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https://www.readbyqxmd.com/read/28512576/applications-of-contact-predictions-to-structural-biology
#1
REVIEW
Felix Simkovic, Sergey Ovchinnikov, David Baker, Daniel J Rigden
Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are important for protein structure or function can lead to covariance between the two positions. Recent methodological advances allow much more accurate contact predictions to be derived from this evolutionary covariance signal. The practical application of contact predictions has largely been confined to structural bioinformatics, yet, as this work seeks to demonstrate, the data can be of enormous value to the structural biologist working in X-ray crystallo-graphy, cryo-EM or NMR...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512575/new-leads-for-fragment-based-design-of-rhenium-technetium-radiopharmaceutical-agents
#2
Alice Brink, John R Helliwell
Multiple possibilities for the coordination of fac-[Re(CO)3(H2O)3](+) to a protein have been determined and include binding to Asp, Glu, Arg and His amino-acid residues as well as to the C-terminal carboxylate in the vicinity of Leu and Pro. The large number of rhenium metal complex binding sites that have been identified on specific residues thereby allow increased target identification for the design of future radiopharmaceuticals. The core experimental concept involved the use of state-of-art tuneable synchrotron radiation at the Diamond Light Source to optimize the rhenium anomalous dispersion signal to a large value (f'' of 12...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512574/crystallographic-and-saxs-studies-of-s-adenosyl-l-homocysteine-hydrolase-from-bradyrhizobium-elkanii
#3
Tomasz Manszewski, Kamil Szpotkowski, Mariusz Jaskolski
S-Adenosyl-l-homocysteine hydrolase (SAHase) from the symbiotic bacterium Bradyrhizobium elkanii (BeSAHase) was crystallized in four ligand complexes with (i) mixed adenosine (Ado) and cordycepin (Cord; 3'-deoxyadenosine), (ii) adenine (Ade), (iii) Ado and (iv) mixed 2'-deoxyadenosine (2'-dAdo) and Ade. The crystal structures were solved at resolutions of 1.84, 1.95, 1.95 and 1.54 Å, respectively. Only the Ade complex crystallized with a dimer in the asymmetric unit, while all of the other complexes formed a crystallographically independent tetrameric assembly...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512573/photoreduction-and-validation-of-haem-ligand-intermediate-states-in-protein-crystals-by-in-situ-single-crystal-spectroscopy-and-diffraction
#4
Demet Kekilli, Tadeo Moreno-Chicano, Amanda K Chaplin, Sam Horrell, Florian S N Dworkowski, Jonathan A R Worrall, Richard W Strange, Michael A Hough
Powerful synergies are available from the combination of multiple methods to study proteins in the crystalline form. Spectroscopies which probe the same region of the crystal from which X-ray crystal structures are determined can give insights into redox, ligand and spin states to complement the information gained from the electron-density maps. The correct assignment of crystal structures to the correct protein redox and ligand states is essential to avoid the misinterpretation of structural data. This is a particular concern for haem proteins, which can occupy a wide range of redox states and are exquisitely sensitive to becoming reduced by solvated electrons generated from interactions of X-rays with water molecules in the crystal...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512572/experimental-strategies-for-imaging-bioparticles-with-femtosecond-hard-x-ray-pulses
#5
Benedikt J Daurer, Kenta Okamoto, Johan Bielecki, Filipe R N C Maia, Kerstin Mühlig, M Marvin Seibert, Max F Hantke, Carl Nettelblad, W Henry Benner, Martin Svenda, Nicuşor Tîmneanu, Tomas Ekeberg, N Duane Loh, Alberto Pietrini, Alessandro Zani, Asawari D Rath, Daniel Westphal, Richard A Kirian, Salah Awel, Max O Wiedorn, Gijs van der Schot, Gunilla H Carlsson, Dirk Hasse, Jonas A Sellberg, Anton Barty, Jakob Andreasson, Sébastien Boutet, Garth Williams, Jason Koglin, Inger Andersson, Janos Hajdu, Daniel S D Larsson
This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles of ∼40 nm in diameter were injected into the submicrometre X-ray focus at a reduced pressure. Diffraction patterns were recorded on two area detectors. The statistical nature of the measurements from many individual particles provided information about the intensity profile of the X-ray beam, phase variations in the wavefront and the size distribution of the injected particles...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512571/mechanochemical-synthesis-of-n-salicylidene-aniline-thermosalient-effect-of-polymorphic-crystals
#6
Sudhir Mittapalli, D Sravanakumar Perumalla, Ashwini Nangia
