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IUCrJ

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https://www.readbyqxmd.com/read/30443370/structure-based-mechanism-of-action-of-a-viral-poly-adp-ribose-polymerase-1-interacting-protein-facilitating-virus-replication
#1
Woo-Chang Chung, Junsoo Kim, Byung Chul Kim, Hye-Ri Kang, JongHyeon Son, Hosam Ki, Kwang Yeon Hwang, Moon Jung Song
Poly(ADP-ribose) polymerase 1 (PARP-1), an enzyme that modifies nuclear proteins by poly(ADP-ribosyl)ation, regulates various cellular activities and restricts the lytic replication of oncogenic gammaherpesviruses by inhibiting the function of replication and transcription activator (RTA), a key switch molecule of the viral life cycle. A viral PARP-1-interacting protein (vPIP) encoded by murine gammaherpesvirus 68 (MHV-68) orf49 facilitates lytic replication by disrupting interactions between PARP-1 and RTA...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443369/-deep-consensus-a-deep-learning-based-approach-for-particle-pruning-in-cryo-electron-microscopy
#2
Ruben Sanchez-Garcia, Joan Segura, David Maluenda, Jose Maria Carazo, Carlos Oscar S Sorzano
Single-particle cryo-electron microscopy (cryo-EM) has recently become a mainstream technique for the structural determination of macromolecules. Typical cryo-EM workflows collect hundreds of thousands of single-particle projections from thousands of micrographs using particle-picking algorithms. However, the number of false positives selected by these algorithms is large, so that a number of different 'cleaning steps' are necessary to decrease the false-positive ratio. Most commonly employed techniques for the pruning of false-positive particles are time-consuming and require user intervention...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443368/crystal-structure-interaction-energies-and-experimental-electron-density-of-the-popular-drug-ketoprophen
#3
Sylwia Pawlędzio, Anna Makal, Damian Trzybiński, Krzysztof Woźniak
The crystal and molecular structure of the pure ( S )-enantiomer of the popular analgesic and anti-inflammatory drug ketoprophen (α-ket) is reported. A detailed aspherical charge-density model based on high-resolution X-ray diffraction data has been refined, yielding a high-precision geometric description and classification of the O-H⋯O interactions as medium strength hydrogen bonds. The crystal structure of the racemic form of ketoprophen (β-ket) was also redetermined at 100 K, at 0.5 Å resolution...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443367/committee-machine-that-votes-for-similarity-between-materials
#4
Duong-Nguyen Nguyen, Tien-Lam Pham, Viet-Cuong Nguyen, Tuan-Dung Ho, Truyen Tran, Keisuke Takahashi, Hieu-Chi Dam
A method has been developed to measure the similarity between materials, focusing on specific physical properties. The information obtained can be utilized to understand the underlying mechanisms and support the prediction of the physical properties of materials. The method consists of three steps: variable evaluation based on nonlinear regression, regression-based clustering, and similarity measurement with a committee machine constructed from the clustering results. Three data sets of well characterized crystalline materials represented by critical atomic predicting variables are used as test beds...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443366/self-adapted-clustering-of-solute-atoms-into-a-confined-two-dimensional-prismatic-platelet-with-an-ellipse-like-quasi-unit-cell
#5
Hongbo Xie, Junyuan Bai, Hucheng Pan, Xueyong Pang, Yuping Ren, Shineng Sun, Liqing Wang, Hong Zhao, Boshu Liu, Gaowu Qin
This paper reports a new structured prismatic platelet, self-assembled by an ellipse-like quasi-unit cell, precipitated in Mg-In-Yb and Mg-In-Ca ternary alloys and aged isothermally at 200°C using aberration-corrected high-angle annular dark-field scanning transmission electron microscopy combined with density functional theory computations. The ordered stacking of solute atoms along the [0001]α direction based on elliptically shaped self-adapted clustering leads to the generation of the quasi-unit cell. The bonding of these ellipse-like quasi-unit-cell rods by the Mg atomic columns along the 〈〉α directions formed a two-dimensional planar structure, which has three variants with a {}α habit plane and full coherence with the α-Mg matrix...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443365/systematic-synthesis-of-a-6-component-organic-salt-alloy-of-naftopidil-and-pentanary-quaternary-and-ternary-multicomponent-crystals
