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IUCrJ

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https://www.readbyqxmd.com/read/27840684/lytic-polysaccharide-monooxygenases-a-crystallographer-s-view-on-a-new-class-of-biomass-degrading-enzymes
#1
REVIEW
Kristian E H Frandsen, Leila Lo Leggio
Lytic polysaccharide monooxygenases (LPMOs) are a new class of microbial copper enzymes involved in the degradation of recalcitrant polysaccharides. They have only been discovered and characterized in the last 5-10 years and have stimulated strong interest both in biotechnology and in bioinorganic chemistry. In biotechnology, the hope is that these enzymes will finally help to make enzymatic biomass conversion, especially of lignocellulosic plant waste, economically attractive. Here, the role of LPMOs is likely to be in attacking bonds that are not accessible to other enzymes...
November 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27840683/resolution-of-ab-initio-shapes-determined-from-small-angle-scattering
#2
Anne T Tuukkanen, Gerard J Kleywegt, Dmitri I Svergun
Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use...
November 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27840682/towards-an-understanding-of-the-propensity-for-crystalline-hydrate-formation-by-molecular-compounds
#3
Alankriti Bajpai, Hayley S Scott, Tony Pham, Kai-Jie Chen, Brian Space, Matteo Lusi, Miranda L Perry, Michael J Zaworotko
Hydrates are technologically important and ubiquitous yet they remain a poorly understood and understudied class of molecular crystals. In this work, we attempt to rationalize propensity towards hydrate formation through crystallization studies of molecules that lack strong hydrogen-bond donor groups. A Cambridge Structural Database (CSD) survey indicates that the statistical occurrence of hydrates in 124 molecules that contain five- and six-membered N-heterocyclic aromatic moieties is 18.5%. However, hydrate screening experiments on a library of 11 N-heterocyclic aromatic compounds with at least two acceptor moieties and no competing hydrogen-bond donors or acceptors reveals that over 70% of this group form hydrates, suggesting that extrapolation from CSD statistics might, at least in some cases, be deceiving...
November 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27840681/angular-correlations-of-photons-from-solution-diffraction-at-a-free-electron-laser-encode-molecular-structure
#4
Derek Mendez, Herschel Watkins, Shenglan Qiao, Kevin S Raines, Thomas J Lane, Gundolf Schenk, Garrett Nelson, Ganesh Subramanian, Kensuke Tono, Yasumasa Joti, Makina Yabashi, Daniel Ratner, Sebastian Doniach
During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution...
November 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27840680/structures-of-parasite-calreticulins-provide-insights-into-their-flexibility-and-dual-carbohydrate-peptide-binding-properties
#5
Christophe Moreau, Gianluca Cioci, Marina Iannello, Emmanuelle Laffly, Anne Chouquet, Arturo Ferreira, Nicole M Thielens, Christine Gaboriaud
Calreticulin (CRT) is a multifaceted protein, initially discovered as an endoplasmic reticulum (ER) chaperone protein, that is essential in calcium metabolism. Various implications in cancer, early development and immunology have been discovered more recently for CRT, as well as its role as a dominant 'eat-me' prophagocytic signal. Intriguingly, cell-surface exposure/secretion of CRT is among the infective strategies used by parasites such as Trypanosoma cruzi, Entamoeba histolytica, Taenia solium, Leishmania donovani and Schistosoma mansoni...
November 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27840679/constructing-covalent-organic-frameworks-in-water-via-dynamic-covalent-bonding
#6
Jayshri Thote, Harshitha Barike Aiyappa, Raya Rahul Kumar, Sharath Kandambeth, Bishnu P Biswal, Digambar Balaji Shinde, Neha Chaki Roy, Rahul Banerjee
The formation of keto-enamine based crystalline, porous polymers in water is investigated for the first time. Facile access to the Schiff base reaction in water has been exploited to synthesize stable porous structures using the principles of Dynamic Covalent Chemistry (DCC). Most credibly, the water-based Covalent Organic Frameworks (COFs) possess chemical as well as physical properties such as crystallinity, surface area and porosity, which is comparable to their solvothermal counterparts. The formation of COFs in water is further investigated by understanding the nature of the monomers formed using hydroxy and non-hydroxy analogues of the aldehyde...