Polymorphs of the dichloro derivative of N-salicylideneaniline exhibit mechanical responses such as jumping (Forms I and III) and exploding (Form II) in its three polymorphs. The molecules are connected via the amide N-H⋯O dimer synthon and C-Cl⋯O halogen bond in the three crystal structures. A fourth high-temperature Form IV was confirmed by variable-temperature single-crystal X-ray diffraction at 180°C. The behaviour of jumping exhibited by the polymorphic crystals of Forms I and III is due to the layered sheet morphology and the transmission of thermal stress in a single direction, compared with the corrugated sheet structure of Form II such that heat dissipation is more isotropic causing blasting...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512570/the-structure-of-denisovite-a-fibrous-nanocrystalline-polytypic-disordered-very-complex-silicate-studied-by-a-synergistic-multi-disciplinary-approach-employing-methods-of-electron-crystallography-and-x-ray-powder-diffraction
#7
Ira V Rozhdestvenskaya, Enrico Mugnaioli, Marco Schowalter, Martin U Schmidt, Michael Czank, Wulf Depmeier, Andreas Rosenauer
Denisovite is a rare mineral occurring as aggregates of fibres typically 200-500 nm diameter. It was confirmed as a new mineral in 1984, but important facts about its chemical formula, lattice parameters, symmetry and structure have remained incompletely known since then. Recently obtained results from studies using microprobe analysis, X-ray powder diffraction (XRPD), electron crystallography, modelling and Rietveld refinement will be reported. The electron crystallography methods include transmission electron microscopy (TEM), selected-area electron diffraction (SAED), high-angle annular dark-field imaging (HAADF), high-resolution transmission electron microscopy (HRTEM), precession electron diffraction (PED) and electron diffraction tomography (EDT)...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512569/unprecedented-phase-transition-sequence-in-the-perovskite-li0-2na0-8nbo3
#8
Charlotte A L Dixon, Jason A McNulty, Steven Huband, Pamela A Thomas, Philip Lightfoot
The perovskite Li0.2Na0.8NbO3 is shown, by powder neutron diffraction, to display a unique sequence of phase transitions at elevated temperature. The ambient temperature polar phase (rhombohedral, space group R3c) transforms via a first-order transition to a polar tetragonal phase (space group P42mc) in the region 150-300°C; these two phases correspond to Glazer tilt systems a(-)a(-)a(-) and a(+)a(+)c(-), respectively. At 500°C a ferroelectric-paraelectric transition takes place from P42mc to P42/nmc, retaining the a(+)a(+)c(-) tilt...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512568/acemetacin-cocrystal-structures-by-powder-x-ray-diffraction
#9
Geetha Bolla, Vladimir Chernyshev, Ashwini Nangia
Cocrystals of acemetacin drug (ACM) with nicotinamide (NAM), p-aminobenzoic acid (PABA), valerolactam (VLM) and 2-pyridone (2HP) were prepared by melt crystallization and their X-ray crystal structures determined by high-resolution powder X-ray diffraction. The powerful technique of structure determination from powder data (SDPD) provided details of molecular packing and hydrogen bonding in pharmaceutical cocrystals of acemetacin. ACM-NAM occurs in anhydrate and hydrate forms, whereas the other structures crystallized in a single crystalline form...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512567/how-many-tricks-can-an-old-perovskite-play
#10
Brendan J Kennedy
The ferroelectric-paraelectric transition in Li0.2Na0.8NbO3 is between two extremely rare perovskite polytypes. How the unprecedented sequence of structures was established shows that even old oxides can play new tricks.
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512566/regulating-thermosalient-behaviour-in-three-polymorphs
#11
Maximilian J Werny, Jagadese J Vittal
Three polymorphs of a di-chloro-N-salicylideneaniline derivative show visually impressive jumping and sudden blasting behaviours on heating due to phase transitions.
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28512565/developments-in-the-structural-science-of-materials
#12
EDITORIAL
C Richard A Catlow
Recent developments in the structural science of materials and the growing power of computational methods in this field are discussed.
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28250957/the-mechanism-behind-the-selection-of-two-different-cleavage-sites-in-nag-nam-polymers
#13
Marko Mihelič, Kristina Vlahoviček-Kahlina, Miha Renko, Stephane Mesnage, Andreja Doberšek, Ajda Taler-Verčič, Andreja Jakas, Dušan Turk
Peptidoglycan is a giant molecule that forms the cell wall that surrounds bacterial cells. It is composed of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) residues connected by β-(1,4)-glycosidic bonds and cross-linked with short polypeptide chains. Owing to the increasing antibiotic resistance against drugs targeting peptidoglycan synthesis, studies of enzymes involved in the degradation of peptidoglycan, such as N-acetylglucos-aminidases, may expose new, valuable drug targets. The scientific challenge addressed here is how lysozymes, muramidases which are likely to be the most studied enzymes ever, and bacterial N-acetylglucosaminidases discriminate between two glycosidic bonds that are different in sequence yet chemically equivalent in the same NAG-NAM polymers...