#6
Rambabu Dandela, Srinu Tothadi, Udaya Kiran Marelli, Ashwini Nangia
The single-crystal X-ray structure of a 6-component organic-salt alloy (hexanary) of naftopidil (1) (an active pharmaceutical ingredient) with benzoic acid (2) and four different hydroxy-substituted benzoic acids, i.e. salicylic acid (3), 2,3-di-hydroxybenzoic acid (4), 2,4-di-hydroxybenzoic acid (5) and 2,6-di-hydroxybenzoic acid (6), is reported. The hexanary assembly originates from the observation that the binary salts of naftopidil with the above acids are isostructural. In addition to the 6-component solid, we also describe five 5-component, ten 4-component, and ten 3-component organic-salt alloys of naftopidil (1) with carboxylic acids (2)-(6)...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443364/determination-of-chemical-ordering-in-the-complex-perovskite-pb-cd-1-3-nb-2-3-o-3
#7
Caiyan Wang, Zhengqian Fu, Nan Zhang, Marek Paściak, Jian Zhuang, Zenghui Liu, Wei Ren, Zuo-Guang Ye
Pure-phase Pb(Cd1/3 Nb2/3 )O3 (PCN) single crystals and ceramics with a complex perovskite structure are synthesized for the first time. The local chemical ordering in PCN has been investigated by X-ray diffraction (including diffuse scattering) and Cs-corrected transmission electron microscopy experiments. It is concluded that the PCN samples have large coherent chemical ordering regions that even extend to the long range, and the ordering model is consistent with β-type chemical ordered regions. The antiphase domain boundaries were also observed...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443363/dynamics-of-soft-nanoparticle-suspensions-at-hard-x-ray-fel-sources-below-the-radiation-damage-threshold
#8
Felix Lehmkühler, Joana Valerio, Dina Sheyfer, Wojciech Roseker, Martin A Schroer, Birgit Fischer, Kensuke Tono, Makina Yabashi, Tetsuya Ishikawa, Gerhard Grübel
The application of X-ray photon correlation spectroscopy (XPCS) at free-electron laser (FEL) facilities enables, for the first time, the study of dynamics on a (sub-)nanometre scale in an unreached time range between femtoseconds and seconds. For soft-matter materials, radiation damage is a major limitation when going beyond single-shot applications. Here, an XPCS study is presented at a hard X-ray FEL on radiation-sensitive polymeric poly( N -isopropylacrylamide) (PNIPAM) nanoparticles. The dynamics of aqueous suspensions of densely packed silica-PNIPAM core-shell particles and a PNIPAM nanogel below the radiation-damage threshold are determined...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443362/tailoring-structural-and-magnetic-properties-of-mn-3-x-fe-x-ga-alloys-towards-multifunctional-applications
#9
Z H Liu, Z J Tang, J G Tan, Y J Zhang, Z G Wu, X T Wang, G D Liu, X Q Ma
This study investigated the structural and magnetic properties of Mn3- x Fe x Ga alloys ( x = 0, 0.2, 0.4, 0.6, 0.8, 1) under different heat-treatment conditions. A tetragonal structure was observed in samples that were heat treated at 623 K for three days followed by quenching in ice water. These tetragonal alloys present large coercive fields in the range 0.8-5 kOe and low saturation magnetization, and have great potential for application in spin-transfer torque-based devices. A hexagonal structure was observed in samples subjected to heat treatment at 883 K for three days following quenching in ice water...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443361/small-angle-neutron-scattering-studies-on-the-ampa-receptor-glua2-in-the-resting-ampa-bound-and-gyki-53655-bound-states
#10
Andreas Haahr Larsen, Jerzy Dorosz, Thor Seneca Thorsen, Nicolai Tidemand Johansen, Tamim Darwish, Søren Roi Midtgaard, Lise Arleth, Jette Sandholm Kastrup
The AMPA receptor GluA2 belongs to the family of ionotropic glutamate receptors, which are responsible for most of the fast excitatory neuronal signalling in the central nervous system. These receptors are important for memory and learning, but have also been associated with brain diseases such as Alzheimer's disease and epilepsy. Today, one drug is on the market for the treatment of epilepsy targeting AMPA receptors, i.e. a negative allosteric modulator of these receptors. Recently, crystal structures and cryo-electron microscopy (cryo-EM) structures of full-length GluA2 in the resting (apo), activated and desensitized states have been reported...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443360/structures-of-collagen-iv-globular-domains-insight-into-associated-pathologies-folding-and-network-assembly
