bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural studies of NenD1, an argininosuccinate lyase involved in the biosynthesis of nenemycin
Authors: Hamel Jérémie , Murphy-Després Xavier , Chen Ruidong , Picard Marie-Ève , Duvignaud Jean-Baptiste , Zhang Changsheng , Shi Rong 
Published: November 2015

Nenemycin is a newly discovered 31-membered cyclodepsipeptide antibiotic isolated from an aquatic Streptomyces. This cyclic molecule contains ester and peptide bonds and is biosynthesized by the combined action of multiple enzymes. Among those is NenD1, an argininosuccinate lyase involved in the synthesis of 2S,3R--2,3-diaminobutanoic acid (DABA), a modified amino acid later added to the cycle of the nenemycin biosynthesis. The structure of NenD1 has been determined at 2.7 Å, showing the homotetrameric arrangement of the enzyme. A new crystal form was obtained after reductive methylation of lysine residues and the resulted 2.9 Å structure reveals features not present in the original. The active site is located at the interface of three subunits and its architecture was compared with other similar enzymes. Our study provides further insights into the synthesis mechanism of the unusual amino acid.
Crystallographic data mining - A path to structure prediction in intermetallics?
Authors: Dshemuchadse Julia , Steurer Walter 
Published: November 2015

Many metals adapt very simple structure types, mainly sphere packings such as cubic and hexagonal close-packed, as well as simple body-centered cubic structures. In contrast, around 2 % of all intermetallic crystal structures exhibit unit cells containing 100 or more atoms [1]. These compounds are also termed "complex intermetallics" and, while the simplest packings approximate metal atoms as spheres and in doing so explain a number of frequent structure types, the existence of such intricate geometries is not immediately evident. From the analysis of a large number of intermetallic structures, we can recognize geometrical patterns (e.g., recurring building blocks) in order to find out more about their general building principles. Among complex intermetallics, two very distinct phenomena can be observed when inspecting the different structures. On one hand, chemically very diverse compounds can crystallize in rather similar structures, as was shown for a group of more than 40 complex face-centered cubic compounds [2]. On the other hand, small compositional changes within select intermetallic systems can yield a number of different structures, which can also belong to the class of complex intermetallics. A showcase system is found among Al-Cu-Ta, where a small range of the ternary phase diagram contains at least four different structures, all of them complex [3]. By gaining deeper knowledge of the factors influencing structure stabilization, we aim at a better understanding of the mechanisms that are responsible for the formation of intermetallic structures. Thus, we hope to contribute to the quest for explaining why certain intermetallic structures form, while countless other theoretically possible structures do not. Consequently, the prediction of intermetallic structures, especially in still largely unknown parts of multinary phase diagrams, will come into reach.
Nidovirus papain-like proteases antagonize the host innate immune response
Authors: Bailey-Elkin Ben , van Kasteren Puck , Snijder Eric , Kikkert Marjolein , Mark Brian 
Published: November 2015

Protein ubiquitination regulates important innate immune responses. Ubiquitin (Ub) can be attached to lysine residues on cellular proteins to promote, among other activities, the innate immune responses of the cell. These pathways can in turn be downregulated by the removal of Ub from cellular proteins by deubiquitinases (DUBs). Viruses of the order Nidovirales have positive-sense, single stranded RNA genomes. Within this order are the families Coronaviridae and Arteriviridae, which include viruses known to cause severe disease in humans and animals, respectively. Members of the families Coronaviridae and Arteriviridae share a common mechanism of gene expression, whereby the viral nonstructural proteins (nsps) are initially expressed as a single polyprotein, which is then cleaved into functional units by papain-like protease (PLP) domains encoded within. Interestingly, while also being necessary for viral replication, a number of Nidovirus PLPs have been shown to remove Ub from host proteins, in order to down-regulate the host innate immune response. Here we present the crystal structure of a Nidovirus PLP in complex with Ub. The structure allowed for the characterization of a Ub-binding interface, and identification of specific residues involved in Ub recognition that are distant from the enzyme active site. The selective inactivation of DUB activity of viral PLP enzymes verses their polyprotein cleavage activity by site directed mutagenesis is allowing us to understand the role of DUB activity in evading innate immune responses of the host, and opens the door for the development of improved live attenuated vaccines against Nidoviruses and other viruses encoding similar dual specificity proteases.
Magnetic electron density in Fe3O4 examined by RXMS at Fe K edge
Authors: Sasaki Satoshi , Okube Maki , Takayasu Shunichi 
Published: November 2015