March 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28250956/the-application-of-tailor-made-force-fields-and-molecular-dynamics-for-nmr-crystallography-a-case-study-of-free-base-cocaine
#14
Xiaozhou Li, Marcus A Neumann, Jacco van de Streek
Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field...
March 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28250955/atom-interaction-propensities-of-oxygenated-chemical-functions-in-crystal-packings
#15
Christian Jelsch, Yvon Bibila Mayaya Bisseyou
The crystal contacts of several families of hydrocarbon compounds substituted with one or several types of oxygenated chemical groups were analyzed statistically using the Hirshfeld surface methodology. The propensity of contacts to occur between two chemical types is described with the contact enrichment descriptor. The systematic large enrichment ratios of some interactions like the O-H⋯O hydrogen bonds suggests that these contacts are a driving force in the crystal packing formation. The same statement holds for the weaker C-H⋯O hydrogen bonds in ethers, esters and ketones, in the absence of polar H atoms...
March 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28250954/incommensurate-atomic-density-waves-in-the-high-pressure-ivb-phase-of-barium
#16
Alla Arakcheeva, Maxim Bykov, Elena Bykova, Leonid Dubrovinsky, Phil Pattison, Vladimir Dmitriev, Gervais Chapuis
The host-guest structures of elements at high pressure discovered a decade ago still leave many open questions due to the lack of precise models based on full exploitation of the diffraction data. This concerns in particular Ba IV, which is stable in the range 12-45 GPa. With the example of phase Ba IVb, which is characterized here for the first time, a systematic analysis is presented of possible host-guest structure models based on high-quality single-crystal diffraction data obtained with synchrotron radiation at six different pressures between 16...
March 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28250953/procedures-for-cryogenic-x-ray-ptychographic-imaging-of-biological-samples
#17
M Yusuf, F Zhang, B Chen, A Bhartiya, K Cunnea, U Wagner, F Cacho-Nerin, J Schwenke, I K Robinson
Biological sample-preparation procedures have been developed for imaging human chromosomes under cryogenic conditions. A new experimental setup, developed for imaging frozen samples using beamline I13 at Diamond Light Source, is described. This manuscript describes the equipment and experimental procedures as well as the authors' first ptychographic reconstructions using X-rays.
March 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28250952/can-x-ray-constrained-hartree-fock-wavefunctions-retrieve-electron-correlation
#18
Alessandro Genoni, Leonardo H R Dos Santos, Benjamin Meyer, Piero Macchi
The X-ray constrained wavefunction (XC-WF) method proposed by Jayatilaka [Jayatilaka & Grimwood (2001) ▸, Acta Cryst. A57, 76-86] has attracted much attention because it represents a possible third way of theoretically studying the electronic structure of atoms and molecules, combining features of the more popular wavefunction- and DFT-based approaches. In its original formulation, the XC-WF technique extracts statistically plausible wavefunctions from experimental X-ray diffraction data of molecular crystals...
March 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28250951/metal-organic-frameworks-for-h2-and-ch4-storage-insights-on-the-pore-geometry-sorption-energetics-relationship
#19
Mohamed H Alkordi, Youssef Belmabkhout, Amy Cairns, Mohamed Eddaoudi
This study aims to assess the possibility of improving H2 and CH4 binding affinity to the aromatic walls of a designed new Metal-Organic Framework (MOF) through simultaneous dispersive interactions. It is suggested here that desirable H2 and CH4 storage media at low pressures require narrow uniform pores associated with large surface area, a trade-off that is challenging to achieve.
March 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28250950/advances-in-mass-spectrometry-based-strategies-to-study-receptor-tyrosine-kinases
#20
REVIEW
Simon Vyse, Howard Desmond, Paul H Huang
Receptor tyrosine kinases (RTKs) are key transmembrane environmental sensors that are capable of transmitting extracellular information into phenotypic responses, including cell proliferation, survival and metabolism. Advances in mass spectrometry (MS)-based phosphoproteomics have been instrumental in providing the foundations of much of our current understanding of RTK signalling networks and activation dynamics. Furthermore, new insights relating to the deregulation of RTKs in disease, for instance receptor co-activation and kinome reprogramming, have largely been identified using phosphoproteomic-based strategies...
March 1, 2017: IUCrJ
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