#11
Patricia Casino, Roberto Gozalbo-Rovira, Jesús Rodríguez-Díaz, Sreedatta Banerjee, Ariel Boutaud, Vicente Rubio, Billy G Hudson, Juan Saus, Javier Cervera, Alberto Marina
Basement membranes are extracellular structures of epithelia and endothelia that have collagen IV scaffolds of triple α-chain helical protomers that associate end-to-end, forming networks. The molecular mechanisms by which the noncollagenous C-terminal domains of α-chains direct the selection and assembly of the α1α2α1 and α3α4α5 hetero-oligomers found in vivo remain obscure. Autoantibodies against the noncollagenous domains of the α3α4α5 hexamer or mutations therein cause Goodpasture's or Alport's syndromes, respectively...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443359/three-beam-convergent-beam-electron-diffraction-for-measuring-crystallographic-phases
#12
Yueming Guo, Philip N H Nakashima, Joanne Etheridge
Under almost all circumstances, electron diffraction patterns contain information about the phases of structure factors, a consequence of the short wavelength of an electron and its strong Coulombic interaction with matter. However, extracting this information remains a challenge and no generic method exists. In this work, a set of simple analytical expressions is derived for the intensity distribution in convergent-beam electron diffraction (CBED) patterns recorded under three-beam conditions. It is shown that these expressions can be used to identify features in three-beam CBED patterns from which three-phase invariants can be extracted directly, without any iterative refinement processes...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443358/unwarping-gisaxs-data
#13
Jiliang Liu, Kevin G Yager
Grazing-incidence small-angle X-ray scattering (GISAXS) is a powerful technique for measuring the nanostructure of coatings and thin films. However, GISAXS data are plagued by distortions that complicate data analysis. The detector image is a warped representation of reciprocal space because of refraction, and overlapping scattering patterns appear because of reflection. A method is presented to unwarp GISAXS data, recovering an estimate of the true undistorted scattering pattern. The method consists of first generating a guess for the structure of the reciprocal-space scattering by solving for a mutually consistent prediction from the transmission and reflection sub-components...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443357/single-particle-imaging-without-symmetry-constraints-at-an-x-ray-free-electron-laser
#14
Max Rose, Sergey Bobkov, Kartik Ayyer, Ruslan P Kurta, Dmitry Dzhigaev, Young Yong Kim, Andrew J Morgan, Chun Hong Yoon, Daniel Westphal, Johan Bielecki, Jonas A Sellberg, Garth Williams, Filipe R N C Maia, Olexander M Yefanov, Vyacheslav Ilyin, Adrian P Mancuso, Henry N Chapman, Brenda G Hogue, Andrew Aquila, Anton Barty, Ivan A Vartanyants
The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443356/signal-to-noise-spatial-resolution-and-information-capacity-of-coherent-diffraction-imaging
#15
Timur E Gureyev, Alexander Kozlov, Yakov I Nesterets, David M Paganin, Andrew V Martin, Harry M Quiney
It is shown that the average signal-to-noise ratio (SNR) in the three-dimensional electron-density distribution of a sample reconstructed by coherent diffractive imaging cannot exceed twice the square root of the ratio of the mean total number of scattered photons detected during the scan and the number of spatially resolved voxels in the reconstructed volume. This result leads to an upper bound on Shannon's information capacity of this imaging method by specifying the maximum number of distinguishable density distributions within the reconstructed volume when the radiation dose delivered to the sample and the spatial resolution are both fixed...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443355/conformational-aspects-of-polymorphs-and-phases-of-2-propyl-1-h-benzimidazole
#16
Fco Javier Zuñiga, Aurora J Cruz-Cabeza, Xabier M Aretxabaleta, Noelia de la Pinta, Tomasz Breczewski, María Mar Quesada-Moreno, Juan Ramón Avilés-Moreno, Juan Jesús López-González, Rosa M Claramunt, Jose Elguero