It is known that a difference-Fourier synthesis of the Fourier series provides a mean for the location of bonding electrons, by subtracting out the electron density of all atoms in the crystal structure. Here the Fourier technique in X-ray diffraction was applied to observe the magnetic electron density of magnetite Fe3O4. An asymmetrical ratio in the resonant X-ray magnetic scattering (RXMS) provides information on the magnetic moments, which can be estimated from an intensity difference between the right-handed and left-handed polarized X rays. The ratio is proportional to the real part of the product of the spin-contributed structure factor F(hkl) and the complex conjugation of charge-scattered F(hkl). Expanding the equations in difference–Fourier formalization, the spin density can be represented with the observed f"m of RXMS. Synchrotron RXMS experiments were performed at the PF-BL-6C beamline using an AFC-5u four-circle diffractometer. Through a diamond phase retarder the incident X rays were circularly polarized at the Fe K absorption edge, where a wavelength of λ = 1.7439 Å (E = 7.1094 keV) was selected within the pre-edge. A spherical crystal of 0.13 mm in diameter was mounted along the a3 axis with the glass fiber on rare-earth magnet and goniometer head. The intensity data of RXMS were collected for Bragg reflections up to 2θ = 1310. After crystal-structure refinements with scaling of the RXMS data, difference-Fourier syntheses were made in triclinic symmetry with a total of 165 reflections by using the software FRAXY. The syntheses are superior in examining the magnetic effect in the polarization difference and eliminating other effects such as charge scattering, experimental errors and the termination effect. The difference of magnetic electron density between left-handed and right-handed circular polarizations at E was estimated in the Fourier series of partially observed F(hkl). The magnetic electron density on Fourier maps will be discussed in the presentation.
How phase measurements can change X-ray crystallography
Authors: Morelhao Sergio , Amirkhanyan Zohrab , Remedios Claudio , Guzzo Cristiane 
Published: November 2015

From inorganic crystals to macromolecular crystals, structure determination with atomic resolution is based on diffraction techniques (electrons, X-rays and neutrons). However, since the coherent scattering cross-section for X-rays by atoms have intermediate values between those for electrons and neutrons, experimental measurements of the phases of structure factors are feasible only for X-rays. Unprecedented results [1-3] have show how phase measurements can reveal important information of the crystalline structure of doped crystals, which are inaccessible by other techniques: "differently from any other method in X-ray crystallography based on structure refinement of intensity data, the presented method pinpoint a specific feature of the structure and directly prove its existence beyond of any reliability parameter or of goodness-of-fitting value." Although there are instrumental and computational challenges, the method can be extended to protein crystallography for improving resolution of poorly solved features of the structures. As depicted in Fig. 1, the structure factor of a given reflection has contributions of distinct groups of atoms. Low resolution at one group can result in phase deviation of Fickle, without significantly affecting its amplitude. For instance, small differences in the symmetry of charge balance at group B can cause great difference in the phase angle of this group, which increases the phase angle of Fickle, Fig. 1 (b). On the other hand, reduction in the scattering amplitude of group E due to atomic disordering decreases the phase angle, Fig. 1 (c). In this presentation, we discuss the current understanding of this method, its perspectives, and importance of providing a tool for structural analysis of macromolecules that is able to go beyond the resolution achieved by the techniques actually in use.
Unprecedented adsorption of molecular hydrogen in the porous hydride framework
Authors: Filinchuk Yaroslav , Tumanov Nikolay , Ban Voraksmy , Oh Hyunchul , Hirscher Michael , Richter Bo , Jensen Torben , Hudson Matthew , Brown Craig , Iles Gail , Jorgensen Scott 
Published: November 2015