November 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27840678/a-multicrystal-diffraction-data-collection-approach-for-studying-structural-dynamics-with-millisecond-temporal-resolution
#7
Robin Schubert, Svetlana Kapis, Yannig Gicquel, Gleb Bourenkov, Thomas R Schneider, Michael Heymann, Christian Betzel, Markus Perbandt
Many biochemical processes take place on timescales ranging from femto-seconds to seconds. Accordingly, any time-resolved experiment must be matched to the speed of the structural changes of interest. Therefore, the timescale of interest defines the requirements of the X-ray source, instrumentation and data-collection strategy. In this study, a minimalistic approach for in situ crystallization is presented that requires only a few microlitres of sample solution containing a few hundred crystals. It is demonstrated that complete diffraction data sets, merged from multiple crystals, can be recorded within only a few minutes of beamtime and allow high-resolution structural information of high quality to be obtained with a temporal resolution of 40 ms...
November 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27840677/synthesis-of-chemically-stable-covalent-organic-frameworks-in-water
#8
Samantha Yu-Ling Chong
The development of environmentally benign and scalable synthetic routes to chemically stable covalent organic frameworks (COFs) is key to their real world application in areas such as gas storage and proton conduction. Banerjee et al. [IUCrJ (2016), 3, 402-407] have exploited the high chemical stability of the keto-enamine linkage to develop a 'green' water-mediated procedure, presenting a scalable route to chemically robust COFs.
November 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27840676/impact-and-influence-of-crystallography-across-the-sciences
#9
EDITORIAL
Samar Hasnain
Crystallography has influenced many of the traditional science disciplines and has opened a number of cross-disciplinary activities often bringing physicists, chemists, biologists and medical scientists together.
November 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27437115/structure-of-a-heterogeneous-glycosylated-lipid-bound-in-vivo-grown-protein-crystal-at-atomic-resolution-from-the-viviparous-cockroach-diploptera-punctata
#10
Sanchari Banerjee, Nathan P Coussens, François-Xavier Gallat, Nitish Sathyanarayanan, Jandhyam Srikanth, Koichiro J Yagi, James S S Gray, Stephen S Tobe, Barbara Stay, Leonard M G Chavas, Subramanian Ramaswamy
Macromolecular crystals for X-ray diffraction studies are typically grown in vitro from pure and homogeneous samples; however, there are examples of protein crystals that have been identified in vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grown in cellulo. Here, an atomic resolution (1.2 Å) crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche...
July 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27437114/serial-crystallography-captures-enzyme-catalysis-in-copper-nitrite-reductase-at-atomic-resolution-from-one-crystal
#11
Sam Horrell, Svetlana V Antonyuk, Robert R Eady, S Samar Hasnain, Michael A Hough, Richard W Strange
Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX) to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1...
July 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27437113/residue-contacts-predicted-by-evolutionary-covariance-extend-the-application-of-ab-initio-molecular-replacement-to-larger-and-more-challenging-protein-folds
#12
Felix Simkovic, Jens M H Thomas, Ronan M Keegan, Martyn D Winn, Olga Mayans, Daniel J Rigden
For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer...
July 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27437112/atomic-structure-and-phason-modes-of-the-sc-zn-icosahedral-quasicrystal
#13
Tsunetomo Yamada, Hiroyuki Takakura, Holger Euchner, Cesar Pay Gómez, Alexei Bosak, Pierre Fertey, Marc de Boissieu
The detailed atomic structure of the binary icosahedral (i) ScZn7.33 quasicrystal has been investigated by means of high-resolution synchrotron single-crystal X-ray diffraction and absolute scale measurements of diffuse scattering. The average atomic structure has been solved using the measured Bragg intensity data based on a six-dimensional model that is isostructural to the i-YbCd5.7 one. The structure is described with a quasiperiodic packing of large Tsai-type rhombic triacontahedron clusters and double Friauf polyhedra (DFP), both resulting from a close-packing of a large (Sc) and a small (Zn) atom...