This paper reports on the polymorphism of 2-propyl-1 H -benzimidazole (2PrBzIm) induced by temperature change. Upon heating, an irreversible reconstructive-type phase transition at T = 384 K from the ordered form I ( P 21 21 21 ) to a new polymorph, form II HT ( Pcam ), was observed. The structural transformation between forms I and II involves significant changes in the crystal packing, as well as a key conformational variation around the propyl chain of the molecule. After the first irreversible phase transition, the II HT form undergoes two further (reversible) phase transitions upon cooling at 361 K ( II RT ) and 181 K ( II LT )...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443354/towards-the-theoretical-limitations-of-x-ray-nanocrystallography-at-high-intensity-the-validity-of-the-effective-form-factor-description
#17
Malik Muhammad Abdullah, Sang-Kil Son, Zoltan Jurek, Robin Santra
X-ray free-electron lasers (XFELs) broaden horizons in X-ray crystallography. Facilitated by the unprecedented high intensity and ultrashort duration of the XFEL pulses, they enable us to investigate the structure and dynamics of macromolecules with nano-sized crystals. A limitation is the extent of radiation damage in the nanocrystal target. A large degree of ionization initiated by the incident high-intensity XFEL pulse alters the scattering properties of the atoms leading to perturbed measured patterns. In this article, the effective-form-factor approximation applied to capture this phenomenon is discussed...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443353/structure-determination-and-crystal-chemistry-of-large-repeat-mixed-layer-hexaferrites
#18
C Delacotte, G F S Whitehead, M J Pitcher, C M Robertson, P M Sharp, M S Dyer, J Alaria, J B Claridge, G R Darling, D R Allan, G Winter, M J Rosseinsky
Hexaferrites are an important class of magnetic oxides with applications in data storage and electronics. Their crystal structures are highly modular, consisting of Fe- or Ba-rich close-packed blocks that can be stacked in different sequences to form a multitude of unique structures, producing large anisotropic unit cells with lattice parameters typically >100 Å along the stacking axis. This has limited atomic-resolution structure solutions to relatively simple examples such as Ba2 Zn2 Fe12 O22 , whilst longer stacking sequences have been modelled only in terms of block sequences, with no refinement of individual atomic coordinates or occupancies...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443352/rayleigh-scattering-microscopy-for-tracking-and-sizing-nanoparticles-in-focused-aerosol-beams
#19
Max F Hantke, Johan Bielecki, Olena Kulyk, Daniel Westphal, Daniel S D Larsson, Martin Svenda, Hemanth K N Reddy, Richard A Kirian, Jakob Andreasson, Janos Hajdu, Filipe R N C Maia
Ultra-bright femtosecond X-ray pulses generated by X-ray free-electron lasers (XFELs) can be used to image high-resolution structures without the need for crystallization. For this approach, aerosol injection has been a successful method to deliver 70-2000 nm particles into the XFEL beam efficiently and at low noise. Improving the technique of aerosol sample delivery and extending it to single proteins necessitates quantitative aerosol diagnostics. Here a lab-based technique is introduced for Rayleigh-scattering microscopy allowing us to track and size aerosolized particles down to 40 nm in diameter as they exit the injector...
November 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/30443351/photocage-initiated-time-resolved-solution-x-ray-scattering-investigation-of-protein-dimerization
#20
Inokentijs Josts, Stephan Niebling, Yunyun Gao, Matteo Levantino, Henning Tidow, Diana Monteiro
This work demonstrates a new method for investigating time-resolved structural changes in protein conformation and oligomerization via photocage-initiated time-resolved X-ray solution scattering by observing the ATP-driven dimerization of the MsbA nucleotide-binding domain. Photocaged small molecules allow the observation of single-turnover reactions of non-naturally photoactivatable proteins. The kinetics of the reaction can be derived from changes in X-ray scattering associated with ATP-binding and subsequent dimerization...
November 1, 2018: IUCrJ
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