Recently the first porous hydride, gamma-Mg(BH4)2, featuring so-called "borohydride framework" and capable to store reversibly guest species was discovered [1]. This example clearly shows that the covalently bound hydride anions, such as borohydride, can act as directional ligands, capable to form molecular and polynuclear complexes, as well as framework structures typically occurring in classical coordination chemistry. Various small molecules are reversibly absorbed in gamma-Mg(BH4)2. In this work we show that molecular hydrogen and nitrogen have different adsorption sites in gamma-Mg(BH4)2, leading to different capacities on saturation and to different H2 and N2 BET areas. Only up to 0.66 N2 molecules are adsorbed per Mg atom, but the saturation capacity is double for the smaller hydrogen molecule. Moreover, at higher pressures, the second hydride phase forms with unprecedented hydrogen content of ~22 weight % (!). The density of hydrogen adsorbed into the pores is much higher than in liquid hydrogen, having no analogues among other porous systems. On the technical side, we will illustrate how in-situ diffraction at neutron and synchrotron sources allows to follow adsorption isobars, aiming for extraction of isosteric heats of adsorption directly from diffraction data, as well as for clarifying the microscopic mechanisms in terms of guest-host and guest-guest interactions.
DIALS – a toolbox for diffraction data analysis
Authors: Fuentes-Montero Luis , Parkhurst James , Winter Graeme , Waterman David , Gildea Richard , Brewster Aaron , Hattne Johan , Sauter Nicholas , Evans Gwyndaf 
Published: November 2015

DIALS is a collaborative initiative to produce an open source software toolbox encompassing all aspects of diffraction data analysis, with an initial focus on X-ray diffraction data from synchrotrons and free-electron lasers for macromolecular crystallography. DIALS [1] has been developed as a modular plug-in framework that permits flexibility not only in the development of new methods and algorithms but also in the application of these methods to data analysis. DIALS builds on the cctbx [2] in addition to its own dedicated tool-kits. We will present the ideas behind DIALS and give examples of its versatility in permitting the use of several spot-finding and indexing schemes, global refinement and both two and three dimensional integration methods.
The 17,803 types of double antisymmetry space groups
Authors: VanLeeuwen Brian , Huang Mantao , Litvin Daniel , Gopalan Venkatraman 
Published: November 2015

Double antisymmetry, as a type of color symmetry, refers to the consideration of two independent color-reversing operations. We found that there are 17,803 types of double antisymmetry space groups. The "types" of double antisymmetry space groups being the proper affine equivalence classes thereof, i.e. if two groups differ only by changes in origin, lattice constants, and angles then they are considered the same type of group, just as with the 230 types of crystallographic space groups. The significance of listing the types of double antisymmetry space groups is that it gives all possible symmetries of a crystal when two independent antisymmetries are considered in conjunction with the conventional 3D Euclidean space symmetry. Examples from our listing of their properties and symmetry diagrams (available online) will be given.
Symmetry in plants: from Bravais' lattices to an explanation of Fibonacci phyllotaxis.
Authors: Gole Christophe 
Published: November 2015

In 1837, fourteen years before publishing his seminal Etude sur la cristallographie Auguste Bravais and his brother Louis wrote an equally seminal work on the arrangement of leaves around the stem of a plant. In this paper, one of the very first truly bio-mathematical work, they introduce and analyze cylindrical lattices and conjecture that only those with the golden angle between successive leaves can exhibit the Fibonacci numbers of spirals predominant in plants. With the advent of the microscope, and following observations of the plants growing tips by Hofmeister, botanists Schwendener and van Iterson developed an accretion model of the plant structures. Their work use ideas of what we now would call renormalization of morphogenetic fronts to understand transitions between successive Fibonacci pairs. This gives rise to a simple explanation of the omni-presence of Fibonacci numbers in plants, which can be verified on digitized plant samples and with systematic computer simulations. This could inform crystallographers in their study of dislocations.
When good ligands go bad
Authors: Merritt Ethan 
Published: November 2015

