonic imaging, scanning electron microscopy, and tear tests are used to investigate the structural characteristics of well pebbled and poorly pebbled cervine leathers. RESULTS: Poorly pebbled leather has a less open structure in the upper grain region than well pebbled leather...
January 10, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28067527/probing-the-acid-induced-packing-structure-changes-of-the-molten-globule-domains-of-a-protein-near-equilibrium-unfolding
#18
Yi-Qi Yeh, Kuei-Fen Liao, Orion Shih, Ying-Jen Shiu, Wei-Ru Wu, Chun-Jen Su, Po-Chang Lin, U-Ser Jeng
Using simultaneously scanning small-angle X-ray scattering (SAXS) and UV-vis absorption with integrated online size exclusion chromatography, supplemental with molecular dynamics simulations, we unveil the long-postulated global structure evolution of a model multidomain protein bovine serum albumin (BSA) during acid-induced unfolding. Our results differentiate three global packing structures of the three molten globule domains of BSA, forming three intermediates I1, I2, and E along the unfolding pathway. The I1-I2 transition, overlooked in all previous studies, involves mainly coordinated reorientations across interconnected molten globule subdomains, and the transition activates a critical pivot domain opening of the protein for entering into the E form, with an unexpectedly large unfolding free energy change of -9...
January 19, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28064019/the-random-co-polymer-glatiramer-acetate-rapidly-kills-primary-human-leukocytes-through-sialic-acid-dependent-cell-membrane-damage
#19
Stig Hill Christiansen, Xianwei Zhang, Kristian Juul-Madsen, Michael Lykke Hvam, Brian Stougaard Vad, Manja Annette Behrens, Ida Lysgaard Thygesen, Babak Jalilian, Jan Skov Pedersen, Kenneth A Howard, Daniel E Otzen, Thomas Vorup-Jensen
The formulation glatiramer acetate (GA) is widely used in therapy of multiple sclerosis. GA consists of random copolymers of four amino acids, in ratios that produce a predominantly positive charge and an amphipathic character. With the extraordinary complexity of the drug, several pharmacological modes-of-action were suggested, but so far none, which rationalizes the cationicity and amphipathicity as part of the mode-of-action. Here, we report that GA rapidly kills primary human T lymphocytes and, less actively, monocytes...
January 5, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28062242/effect-of-reaction-solvents-on-the-multi-scale-structure-of-potato-starch-during-acid-treatment
#20
Binghua Sun, Yaoqi Tian, Benxi Wei, Long Chen, Yanhong Bi, Zhengyu Jin
Potato starch was treated with 0.36% HCl in ethanol and water for various time periods, and its structural changes were evaluated and compared in this study. Acid-ethanol treated starch (AET-s) had relatively low average molecular weight (Mw) and z-average radius of gyration (Rg), and its solubility was higher than that of the counterpart acid-water treated starch (AWT-s). The granular appearance and differential scanning calorimetry (DSC) profile demonstrated that acid in ethanol and in water exhibited different attack pathways on the granules...
January 3, 2017: International Journal of Biological Macromolecules
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