July 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27437111/quantum-crystallographic-charge-density-of-urea
#14
Michael E Wall
Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods...
July 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27437110/isolation-and-evolution-of-labile-sulfur-allotropes-via-kinetic-encapsulation-in-interactive-porous-networks
#15
Hakuba Kitagawa, Hiroyoshi Ohtsu, Aurora J Cruz-Cabeza, Masaki Kawano
The isolation and characterization of small sulfur allotropes have long remained unachievable because of their extreme lability. This study reports the first direct observation of disulfur (S2) with X-ray crystallography. Sulfur gas was kinetically trapped and frozen into the pores of two Cu-based porous coordination networks containing interactive iodide sites. Stabilization of S2 was achieved either through physisorption or chemisorption on iodide anions. One of the networks displayed shape selectivity for linear molecules only, therefore S2 was trapped and remained stable within the material at room temperature and higher...
July 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27437109/mysteries-of-icosahedral-quasicrystals-how-are-the-atoms-arranged
#16
Tsutomu Ishimasa
Higher-dimensional structure analysis of quasicrystals is now possible. Yamada et al. [IUCrJ (2016), 3, 247-258] have solved the atomic structure of icosahedral ScZn7.33 including the characteristic imperfections.
July 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27437108/imaging-enzyme-kinetics-at-atomic-resolution
#17
John Spence, Eaton Lattman
Serial crystallography at a synchrotron has been used to obtain time-resolved atomic resolution density maps of enzyme catalysis in copper nitrite reductase. Similar XFEL studies, intended to out-run radiation damage, will also soon appear.
July 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27437107/challenges-in-the-structural-science-of-materials
#18
C Richard A Catlow
Articles published recently in IUCrJ continue to exemplify the developments and challenges in the structural science of materials.
July 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27158508/peculiar-orientational-disorder-in-4-bromo-4-nitrobiphenyl-bnbp-and-4-bromo-4-cyanobiphenyl-bcnbp-leading-to-bipolar-crystals
#19
Matthias Burgener, Hanane Aboulfadl, Gaël Charles Labat, Michel Bonin, Martin Sommer, Ravish Sankolli, Michael Wübbenhorst, Jürg Hulliger
180° orientational disorder of molecular building blocks can lead to a peculiar spatial distribution of polar properties in molecular crystals. Here we present two examples [4-bromo-4'-nitrobiphenyl (BNBP) and 4-bromo-4'-cyanobiphenyl (BCNBP)] which develop into a bipolar final growth state. This means orientational disorder taking place at the crystal/nutrient interface produces domains of opposite average polarity for as-grown crystals. The spatial inhomogeneous distribution of polarity was investigated by scanning pyroelectric microscopy (SPEM), phase-sensitive second harmonic microscopy (PS-SHM) and selected volume X-ray diffraction (SVXD)...
May 1, 2016: IUCrJ
https://www.readbyqxmd.com/read/27158507/in-situ-ultra-small-angle-x-ray-scattering-study-under-uniaxial-stretching-of-colloidal-crystals-prepared-by-silica-nanoparticles-bearing-hydrogen-bonding-polymer-grafts
#20
Ryohei Ishige, Gregory A Williams, Yuji Higaki, Noboru Ohta, Masugu Sato, Atsushi Takahara, Zhibin Guan
A molded film of single-component polymer-grafted nanoparticles (SPNP), consisting of a spherical silica core and densely grafted polymer chains bearing hydrogen-bonding side groups capable of physical crosslinking, was investigated by in situ ultra-small-angle X-ray scattering (USAXS) measurement during a uniaxial stretching process. Static USAXS revealed that the molded SPNP formed a highly oriented twinned face-centered cubic (f.c.c.) lattice structure with the [11-1] plane aligned nearly parallel to the film surface in the initial state...
May 1, 2016: IUCrJ
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