Tools for validating structural models of proteins are relatively mature and widely implemented. New protein crystallographers are introduced early on to the importance of monitoring conformance with expected φ/ψ values, favored rotamers, and local stereochemistry. The protein model is validated by the PDB at the time of deposition using criteria that are also available in the standard software packages used to refine the model being deposited. By contrast, crystallographers are typically much less familiar with procedures to validate key non-protein components of the model – cofactors, substrates, inhibitors, etc. It has been estimated that as many as a third of all ligands in the PDB exhibit preventable errors of some sort, ranging from minor deviations in expected bond angles to wholly implausible placement in the binding pocket. Following recommendations from the wwPDB Validation Task Force, the PDB recently began validating ligand geometry as an integral part of deposition processing. This means that many crystallographers will soon receive for the first time a "grade" on the quality of ligands in the structure they have just deposited. Some will be surprised, as I was following my first PDB deposition of 2014, at how easily bad ligand geometry can slip through the cracks in supposedly robust structure refinement protocols that their lab has used for many years. I will illustrate use of current tools for generating ligand restraints to guide model refinement. One is the jligand+coot+cprodrg pipeline integrated into the CCP4 suite. Another is the Grade web server provided as a community resource by Global Phasing Ltd. Furthermore I will show examples from recent in-house refinements of how things can still go wrong even if you do use these tools, and how we recovered. The new PDB deposition checks may expose errors in your ligand descriptions after the fact. This presentation may help you avoid introducing those errors in the first place.
Mechanical Effects in Molecular Crystals – A Revival
Authors: Naumov Panče , Panda Manas , Sahoo Subash , Nath Naba , Husain Ahmad , Nauha Elisa 
Published: November 2015

The classical perception of single crystals of molecular materials as rigid and brittle entities has downsized the research interest in mechanical effects that had been initiated and was active back in the 1980s. More recently, the modern analytical techniques for mechanical, electron-microscopic, structural, spectroscopic and kinematic characterization have contributed to accumulate compelling evidence that under certain circumstances, even some seemingly rigid single crystals can deform, bend, twist, hop, wiggle or perform other "acrobatics" that are atypical for non-soft matter. These examples contribute to a paradigm shift in our understanding of the elasticity of molecular crystals and also provide direct mechanistic insight into the structural perturbations at the limits of the susceptibility of ordered matter to internal and external mechanical force. As the relevance of motility and reshaping of molecular crystals is being recognized by the crystal research community as a demonstration of a very basic concept–conversion of thermal or light energy into work–a new and exciting crystal chemistry around mechanically responsive single crystals rapidly unfolds.
Three-dimensional imaging of acoustic phonons using an X-ray laser
Authors: Clark Jesse , Robinson Ian 
Published: November 2015

Key insights into the behaviour of materials can be gained by observing their structure when they undergo lattice distortion. Laser pulses on the femtosecond time scale can be used to induce disorder in a ``pump-probe" experiment with the ensuing transients being probed stroboscopically using femtosecond pulses of visible light, X-rays or electrons (Fig. 1 A). Here we report two- and three-dimensional imaging of the generation and subsequent evolution of coherent acoustic phonons on the picosecond time scale within single gold nanocrystals using an X-ray free electron laser (Fig. 1 B). Our results allow comparisons between experiment and predictive models based on continuum elasticity theory and molecular dynamics simulations (Fig. 1 B). *Full author list - J.N. Clark L. Beitra, G. Xiong, A. Higginbotham, D. M. Fritz, H. T. Lemke, D. Zhu, M. Cholle, G. J. Williams, M. Messerschmidt, B. Abbey, R. J. Harder, A. M. Korsunsky, J. S. Wark, D. Reis, I. K. Robinson.
Temperature dependence of Uiso constraints in riding hydrogen treatments
Authors: Luebben Jens , Grabowsky Simon , Edwards Alison , Morgenroth Wolfgang , Sheldrick George , Dittrich Birger 
Published: November 2015

Anisotropic parametrisation of the thermal displacements of hydrogen atoms in single-crystal X-ray structure refinement is not possible with independent atom model (IAM) scattering factors. This is due to the weak scattering contribution of hydrogen atoms. Only when aspherical scattering factors are used can carefully measured Bragg data provide such information. For conventional structure determinations parameters of "riding" hydrogen atoms are frequently constrained to values of their "parent" heavy atom. Usually values of 1.2 and 1.5 times X-U_eq are assigned to H-U_iso in these cases. Such constraints yield reasonable structural models for room-temperature data. However, todays small molecule X-Ray diffraction experiments are usually carried out at significantly lower temperatures. To further study the temperature dependence of ADPs we have evaluated several data sets of N-Acetyl-L-4-Hydroxyproline Monohydrate at temperatures ranging from 9 K to 250 K. Methods compared were HAR [1], Invariom refinement [2], time-of-flight Neutron diffraction and the TLS+ONIOM approach [3]. In the TLS+ONIOM approach non-hydrogen ADPs from Invariom refinement provided ADPs for the TLS-fit. Hydrogen atoms in all methods were grouped and analyzed according to their Invariom name. We reach a good agreement of the temperature dependence of H-U_iso/X-U_eq. At very low temperatures the ratio H-U_iso/X-U_eq can be as high as 4, e.g. for Hydrogen attached to a sp3 carbon atom with three non-Hydrogen atom neighbors. Since all methods consistently show that the H-U_iso/X-U_eq ratio is temperature dependent, this effect should be taken into account in conventional structure determinations.
Modulated order in ionic conductors: a fine line between helping and hindering
Authors: Ling Chris 
Published: November 2015

Solid-state ionic conduction relies on essentially conflicting structural properties: long-range crystalline order, to provide structural stability (as fuel cell membranes, battery cathodes etc.); and short-range disorder, to provide smooth conduction pathways without deep local energy minima that could trap the conducting species. Materials that combine these features are generally metastable, and prone to ordering into complex modulated structured that can only be described in (3+n) dimensions using the superspace formalism. Such ordering would normally be expected to seriously compromise conduction properties. However, low-temperature modulated structures can be effective and stable precursors to high-temperature ionic conductors - and, in some cases, can coexist with regions of local disorder that actually enhance conduction. The relationship between modulated order and ionic conduction is relatively little studied, but some of our recent work points to its potential importance. This presentation will focus on two examples: the (3+3)-dimensional commensurately modulated proton conductor Ba4Nb2O9.1/3H2O; [1,2] and the (3+3)-dimensional incommensurately modulated oxide ion conductor "Type II" Bi2O3.xNb2O5 (for which a single-crystal neutron diffraction pattern and the refined structure are shown below). [3] The aim is to show how modulated structures can be designed and manipulated to optimise technological performance by striking a balance between stabilising the overall framework while destabilising the conduction pathways.
Exploring consumer preferences for hedonic and utilitarian food attributes
Authors: Maehle Natalia , Iversen Nina , Hem Leif , Otnes Cele 
Published: November 2015

Purpose
– The purpose of this paper is to identify the relative importance of four main attributes of food products for consumer’s choice. These are price, taste, environmental friendliness and healthfulness, tested across hedonic and utilitarian food products (milk and ice-cream). The weighting of attributes involved in food choices is a complex phenomenon, as consumers must consider contradictory requirements when making their choices. Consumers’ decision-making processes might also be influenced by food category. Some food products are mostly consumed for pleasure, whereas others are consumed because of their nutritional value.

Design/methodology/approach
– The study employs a choice-based conjoint technique, which addresses how consumers make trade-offs across a set of product attributes.

Findings
– The results indicate that price and taste attributes are rated as the most important for both hedonic and utilitarian food products. However, when the authors group consumers according to their product preferences, the relative importance of product attributes changes. Specifically, the importance of environmental friendliness and healthfulness is much higher among the health-conscious and environmentally conscious segments than for other segments.

Originality/value
– To the knowledge, this is the first study comparing the importance of this combination of product attributes (price, taste, calorie content and eco-label) across hedonic and utilitarian foods in a choice-based conjoint setting. Moreover, a new way of grouping consumers according to their ethical-value profiles enables the authors to create a psychographic description of these segments, and to relate it to their food attribute preferences.